2020

Science Review

An annual compilation ofresearch data uses enabled by

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GBIF Science Review 2020
GBIF Secretariat
February 2021

Citation:
GBIF Secretariat. (2021). GBIF Science Review 2020. https://doi.org/10.35035/bezp-jj23
Licence:
The GBIF Science Review is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.
Cover photo:
Pangolin (Manis pentadactyla subsp. pentadactyla) by CHUNG CHANG-LIN via iNaturalist. Licensed under a Creative
Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license.

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Foreword
This edition of the GBIF Science Review presents a
selection of some of the key research uses of GBIFmediated data published during calendar year 2019.
The COVID-19 pandemic forced the GBIF Secretariat
to reassess our normal work timelines in 2020. The
Review itself was not unaffected, but that has led to a
happy coincidence.
As we go to press (or "press"), the Proceedings of
the National Academy of Sciences has published acomprehensive analysis and review of more than
4,000 peer-reviewed studies published between 2003
and 2019 that rely on data from the GBIF network(a https://doi.org/10.1073/pnas.2018093118).
Led by J. Mason Heberling of the Carnegie Museumof Natural History assisted by Scott B. Weingart ofCarnegie Mellon University and Secretariat staff, thispaper explores the wider network of interdisciplinary
knowledge generated through the efforts of GBIF's
formal participants and data publishers in more than
130 countries.

The data uses featured in the 2020 Science Review
represent part of an impressive and rapidly growing
corpus of work. The data resources on which they're
built supported 743 peer-reviewed publications in
2019—a rate of roughly two research articles everyday. In comparison, the cumulative number of studies
published between 2003 and 2009 amounted to just
157 papers.
As even this small sample of 67 summaries shows,
the range of research investigations explored withthe help of data from the GBIF network remains
diverse and dynamic. We hope you find insight andinspiration in equal measure—and, of course, wheredata references #CiteTheDOI, you can also find theevidence base and sources of those studies. Happy
hunting!

Joe Miller
GBIF Executive Secretary

BALTIMORE ORIOLE (ICTERUS GALBULA) OBSERVED IN KENNEBUNK, ME, USA BY KEN JANES. PHOTO VIA INATURALIST (CC BY-NC 4.0)

5About the Science Review
The GBIF Science Review provides an annual survey
drawn from the Secretariat’s ongoing literature
tracking programme, which identifies researchuses and citations of biodiversity information
accessed through GBIF’s global infrastructure. The
peer-reviewed articles summarized in the following
pages offer a partial but instructive view of research
investigations supported and enabled by free andopen access to biodiversity data from the GBIF
network.

As in previous years, the categories used here areintended to help readers navigate the major subject
areas of GBIF-assisted research, despite the factthat some papers may cut across multiple topics.
For clarity’s sake, articles appear under only one
category in the Review. Countries assigned to authors
are based on the location of the institutions identified
in the author information, while funding information
included for the highlighted papers draws upon thepapers’ acknowledgements.

We have labelled open-access scientific articles
using the symbol a. We feel this step serves thoseinterested in reading the research at a time ofchanging institutional journal subscriptions.

Those interested in sharing research uses that
may have escaped our attention can write to us atcommunication@gbif.org.

The comprehensive list of this year’s uses (aswell as current and previous ones) is separate
from the printed version of the Science Review
and is available exclusively through the online
literature index at https://www.gbif.org/resource/
search?contentType=literature.

CONTENTS
Uses and trends����������������������������������������������������������������������������������������������������������������� 6
Biodiversity conservation������������������������������������������������������������������������������������������������ 8
Ecology����������������������������������������������������������������������������������������������������������������������������� 14
Environmental sciences������������������������������������������������������������������������������������������������� 22
Evolutionary biology������������������������������������������������������������������������������������������������������� 24
Multidisciplinary sciences��������������������������������������������������������������������������������������������� 27
Other research topics�����������������������������������������������������������������������������������������������������34

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Uses and trends
These visualizations of the use of GBIF-mediated data serve to show not just the growing number ofpeer-reviewed publications appearing each year, but also the increasing geographic distribution of
institutions hosting authors who apply the data in their research articles. Each trend highlights the
GBIF network’s widening sphere of influence and impact on scientific research related to the biologicaldomain.

ANNUAL NUMBER OF PEER-REVIEWED ARTICLES USING GBIF-MEDIATED DATA
2020

981

2019

743

2018

675

2017

696

2016

438

2015

407

2014

350

2013

249

2012

229

2011

169

2010

148

2009

89

2008

52
0

100

200

300

400

500

600

700

800

900

1000

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NUMBER OF ARTICLES WITH AUTHORS BY COUNTRY/ISLAND/TERRITORY

countries, islands &territories with authors who
used GBIF-mediated datain peer-reviewed papers
published in 2019

104
Brunei Darussalam
Hong Kong
Macao
Singapore

Trinidad and Tobago

Cook Islands
French Polynesia
New Caledonia> 100 | 50-100 | 20-49 | 10-19 | < 9

NUMBER OF ARTICLES WITH AUTHORS BY REGION
Europe & Central Asia

597

North America

261

Latin America

255

Asia

220

Oceania78

Africa58

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Biodiversity Conservation

SCINAX FUSCOVARIUS OBSERVED IN ALTAMIRO DE MOURA PACHECO STATE PARK, BRAZIL BY WERTHER. PHOTO VIA INATURALIST (CC BY-NC 4.0)

THE ROLE OF NATURAL HISTORY COLLECTIONSIN BIODIVERSITY KNOWLEDGE GENERATION IN
ANGOLADATA USED: 149,701 SPECIES OCCURRENCES

a Figueira R and Lages F (2019) Museum and Herbarium
Collections for Biodiversity Research in Angola.
Biodiversity of Angola. Springer International Publishing
513–542. Available at:https://doi.org/10.1007/978-3-030-03083-4_19
Author countries/areas: Angola, Portugal

Natural history collections in museums and herbaria
are of great importance to biodiversity science,
particularly in countries and regions with high levels ofendemism and rare species. This is especially true forAngola with its unique mixture of landscapes where
tropical humid climates interface with arid deserts.
Authors of this book chapter set out to strengthen
knowledge of Angolan natural history collections
and their role in biodiversity knowledge generation.
Reviewing the history of collections in Angola, theauthors provide a detailed account of 150 years ofexpeditions and studies in the country, while using
GBIF-mediated occurrence data to summarize thecurrent status of collections of Angolan biodiversity—
held both in local institutions and in other countries.

In addition to simply preserving and documenting
biodiversity, the chapter highlights how collections
underpin multiple branches of scientific researchand conservation science, including supporting
sustainable food production and evaluating impactsof environmental changes.

ASSESSING THE FUNCTIONAL IMPACT ONECOSYSTEMS OF SUNDALAND FRESHWATERSPECIES LOSSDATA USED: 893 SPECIESChua KWJ, Tan HH and Yeo DCJ (2019) Loss of endemic fish
species drives impacts on functional richness, redundancy
and vulnerability in freshwater ecoregions of Sundaland.
Biological Conservation. Elsevier BV 234: 72–81. Available
at: https://doi.org/10.1016/j.biocon.2019.03.019
Author countries/areas: Singapore

Not only a terrestrial biodiversity hotspot, thebiogeographical region of Sundaland in southeast
Asia is also a global hotspot for freshwater diversity.
Large-scale agricultural conversion of rainforests
poses a major threat to freshwater fishes and theecosystems they help support.
By assessing functional richness, redundancy
and vulnerability of Sundaic freshwater fishes,

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IMPACTS OF GLOBAL LAND-USE AND CLIMATECHANGE ON PLANT BIODIVERSITY

Compiling knowledge from a wide range of sources—
including GBIF—of all occurring fishes across 13
ecoregions, the authors describe functional traits for893 species. The distribution of trait entities varies
from less than 30 per cent of the total variation in trait
entities in Java to more than 85 per cent in the Malay
peninsula.

Di Marco M, Harwood TD, Hoskins AJ, Ware C, Hill SLL andFerrier S (2019) Projecting impacts of global climate
and land-use scenarios on plant biodiversity using
compositional-turnover modelling. Global Change Biology.
Wiley 25(8): 2763–2778.
Available at: https://doi.org/10.1111/gcb.14663

When modelling loss of extinction-prone species,
they show a general pattern of accelerating impacts
on functional diversity. With low levels of functional
redundancy and thus high vulnerability to impactsof species loss, the Malay Peninsula Eastern Slope issingled out as the most urgent target for conservation
efforts.

In response to accelerating rates of biodiversity loss,
the global community is considering new, ambitious
conservation targets. To inform policy decisions,fine-scale assessments predicting future impacts ofthreats to biodiversity are therefore crucial.

PROTECTING FROGS OF THE FUTURE IN BRAZILIAN
BIOMESDATA USED: 500 SPECIES

Vasconcelos TS and Prado VHM (2019) Climate change
and opposing spatial conservation priorities for anuran
protection in the Brazilian hotspots. Journal for Nature
Conservation. Elsevier BV 49: 118–124. Available at:https://doi.org/10.1016/j.jnc.2019.04.003
Author countries/areas: Brazil
Research funding: Conselho Nacional de Desenvolvimento
Científico e Tecnológico

Distinguished by high levels of diversity andendemism, the Atlantic Forest and Cerrado biomes
in Brazil are recognized as hotspots of biodiversity.
Home to hundreds of frog species, many of which areendemic, these regions and their anuran fauna are ofparticular interest to conservation biologists.
Modelling the ecological niches of more than 500 frog
species, authors of this study outline conservation
priorities across space and time. Their results showthat for both biomes in the baseline climate, total
representation is achievable in just ~9 per cent of
50x50 km grid cells.
In future climates, the Atlantic Forest anurans will
require an increased area in the number of grid cells
for total coverage, whereas the opposite is the casefor the Cerrado. In fact, fewer than a third of thebaseline Cerrado cells appear to have relevance foranuran conservation across all time frames.

DATA USED: 52 MILLION SPECIES OCCURRENCES

Author countries/areas: Australia, Italy, UK

This study examined the effects of climate change
and land-use since 1900 on global vascularplant biodiversity using models of compositional
turnover, based on 52 million GBIF-mediated species
occurrences. By applying future scenarios of different
degrees of climate and land-use change, the authors
used the models to predict the proportion of vascularplants expected to go extinct by 2070.
Between 1900 and 2015 plant extinctions increased
by 60 per cent. When considering land-use scenarios
alone, sustainable socio-economic development could
slow this down moving forward. Unfortunately, under
all considered climate change scenarios, rates ofextinction are predicted to be 3-4 times higher than in
the most pessimistic land-use scenario alone.
The combined results of the paper suggest thatunless climate change is halted, efforts to introduce
sustainable land-use planning will not be enough toprevent dramatic biodiversity loss.

USING RARITY AS A SURROGATE MEASURE FOR
BIODIVERSITYDATA USED: 2,380,424 SPECIES OCCURRENCES

a Astudillo-Scalia Y and de Albuquerque FS (2019)
Evaluating the performance of rarity as a surrogate in site
prioritization for biodiversity conservation. Global Ecology
and Conservation. Elsevier BV 18: e00639. Available at:https://doi.org/10.1016/j.gecco.2019.e00639
Author countries/areas: USA

In conservation planning, several metrics can be used
when seeking to identify how to cover the greatest
number of species in the least number of sites. Widelyused, species richness, however, appears to be one of
the least effective.
(continued on next page...)biodiversity conservation

researchers behind this study give insights into thecurrent status of ichthyofaunal diversity and potential
impacts of species loss on ecosystems.

biodiversity conservation

10

This study assesses the performance of threerarity-based indices as new potential surrogates of
biodiversity for solving the minimum-set coverage
problem: rarity-weighted richness (RWR), index ofsummed rarity (ISR) and index of relative rarity (IRR).
The authors tested the indices in 14 datasets—eight
mediated by GBIF—spanning a broad range of taxa,
spatial extent and resolution.

FILLING KNOWLEDGE GAPS WITH ROADKILL DATA

In all 14 datasets, rarity indices outperformed species
richness and in some cases, also complementarity
algorithms. The best performing index was RWR.

Author countries/areas: USA

With few or no requirements for specialized software,computing power or programming skills, theproposed indices may represent a simple, yet reliable
alternative to prohibitively long computation times ofinteger programming and heuristic algorithms in site
prioritization for biodiversity conservation.

GLOBAL ANALYSIS OF GAPS IN BUTTERFLY DATADATA USED: 41,077,368 SPECIES OCCURRENCES

Girardello M, Chapman A, Dennis R, Kaila L, Borges PAV andSantangeli A (2019) Gaps in butterfly inventory data: A
global analysis. Biological Conservation. Elsevier BV 236:
289–295. Available at:https://doi.org/10.1016/j.biocon.2019.05.053
Author countries/areas: Finland, Greece, Portugal, UK

Biodiversity data is the main pillar of conservation
planning. The quality of species assessments,
however, relies on the availability and standard ofoccurrence data. If data is scarce—the Wallacean
Shortfall—results may be unreliable.
Large, colourful and with plenty of aesthetic
appeal, butterflies are a remarkable exception toundersampling of insects. In this study, researchers
used GBIF-mediated occurrences of six butterfly
families containing more than 8,000 species to
identify gaps in inventory data at the global level.
The authors found a positive trend in record
accumulation in the past century—particularly
since 1990—in most of the world with the exceptionof Central Africa. The highest levels of inventory
completeness are found in Europe, North America,
coastal Australia and Southern Africa.
While using regression models to identify predictorsof inventory completeness, the authors found roaddensity (i.e. accessibility) to be important, however,this was only at the finest resolution. At a large scale,completeness was better predicted by elevation anddensity of protected areas.

DATA USED: 26,853,168 SPECIES OCCURRENCES

Tiedeman K, Hijmans RJ, Mandel A, Waetjen DP and
Shilling F (2019) The quality and contribution of volunteer
collected animal vehicle collision data in ecologicalresearch. Ecological Indicators. Elsevier BV 106: 105431.
Available at:https://doi.org/10.1016/j.ecolind.2019.05.062

Knowledge about the distributions of species
is increasingly being improved thanks to datacollected by volunteers through citizen science
projects. Dominated by non-experts, some projects
rely on experts for validation while others verify
identifications through community efforts.
This study seeks to evaluate the quality of a volunteerbased animal-vehicle collision programme—theCalifornia Roadkill Observation System (CROS)—and
its contribution to knowledge about species ranges.
Assessing more than 35,000 observations of morethan 400 species, the authors found that species
identification accuracy was high for both professional(99 per cent) and non-professional users (95 percent).
The ranges derived from the CROS dataset overlapped
to a large extent with GBIF-mediated occurrences.
However, for 139 species the roadkill data expanded
ranges by a mean of 3,735 km². For some ten per centof species, this would increase their environmental
niche—0.13 degrees C for mammals, suggesting aclear significance of the dataset, that if published to
GBIF could fill gaps in knowledge.

ASSESSING SAMPLING EFFORT IN THE CAATINGAUSING IGNORANCE SCORESDATA USED: 1,218,897 SPECIES OCCURRENCES

Correia RA, Ruete A, Stropp J, Malhado ACM, dos Santos
JW, Lessa T, Alves JA and Ladle RJ (2019) Using ignorance
scores to explore biodiversity recording effort for multiple
taxa in the Caatinga. Ecological Indicators. Elsevier BV 106:105539. Available at:https://doi.org/10.1016/j.ecolind.2019.105539
Author countries/areas: Brazil, Iceland, Portugal, Sweden

Making informed decisions in conservation planningrequires good knowledge about species distributions.
Gaps and biases in spatial data, however, may skew
results and affect our ability to accurately predict the
distribution of species.
This study explores the use of ‘ignorance scores’ toevaluate sampling effort and bias—in a case studyof species present in the Caatinga semi-arid tropical

11

Their results showed a staggering taxonomic bias withhigh ignorance scores across the vast majority of cells
for all groups, except plants—suggesting a preference
towards plant recording in the region. For amphibians,the percentage of grid cells with no records was morethan 99 per cent.
Exploring reasons for recording biases, the authors
point to road density as a main factor, while
population density and distance to nearest university
are secondary predictors.

TARGETING THE KNOWN UNKNOWNS OF THE
BOTANICAL WORLDDATA USED: 214,964,486 SPECIES OCCURRENCES

Cornwell WK, Pearse WD, Dalrymple RL and Zanne AE(2019) What we (don’t) know about global plant diversity.
Ecography. Wiley 42(11): 1819–1831. Available at:https://doi.org/10.1111/ecog.04481
Author countries/areas: Australia, USA

This study by an Australian and U.S. team compares
the coverages and overlaps between the mostcomprehensive sources of geographic, genetic andtrait-based botanical data to provide an actionable
view of the current presence and absence ofknowledge about the world's plants.
Their analysis draws on nearly 215 million plant
records from GBIF.org and compares their coveragewith data aggregated in GenBank and TRY, placing
each of the 350,699 species names in The Plant List
into one of three groups: 1) broadly covered species(17.7 per cent) where at least some knowledge of theirlocations, genes and traits exists; 2) patchily covered
species (55.6 per cent) missing from at least one data
source; or 3) species with no information other thantheir names (26.7 per cent).

PUTTING A PRICE ON NATURE’S CONTRIBUTION TO
PEOPLEa Hipólito J, Sousa B dos SB, Borges RC, Brito RM de, Jaffé
R, Dias S, Imperatriz Fonseca VL and Giannini TC (2019)
Valuing nature’s contribution to people: The pollination
services provided by two protected areas in Brazil. Global
Ecology and Conservation. Elsevier BV 20: e00782.
Available at: https://doi.org/10.1016/j.gecco.2019.
e00782
Author countries/areas: Brazil
Research funding: Conselho Nacional de Desenvolvimento
Científico e Tecnológico

Directly contributing to human well-being, pollinationis one of the most studied ecosystem services,
the effect of which can be measured in order toincentivize preservation.
Focused on two protected areas in Brazil—Serra da
Bocaina in the Amazon Forest and Mata do Jambreiro
in the Atlantic Forest—this study calculates bothmonetary and non-monetary values of pollination
services provided by bees in the surroundings.
Using data on land cover and use, the authors
estimated the size of agricultural areas and theirdependence on animal pollination. Derived fromGBIF-mediated occurrences, they compiled a list ofbee species and estimated their maximum foraging
distance.
In Serra da Bocaina, they identified 17 agricultural
crops with varying levels of pollination dependence,
the annual value of which is estimated to $564,500.
For Mata do Jambreiro, 16 crops are cultivated, of
which half depend on pollination—estimated at avalue of $246,000 per year.
The non-monetary valuation of pollination services
provided by the two protected areas identified
important areas with higher potential for nesting andfood resources in Canaã dos Carajás and Parauapebas
for Bocaina—and, especially, Nova Lima forJambreiro.

While the GBIF network provides the most complete
species coverage (73.3 per cent), the results outline
the shapes of some well-known but previously
unquantified shortfalls in botanical knowledge.
By providing clear targets for data collection andspecimen digitization, the authors present reasons
to be optimistic about their stated hope of "turn[ing]what appears to be an insurmountable task into amanageable checklist of gaps to be filled."
COMMON ROSE (PACHLIOPTA ARISTOLOCHIAE) OBSERVED IN THAILAND
BY TVP. PHOTO VIA INATURALIST (CC BY-NC-ND 4.0)

biodiversity conservation

forest in Brazil. Downloading all GBIF-mediatedoccurrences in the region, researchers organized
the data into taxonomic reference groups of similarcollection methods and calculated scores for each
10x10 km cell.

biodiversity conservation

12

HOW LAND USE AFFECTS BIODIVERSITY IN
DRYLANDS AND MEDITERRANEAN ENVIRONMENTS
a García-Vega D and Newbold T (2019) Assessing theeffects of land use on biodiversity in the world’s drylands
and Mediterranean environments. Biodiversity andConservation. Springer Science and Business Media LLC
29(2): 393–408. Available at:https://doi.org/10.1007/s10531-019-01888-4
Author countries/areas: UK
Research funding: Natural Environment Research Council

Human land uses, such as agriculture, urbanizationand plantation forests, are expanding worldwide,
destroying habitats and leading to local species
extinctions. The effects of land use on biodiversity,
however, vary across ecosystem types, as a crop field
may reduce biodiversity in tropical rainforests but
may increase it in a desert.
This study focuses on drylands and Mediterranean
ecosystems, estimated to have experienced thelargest land-use derived declines in biodiversity todate. Assembling a dataset of biodiversity surveys inthese biomes, the authors create a model comparing
species richness, abundance, diversity, endemism
and compositional turnover across different types ofland use.
To assess effects on endemism and composition, theauthors used GBIF-mediated occurrence data to define
species range occupancy, which was also modelled asa function of land use.
The overall results showed strong negative responses
to land use in Mediterranean environments. Relative toundisturbed natural habitat, all measured parameters
showed decline across all land uses. For drylands,
however, the results showed a strong turnover in
species composition, but no significant response in
any other measures.

CLIMATE CHANGE THREATENS THE MOST
BIODIVERSE REGIONS OF MEXICODATA USED: 1,927,034 SPECIES OCCURRENCES

Esperon-Rodriguez M, Beaumont LJ, Lenoir J, Baumgartner
JB, McGowan J, Correa-Metrio A and Camac JS (2019)
Climate change threatens the most biodiverse regions of
Mexico. Biological Conservation. Elsevier BV 240: 108215.
Available at:https://doi.org/10.1016/j.biocon.2019.108215
Author countries/areas: Australia, France, Mexico

Climate change poses a major threat to global
biodiversity, however, identifying and conserving
potential stable climate refugia may help limit
biodiversity losses.

Harbouring nearly 10 per cent of the world’s
biodiversity, Mexico is a megadiverse country. In
this study, researchers focused on five bioclimatic
variables to assess the vulnerability to climate changeof 40 protected areas (PA) in Mexico. Using GBIFmediated occurrences in the same areas, the authors
analysed species richness and composition undercurrent and future climates.
Their results showed temperature increases for all
PAs, and for 31 PAs—habitat to more than 22,000
species—the climate will change completely by 2050.
The remaining nine PAs are predicted to retain about
half their baseline climatic space, and may to somedegree constitute potential refugia.
Species composition varied among PAs and the mostvulnerable appeared to cluster broadly in the central
mountainous regions and the tropical south-easternpart of Mexico. Considering all factors, the study
points to los Tuxtlas as the most vulnerable protected
area, and Tiburon Ballena as the least vulnerable.

ESTIMATING RANGE SIZES USING OPEN ACCESSBIODIVERSITY DATAa Smith JA, Benson AL, Chen Y, Yamada SA and Mims MC(2020) The power, potential, and pitfalls of open accessbiodiversity data in range size assessments: Lessons fromthe fishes. Ecological Indicators. Elsevier BV 110: 105896.
Available at:https://doi.org/10.1016/j.ecolind.2019.105896
Author countries/areas: USA
Research funding: Natural Environment Research Council

When prioritizing conservation efforts, the range sizeof a species is often used as a measure of rarity and to
determine its intrinsic risk of extinction. How ranges
are defined or estimated, however, may affect how
rare or common a species is seen to be, and whether
conservation efforts are justified.
Stream-dwelling organisms, such as freshwater
fishes constrained to river networks, may present a
particular challenge, and in this study, researchers
compared different methods of range size estimation
for freshwater species.
Initially selecting a wide taxonomic and geographic
representation of species, the authors gathered
GBIF-mediated occurrences of 128 fish species in
the conterminous United States and calculated range
sizes based on minimum convex polygons.
They then compared the GBIF-based results to range
sizes derived from NatureServe maps—considered
the best available estimates of current distributions—13

Importantly, both analytical approaches consistently
identified the rarest and perhaps most vulnerable
species, suggesting an important role of open datain filling fundamental knowledge gaps, especially forpoorly understood taxa.

Species richness was the most important factor
in explaining both collection density (positive
correlation) and inventory incompleteness (negative
correlation) across the region. The authors highlightthe importance of digitization and prioritizing futurecollection efforts, especially in low-density areas of
Kenya and Tanzania

USEFULNESS OF GBIF-MEDIATED OCCURRENCEDATA IN SPIDER RED LISTINGDATA USED: 4,528,821 SPECIES OCCURRENCES

a Shirey V, Seppälä S, Branco V and Cardoso P (2019)
Current GBIF occurrence data demonstrates both promise
and limitations for potential red listing of spiders.
Biodiversity Data Journal. Pensoft Publishers 7.
Available at: https://doi.org/10.3897/bdj.7.e47369
Author countries/areas: Finland, USA

Assessing the extinction risk status of a species, andprioritizing conservation efforts, require knowledge on
species populations and trends. With such data often
lacking, GBIF-mediated occurrence data can aid in
documenting species ranges and changes over time.
PELEGRINA AENEOLA OBSERVED IN GOAT MARSH, WASHINGTON, USA BY
CORNDOG. PHOTO VIA INATURALIST CC BY-NC 4.0.

PLANT INVENTORY COMPLETENESS AND
COLLECTION PATTERNS IN TROPICAL EAST AFRICADATA USED: 32,536,833 SPECIES OCCURRENCES

Wang S, Zhou Y, Musili PM, Mwachala G, Hu G and Wang Q(2020) Inventory incompleteness and collecting priority
on the plant diversity in tropical East Africa. BiologicalConservation. Elsevier BV 241: 108313. Available at:https://doi.org/10.1016/j.biocon.2019.108313
Author countries/areas: China, Kenya
Research funding: National Natural Science Foundation of
China

Primary biodiversity data is crucial to understanding
biogeographic patterns of species richness and forbeing able to predict impacts of climate change oranthropogenic activity on biodiversity.
Tropical East Africa has a very rich flora with
important hotspots. In this study, researchers use
plant data from GBIF and other sources to assess thecompleteness and collection patterns in the region.
Authors of the study find extremely uneven collection
densities across the region—with very low density innorthern Kenya and southern Tanzania. By comparing
richness observed in occurrence data with predictedrichness modelled using Maxent, the authors revealthat collection effort in half of East Africa is indeed
incomplete.

In this study, a group of researchers—including
one of the 2020 GBIF Young Researchers Awardwinners—assessed the usefulness of GBIF-mediatedoccurrences in deriving IUCN Red List classifications
based on Extent of Occurrence (EOO) calculations ina largely under-sampled taxon—spiders (Araneae)—by comparing hypothetical Red List classifications
derived from literature, GBIF data, and both combined.
The analysis showed that while GBIF data alone was
not sufficient for 88.7 per cent of the study species,
it enabled assessment of some species (3.3 percent) not classifiable based on literature alone. Ina few species, the addition of GBIF data changed
the hypothetical classification—in one species,
Myrmarachne bicolor, from Vulnerable to Least
Concern.
The results show the potential of using GBIF-mediateddata in extinction risk assessments, while highlighting
the importance of promoting increased digitizationand mobilization of data to GBIF.

biodiversity conservation

finding strong correlations between the approacheswith no detectable taxonomic bias.

14

Ecology

PRETZEL SLIME MOLD (HEMITRICHIA SERPULA) BY ALEXANDER SHIROKIKH VIA INATURALIST. PHOTO LICENSED UNDER CC BY-NC 4.0.

COORDINATECLEANER: FAST AND STANDARDIZEDCLEANING OF SPECIES OCCURRENCE DATADATA USED: 116M SPECIES OCCURRENCES

Zizka A, Silvestro D, Andermann T, Azevedo J, Duarte
Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R,
Svanteson S, Wengström N, Zizka V and Antonelli A (2019)
CoordinateCleaner: standardized cleaning of occurrence
records from biological collection databases. Methods in
Ecology and Evolution. Wiley. Available at:https://doi.org/10.1111/2041-210X.13152
Author countries/areas: Germany, Norway, Sweden,
Switzerland

With more than two scientific articles relying
on species occurrence data from GBIF.org
published every day, ensuring the data qualityof this indispensable resource is critical. Whilesmall datasets may be inspected visually, this is
impractical–if not impossible–for studies using
thousands or millions of records.
Faced with this challenge, a team of researchers
including the 2nd prize winner of the 2016 Ebbe
Nielsen Challenge developed CoordinateCleaner–a
new open source R library for standardized cleaningof species occurrence records. Based on a reference
database of coordinates indicating typical geolocation
problems, e.g. country centroids and capitals, aswell as coordinates of biodiversity institutions (e.g.
museums), CoordinateCleaner quickly flags records
with potential issues. The software also employs
novel algorithms to spot datasets including records
with systemized coordinate conversion and rasterized
sampling bias.
In an example using all GBIF-mediated recordsof flowering plants (~91 million records) and the
Paleobiology Database (19,000 records), the authors
demonstrate how CoordinateCleaner flags 3.6 per centof GBIF-mediated records and 6.3 per cent of PBDB
records as having potential geolocation issues. At
the contributing dataset level, the example flagged
four per cent of datasets for potential coordinate
conversion bias and 18.5 per cent of datasetsfor potential rounding or rasterization. While theoutput should not be taken as immediate grounds
for exclusion, it provides researchers with a moreobjective means of flagging datasets for manual caseby-case validation.
CoordinateCleaner provides a comprehensive setof routines that can help researchers perform fast,systematic and reproducible cleaning of occurrence
data for use in ecological, biogeographic andpaleontological studies.

15

DIVERSITY OF SLIME MOULDS–MUCH MORE THANMEETS THE EYE
Shchepin ON, Schnittler M, Erastova DA, Prikhodko IS,
Borg Dahl M, Azarov DV, Chernyaeva EN and Novozhilov YK(2019) Community of dark-spored myxomycetes in ground
litter and soil of taiga forest (Nizhne-Svirskiy Reserve,
Russia) revealed by DNA metabarcoding. Fungal Ecology.
Elsevier BV 39: 80–93. Available at:https://doi.org/10.1016/j.funeco.2018.11.006

Myxomycetes–or slime moulds–are fascinating
lifeforms with a complex life cycle involving a singlecell amoeba-like stage followed by multinuclear
aggregates, culminating in a fruiting body-likestructure with airborne spores restarting the cycle.
In a study of so-called dark-spored slime moulds,
researchers used DNA metabarcoding to assessthe diversity of myxomycetes in the lowland pine
forests of Nizhne-Svirskiy Reserve, Russia. Sampling
both ground litter and soil in separate study plots
representing four different stages after a forest
fire, followed by DNA extraction, amplification andsequencing, the authors produced more than 300,000
sequence reads based on myxomycete-specificprimers. These sequences clustered to fewer than
200 operational taxonomic units (OTU), of which theauthors identified 15 species and nine genera.

Reconstructing a complete angiosperm phylogeny
while gathering data on chromosome numbers andGBIF-mediated occurrences, this study maps theglobal distribution of polyploid frequency amongnearly 135,000 plant species. The resulting maps
show a clear latitudinal pattern with polyploidy
increasing towards the poles. At the biome-level, mostpolyploid plants are found in tundras. Most ecoregions
show the same patterns as their biomes—with somenotable polyploid-rich tropical ecoregions, such as theAndes and Hawaii.
Exploring possible environmental drivers, the authors
show that polyploidy is correlated with temperature,
prevailing in cooler climates. The effect, however,appears predominantly mediated by the indirect
impact of temperature on the floral composition of
ecoregions.

Comparing identified taxa against GBIF-mediatedoccurrences, the authors found four species new
to the Leningrad region. While the myxomycete
composition shifted significantly with the fire historyof a plot, the authors were unable to find a clear
chronosequence, suggesting that factors shaping
assemblages are not simply a linear product of time
passed since a fire.
The study identifies DNA metabarcoding as a useful
tool in describing slime mould diversity, as invisible
amoeba-stage populations are much more widespreadthan the recordings of visible fruiting bodies.

THE GLOBAL DISTRIBUTION AND DRIVERS OF
POLYPLOIDY IN PLANTSDATA USED: 113,504,266 SPECIES OCCURRENCES

Rice A, Šmarda P, Novosolov M, Drori M, Glick L, Sabath
N, Meiri S, Belmaker J and Mayrose I (2019) The global
biogeography of polyploid plants. Nature Ecology &Evolution. Springer Science and Business Media LLC 3(2):265–273.
Available at: https://doi.org/10.1038/s41559-018-0787-9
Author countries/areas: Czechia, Israel

A HEXAPLOID, CALIFORNIA REDWOOD (SEQUOIA SEMPERVIRENS) HAS SIX
COPIES OF EACH CHROMOSOME. PHOTO BY VENETIAN3 (CC BY-NC 4.0).

ecology

Author countries/areas: Germany, New Zealand, Russia

Polyploidy—having more than two copies of eachchromosome—is often lethal in animals, but notan uncommon phenomenon in plants. In fact, allangiosperm species are believed to have undergone
one or more polyploidization events in their lifetime.
Allopolyploidy—when the genomes of two different
species merge and hybrids arise—can result in higher
capacity for adaptation, but what are the drivers andhow are the polyploid plants distributed globally?

16

THE ROLE OF HORTICULTURE IN FACILITATING
PLANT INVASIONS

ecology

Guo W, van Kleunen M, Pierce S, Dawson W, Essl F, Kreft
H, Maurel N, Pergl J, Seebens H, Weigelt P and Pyšek P(2019) Domestic gardens play a dominant role in selecting
alien species with adaptive strategies that facilitate
naturalization. Global Ecology and Biogeography. Wiley
28(5): 628–639. Available at:https://doi.org/10.1111/geb.12882
Author countries/areas: China, Czechia, Denmark, Germany
Research funding: Austrian Science Fund, Deutsche
Forschungsgemeinschaft, Akademie Věd České Republiky,
Grantová Agentura České Republiky

More than 13,000 naturalized alien species ofvascular plants have been recorded worldwide, andhorticulture is the major pathway of plant invasions.
Botanic gardens play a vital role in conserving plant
diversity and preventing extinction, but they also
cultivate many species with invasion potential.
Examining the role of horticulture in plant invasions,this study rigorously examines the direct and indirect
relationships between species traits, horticulturaluse, native range size and naturalization success.
Using a dataset—downloaded from GBIF and othersources—of nearly 4,000 species with defined
adaptive strategies, the authors reveal that speciesgrown in botanic or domestic gardens are significantly
more likely to become naturalized than those notcultivated.
The study finds that naturalization is linked toparticular adaptation strategies among plant species,
but that species using these strategies are also more
likely to be cultivated. In other words—horticulture is
not just a major pathway for invasions, it also tends
to select alien species with the highest invasive
potential.

TERRESTRIAL HOTSPOTS OF EVOLUTIONARY
DIVERSITY POINT TO NEW PRIORITIES FORCONSERVATIONDATA USED: OCCURRENCES OF 6,483 GENERA

Daru BH, le Roux PC, Gopalraj J, Park DS, Holt BG and Greve
M (2019) Spatial overlaps between the global protectedareas network and terrestrial hotspots of evolutionary
diversity. Global Ecology and Biogeography. Wiley 28(6):757–766. Available at:https://doi.org/10.1111/geb.12888
Author countries/areas: Denmark, South Africa, UK, USA

Identifying biodiversity hotspots is a common
approach for prioritizing conservation. Most suchdesignations, however, rely on species-level metrics
and largely ignore phylogenetics. Although notnecessarily more informative than species-level
hotspots, phylogenetic diversity hotspots canrepresent evolutionary history and, potentially,
adaptive capacity.
Integrating data on phylogeny and geographicaldistribution of amphibians, mammals, birds andangiosperms mediated by GBIF, this study identifies
29 clusters of phylogenetic diversity worldwide. Whilea large proportion of these overlap with specieslevel hotspots, the study finds novel hotspots ofphylogenetic diversity in Central Chile, Honshu(Japan), New Caledonia, the Appalachian Mountains
and parts of Texas.
Across all taxonomic groups, the most
phylogenetically diverse concentrations were foundin tropical regions, and overall, fewer than 10 per centof phylogenetic diversity hotspots are designated asprotected areas.

COMMON STAR-OF-BETHLEHEM (ORNITHOGALUM UMBELLATUM) OBSERVED IN ATLANTA, USA BY MRSDYNE. PHOTO VIA INATURALIST (CC BY-NC 4.0)

17

The resulting phylogeny revealed a major classwide species radiation in the Jurassic, coinciding
with angiosperm expansions. Several clade-specificadaptive radiations also took place, offering an
explanation for mushroom genera with thousands ofspecies.

VELVET FOOT (FLAMMULINA VELUTIPES) OBSERVED IN KURSK OBLAST,RUSSIA BY RYZHKOV OLEG. PHOTO VIA INATURALIST (CC BY-NC 4.0)

GLOBAL ANALYSIS OF EVOLUTIONARY HISTORY OF
MUSHROOM-FORMING FUNGIDATA USED: 5,884,445 SPECIES OCCURRENCES

a Varga T, Krizsán K, Földi C, Dima B, Sánchez-García
M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V,
Albert L, Andreopoulos W, Angelini C, Antonín V, Barry KW,
Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P,
Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml
J, Haridas S, Hughes K, Justo A, Karasiński D, Kautmanova
I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE,
Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado
LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B,
Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop
K, Spirin V, Szebenyi C, Tomšovský M, Tulloss RE, Uehling
J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O,
Hibbett DS and Nagy LG (2019) Megaphylogeny resolves
global patterns of mushroom evolution. Nature Ecology &Evolution. Springer Science and Business Media LLC 3(4):
668–678. Available at:https://doi.org/10.1038/s41559-019-0834-1
Author countries/areas: Argentina, Australia, Austria,
Canada, Czechia, Dominican Republic, Estonia, Finland,
France, Hungary, Italy, Netherlands, New Zealand, Norway,
Poland, Russia, Slovakia, Sweden, USA

Playing a variety of roles in ecosystems, mushroomforming fungi (Agaricomycetes) are the most diverseand complex group within the fungal kingdom, withmore than 20,000 described species.
In this paper, researchers from institutions in
19 countries present a new, comprehensive
megaphylogeny of mushroom-forming fungi,
comprising 5,284 species of which more than 1,200
species were specifically sampled as part of thestudy.

The classic toadstool morphology is associated withincreased rates of lineage diversification and thus
appears to have been a key innovation in the evolutionof mushroom-forming fungi, shaping the extant
diversity of the class.

MAPPING ENVIRONMENTAL PROPERTIES IN
DATA-POOR AREAS USING SPECIES OCCURRENCESDATA USED: 30,000 SPECIES OCCURRENCES

Zuquim G, Stropp J, Moulatlet GM, Van doninck Jasper,
Quesada CA, Figueiredo FOG, Costa FRC, Ruokolainen K
and Tuomisto H (2019) Making the most of scarce data:
Mapping soil gradients in data-poor areas using species
occurrence records. Methods in Ecology and Evolution.
Wiley 10(6): 788–801. Available at:https://doi.org/10.1111/2041-210X.13178
Author countries/areas: Brazil, Ecuador, Finland

Environmental data is commonly used to define
ecological niches and to model species distributions.
When environmental data is scarce, however, thepresence of indicator species can be used to inferenvironmental conditions.
In this study, authors outline a method for generating
environmental maps derived from plot data in threelayers: 1) indicator species with known environmental
tolerances, 2) species occurrences from e.g. GBIF, and
3) environmental data only.
From the first layer, the authors are able to derive
an environmental optimum. In the next step, thiscan be used to infer estimates of environmental
properties at species-only plots. These estimates,when interpolated with known environmental plots,
generate a map of an area of interest that can bevalidated using an external dataset.
The authors employ the proposed framework tosuccessfully produce a map of soil quality (asmeasured through the concentration of positively
charged ions) for Amazonia using ferns andlycophytes as indicator species, leading to a 12-foldincrease in environmental data.

ecology

Using GBIF-mediated mushroom occurrences, theauthors found the highest speciation rates in thetemperate zone, contrasting with the latitudinal
diversity gradient observed in plants and animals, forwhich diversity tends to be higher in the tropics.

18

EXPLORING THE GLOBAL DISTRIBUTION OF
MYCOHETEROTROPHIC PLANTSDATA USED: 32,752 SPECIES OCCURRENCES

ecologya Gomes SIF, van Bodegom PM, Merckx VSFT and
Soudzilovskaia NA (2019) Global distribution patternsof mycoheterotrophy. Global Ecology and Biogeography.
Wiley. Available at: https://doi.org/10.1111/geb.12920
Author countries/areas: Netherlands
Research funding: Nederlandse Organisatie voor
Wetenschappelijk Onderzoek

In mycorrhizal symbioses, plants exchange
photosynthesized carbohydrates for mineral
nutrients from fungi in the soil. Mycoheterotrophic
plants, however, cheat—and obtain carbon from theirfungal partners as well, sometimes leading to thecomplete loss of photosynthesis.
In this study, Dutch researchers explore theenvironmental preferences of mycoheterotrophic
plants and drivers of their global distribution.
Using GBIF-mediated occurrences of all known
mycoheterotrophic species, the authors compile alarge dataset with information on soil, climate, type ofmycorrhizal fungi and autotrophic hosts.
Their analysis shows that mycoheterotrophic plants
tend to avoid cold and highly seasonal climates.
Plants associated with so-called arbuscular fungi arefound in broadleaved tropical forests, whereas those
preferring the company of ectomycorrhizal fungi
occur in temperate regions—primarily needle-leaved
forests.
This pattern appears to be driven by climatic factors—
primarily temperature and precipitation—rather thanabundance of specific autotrophic hosts from which
the fungi-mediated nutrients are derived.

ESTIMATING RANGE EXTENTS OF MUSHROOMFORMING FUNGI USING OTUS
DATA USED: 155,363 SPECIES OCCURRENCES

Accurate knowledge on fungus distributional ranges,
however, may be hampered by overestimations due tobroad species delimitations.
Using genetically defined operational taxonomic
units (OTUs) from the UNITE database, this study
by Canadian researchers attempts to improve
this knowledge by analysing global data from 12
mushroom-forming fungus genera. They augmented
this dataset by sampling 600+ mushroom specimens
found in Washington and British Columbia.
As many OTU records lack precise locality data, theauthors used country centroids to estimate ranges—amethodology they verified by comparing estimatedrange extents with GBIF-mediated occurrences of
species of four well-studied tree genera.
The overall results put the median range extent ofmushroom OTUs at 1,200 to 4,039 km and suggest
a biogeographic structure as opposed to global
distributions—of mushroom-forming fungi.

COLD-ADAPTED PLANT RICHNESS IN THE
NORTHERN HEMISPHEREDATA USED: 140,229,903 SPECIES OCCURRENCES

Hagen O, Vaterlaus L, Albouy C, Brown A, Leugger F, Onstein
RE, Santana CN, Scotese CR and Pellissier L (2019)
Mountain building, climate cooling and the richness ofcold-adapted plants in the Northern Hemisphere. Journalof Biogeography. Wiley 46(8): 1792–1807. Available at:https://doi.org/10.1111/jbi.13653
Author countries/areas: France, Switzerland, Germany, USA
Research funding: Deutsche Forschungsgemeinschaft

Plants in cold climates have evolved to have lower
stature, tougher leaves, and biochemical properties
preventing the formation of ice crystals. Even thoughlineages of such cold-adapted vascular plantsfrom mid-latitude mountain regions—such as theHimalayas and Rocky Mountains—are also found in
Arctic regions, species richness is lower in the Arctic.

Author countries/areas: Canada
Research funding: Natural Sciences and Engineering
Research Council of CanadaThis study used GBIF-mediated occurrences ofmore than 5,000 species occupying cold climatesto generate stacked distribution maps confirming
this observation. The authors used a model to derive
environmental predictors of cold-adapted richness
patterns, showing that richness is strongly associatedwith ecoregions.

Genetically more closely related to animals thanto plants, fungi constitute the third kingdom ofeukaryotic organisms. Essential to terrestrial
ecosystems, they facilitate wood decay and form
mycorrhizal symbioses with autotrophic plants.

Mapping the cold climate of the entire Northern
Hemisphere from 60 million years ago to now, theauthors showed that while cold regions—with
temperatures below 0°C—started appearing in midlatitude regions with the Himalayan uplift about 42

Bazzicalupo AL, Whitton J and Berbee ML (2019) Over thehills, but how far away? Estimates of mushroom geographic
range extents. Journal of Biogeography. Wiley. Available at:https://doi.org/10.1111/jbi.13617

19

million years ago, cooling in the Arctic did not start
until about 10 million years later, and the region as awhole was not comparably cold until much later.
The overall results indicate that early cooling of alpine
regions allowed for evolution and diversification ofcold-adapted vascular plants, followed much later bycolonization of the Arctic.

DATA USED: 247,231,174 SPECIES OCCURRENCES

a Staude IR, Navarro LM and Pereira HM (2019) Range
size predicts the risk of local extinction from habitat loss.
Global Ecology and Biogeography. Wiley 29(1): 16–25.
Available at: https://doi.org/10.1111/geb.13003
Author countries/areas: Germany
Research funding: Deutsche Forschungsgemeinschaft

At the global scale, species with small ranges are more
likely to face extinction when threatened by changes
in climate or land use. It is not well-documented,
however, whether this risk also applies at the local
level.
This study by researchers from Germany usedhistorical land-use data combined with GBIF-mediatedplant occurrences to derive species range based on
the number of grid cells occupied by a given species.
They then identified cells that had experienced natural
habitat loss and the species present before and after
the change.

At 80 per cent habitat loss, for example, theprobability of persisting for species with larger ranges
is higher than 85 per cent, while small-range species
have a significantly lower persistence probability of
75 per cent.

DISCRIMINATION ACCURACY UNINFORMATIVE
WHEN EVALUATING SPECIES DISTRIBUTIONMODELSDATA USED: 5,969,252 SPECIES OCCURRENCES

a Warren DL, Matzke NJ and Iglesias TL (2019)
Evaluating presence-only species distribution models
with discrimination accuracy is uninformative for many
applications. Journal of Biogeography. Wiley 47(1):167–180. Available at: https://doi.org/10.1111/jbi.13705
Author countries/areas: Australia, Germany, Japan,
New ZealandResearch funding: Macquarie University, Australian
Research Council

Species distribution models (SDMs) are popular
tools—easy to build using data freely available—and,in some cases the only tractable means of estimating
habitat suitability. The ability to predict withheld
data (discrimation accuracy) is often used to makedecisions on models, methods and data.
Using a simulation approach, this study evaluates
the relationship between discrimination accuracy
and functional accuracy to assess commonlyused methods for selection of models. The authors
simulated occurrence data across 11 levels ofsampling bias—modelled using GBIF-mediated data ofall plants in Australia—performing 20 simulations foreach and using four experimental scenarios to build
models based on seven algorithms, resulting in a totalof 6,160 models.
The results showed a fairly good functional accuracyof models overall—that is, modelled suitability
matched true suitability of habitat. However, acrossnearly all algorithms and levels of complexity thediscrimination capacity was a very poor predictor offunctional accuracy, indicating that assessing models
based on this approach might be less than ideal.

GENTIANA DEPRESSA OBSERVED IN LANGTANG, NEPAL BY YALING LIN.
PHOTO VIA INATURALIST (CC BY-NC 4.0)

ecology

HIGHER RISK OF LOCAL EXTINCTION FOR SPECIESWITH SMALL RANGESGrouping species into small or large ranges, the author
calculated the probability of a group persisting at agiven amount of habitat loss, showing that smallrange species have a steeper decline than large-range
plants.

20

DESCRIBING BROAD-SCALE DIVERSITY PATTERNSUSING HERBARIUM DATADATA USED: 4,251,424 SPECIES OCCURRENCES

ecology

Bottin M, Peyre G, Vargas C, Raz L, Richardson JE andSanchez A (2019) Phytosociological data and herbarium
collections show congruent large-scale patterns but differ
in their local descriptions of community composition.
Journal of Vegetation Science. Wiley 31(1): 208–219.
Available at: https://doi.org/10.1111/jvs.12825
Author countries/areas: Colombia, UK

The study of vegetation turnover, composition
gradients and beta-diversity requires systematicallycollected sampling data from vegetation plots andrelevés. Occurrence data from museum and herbarium
specimens, however, may be used in cases wheresuch data is scarce.
This study compares phytosociological vegetation
data with mainly GBIF-mediated herbarium data frompáramos (alpine ecosystems) in Colombia in theirability to describe diversity patterns and species
composition gradients.
The authors show that overall species compositiondiffered between the two datasets—perhaps
explained by a bias towards charismatic and/or
rare species in the herbarium data. So while a large

number of species were present in a few locations in
the herbarium data—and absent from the plot data—
many species present in the plot data were common
to a larger number of plots than described by theherbarium data.
Pairwise beta-diversity analyses showed nosignificant differences between the datasets, andamong common species, ecological distributions
patterns were similar. The authors conclude thatwhile plot data is best for describing local patterns,
combining data from the two sources may be efficientat broader scales.

ECO-GEOGRAPHICAL ANALYSIS OF RARE ENDEMIC
PLANTS OF SIBERIA
Baikov KS, Baikova EV and Banaev EV (2019) Ecologicaland Geographical Analysis of Endemic Vascular Plants
in Siberia and Problems of Their Conservation Ex Situ.
Contemporary Problems of Ecology. Pleiades Publishing
Ltd 12(5): 418–433. Available at:https://doi.org/10.1134/S1995425519050032
Author countries/areas: Russia

Endemic species are only found in a single
geographical location, zone or habitat type.
Some very rare species are only known from thefirst location in which they were originally described(stenoendemics).
In this study, researchers from Russia developed
a custom nine-point ranking system based on
characteristics such as stenoendemism, typificationand inclusion in red lists to identify the 50 rarest
vascular plant species in Siberia. Using herbarium
data published through GBIF, the authors analysed
the taxonomic composition and eco-geographicalfeatures of these species in order to develop scientificrecommendations for their conservation.
The 50 identified species make up about 1.1 percent of the total number of known vascular plants
in Siberia. The most widely represented families
are Asteraceae (nine species), Rosaceae (sevenspecies), and Ranunculaceae (four species). Morethan 80 per cent of the studied species are found in
the southern hemi-boreal zone (areas of mixed boreal
and temperate forests), and nearly half belong to the
Altai-Siberian ecoregion.
The study finds a low level of state protection of
the studied species and recommends inclusionof endemic Siberian species into lists of rare andendangered plants of Russia.

ALCHEMILLA CIRCULARIS RECORDED IN CHAYKOVSKIY RAYON, PERM KRAI,RUSSIA BY OVESNOV A. PHOTO VIA MOSCOW STATE UNIVERSITY (CC BY 4.0)

21

Help promote open biodiversity data

SAULCY'S LEAFCUTTER (MEGACHILE SAULCYI) OBSERVED IN SANTIAGO, CHILE BY ORLANDOMONTES. PHOTO VIA INATURALIST (CC BY-NC 4.0)

☑ You can provide at least one example in which you haveshared biodiversity data through GBIF, used GBIF-mediateddata, and/or advocated open data in your professional
capacity☑ You agree with the ICSU-World Data System Data Sharing

Principles—in short, that data should be shared openly ina timely manner, with the fewest restrictions possible andused with proper citation☑ You agree to share your contact information on GBIF.org, andpossibly on websites run by GBIF nodes and partners☑ You allow the GBIF Secretariat and GBIF nodes to contact you
about opportunities to promote open biodiversity data at
specific events☑ You commit to providing details annually about at least one

event, publication or process in which you have advocatedfor open biodiversity data

If you can check all of the above, then maybe you’re the next Biodiversity Open Data Ambassador!
For more information about the programme and how to apply, please visit

http://bit.ly/bodamba

22

Environmental Sciences

POLAR BEARS (URSUS MARITIMUS) BY SANDRA EGLĪTE VIA INATURALIST. PHOTO LICENSED UNDER CC BY-NC 4.0.

AMAZONIA FACING THREATS OF DEFORESTATIONAND CLIMATE CHANGEDATA USED: OCCURRENCES OF 6,394 SPECIES

Gomes VHF, Vieira ICG, Salomão RP and ter Steege H (2019)
Amazonian tree species threatened by deforestation andclimate change. Nature Climate Change. Springer Scienceand Business Media LLC 9(7): 547–553. Available at:https://doi.org/10.1038/s41558-019-0500-2
Author countries/areas: Brazil, Netherlands

Holding close to 13 per cent of all trees of the world,
the Amazonian lowlands is the largest rainforest blockon Earth with a richness of up to 16,000 species.
This immense tree diversity is threatened by bothdeforestation and climate change, and assessing
the relative impacts of these threats is crucial toconservation.
In this study, researchers used environmental
suitability models based on GBIF-mediatedoccurrences of nearly 7,000 Amazonian trees toestimate impacts of climate change. They also usedhistorical deforestation data to predict future losses.
The authors found that by 2050, deforestation alone
may cause a decline in richness of 19-36 percent,while climate change may account for 31-37 per cent.
Combined, however, the effect may reach 58 per centloss of richness—with the worst outlook in the portionof the Amazonian forest outside current protectedareas, accounting for roughly half of the total.
With the major importance of the rainforest inabsorbing atmospheric C02 and regulating climate,this study urges expanded protected area networks
and an urgent halt to deforestation, to help mitigate
climate change and avoid species collapse inAmazonia.

FRESHWATER MANAGEMENT USING MULTIOBJECTIVE OPTIMIZATION OF SPECIESDISTRIBUTION MODELSDATA USED: 65,000 SPECIES OCCURRENCES

GGobeyn S and Goethals PLM (2019) Multi-objective
optimisation of species distribution models for rivermanagement. Water Research. Elsevier BV 163: 114863.
Available at:https://doi.org/10.1016/j.watres.2019.114863
Author countries/areas: Belgium

Modelling freshwater species distributions canbe challenging, as biases in the case of species
that are obscure or difficult to observe may lead tounderestimating the true habitat suitability. In thispaper, authors present a solution to this problem
involving optimizing models based on multiple

23

Under the Paris Agreement of the UN Framework
Convention on Climate Change, countries have
Using data from the GBIF-mediated Limnodata
pledged to reduce greenhouse gas emissions in order
Neerlandica dataset, the authors evaluated theperformance of their multi-objective optimization (MOO) to limit global warming. Current data, however, showsthat contributions are falling short of the required
approach—called the non-dominated sorting genetic
levels towards limiting warming to even 2°C above prealgorithm II—against regular single objective models
industrial levels.
of 11 pollution-sensitive macroinvertebrate species
objectives rather than just one.

(including Cloeon dipterum shown above).

THE IMPLICATIONS OF THE PARIS AGREEMENT ON
CLIMATE CHANGE FOR GLOBAL BIODIVERSITY
HOTSPOTSDATA USED: OCCURRENCES OF 80,000 SPECIESa Warren R, Price J, VanDerWal J, Cornelius S and Sohl
H (2018) The implications of the United Nations Paris
Agreement on climate change for globally significant
biodiversity areas. Climatic Change. Springer Science andBusiness Media LLC 147(3-4): 395–409. Available at:https://doi.org/10.1007/s10584-018-2158-6
Author countries/areas: Australia, UK
Research funding: Natural Environment Research Council

The results show that without mitigation, on average
only 33 per cent of each conservation area will
be available as a climate refugium. If warming islimited to 2°C, however, the average refugium area isdoubled. The authors conclude that limiting warming
to well below 2°C would further reduce risk of local
extinctions.

CROP SECURITY AND ADAPTIVE STRATEGIES IN
SUB-SAHARAN AFRICA UNDER CLIMATE CHANGEDATA USED: OCCURRENCES OF 807 SPECIESPironon S, Etherington TR, Borrell JS, Kühn N, Macias-Fauria
M, Ondo I, Tovar C, Wilkin P and Willis KJ (2019) Potential
adaptive strategies for 29 sub-Saharan crops under futureclimate change. Nature Climate Change. Springer Scienceand Business Media LLC 9(10): 758–763. Available at:https://doi.org/10.1038/s41558-019-0585-7
Author countries/areas: New Zealand, UK

With climate change expected to negatively impact
agriculture, devising adaptive strategies for crops is
an important step in overcoming this global challenge.
In this study, researchers developed an analyticalframework for assessing crop security and mitigating
strategies for agriculture in sub-Saharan Africa,
considered especially at risk due to its tropicallocation, socioeconomic policy and farming
characteristics.
Based on occurrence data from GBIF and othersources, the authors modelled the climatic niches of
29 major crops and 778 of their wild relatives—now
and in the future—to determine crop security.

CARRION CROW BUSH (SENNA RETICULATA) OBSERVED IN MANAUS, BRAZILBY CRAX. PHOTO VIA INATURALIST (CC BY-NC 4.0)

For each crop they then assessed the potential
success of three strategies: switching to cultivars
from other continents, using wild relatives, or—in theworst cases—replacing with another sub-SaharanAfrican crop.

environmental sciences

Their results showed that the MOO approach is twoto-four times more efficient at identifying large range
distributions, while only requiring four per cent longer
runtimes per training. To support decision-making,the authors propose a closer collaboration between
model developers and freshwater managers to set
environmental standard limits on a more objective
basis.

In this study, researchers modelled the distributionsof ~80,000 plants and animals using GBIF-mediateddata to assess the risks to species in globallysignificant biodiversity conservation areas,
quantifying the benefits of national emission
reductions and the effects of limiting warming to 2°C
against 4.5°C in the unmitigated scenario.

24

evolutionary biology

Evolutionary Biology

MACRACANTHA ARCUATA OBSERVED IN GUNUNG MULU NATIONAL PARK, MALAYSIA. PHOTO 2019 KAL SQUIRES VIA INATURALIST UNDER (CC BY-NC 4.0)

EFFECTS OF SAMPLING BIAS ON STABILITY OF
AREAS OF ENDEMISMDATA USED: 34,000 SPECIES OCCURRENCES

Casagranda MD and Goloboff PA (2019) On stability
measures and effects of data structure in the recognitionof areas of endemism. Biological Journal of the Linnean
Society. Oxford University Press (OUP) 127(1): 143–155.
Available at: https://doi.org/10.1093/biolinnean/blz019
Author countries/areas: Argentina

Biases in data—whether geographic or taxonomic—all
introduce uncertainty in downstream analyses which
can affect results and misrepresent the real world.
This study attempts to quantify the effects ofdifferent types of biases by introducing two
stability measures—one for geography and one fortaxonomy—to indicate the degree to which a biased
dataset agrees with its unbiased version.
Using three datasets, including a GBIF download of
all Amazonian amphibians, researchers artificiallyintroduced "biases" by randomly removing increasing
fractions of records for 1) all species, 2) specificsubsets of species, and 3) within defined geographicalsectors—to emulate problems of poor sampling,
uneven sampling and geographical bias, respectively.
In analyses focused on specific areas of endemism,
the authors compared results from the original datawith intentionally biased data to uncover measures ofstability—that is, the degree to which the biased data
leads to the same predictions as the unbiased data.

In nearly all cases, stability diminished with increased
removal of data. However, it seems that data
incompleteness had a bigger impact on taxonomic
stability, indicating perhaps on a positive notethat even scattered data can lead to fair spatial
identification of areas of endemism.

UNTANGLING THE PHYLOGENETIC WEBS OF
ORB-WEAVING SPIDERSDATA USED: 66,479 SPECIES OCCURRENCES

Scharff N, Coddington JA, Blackledge TA, Agnarsson I,
Framenau VW, Szűts T, Hayashi CY and Dimitrov D (2019)
Phylogeny of the orb-weaving spider family Araneidae(Araneae: Araneoidea). Cladistics. Wiley 36(1): 1–21.
Available at: https://doi.org/10.1111/cla.12382
Author countries/areas: Australia, Denmark, Hungary,
Norway, USA

The third-most speciose family of spiders, Araneidae(the orb-weaving spiders) has been widely studied
from within various branches of research including
behavioral science, ecology, material science,
genomics and pharmacology. Modern phylogenetic
revisions of the family, however, have been
geographically limited.
Continuing previous work on Araneid evolution anddiversification, the authors of this study present a
new phylogeny, based on genetic samples from 158
taxa. Using GBIF-mediated occurrences they generate
a map of the global distribution of Araneid species andadd many understudied species from the southernhemisphere to get a true global representation of

25

the family. Surprisingly, many clades named in the
new phylogeny cannot be corroborated by current
knowledge from morphological or behavioral studies.
Based on the phylogeny, the authors also analysed
the evolution of sexual size dimorphism and web
architecture. While genera exhibiting the former
did not form a distinct clade, several patterns
were discovered for web architecture including amonophyletic group of spanning thread web spiders.

EXPLORING THE MECHANISMS UNDERLYINGCONIFER HOTSPOT FORMATIONDATA USED: 324,485 SPECIES OCCURRENCES

Author countries/areas: USA

Biodiversity is not distributed evenly across theplanet, but follows patterns such as the latitudinal
species gradient or assemblages in regional
hotspots. Understanding these differences in spatial
distribution and what causes them is a crucial aspectof evolutionary ecology.
This paper uses the global distribution of conifers to
explore mechanisms underlying biodiversity hotspot
formation. Its authors derived species ranges and—
subsequently—assemblages from GBIF-mediatedoccurrence data to identify eight richness hotspots,
while analysing a wide range of characteristics tocompare these with non-hotspots.
In their analysis, they find greater topographic
heterogeneity in hotspots than surrounding areas,
although not consistently associated with differencesin climate or soil types. Comparing traits, the authors
show minor, but non-consistent differences between
hotspot and non-hotspot species.

SEX BIASES IN NATURAL HISTORY COLLECTIONSDATA USED: 6.6 M SPECIES OCCURRENCES

Cooper N, Bond AL, Davis JL, Portela Miguez R, Tomsett
L and Helgen KM (2019) Sex biases in bird and mammal
natural history collections. Proceedings of the Royal
Society B: Biological Sciences. The Royal Society
286(1913): 20192025. Available at:https://doi.org/10.1098/rspb.2019.2025
Author countries/areas: Australia, UK

Often treated as a nuisance variable—or overlooked
altogether—the biological sex of an organism is
an important factor affecting many aspects of theindividual's ecology and behaviour. Among museum
collection specimens, biased sex ratios could haveserious implications for studies that rely on them.
This study examines GBIF-mediated records of morethan 2.4 million bird and mammal specimens fromfive major international museums. For birds, 20 per
cent were female, 31 per cent male and 49 per centunsexed, while for mammals—likely easier to sex—
only 15 per cent of specimens were unsexed, 44 percent were male and 41 per cent were female.
This bias was not due to unsexed specimens
being female. Even species that exhibit femaleskewed ratios in the wild, showed male bias among
specimens.
The authors found no significant improvement in sex
balance over the last 130 years.
The most notable finding of the study was among thename-bearing type specimens (holotypes, syntypes,
lectotypes, and neotypes), where only 25 per cent ofbirds and 39 per cent of mammals were females.

FEMALE SPECIMEN OF A NORTHERN YELLOW-SHAFTED FLICKER (COLAPTES AURATUS SUBSP. LUTEUS) COLLECTED IN EVANSTON, ILLINOIS, USA.
PHOTO VIA THE FIELD MUSEUM (CC-BY-NC 4.0)

evolutionary biology

Sundaram M, Donoghue MJ, Farjon A, Filer D, Mathews
S, Jetz W and Leslie AB (2019) Accumulation overevolutionary time as a major cause of biodiversity hotspots
in conifers. Proceedings of the Royal Society B: Biological
Sciences. The Royal Society 286(1912): 20191887.
Available at: https://doi.org/10.1098/rspb.2019.1887

Overall, the study suggests a bigger role played bygeography than biology, and that hotspots form not asa result of unique diversification processes, but rather
a simple accumulation of regional diversity in stable,
mountainous areas.

26

DISTURBANCE SHAPING THE ELEVATION RANGESOF TREES IN COSTA RICADATA USED: 126,066 SPECIES OCCURRENCES

a Muñoz Mazón M, Klanderud K, Finegan B, Veintimilla
D, Bermeo D, Murrieta E, Delgado D and Sheil D (2019)
Disturbance and the elevation ranges of woody plant
species in the mountains of Costa Rica. Ecology and
Evolution. Wiley 9(24): 14330–14340. Available at:https://doi.org/10.1002/ece3.5870

evolutionary biology

Author countries/areas: Costa Rica, Germany, Norway
Research funding: Norges Miljø- og Biovitenskapelige
Universitet

In ecology, disturbance caused by transient reduction
in competition resulting from vegetation death orremoval—through e.g. grazing, mowing or controlledburning—can help promote species diversity at local
scales, but how it might shape distributions at larger
scales is unknown.

In this study, researchers examined and compared theelevation range limits of tree species in undisturbed
old-growth and secondary forests of Costa Rica.
Using plot data and GBIF-mediated occurrences of
7,750 individual tree stems representing more than
490 species, the authors calculated elevation rangesof all species and analysed relationships with otherparameters.
In their results, species ranges increased withelevation. Consistent with the authors' predictions,species in secondary growth forests had wider
elevation ranges than species in old growth—apattern also seen in larger stems compared tosmaller stems. Despite some noise and uncertainty,
these results together add evidence to the role ofdisturbance in expanding tree elevation ranges.

QUERCUS COSTARICENSIS OBSERVED IN COSTA RICA BY BOTANICALKATZ. PHOTO VIA INATURALIST (CC BY-NC 4.0)

27

Multidisciplinary Sciences

HARLEQUIN RACERUNNER (PLICA UMBRA) OBSERVED IN BORBA, AMAZONAS, BRAZIL BY JONATHAN NEWMAN. PHOTO VIA INATURALIST (CC BY-NC 4.0)

REDUCING EFFECTS OF SAMPLING GAPS INCONSERVATION MAPPINGDATA USED: 659,062 SPECIES OCCURRENCES

a Oliveira U, Soares-Filho BS, Santos AJ, Paglia AP,
Brescovit AD, de Carvalho CJB, Silva DP, Rezende DT, Leite
FSF, Batista JAN, Barbosa JPPP, Stehmann JR, Ascher JS,
Vasconcelos MF, Marco PD, Löwenberg-Neto P and Ferro
VG (2019) Modelling Highly Biodiverse Areas in Brazil.
Scientific Reports. Springer Science and Business MediaLLC 9(1). Available at:https://doi.org/10.1038/s41598-019-42881-9
Author countries/areas: Argentina, Brazil, Singapore

In megadiverse regions and countries, gaps inbiological sampling can make traditional mapping
approaches for conservation difficult. Strategies
developed for well-sampled regions may produce
unsatisfactory results when applied in countries withless even sampling—such as Brazil.
In this study, authors developed a new comprehensive
spatial framework for mapping highly biodiverse areas
in Brazil using species occurrences as mediated by
GBIF and applying special techniques to reduce theeffect of irregular sampling. From thoroughly cleaned
species records and a phylogenetic supertree, theauthors derive a range of quantitative biodiversity
variables, including composition, richness andendemism—both at the species and phylogenetic
level.
Summarizing the quantitative variables at a regional
scale, the model identifies the smallest possible

areas with the most unique biodiversity, producing
a map of relevant priority areas for biodiversity
conservation. In the optimal solution, the model isable to encompass ~90 per cent of known biodiversity
in only 10 per cent of the country's area.

PALEOCLIMATIC ANALYSIS OF EARLY EOCENE
TRANSIENT GLOBAL WARMING EVENTSDATA USED: 6,282,569 SPECIES OCCURRENCES

Willard DA, Donders TH, Reichgelt T, Greenwood DR,
Sangiorgi F, Peterse F, Nierop KGJ, Frieling J, Schouten S
and Sluijs A (2019) Arctic vegetation, temperature, andhydrology during Early Eocene transient global warming
events. Global and Planetary Change. Elsevier BV 178:
139–152. Available at:https://doi.org/10.1016/j.gloplacha.2019.04.012
Author countries/areas: Canada, Netherlands, USA

Global temperatures have been both much higher
and much lower than the current average, andunderstanding paleoclimatic variations is importantas they provide valuable analogues for models of
future climate change.
This study examines two transient warming events—
the Paleocene-Eocene Thermal Maximum (PETM) andthe Eocene Thermal Maximum (ETM2)—in which thetemperature increased by 4-8°C for periods of lessthan 200,000 years each.
Applying pollen and spore microfossil analyses ofmarine sediment cores from nearly 400 metres below(continued on next page...)28

the Arctic Ocean seabed, researchers reconstructed
the terrestrial vegetation of PETM and ETM2.
Using a bioclimatic analysis of GBIF-mediatedoccurrences of modern living relatives assumed tohave similar climatic niches, the authors then derived
climate parameters during the two events.
Based on pollen taxa present and bioclimaticreconstructions, the study provides evidence of Arctic
broad-leaved swamp forests during both PETM andETM2. PETM mean annual temperatures and mean
winter temperatures were both ~2 to 3.5°C warmer
than the late Paleocene.

PRIORITIZING IN SITU CONSERVATION OF CROPWILD RELATIVES

multidisciplinary

DATA USED: 136,576 SPECIES OCCURRENCES

a Vincent H, Amri A, Castañeda-Álvarez NP, Dempewolf
H, Dulloo E, Guarino L, Hole D, Mba C, Toledo A and Maxted
N (2019) Modeling of crop wild relative species identifies
areas globally for in situ conservation. Communications
Biology. Springer Science and Business Media LLC 2(1).
Available at: https://doi.org/10.1038/s42003-019-0372-z
Author countries/areas: Colombia, Germany, Italy, Macao,
Morocco, UK, USA
Research funding: Bioforsk, University of Birmingham

The wild cousins of agricultural plants, crop wild
relatives (CWRs) are important sources of genetic
diversity with potential for breeding more nutritious
varieties with higher yields and climate change
tolerance.
Exploring relevant areas for in situ conservationof CWRs, this study applies species distribution
modelling to 1,261 wild species from 167 major crop
gene pools using a global CWR database mediated by
GBIF. The models reveal the highest concentrationsof CWRs in the Mediterranean basin with a hotspot on
the northeast Lebanese/Syrian border.

MODELLING THE GLOBAL DIVERSITY OF
PHYTOPLANKTONDATA USED: 790,000 SPECIES OCCURRENCES

a Righetti D, Vogt M, Gruber N, Psomas A and Zimmermann
NE (2019) Global pattern of phytoplankton diversity driven
by temperature and environmental variability. Science
Advances. American Association for the Advancement of
Science (AAAS) 5(5): eaau6253.
Available at: https://doi.org/10.1126/sciadv.aau6253
Author countries/areas: Switzerland

Marine phytoplankton play a crucial role in ocean
productivity, yet very little is known about the global
patterns of diversity of these extremely diverse
marine organisms, varying from photosynthesizing
cyanobacteria to plant-like diatoms.
Combining more than a million occurrence records
from GBIF, the Ocean Biodiversity Information System(OBIS), and others with 10 environmental variables
representing key dimensions of phytoplankton
ecological niches, authors of this paper modeled the
distributions of more than 500 species and globally
projected the models onto monthly data fields.
Based on these projections, the authors produced aglobal phytoplankton map, showing threefold richness
in the tropics compared to higher latitudes, confirming
the metabolic theory, with sea surface temperature as
the most important predictor.
In cooler waters, however, richness is lower than
expected, with regions between 35 and 60 degrees
latitude showing the greatest divergence. The authors
suggest that environmental variability may play arole in reducing richness—either directly or throughenhancing competitive exclusion.

In future climates, the crop types with the most
CWRs predicted to lose more than 50 per cent of
their distribution potential are root, bulb or tuberous
vegetables, but cereals and legumes are also likely
to face substantial losses. Citrus is the least affected
crop.
While prioritizing areas for conservation, the authors
find that protecting the top 150 sites would only
involve 0.01 per cent of the total terrestrial area of theworld. The conservation of just the top 10 sites insideand outside existing protected areas, respectively,
would protect 475 CWR species and more than 1,200
CWR/crop combinations.

VIRGINIA STRAWBERRY (FRAGARIA VIRGINIANA) OBSERVED IN AMHERST,
MA, USA BY AARON HULSEY. PHOTO VIA INATURALIST (CC BY-NC 4.0)

29

UNDERSTANDING MACROEVOLUTIONARY
PROCESSES IN TEMPERATE BIOTASDATA USED: 1,650,109 SPECIES OCCURRENCES

a Folk RA, Stubbs RL, Mort ME, Cellinese N, Allen JM,
Soltis PS, Soltis DE and Guralnick RP (2019) Rates of nicheand phenotype evolution lag behind diversification in atemperate radiation. Proceedings of the National Academyof Sciences. Proceedings of the National Academy of
Sciences 116(22): 10874–10882.
Available at: https://doi.org/10.1073/pnas.1817999116
Author countries/areas: Switzerland, USA

Evolution takes place all the time. When shifts
in environmental regimes provide ecologicalopportunities, diversification can happen fast. New
ecological niches and phenotypic traits evolve, butwhat might explain shifts in rates—and is there an
association between the timing of diversification of
species, niche and traits?

Their results showed that in Saxifragales, species
first diversified 15 million years ago, driven by the
Earth's cooling climate. It wasn't, however, until
about five million years later that these plants
invaded new habitats and evolved new physicaltraits. This suggests an evolutionary pattern neverobserved before, involving a strong temporal lag
with diversification preceding niche and phenotype
evolution in temperate biotas.

CLIMATE-INDUCED CO-EXTINCTIONS IN SEVENEUROPEAN POLLINATOR NETWORKSDATA USED: OCCURRENCES OF 59 SPECIESa Bascompte J, García MB, Ortega R, Rezende EL andPironon S (2019) Mutualistic interactions reshuffle theeffects of climate change on plants across the tree oflife. Science Advances. American Association for the
Advancement of Science (AAAS) 5(5): eaav2539.
Available at: https://doi.org/10.1126/sciadv.aav2539
Author countries/areas: Spain, Switzerland, UK
Research funding: Ministerio de Ciencia y Tecnología

Species distribution models are commonly used forpredicting the effects of climate change including
potential extinctions.

Based on a rich trait dataset of seven European
pollinator networks, this study explores potential
climate-induced extinctions while considering mutual
dependencies and thus co-extinctions. Adding
GBIF-mediated occurrences, authors progressively
projected models of 244 plant species into futureclimates, assigning a co-extinction probability eachtime an interaction would be lost.
The results show substantial variability acrossnetworks with dramatic increases in co-extinction
rates in the Mediterranean networks—compared tothe other networks. In fact, the 2080 projection showsa near-doubling of climate-induced extinctions whenpotential co-extinctions are considered.
Not surprisingly, some trait profiles are less likely tobe driven to climatic extinction than others, however,the same profile may indeed have a significantly
larger risk of disappearing through subsequent coextinctions.

REPLACING COFFEE WITH COCOA TO OVERCOME
EFFECTS OF CLIMATE CHANGEDATA USED: 48,239 SPECIES OCCURRENCES

a De Sousa K, van Zonneveld M, Holmgren M, Kindt R
and Ordoñez JC (2019) The future of coffee and cocoa
agroforestry in a warmer Mesoamerica. Scientific Reports.
Springer Science and Business Media LLC 9(1). Available at:https://doi.org/10.1038/s41598-019-45491-7
Author countries/areas: Costa Rica, Ecuador, Kenya,
Netherlands, Norway, Peru, Taiwan

With productivity of Arabica coffee projected to
decline drastically, replacing coffee with cocoa(Theobroma cacao) and integrating trees incombined agroforestry systems may become an
important strategy for climate change adaptation in
Mesoamerica.
This study investigated the feasibility of this strategy
by assessing current and future climatic suitabilityof coffee, cocoa and 100 common agroforestry trees
using primarily GBIF-mediated occurrences.
By modelling distributions of all species andprojecting these into 2050 climate scenarios, theauthors showed that coffee is indeed more vulnerable
to climate change than cocoa, as up to 62 per cent of
current areas for production may become unsuitableby 2050. Eighty-five per cent of these vulnerable
areas may, however, remain suitable for cocoa.
(continued on next page...)multidisciplinary

Focusing on a major flowering plant clade—
Saxifragales—a group of nearly 2,500 species
encompassing trees such as sweet gum and shrubs
such as gooseberry, authors of this study built aphylogenetic tree of 1,736 species and addressed
macroevolutionary questions through analyses oftraits and ecological niches, derived from 1.6 million
GBIF-mediated occurrences and climate data.

Such models treat species independently and neglect
interactions between species.

multidisciplinary30

The results also showed that despite overall losses
in suitability for the most popular tree species,
agroforestry may remain a viable alternative, as 72
per cent of future coffee areas will be able to support
more than 30 tree species. For cocoa, the agroforestry
potential is even higher—with 95 per cent of areas
suitable for more than 30 species..

The results of their analysis point to major transitions
in mean climate state including series of abruptchanges in water availability of up 70 per cent—eachlasting 500–2,000 years. The authors speculate thatthese changes may have driven a speciation pump,ultimately responsible for the high diversity in thewestern CFR today.

USING MAMMAL EXCREMENT TO EXPLAIN THE
RICHNESS OF THE CAPE FLORISTIC REGIONAGE AND PATTERNS OF ENDEMISM ON ISLANDSWORLDWIDEDATA USED: 165,365,849 SPECIES OCCURRENCESDATA USED: 160,301,578 SPECIES OCCURRENCES

Chase BM, Boom A, Carr AS, Chevalier M, Quick LJ, Verboom
GA and Reimer PJ (2019) Extreme hydroclimate response
gradients within the western Cape Floristic region of South
Africa since the Last Glacial Maximum. Quaternary Science
Reviews. Elsevier BV 219: 297–307. Available at:https://doi.org/10.1016/j.quascirev.2019.07.006

a Veron S, Haevermans T, Govaerts R, Mouchet M and
Pellens R (2019) Distribution and relative age of endemism
across islands worldwide. Scientific Reports. Springer
Science and Business Media LLC 9(1). Available at:https://doi.org/10.1038/s41598-019-47951-6

Author countries/areas: France, South Africa, Switzerland,
UK

Isolated from continental life, evolution on islands cantake its own course, allowing many unique lineages
and high levels of endemism. In some sites, the age ofendemic species varies significantly from the average,a phenomenon thought to be associated with theorigin of the island. Recent endemism is associatedwith oceanic islands, i.e. islands formed de novo,
whereas ancient endemism is linked to continental
islands, i.e. islands formed by fragmentation.

One of the world's biodiversity hotspots, the Cape
Floristic Region (CFR) in South Africa is characterized
by remarkable vegetation with high levels ofendemism and species richness. The floral diversityof the CFR is thought to be driven by relative climaticstability, but it is not homogenous across the whole
region.
This study uses GBIF-mediated occurrences of nineclasses of vascular and non-vascular plants to map
the species richness of the CFR—highlighting theextreme diversity in the southwestern part of theregion. Using high-resolution paleoclimatic data
derived from stable isotope analysis of hyraceum
samples (fossilized faeces and urine of the rockhyrax) up to ~20,000 years old, the authors explore
the climate change dynamics in the western CFR.

Author countries/areas: France, UK

Focusing on monocots, this study sought to identify
islands with significant endemic flora of more recent,ancient or mixed lineages, and to investigate factors
contributing to these patterns. Using GBIF-mediatedplant occurrences representing 15,964 species foundon 4,306 islands, the authors calculated a measure ofphylogenetic endemism and identified 142 islands as
being either recent, ancient or mixed—with a subset
of 42 islands being 'super-endemic', an extreme caseof the last category.

ROCK HYRAX (PROCAVIA CAPENSIS SUBSP. CAPENSIS) OBSERVED IN SOUTH AFRICA BY MICHELE BERTONCINI. PHOTO VIA INATURALIST (CC BY-NC 4.0).

31

The islands identified—irreplaceable for uniquenessand evolutionary history—can help guide biodiversity
conservation. While distributed across the entire
world, most are present at low latitudes. In addition,
the authors found that habitat availability and climate
stability were the most important environmental
factors contributing to endemism.

THE ROLE OF WILDERNESS AREAS IN PROTECTING
BIODIVERSITYDATA USED: 65,733,880 SPECIES OCCURRENCESDi Marco M, Ferrier S, Harwood TD, Hoskins AJ and Watson
JEM (2019) Wilderness areas halve the extinction riskof terrestrial biodiversity. Nature. Springer Science andBusiness Media LLC 573(7775): 582–585. Available at:https://doi.org/10.1038/s41586-019-1567-7
Author countries/areas: Australia, Italy, USA

Seeking to quantify the value of wilderness areas, thisstudy applied models of compositional turnover—or beta-diversity—based on more than 65 million
GBIF-mediated occurrences of vascular plants andinvertebrates to predict differences in composition
between wilderness and non-wilderness.
By identifying the areas on every continent that makethe highest relative contribution to persistence of
biodiversity, the study finds that wilderness buffers
extinction risks in all biogeographical realms. The
effect is more pronounced, however, in areas withlarger remaining extent of wilderness, such as the
Palearctic.
Overall, the probability of species extinction in nonwilderness areas is more than twice as high as inwilderness areas, and for some communities the lossof a single square km grid cell of wilderness signifies a
reduction in species persistence of up to 14 per cent.

THE IMPACT OF CLIMATE CHANGE ON ISLANDSDATA USED: 2,550,396 SPECIES OCCURRENCES

a Veron S, Mouchet M, Govaerts R, Haevermans T and
Pellens R (2019) Vulnerability to climate change of islands
worldwide and its impact on the tree of life. Scientific
Reports. Springer Science and Business Media LLC 9(1).
Available at: https://doi.org/10.1038/s41598-019-51107-x
Author countries/areas: France, UK

Having evolved in isolation, islands represent
unique communities with extremely high rates of

To understand the impact a changing climate may
have on islands, this study investigated relative
vulnerability of monocots, a major group of flowering
plants with many taxa of high economic value (e.g.
palms and bananas).
Analysing 1,497 monocot genera distributed across5,565 islands worldwide, the authors calculated
the overall vulnerability of all islands to shifts in sea
level, temperature and rainfall, and linked this tothe expected phylogenetic diversity, derived fromassessing 2.5 million GBIF-mediated occurrences,and the phylogenetic losses from predicted climateinduced local extinctions.
The most vulnerable islands were mainly situated at
low latitudes and/or in the Southern Hemisphere, while
the highest estimated phylogenetic losses mainly
occurred in the Eastern Hemisphere. Consideringboth factors, the study highlights Cuba and New
Guinea as highly vulnerable, both representing large
phylogenetic diversity at stake.

ONE THIRD OF TROPICAL AFRICAN FLORA MAY BE
FACING EXTINCTIONa Stévart T, Dauby G, Lowry PP, Blach-Overgaard A,
Droissart V, Harris DJ, Mackinder BA, Schatz GE, Sonké B,
Sosef MSM, Svenning J-C, Wieringa JJ and Couvreur TLP(2019) A third of the tropical African flora is potentiallythreatened with extinction. Science Advances. American
Association for the Advancement of Science (AAAS) 5(11):eaax9444. Available at:https://doi.org/10.1126/sciadv.aax9444
Author countries/areas: Belgium, Denmark, France, USA
Research funding: Fondation pour la Recherche sur la
Biodiversite

Despite their crucial importance for terrestrial
ecosystems, most tropical plants lack extinction
risk assessments. IUCN Red List assessments are
generated species-by-species, requiring knowledge,
reliable data and thus, time. In 2019, less than eightper cent of the estimated number of plant species
worldwide had been assessed.
(continued on next page...)multidisciplinary

Wilderness areas—nature with no or minimal humandisturbance—are rapidly decreasing in global
extent. How important this last stronghold of intact
ecosystems is in mitigating the biodiversity crisis,
however, is unknown.

endemism—exceeding mainland species almost
tenfold. This uniqueness, however, also makes insularcommunities especially vulnerable to rapid changes
caused by human activities, such as climate change.

32

Preliminary Automated Conservation Assessments(PACA) may help the process along, as suggested bythis paper, in which researchers used the RAINBIO
dataset of tropical African plants to carry out asimultaneous extinction risk analysis of more than
22,000 vascular plant species in tropical Africa.
The authors used GBIF-mediated data to filter out
non-endemics with wide distributions outside thecontinent.
The final results of the PACA analysis, based on two
IUCN Red List criteria, placed more than 30 per centof species in the "likely/potentially threatened"category—with highest proportion of these found in
Ethiopia, West Africa, Central Tanzania and southern
Democratic Republic of the Congo.

CLIMATE STABILIZATION—A DOUBLE-EDGED
SWORD?

multidisciplinary

DATA USED: 566,184,545 SPECIES OCCURRENCES

a Ohashi H, Hasegawa T, Hirata A, Fujimori S, Takahashi
K, Tsuyama I, Nakao K, Kominami Y, Tanaka N, Hijioka Y
and Matsui T (2019) Biodiversity can benefit from climate
stabilization despite adverse side effects of land-based
mitigation. Nature Communications. Springer Science andBusiness Media LLC 10(1). Available at:https://doi.org/10.1038/s41467-019-13241-y
Author countries/areas: Austria, Japan

Climate change is a threat to all life on Earth andreducing greenhouse gas (GHG) emissions is a
crucial mission of The Paris Agreement within the UN
Framework Convention on Climate Change. Substantial
GHG mitigation, however, may require significant
land-use change, such as large-scale bioenergy crop
production and afforestation. With land-use change
being the largest driver of biodiversity loss to date,can the positive effects of GHG mitigation outweighthe negative effects of land-use change?
By comparing a GHG mitigation scenario to baselinein terms of changes to distribution models poweredby GBIF-mediated data of more than 8,000 species ofplants and animals, this study by researchers fromJapan suggests that biodiversity overall can benefit
from climate stabilization despite potential side
effects of land-based mitigation.
Their results show that while some regions with muchgrowth in land-based mitigation efforts (i.e., Europe
and Oceania) are projected to suffer biodiversity
losses, stringent GHG mitigation may bring a net
benefit to global biodiversity—particularly in thelatter half of the century.

WHY ARE SOME SPECIES COMMON WHILE OTHERSARE RARE?
a Enquist BJ, Feng X, Boyle B, Maitner B, Newman EA,
Jørgensen PM, Roehrdanz PR, Thiers BM, Burger JR, Corlett
RT, Couvreur TLP, Dauby G, Donoghue JC, Foden W, Lovett
JC, Marquet PA, Merow C, Midgley G, Morueta-Holme N,
Neves DM, Oliveira-Filho AT, Kraft NJB, Park DS, Peet RK,
Pillet M, Serra-Diaz JM, Sandel B, Schildhauer M, Šímová I,
Violle C, Wieringa JJ, Wiser SK, Hannah L, Svenning J-C and
McGill BJ (2019) The commonness of rarity: Global andfuture distribution of rarity across land plants. Science
Advances. American Association for the Advancement of
Science (AAAS) 5(11): eaaz0414. Available at:https://doi.org/10.1126/sciadv.aaz0414
Author countries/areas: Brazil, Chile, China, Czechia,
Denmark, France, Netherlands, New Zealand, South Africa,
UK, USA
Research funding: National Science Foundation

The phenomenon that some species are very common
while others incredibly rare has always puzzled
ecologists. Studies have investigated this on a local
scale, but as most species are common in some partsof their ranges while rare in others, results are usuallypoor estimates of true global rarity.
This paper uses the Botanical Information and Ecology
Network (BIEN) global plant database, which draws
on GBIF as the main source of occurrences, to perform33

an unprecedented assessment of global patterns ofrarity. By quantifying the global species abundance
distribution (gSAD)—a functional measure of true
abundance—of 435,000 species, the authors showedthat 36.5 per cent are rare, with just five records or
fewer.
While distributed globally, very rare species are morecommon in hotspots found in Central and SouthAmerica, southern Africa and Madagascar, and acrossAsia-Pacific from China to New Guinea.
When exploring drivers of rarity, models showedthat the most important predictor of plant rarity is astable climate, and that rapid changes in temperaturenegatively affects retention of rare species.

CHOOSING LIFE ON MARSa Vaz E and Penfound E (2020) Mars Terraforming: A
Geographic Information Systems Framework. Life Sciencesin Space Research. Elsevier BV 24: 50–63. Available at:https://doi.org/10.1016/j.lssr.2019.12.001

This study explores the potential of Mars terraforming
through a suitability analysis identifying places on
Earth with Mars-like environments, i.e. the coldest,driest and sunniest places on the planet, and using
GBIF-mediated occurrences in these locations to
identify relevant species likely to withstand hostile
Martian environments.
Having the most Mars-like conditions, The Antarctic
Peninsula and Ellesmere and Devon Islands in the
Arctic were the focus of a vegetation analysis, in which
the authors identified 21 tracheophyte and bryophyte
genera with significantly higher proportions ofoccurrences within two of the study areas.
Further analysis indicated that the Arctic areas
might be the better option in terms of finding suitable
vegetation for Mars terraforming—and pointed toBluegrass (Poa) as the most promising genus forfurther studies.

Author countries/areas: Canada

AN ARTIST’S IMPRESSION OF MARS FOUR BILLION YEARS AGO BY EUROPEAN SOUTHERN OBSERVATORY / M. KORNMESSER
VIA WIKIMEDIA COMMONS (CC BY-SA 4.0)

multidisciplinary

Home to millions of species, Earth is the only planet
in our solar system able to sustain life as we know it.
Travelling to and settling on other planets, like Mars,
remains a fascination of humans, however, one thatwill require bringing hardy oxygen-producing plants to
the Red Planet from Earth.

34

Other research

HARVESTING CASSAVA BY IKHLASUL AMAL VIA FLICKR (CC BY-NC 2.0)

GLOBAL ANALYSIS OF POTENTIAL MARGINAL LANDRESOURCES OF CASSAVADATA USED: 290,447 SPECIES OCCURRENCES

Jiang D, Wang Q, Ding F, Fu J and Hao M (2019) Potential
marginal land resources of cassava worldwide: A datadriven analysis. Renewable and Sustainable Energy
Reviews. Elsevier BV 104: 167–173. Available at:https://doi.org/10.1016/j.rser.2019.01.024
Author countries/areas: China

A drought-resistant tropical shrub capable ofproducing a rich, starchy root in marginal soil, cassava
has been shown to be a suitable source of biofuel anda useful alternative to petroleum-based fuels.
Seeking to evaluate the potential of cassava to begrown on marginal lands at a global scale as a biofuel,researchers from the Chinese Academy of Sciences(CAS) used GBIF-mediated cassava occurrences
combined with data on land use, climate and soil tocreate a boosted regression tree model mapping theenvironmental suitability of the plant.
With high accuracy and good performance, theobtained model was influenced primarily by land coverand annual precipitation with relative contributions of
46 and 35 per cent, respectively.

Focusing on relevant biomes, i.e. shrubland, savanna
and grassland, the researchers estimated theworldwide marginal land area suitable for cassava
to be 1.6 billion hectares—half of which are in Africa.
With 394 million hectares, Brazil has the largest
suitable land area followed by Angola with 105 million
hectares.

A NOVEL APPROACH TO CREATING AGGREGATEDMAPS OF SPECIES OCCURRENCESDATA USED: 64M SPECIES OCCURRENCES

Beilschmidt C, Mattig M, Fober T and Seeger B (2019)
An efficient aggregation and overlap removal algorithm
for circle maps. GeoInformatica. Springer Science andBusiness Media LLC 23(3): 473–498. Available at:https://doi.org/10.1007/s10707-019-00342-5
Author countries/areas: Germany
Research funding: Deutsche Forschungsgemeinschaft

Visualizing spatial data is an important tool whenworking with large volumes of species occurrences.
Plotting millions of points on maps, however, iscomputationally expensive and overlaps can lead to
occluded visualization.
In an attempt to overcome this, researchers from the
University of Marburg in Germany designed a novel
visualization algorithm for creating aggregated,35

non-overlapping circle representation maps ofpoint coordinates. Their approach—Circle Merging
Quadtree—is based on an iterative transformationof all points into circles of a certain radius and thenmerging and (thus expanding) overlapping circles
until no circles overlap.
Using GBIF-mediated occurrences of 50 species,
varying from hundreds to millions of records per
species, the authors compared the performanceand quality of their algorithm to existing methods.
While providing similar or better quality than theother tested methods, CMQ proved superior interms of processing runtime—at up to two orders ofmagnitude.

WIKIPEDIA PAGEVIEWS REFLECT OBSERVABLEPATTERNS IN PHENOLOGYa Mittermeier JC, Roll U, Matthews TJ and Grenyer R(2019) A season for all things: Phenological imprints in
Wikipedia usage and their relevance to conservation. PLOS
Biology. Public Library of Science (PLoS) 17(3): e3000146.
Available at:https://doi.org/10.1371/journal.pbio.3000146
Author countries/areas: Israel, Portugal, UK

Using three years of log data from the online
encyclopedia, Wikipedia, authors of this study
analysed pageviews of articles of more than 31,000
species matched against the GBIF taxonomic
backbone across 245 languages, to explore seasonalpatterns in Wikipedia activity.
They found seasonal variation in more than 20 per
cent of species pages, compared to just 6.5 per centin a random sample of non-species pages. Most pages
showed a single annual peak, while ~10 per cent had
two annual peaks.

a Piñar G, Poyntner C, Tafer H and Sterflinger K (2019)
A time travel story: metagenomic analyses decipher the
unknown geographical shift and the storage history of
possibly smuggled antique marble statues. Annals ofMicrobiology. Springer Science and Business Media LLC
69(10): 1001–1021. Available at:https://doi.org/10.1007/s13213-019-1446-3
Author countries/areas: Austria

In forensic science, even the smallest traces of DNA
can be used as biological markers to signify thepresence of a person or object in a given context. But
when no knowledge of context is available, advancesin metagenomic barcoding coupled with knowledge of
species distributions may be usefully exploited.
In this study, researchers from Austria sampled threemarble statues of unknown origin for DNA extraction.
They amplified the collected DNA and constructedlibraries for quantification and taxonomic assignment.
Matching the identified taxa with distributions of
GBIF-mediated occurrences, the authors were able todraw some conclusions on the possible origins of thestatues.
Two of the statues, representing torsos, appear tohave been stored in agricultural soil, perhaps near an
animal farm. As the genetic fingerprints were similar,
the torsos are likely to have been stored together
in recent times. Both carried sequences matchingtaxa endemic to Eastern Asia. The third statue,
representing a head, however, differed considerablywith a microbiome indicating longer storage time inarid conditions as well as marine environments in thepast.
The most relevant find was the relative abundance of
DNA of the genus Taiwania present on one torso. Witha single extant species growing in the mountains ofcentral Taiwan and locally in Southwest China, thetorso is likely to have stayed or been transported
through these areas.

Reflecting actual phenological patterns, pageviewsfor groups like insects and flowering plants exhibited
higher seasonality than mammals. Seasonal patterns
were not consistent across Wikipedia languages, as
fewer than two per cent of species showed the same
pattern in all languages, with greater seasonality
shown for languages spoken at higher latitudes, i.e.
further from the Equator.
THREE ANTIQUE MARBLE STATUES OF UNKNOWN ORIGIN ANALYSED IN THE
STUDY. PHOTO FROM FIGURE 1 IN PIÑAR ET AL. 2019 (CC BY 4.0)

other research

Seasonal and interannual variations affect plant andanimal life cycle events, such as flowers blooming andbirds migrating. Phenology, the study of such events,
can play a role in how and when humans interact withnature, a phenomenon with potential importance toconservation.

RELYING ON BIODIVERSITY SCIENCE TO INFORM
ART HISTORY36

SPATIOTEMPORAL BIASES IN ARCTIC HERBARIUM
SPECIMEN COLLECTIONSDATA USED: 29,749 SPECIES OCCURRENCES

a Panchen ZA, Doubt J, Kharouba HM and Johnston
MO (2019) Patterns and biases in an Arctic herbarium
specimen collection: Implications for phenologicalresearch. Applications in Plant Sciences. Wiley 7(3):e01229. Available at: https://doi.org/10.1002/aps3.1229
Author countries/areas: Canada
Research funding: Natural Sciences and Engineering
Research Council of Canada, Killam Trusts

Biases in natural history collections may arise aroundcertain climates and in remote areas, which in turn
may impact the results of scientific studies basedon data from such collections. This can be especiallypronounced in time-sensitive phenological studies.

other researchThis study examines 29,000 herbarium specimensfrom Nunavut—the largest and most northerly
territory of Canada—deposited at the National
Herbarium of Canada (available through GBIF) toassess biases across time, space, and phenology,
among others.
The limited access to the region as well as very shortsnow-free periods are apparent in the results of thestudy, showing 85 per cent of specimens collected
in July and August. In terms of spatial distribution,
only 0.63 per cent of the region contained one or more
specimens—with the highest density of records foundnear the capital, Iqaluit.
The study also finds a preference towards collecting
flowering plants in peak flower, as more than twothirds of specimens fall into these categories whenassessing phenological phase and flowering stage,
respectively.

THE EVOLUTION OF CLEANING BEHAVIOUR IN
MARINE FISHESDATA USED: OCCURRENCES OF FIVE FAMILIESDOTTED MAORI (CHEILINUS CHLOROURUS) BEING TENDED TO BY A
BLUESTREAK CLEANER WRASSE (LABROIDES DIMIDIATUS). PHOTO BYMARK ROSENSTEIN VIA INATURALIST (CC BY-NC-SA 4.0)

In this study, researchers examined the evolutionary
history of cleaning in five marine fish families in orderto determine how and when this behaviour arose andwhether the trait is restricted to species of a certain
shape or size.
The authors found that cleaning evolved relatively
recently with no one common ancestor in any family.
By assigning species to distinct non-overlapping
biogeographic regions using GBIF-mediatedoccurrences, they show that obligate cleaners in two
families evolved in parallel and almost at same time inseparate regions of the world: Labroides in the Indian
Ocean and Elacatinus in the Western Atlantic.
By comparing photos of cleaner species withsuperimposed digitized body shape landmarks, theyalso showed that obligate cleaning is only present
in elongate-bodied species with anterior pectoral fin
attachment and eye positioning.

OPENBIODIV: A KNOWLEDGE GRAPH FOR LINKED
OPEN BIODIVERSITY DATADATA USED: GBIF TAXONOMIC BACKBONE

Baliga VB and Mehta RS (2019) Morphology, Ecology, andBiogeography of Independent Origins of Cleaning Behavior
Around the World. Integrative and Comparative Biology.
Oxford University Press (OUP) 59(3): 625–637. Available
at: https://doi.org/10.1093/icb/icz030

a Penev L, Dimitrova M, Senderov V, Zhelezov G,
Georgiev T, Stoev P and Simov K (2019) OpenBiodiv:
A Knowledge Graph for Literature-Extracted Linked
Open Data in Biodiversity Science. Publications. MDPI
AG 7(2): 38. Available at: https://doi.org/10.3390/
publications7020038

Author countries/areas: USA

Author countries/areas: Bulgaria, Sweden

Cleaning is an often mutualistic behaviour amongsome marine species in which typically small and/or juvenile fishes (cleaners) locate and feed on
ectoparasites off the bodies of larger taxa (clients).
Some species obtain nearly all calories throughcleaning while others use cleaning as a supplement.

Decades of biodiversity research have contributed
immense knowledge about life on Earth. To fully
exploit this knowledge, data must be available, openly
and freely, while sources of data should be linkablethrough the use of stable and unique identifiers.

37

OpenBioDiv is a Open Biodiversity Knowledge
Management System that uses semantic publishing
workflows, graph database technologies, and text anddata mining to establish a robust infrastructure formanaging biodiversity knowledge.
Presented as a Linked Open Dataset, OpenBioDivbuilds on data extracted from more than 5,000
scientific articles from Pensoft Publishers and evenmore taxonomic treatments mediated by Plazi. All thisdata is matched against an RDF version of the GBIF
backbone taxonomy to ensure consistency.
The tool enables fast answers to complicatedquestions that would otherwise require querying
numerous separate databases—e.g. "how many
articles about taxon X has author Y published in thepast 10 years", or, "which taxon treatments mention
both scientific name X and Y?". Users can perform
simple searches in the web portal while more complex
queries are possible through a SPARQL endpoint.

INSECTS OF MADAGASCARDATA USED: 286,764 SPECIES OCCURRENCES

Author countries/areas: Italy

One of the world's most important biodiversity
hotspots, Madagascar is home to a disproportionately
large and diverse flora and fauna with high levels ofcryptic diversity and endemism.
This study examines available GBIF-mediatedspecies occurrences of nine insect orders to evaluate
the current coverage in knowledge of Malagasy
entomofauna. With access to a dataset of 286,000
occurrences, researchers mapped and identified
areas of high and low sampling, while investigating
potential associations with specific ecosystems,
protected areas and access infrastructure.

The current protected areas of Madagascar housearound 70 per cent of insect occurrences. A proposed
expansion of the PA system would significantly
improve this, especially for orders that are notcurrently well represented within PAs—Neuroptera,
Odonata and Lepidoptera.

XGBOOST: ACCURATE HIGH-RESOLUTIONVEGETATION MAPPINGDATA USED: OCCURRENCES FROM 11,234 VEGETATION SURVEY PLOTSa Zhang H, Eziz A, Xiao J, Tao S, Wang S, Tang Z, Zhu J andFang J (2019) High-Resolution Vegetation Mapping Using
eXtreme Gradient Boosting Based on Extensive Features.
Remote Sensing. MDPI AG 11(12): 1505. Available at:https://doi.org/10.3390/rs11121505
Author countries/areas: China, France
Research funding: National Key Research and Development
Program of China, National Natural Science Foundation of
China

Mapping of ecosystems and vegetation types isimportant for environmental planning and resource
management, but producing accurate, high-resolution
maps is a challenge due to mosaic and heterogeneousenvironments.
This paper presents a workflow to produce highresolution multiclass vegetation maps based ona machine learning algorithm for regression andclassification referred to as XGBoost—or extreme
gradient boosting.
To demonstrate the workflow, researchers used two
strikingly different cases. First, they surveyed the
Dzungarian Basin in China by photographic sampling
covering more than 3,000 points 1-2 km apart.
From the photos, they identified plant species anddeveloped a hierarchical vegetation classification
system.
In the second case, they gathered GBIF-mediatedvegetation survey data for New Zealand. The authors
supplemented both datasets with an extensive suiteof bioclimatic data and remote sensing data.

CALLIMATION VENUSTUM OBSERVED IN MORAMANGA, MADAGASCAR BY
DAVID RABEHEVITRA. PHOTO VIA INATURALIST (CC BY-NC 4.0)

In both cases, the authors used the XGBoost approachto produce high-resolution vegetation maps,
effectively separating vegetation classes with higher
accuracy than other mapping projects.

other researcha PIannella M, D’Alessandro P and Biondi M (2019)
Entomological knowledge in Madagascar by GBIF datasets:
estimates on the coverage and possible biases (Insecta).
Fragmenta Entomologica. PAGEPress Publications 51(1):1–10. Available at: https://doi.org/10.4081/fe.2019.329

Their analysis revealed that the Eastern Madagascar
subhumid forest and lowland rainforest host asignificantly higher number of insect records than
expected. More than 60 per cent of sampling happens
within 1 km of a road, while no records are present
beyond 10 km from a road.

38

FORMAL DESCRIPTION IS A PREDICTOR OF
EXTINCTION RISK IN WEAKLY ELECTRIC FISHES
Tagliacollo VA, Camelier P, Zanata AM and Reis RE (2019)
A shocking discovery of threat risks on newly described
species of weakly electric fishes. Journal of Fish Biology.
Wiley 96(5): 1077–1086. Available at:https://doi.org/10.1111/jfb.14096
Author countries/areas: Brazil

Among the most diverse of all vertebrate groups withnearly 16,000 described species, freshwater fishes
are also the most highly threatened. Body and range
size are good predictors of extinction risk, which has
the implication that newly described species—usuallysmall in size and with narrow ranges—could be more
likely to be threatened.

other researchThis study examines the relationship between species
traits, publication date and extinction risk in two
groups of weakly electric fishes—Mormyroidea andGymnotiformes. The authors compiled data on bodysize from FishBase and derived species distributions
based on IUCN range maps or GBIF-mediatedoccurrences for 470 species.
Their analyses revealed that all except one of thelarger species are considered Least Concern (LC)or Data Deficient (DD), while all widespread species
are listed as LC. The models confirmed that newlydescribed species are more often small-bodied withnarrow ranges and likely to be prone to extinction—
especially in the African mormyroids, suggesting that
their existence after being described may be shortlived.

USING WW FOR SPECIES DISTRIBUTIONMODELLINGDATA USED: 291,392 SPECIES OCCURRENCES

Deneu B, Servajean M, Botella C and Joly A (2019)
Evaluation of Deep Species Distribution Models Using
Environment and Co-occurrences. Experimental IR Meets
Multilinguality, Multimodality, and Interaction. Springer
International Publishing 213–225. Available at:https://doi.org/10.1007/978-3-030-28577-7_18
Author countries/areas: France

Species distribution models (SDM) are key tools to
obtaining knowledge about the spatial distributionof species, often achieved through ecological nichemodelling, where environmental features are used to
predict where species may occur.
Based on a conference challenge, this paper
explores the use of deep neural networks (NN)in species distribution modelling, introducing
a novel, convolutional NN model based on

environmental features and co-occurrences (species
interdependencies) combined, and comparing its
performance to three other SDM approaches.
The authors use a GBIF-mediated dataset of 3,300
plant species occurring in France, of which threequarters were used for training models and one
quarter for testing. They showed that all models
performed well, with environment-based models
scoring highest. While the novel NN combined withco-occurrence data did get the highest score, its
performance was not significantly higher than themodel based on environmental features alone.
The study highlights that while NN can improve theperformance of SDM, performance of models based
solely on environmental data is outperformed bymodels capturing species interdependencies as well.

CHECKLIST, TAXONOMY AND DISTRIBUTION OF
RODENTS IN ETHIOPIADATA USED: 4,299 SPECIES OCCURRENCES

DBryja J, Meheretu Y, Šumbera R and Lavrenchenko LA(2019) Annotated checklist, taxonomy and distribution ofrodents in Ethiopia. Folia Zoologica. Institute of Vertebrate
Biology, Academy of Sciences of the Czech Republic 68(3):117. Available at: https://doi.org/10.25225/fozo.030.2019
Author countries/areas: Czechia, Ethiopia, Russia

Specialized to particular ecosystems and withlow dispersal ability, rodents are generally good
indicators of biodiversity levels. In eastern Africa,
the geomorphologically diverse country of Ethiopia
provides habitat for rich vertebrate fauna, yet thelatest checklist of Ethiopian rodents is almost 25
years old.
Aimed at providing up-to-date knowledge on thebiodiversity of rodents on Ethiopia, this paper
compiles critically-reviewed data from literature,unpublished museum collections, field surveys and
GBIF, providing maps of known distributions of 104
rodent species—including 40 species not included in
the previous checklist (Yalden et al. 1996)
The study also produces complete taxonomic andecological accounts for each species. The authors
note the highest proportion of endemic species in the
Ethiopian highlands and indicate that rodent diversity
in Ethiopia is much higher than in other Africancountries of comparable size.

39

USING GENETIC HEAT INDEX (GHI) FORCONSERVATION PRIORITIZATIONENVIRONMENTAL INFLUENCE ON ANGIOSPERM
DIVERSITY OF DIFFERENT GROWTH FORMS

Hawthorne WD and Marshall CAM (2019) Rapid Botanic
Survey, Bioquality and improving botanical inventory inthe tropics by integrating across spatial scales. Gardens’
Bulletin Singapore. National Parks Board 71(suppl.2):
315–333. Available at:https://doi.org/10.26492/gbs71(suppl.2).2019-21

Zhou Y, Boru BH, Wang S and Wang Q (2020) Species
richness and phylogenetic diversity of different growthforms of angiosperms across a biodiversity hotspot in thehorn of Africa. Journal of Systematics and Evolution. Wiley.
Available at: https://doi.org/10.1111/jse.12559

Author countries/areas: UK

Identifying areas of high biodiversity is importantwhen prioritizing areas for conservation. Suchhotspots can be defined by the number of species orlevels of endemism, but richness alone is considered
to have limited value for highlighting conservation
priorities.
In this study, researchers propose 'bioquality' as anovel indicator of conservation priority—defined as
biodiversity value measured by the concentrationof globally rare taxa in a given plant community.
Calculated by categorizing species based on
an assessment of their global range and thensummarizing in a Genetic Heat Index (GHI), bioquality
can complement other parameters like richness andrarity.

The environment affects the evolutionary andbiogeographical history of all species, affecting
both richness and phylogenetic diversity. However,different forms of organisms may respond in different
ways in their adaptation to changes.
In this study, researchers assessed patterns ofspecies richness and phylogenetic diversity inangiosperm plants of East Africa, while considering
differences between groups of woody and herbaceous
species.
Using GBIF-mediated occurrences of more than 5,600
species, the authors analysed correlations between
environmental variables and plant diversity metrics,
finding similar tendencies among both angiospermgroups with positive responses to precipitation
measures, topography and soil nutrients.
The results did, however, also show thatenvironmental variables explained larger variance in
phylogenetic diversity for woody plants compared toherbaceous plants, suggesting a greater role of theenvironment in shaping community structures among
trees and shrubs than herbs.

DRACAENA OMBET OBSERVED NEAR ABALA, ETHIOPIA BY PFAUCHER. PHOTO VIA INATURALIST (CC BY-NC 4.0)

other researchCompiling occurrence data for more than 40,000
plant species from GBIF and other sources, theauthors derive GHI scores for East Africa at varying
resolutions, identifying hotspots and data gaps at
both regional and local levels. To help fill gaps insampling, the paper suggests Rapid Botanic Surveys,
combining strengths of taxonomic and ecologicalrecording, aiming to provide information about allplant species, community types and location of
hotspots in a given area.

Author countries/areas: China, Ethiopia

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