cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.90329
title: Data from: How ants, birds and bats affect crop yield along shade gradients in tropical cacao agroforestry

description: Tropical agroforests are diverse systems where several predator groups
 shape animal communities and plant–arthropod interactions. Ants, birds and
 bats in particular can reduce herbivore numbers and thereby increase crop
 yield. However, the relative importance of these groups, whether they
 interact, and how this interaction is affected by management and landscape
 context, is poorly understood. We jointly manipulated access of ants,
 birds and bats in Indonesian smallholder cacao agroforestry across
 gradients of shade and distance to natural forest. We quantified arthropod
 abundance, pest damage and yield. In control treatments, yield was highest
 under 30–40% canopy cover. Ant exclusion strongly reduced yield (from 600
 to 300 kg ha−1 year−1) at 15% canopy cover. Bird exclusion impaired yield
 (from 400 to 250 kg ha−1 year−1) at 60% and enhanced yield (from 600 to
 900 kg ha−1 year−1) at 15% canopy cover, while bats had no effect. Yield
 increased with forest proximity, a pattern not related to predator access.
 No interactive effects among predator exclusions on yield, pest damage and
 arthropod communities were found. Ant exclusion increased numbers of
 herbivores below 30% canopy cover, without reducing spider abundances.
 Bird exclusion reduced herbivore and increased spider abundances.
 Synthesis and applications. Using exclusion studies, we estimated that
 ants and birds cause cacao yield to vary between 100 to 800 kg ha−1
 year−1, depending on shade-tree management. In all but the most shaded
 agroforests, ants were pivotal in supporting yields. Yields under
 low-canopy cover were strongly dependent on access by predator groups,
 with birds reducing rather than increasing yield. Hence, cacao farmers
 should refrain from disturbing ant communities and maintain 30–40%
 shade-tree canopy cover not only for ecophysiological reasons but also to
 buffer variability in predator communities.
description: Cacao_yield_fruit_arthropod_abundance_indonesia2011_12The data was collected during a ant, bird and bat exclusion experiment in smallholder cacao cacao plantations in Central Sulawesi, Indonesia. Yield measurement, counted fruits and leaves are aggregated over the study duration (April 2011 - May 2012). The fruits were classified by size/development and presence/absence of pest and disease symptoms. The yield was separated for damaged and marketable yield. Abundances of arthropods were gathered through fogging (5% Malathion) the experimental trees at the end of the experiment. Moreover we provide data regarding cacao tree phenology and biotic as well as abiotic environmental conditions.Harvest_fruit_arthropod_count_cacao2011-2012.xlsx
DOI: 10.5061/dryad.r86pk
title: Data from: Climate and sea-level changes across a shallow marine Cretaceous–Palaeogene boundary succession in Patagonia, Argentina

description: Upper Maastrichtian to lower Paleocene, coarse-grained deposits of the
 Lefipán Formation in Chubut Province, (Patagonia, Argentina) provide an
 opportunity to study environmental changes across the
 Cretaceous–Palaeogene (K–Pg) boundary in a shallow marine depositional
 environment. Marine palynological and organic geochemical analyses were
 performed on the K–Pg boundary interval of the Lefipán Formation at the
 San Ramón section. The palynological and organic geochemical records from
 the San Ramón K–Pg boundary section are characteristic of a highly
 dynamic, nearshore setting. High abundances of terrestrial palynomorphs,
 high BIT-index values and the occasional presence of plant fossils are
 indicative of a large input of terrestrial organic material. The
 organic-walled dinoflagellate cyst (dinocyst) assemblage is generally
 dominated by Senegalinium and other peridinioid dinocyst taxa, indicative
 of high-nutrient conditions and decreased salinities, probably associated
 with a large fluvial input. The reconstructed sea surface temperatures
 range from 25°C to 27°C, in accordance with the tropical climate inferred
 by palynological and megafloral studies. As in the Bajada del Jagüel
 section, ~500 km north-north-east of San Ramón, peaks of Senegalinium spp.
 were recorded below and above the K–Pg boundary, possibly related to
 enhanced runoff resulting from more humid climatic conditions. The
 lithological, palynological and organic geochemical records suggest the
 occurrence of a sea-level regression across the K–Pg boundary, resulting
 in a hiatus directly at the boundary in both sections, followed by a
 transgression in the Danian.
description: Vellekoop et al
 Supplementary dataset S1organic geochemical data
 San Ramón sectionVellekoop et al
 Supplementary dataset S2palynological data San
 Ramón sectionVellekoop et al
 Paleontology Supporting Informationlist of encountered
 dinocyst taxa
DOI: 10.5061/dryad.k94p3
title: Data from: Reproductive isolation and local adaptation quantified for a chromosome inversion in a malaria mosquito

description: Chromosome inversions have long been thought to be involved in speciation
 and local adaptation. We have little quantitative information, however,
 about the effects that inversion polymorphisms have on reproductive
 isolation and viability. Here we provide the first estimates from any
 organism for the total amount of reproductive isolation associated with an
 inversion segregating in natural populations. We sampled chromosomes from
 751 mosquitoes of the malaria vector Anopheles funestus along a 1421 km
 transect in Cameroon that traverses savannah, highland, and rainforest
 ecological zones. We then developed a series of population genetic models
 that account for selection, migration, and assortative mating, and fit the
 models to the data using likelihood. Results from the best-fit models
 suggest there is strong local adaptation, with relative viabilities of
 homozygotes ranging from 25% to 130% compared to heterozygotes.
 Viabilities vary qualitatively between regions: the inversion is
 underdominant in the savannah, while in the highlands it is overdominant.
 The inversion is also implicated in strong assortative mating. In the
 savannah, the two homozygote forms show 92% reproductive isolation,
 suggesting that this one inversion can generate most of the genetic
 barriers needed for speciation.
description: KaryotypeCountsField data. Number of Anopheles funestus collected in populations of Cameroon, by the type of arrangement in3Ra. Columns are: The name of the village, Longitude and Latitude (in WGS84 UTM Zone 33 North), the distance in km from the start of the transect, the counts of Standard homozygotes (SS), Heterozygotes (SI), and Inverted Homozygotes (II), and the total of individuals collectedSource CodeCode.zip
DOI: 10.5061/dryad.ts679
title: Data from: Parasite escape through trophic specialization in a species flock

description: Adaptive radiation occurs when species diversify rapidly to occupy an
 array of ecological niches. Since opportunities for parasite infection and
 transmission may greatly vary among these niches, adaptive radiation is
 expected to be associated with a turnover of the parasite community. As
 major agents of natural and sexual selection, parasites may play a central
 role in host diversification. The study of parasite turnover may thus be
 of general relevance and could significantly improve our understanding of
 adaptive radiation. In the present study, we examined the parasite faunas
 of eleven species belonging to the tribe Tropheini, one of several
 adaptive radiations of cichlid fishes in Lake Tanganyika. The most
 parsimonious ancestral foraging strategy among the Tropheini is relatively
 unselective substrate browsing of aufwuchs. Several lineages evolved more
 specialized foraging strategies, such as selective combing of microscopic
 diatoms or picking of macro-invertebrates. We found that representatives
 of these specialized lineages bear reduced infection with food-web
 transmitted acanthocephalan helminths, but not with parasites with a
 direct life cycle. Possibly, the evolution of selective foraging
 strategies entailed reduced ingestion of intermediate invertebrate hosts
 of acanthocephalans. We conclude that some species belonging to the
 Tropheini virtually escape acanthocephalan infection as a by-product
 effect of trophic specialization.
description: Data on parasite
 infection and host characteristicesData on parasite
 infection and host characteristicesHablutzel et al. 2017 Parasite
 escape data.xls
DOI: 10.5061/dryad.cn946
title: Data from: Patterns and processes in complex landscapes: testing alternative biogeographic hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i

description: The Island of Hawai‘i is a dynamic assemblage of five volcanoes with wet
 forest habitat currently existing in four distinct natural regions that
 vary in area, age, and geographic isolation. In this complex landscape,
 alternative assumptions of the relative importance of specific habitat
 characteristics on evolutionary and ecological processes predict
 strikingly different general patterns of local diversity and regional
 similarity. In this study we compare alternative a priori hypotheses
 against observed patterns within two distinct biological systems and
 scales: community composition of wet forest vascular plant species and
 mitochondrial and nuclear genes of Drosophila sproati, a wet forest
 restricted endemic. All observed patterns display strong and similar
 regional structuring, with the greatest local diversity found in Kohala
 and the windward side of Mauna Loa, the least in Ka‘ū and Kona, and a
 distinctive pattern of regional similarity that likely reflects the
 historical development of this habitat on the island. These observations
 largely corroborate a biogeographic model that integrates multiple lines
 of evidence, including climatic reconstruction, over those relying on
 single measures, such as current habitat configuration or substrate age.
 This method of testing alternative hypotheses across biological systems
 and scales is an innovative approach for understanding complex landscapes
 and should prove valuable in diverse biogeographic systems.
description: Hawaii Wet Forest
 PlantsTo determine which plant
 species occur within each region, we drew from a database of angiosperm
 distributions (Price, 2004), with additional data for ferns (Palmer, 2003)
 to represent all vascular plants. These data come from numerous sources,
 including herbarium specimens, species lists, historical accounts, and
 field records from numerous biologists. Where possible, specific localties
 place a species solidly within a given biogeographic region or moisture
 zone according to maps developed by Price et al. (2007); in some cases
 more general records were necessary, such as presence noted in a checklist
 from a given area or general herbarium label information ("Kohala
 Mountains"). We followed Price (2004) and considered a species to
 inhabit a wet forest habitat region if it was recorded from any of the
 volcanoes that make up the region and is known to occur in wet forest
 somewhere within its range.HawaiiWetForestPlants.xlsD. sproati collection informationDetailed collection information for all D. sproati individuals sequenced in this study.D. sproati collection info (complete and revised).xls
DOI: 10.5061/dryad.3723v
title: Data from: The social factors driving settlement and relocation decisions in a solitary and aggregative spider

description: Both ecological and social factors play an important role in determining
 the structure of animal settlement patterns. While the ecological factors
 determining animal settlement are generally well known, the relative
 importance of social factors in mediating fine-scale settlement choices is
 poorly understood. As a result, we have little knowledge of why
 individuals choose to settle near specific neighbors. Here we used a
 web-building spider (Nephila plumipes) that settles both solitarily and
 next to neighbors within aggregations to examine the specific social
 factors that influence settlement decisions. Within experimental
 enclosures we observed the settlement patterns of females pre- and
 post-male release. This allowed us to compare two models of aggregative
 settlement in lekking species, the hotshot and preferences models, to
 examine the relative importance of a female’s phenotype and mate
 attraction to further dissect settlement and relocation decisions. We show
 that mate attraction increased with aggregation size, and that larger
 females were generally preferred, supporting both the hotshot and
 preference models of aggregative settlement. We further demonstrate that
 smaller females that attracted fewer males within an aggregation were most
 likely to relocate. Our results demonstrate how social feedback can affect
 initially state-dependent settlement decisions, thereby highlighting the
 dynamic nature of settlement.
description: Kasumovic_Jordan_AnalysesData for the main analyses of the paperData for subsampling analysesKasumovic_Jordan_Subsampling.xls
DOI: 10.5061/dryad.8852
title: Data from: Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae)

description: The diversity of geographic scales at which marine organisms display
 genetic variation mirrors the biophysical and ecological complexity of
 dispersal by pelagic larvae. Yet little is known about the effect of
 larval ecology on genetic population patterns, partly because detailed
 data of larval ecology do not yet exist for most taxa. One species for
 which this data is available is Eleutheronema tetradactylum, a tropical
 Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial
 cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to
 survey the genetic structure of E. tetradactylum across northern
 Australia. Structure was found throughout the range and isolation by
 distance was strong, explaining approximately 87 and 64% of the genetic
 variation in microsatellites and mtDNA, respectively. Populations
 separated by as little as 15 km also showed significant genetic structure,
 implying that local populations are mainly insular and self-seeding on an
 ecological time frame. Because the larvae of E. tetradactylum have lower
 swimming performance and poor orientation compared with other tropical
 fishes, even modest larval abilities may permit self-recruitment rather
 than passive dispersal.
description: E_tetradactylumExcel spreadsheet of microsatellite scores, Genalex format.
DOI: 10.5061/dryad.fb128m1
title: Data from: Using an integral projection model to assess the effect of temperature on the growth of gilthead seabream Sparus aurata

description: Accurate information on the growth rates of fish is crucial for fisheries
 stock assessment and management. Empirical life history parameters (von
 Bertalanffy growth) are widely fitted to cross-sectional size-at-age data
 sampled from fish populations. This method often assumes that
 environmental factors affecting growth remain constant over time. The
 current study utilized longitudinal life history information contained in
 otoliths from 412 juveniles and adults of gilthead seabream, Sparus
 aurata, a commercially important species fished and farmed throughout the
 Mediterranean. Historical annual growth rates over 11 consecutive years
 (2002-2012) in the Gulf of Lions (NW Mediterranean) were reconstructed to
 investigate the effect of temperature variations on the annual growth of
 this fish. S. aurata growth was modelled linearly as the relationship
 between otolith size at year t against otolith size at the previous year
 t-1. The effect of temperature on growth was modelled with linear mixed
 effects models and a simplified linear model to be implemented in a cohort
 Integral Projection Model (cIPM). The cIPM was used to project S. aurata
 growth, year to year, under different temperature scenarios. Our results
 determined current increasing summer temperatures to have a negative
 effect on S. aurata annual growth in the Gulf of Lions. They suggest that
 global warming already has and will further have a significant impact on
 S. aurata size-at-age, with important implications for age-structured
 stock assessments and reference points used in fisheries.
description: Allometry
 DataSparus aurata otolith
 radius (rad4) and fish length or weight, to be used in an allometry
 model.allometrydata.csvGrowth DataGrowth and temperature data to be used in the integral projection model.for_analysis4.csvSummer temperatures for lagoonsMean summer temperatures for the four coastal lagoons in the Gulf of Lions. Downloaded from www.myocean.eu in the form of ‘reanalysis temperature data’.summer_temps.csvOxygen and Temperature for LagoonsMean summer dissolved oxygen and water surface temperature values for the four major costal lagoons in the Gulf of Lions. Downloaded from www.ifremer.fr/surval2/ (n=57 data buoys).lagoon_data_sub.csv
DOI: 10.5061/dryad.41r04
title: Data from: Multi-segmented arthropods from the middle Cambrian of British Columbia (Canada)

description: A new arthropod, Kootenichela deppi n. gen. n. sp., is described from the
 Stanley Glacier exposure of the middle Cambrian (Series 3, Stage 5)
 Stephen Formation in Kootenay National Park (British Columbia, Canada).
 This taxon possesses a number of primitive arthropod features such as an
 elongate, homonomous trunk (consisting of at least 29 segments), poorly
 sclerotised trunk appendages, and large pedunculate eyes associated with
 an anterior (ocular) sclerite. The cephalon encompasses a possible
 antenna-like appendage and enlarged raptorial appendages with a bipartite
 peduncle and three spinose distal podomeres, indicative of megacheiran
 (“great-appendage” arthropod) affinities. The relationships of
 megacheirans are controversial, with them generally considered as either
 stem-euarthropods or a paraphyletic stem-lineage of chelicerates. An
 extensive cladistic analysis resolved Kootenichela as sister-taxon to the
 enigmatic Worthenella cambria from the middle Cambrian (Series 3, Stage
 5), Burgess Shale Formation in Yoho National Park (British Columbia),
 which is herein reinterpreted as a megacheiran arthropod. Based on their
 sister-group relationship, both taxa were placed in the new family
 Kootenichelidae, to which Pseudoiulia from the Chengjiang biota is also
 tentatively assigned. All of these taxa possess an elongate,
 multi-segmented body and subtriangular exopods. This family occupies a
 basal position within a paraphyletic Megacheira, the immediate outgroup of
 Euarthropoda (crown-group arthropods). The resultant topology indicates
 that analyses that have resolved megacheirans as stem-chelicerates have
 done so because they have rooted on inappropriate taxa, e.g.,
 trilobitomorphs and marrellomorphs.
description: Kootenichela
 NEXUSPhylogenetic data set in
 NEXUS file format.
DOI: 10.5061/dryad.2m2r2
title: Data from: The colour of paternity: extra-pair paternity in the wild Gouldian finch does not appear to be driven by genetic incompatibility between morphs

description: In socially monogamous species, individuals can use extra-pair paternity
 and offspring sex allocation as adaptive strategies to ameliorate costs of
 genetic incompatibility with their partner. Previous studies on
 domesticated Gouldian finches (Erythrura gouldiae) demonstrated a genetic
 incompatibility between head colour morphs, the effects of which are more
 severe in female offspring. Domesticated females use differential sex
 allocation, and extra-pair paternity with males of compatible head colour,
 to reduce fitness costs associated with incompatibility in mixed-morph
 pairings. However, laboratory studies are an oversimplification of the
 complex ecological factors experienced in the wild, and may only reflect
 the biology of a domesticated species. This study aimed to examine the
 patterns of parentage and sex-ratio bias with respect to colour pairing
 combinations in a wild population of the Gouldian finch. We utilized a
 novel PCR assay that allowed us to genotype the morph of offspring before
 the morph phenotype develops, and to explore bias in morph paternity and
 selection at the nest. Contrary to previous findings in the laboratory, we
 found no effect of pairing combinations on patterns of extra-pair
 paternity, offspring sex ratio, or selection on morphs in nestlings. In
 the wild, the effect of morph incompatibility is likely much smaller, or
 absent, than was observed in the domesticated birds. Furthermore, the
 previously studied domesticated population is genetically differentiated
 from the wild population, consistent with the effects of domestication. It
 is possible that the domestication process fostered the emergence (or
 enhancement) of incompatibility between colour morphs previously
 demonstrated in the laboratory.
description: 2009
 GenotypesGenotypes for
 individuals caught in 2009 for CERVUS analysis. In CERVUS format. Age
 classes & sexes in the Readme.2009_genotypes.csv2008 GenotypesGenotypes for individuals used in CERVUS analysis caught in 2008. Readme includes the age and sex of individuals used.2008_genotypes.csvAdultsDetails for each Adult caught over 2008-2009.ChicksDetails of all offspring in this study including results from parentage analysis.Nest data for Spatial EPP analysisAll breeding observations in nestboxes and hollows (without genetic samples) at Wyndham in 2008-2009, including anonymised co-ordinates for nest locations, where inter nest differences are preserved but do not reflect the real position on the globe. README file also includes the code used to calculate the number of synchronous nests and how far away they are.Nests.csvGenotypes of Wild and Captive birdsGenotypes of the wild and captive birds in Arlequin format. Readme file includes the key that will allow the ID numbers to be broken down into which morph they are.WvC.arp
DOI: 10.5061/dryad.8d22h
title: Data from: Quantitative trait loci for light sensitivity, body weight, body size, and morphological eye parameters in the bumblebee, Bombus terrestris

description: Bumblebees such as Bombus terrestris are essential pollinators in natural
 and managed ecosystems. In addition, this species is intensively used in
 agriculture for its pollination services, for instance in tomato and
 pepper greenhouses. Here we performed a quantitative trait loci (QTL)
 analysis on B. terrestris using 136 microsatellite DNA markers to identify
 genes linked with 20 traits including light sensitivity, body size and
 mass, and eye and hind leg measures. By composite interval mapping (IM),
 we found 83 and 34 suggestive QTLs for 19 of the 20 traits at the linkage
 group wide significance levels of p = 0.05 and 0.01, respectively.
 Furthermore, we also found five significant QTLs at the genome wide
 significant level of p = 0.05. Individual QTLs accounted for 7.5-53.3% of
 the phenotypic variation. For 15 traits, at least one QTL was confirmed
 with multiple QTL model mapping. Multivariate principal components
 analysis confirmed 11 univariate suggestive QTLs but revealed three
 suggestive QTLs not identified by the individual traits. We also
 identified several candidate genes linked with light sensitivity, in
 particular the Phosrestin-1-like gene is a primary candidate for its
 phototransduction function. In conclusion, we believe that the suggestive
 and significant QTLs, and markers identified here, can be of use in
 marker-assisted breeding to improve selection towards light sensitive
 bumblebees, and thus also the pollination service of bumblebees.
description: geno_phenotypes