cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7s94q
title: Data from: Hologenomic speciation: synergy between a male-killing bacterium and sex-linkage creates a ‘magic trait’ in a butterfly hybrid zone

description: Danaus chrysippus (L.) in Africa comprises four substantially isolated
 semispecies that are migratory and hybridize on a seasonal basis
 throughout the eastern and central part of the continent. In the hybrid
 zone (but not elsewhere), the butterfly is commonly host to a male killing
 endosymbiotic bacterium, Spiroplasma sp., which principally infects one
 semispecies, Danaus chrysippus chrysippus in Kenya. A W-autosome mutation,
 inherited strictly matrilinearly, links B and C colour gene loci, which
 have thus gained sex-linkage in chrysippus. We have monitored variation in
 sex ratio and genotype at the A and C colour gene loci for two extended
 periods of 18 months (2004–5) and 12 months (2009–10) in adults reared
 from wild eggs laid on trap plants in Kasarani, near Nairobi, Kenya.
 Additionally, in 2009–10, all surviving adult butterflies were screened
 for Spiroplasma infection. The hybridizing Kasarani population is highly
 atypical in three respects, and has apparently been so for some 30 years:
 first, the sex ratio is permanently female-biased (as expected), although
 subject to seasonal fluctuation, being lowest (male/female) when D. c.
 chrysippus (cc) peaks and highest when Danaus chrysippus dorippus (CC)
 predominates; second, the population is invariably dominated by Cc
 heterozygotes of both sexes but especially females; and third, cc males
 are always scarce because they are systematically eliminated by male
 killing, whereas the CC genotype is male-biased. It is this imbalance of
 sex versus genotype that determines the massive departure from
 Hardy–Weinberg equilibrium in the population, in part because cc females
 have little choice but to pair with C- males. We suggest that: first, Cc
 hybrids of both sexes fail to disperse in the company of either parental
 semispecies; second, Spiroplasma positive females carrying the W-autosome
 mutation have a selective advantage over females that lack the
 translocation; third, the endoparasite and the translocation create a
 ‘magic trait’ linkage group that underlies hologenomic reproductive
 isolation between two emerging species, D. c. chrysippus and D. c.
 dorippus; and, fourth, that the predominance of males in dorippus suggests
 that individuals must be protected by a male-killing suppressor gene. By
 contrast to the C locus, Aa heterozygotes are in substantial and permanent
 deficit, suggesting either assortative mating between AA (chrysippus and
 dorippus) and aa (Danaus chrysippus alcippus), or heterozygote unfitness,
 or both.
description: BLJS 2895.R1. Sex ratio
 model revisedData collected in the
 field for this publication, population genetic model and its
 parametersBJLS-2895.R1.Raw data
 set for tables 1-5Excel data sheet giving
 all data on butterflies reared for this publication
DOI: 10.5061/dryad.3p5r6
title: Data from: Survival of the feces: does a nematode lungworm adaptively manipulate the behavior of its cane toad host?

description: Parasites can enhance their fitness by modifying the behavior of their
 hosts in ways that increase rates of production and transmission of
 parasite larvae. We used an antihelminthic drug to experimentally alter
 infections of lungworms (Rhabdias pseudosphaerocephala) in cane toads
 (Rhinella marina). We then compared subsequent behaviors of dewormed toads
 versus toads that retained infections. Both in the laboratory and in the
 field, the presence of parasites induced hosts to select higher body
 temperatures (thereby increasing rates of lungworm egg production), to
 defecate in moister sites, and to produce feces with higher moisture
 content (thereby enhancing survival of larvae shed in feces). Because
 those behavioral modifications enhance rather than decrease parasite
 fitness, they are likely to have arisen as adaptive manipulations of host
 behavior rather than as host adaptations to combat infection or as
 nonadaptive consequences of infection on host physiology. However, the
 mechanisms by which lungworms alter cane toad thermal preference and
 defecation are not known. Although many examples of host manipulation by
 parasites involve intermediate hosts facilitating their own demise, our
 findings indicate that manipulation of definitive hosts can be as subtle
 as when and where to defecate.
description: Finnerty_et_al_DataCollected data in separate labeled tabs
DOI: 10.5061/dryad.c6f1g
title: Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations

description: Spatial variation in disease risk in wild populations can depend both on
 environmental and genetic factors. Understanding the various contributions
 of each factor requires experimental manipulation of both the environment
 and genetic composition of populations under natural field conditions. We
 first examined natural patterns of oomycete composition and infection in
 the eggs of 13 populations of the spotted salamander Ambystoma maculatum.
 We then performed a fully factorial field transplant of the eggs of six
 populations to separate the contributions from population of origin and
 the environment on oomycete resistance in spotted salamanders. Among wild
 ponds, we found strong variation in oomycete infections in spotted
 salamander populations and differences in the composition of oomycete
 communities. In transplant experiments, salamander populations differed in
 their resistance to oomycete infections via a significant interaction
 between population of origin and environment. However, not all populations
 were locally adapted to local conditions. One population was significantly
 adapted to its home environment, and another one was significantly
 maladapted. These population effects could originate from differential
 adaptation of salamander populations to local oomycete communities or
 environmental conditions that mediate resistance, local adaptation and
 maladaptation of oomycetes to hosts, or from maternal transmission.
 Accounting for both environment and population of origin will often be
 necessary to understand disease dynamics in wild populations.
description: Urban et al. Oikos data
 for dryadRaw data from field
 surveys of oomycete infections in 2010 and 2011 as well as infection
 results from transplant experiment.
DOI: 10.5061/dryad.8cs37
title: Data from: Terrestrial-focused protected areas are effective for conservation of freshwater fish diversity in Lake Tanganyika

description: Freshwater protected areas are rarely designed specifically for this
 purpose and consequently their conservation benefit cannot be guaranteed.
 Using Lake Tanganyika as a test case we investigated the benefits of
 terrestrial-focussed protected areas on the alpha and beta taxonomic and
 functional diversity of the diverse endemic rocky-shore cichlid fishes.
 Lake Tanganyika has limited protected shorelines and continued human
 population growth in its catchment, which has potential for negative
 impacts on habitat quality and key biological processes. We conducted 554
 underwater surveys across a gradient of human disturbance including two
 protected areas, along 180 km of Tanzanian coastline, sampling 70 cichlid
 species representing a diverse range of life-histories and trophic groups.
 Alpha diversity was up to 50% lower outside of protected areas, and
 herbivores appeared most affected. Turnover dominated within-locality
 variation in beta diversity, but the nestedness component was positively
 related to human disturbance indicating an increase in generalist species
 outside of protected areas. Within protected areas the decline in zeta
 diversity (the expected number of shared species across multiple surveys)
 was best described by power law functions, which occur when local
 abundance is predicted by regional abundance; but declined exponentially
 in unprotected waters indicating a dominance of stochastic assembly.
 Despite not being designed for the purpose, the protected areas are
 clearly benefitting cichlid taxonomic and functional diversity within Lake
 Tanganyika, probably through local reduction in sediment deposition and/or
 pollution, but as cichlids can be poor dispersers protected area coverage
 should be expanded to benefit isolated communities.
description: Kigoma Town Cichlid
 Community MatrixBrittonEtAl2017_KigomaTown.csvKigoma Deforested Cichlid Community MatrixBrittonEtAl2017_KigomaDeforested.csvKalilani Village Cichlid Community MatrixBrittonEtAl2017_KalilaniVillage.csvJakobsen's Beach Cichlid Community MatrixBrittonEtAl2017_Jakobsen'sBeach.csvGombe Stream National Park Cichlid Community MatrixBrittonEtAl2017_GombeNP.csvMahale Mountain National Park S1 Cichlid Community MatrixBrittonEtAl2017_MahaleNPS1.csvMahale Mountain National Park S2 Cichlid Community MatrixBrittonEtAl2017_MahaleNPS2.csv
DOI: 10.5061/dryad.7h8v1
title: Data from: A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity

description: The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the
 Indian Ocean and largely responsible for shaping the unique ecosystem
 found throughout the island’s rainforests. However, the introduction and
 establishment of supercolonies of the highly invasive yellow crazy ant,
 Anoplolepis gracilipes, has decimated red crab numbers over the last
 several decades. This poses a significant risk to the future conservation
 of G. natalis and consequently threatens the integrity of the unique
 island ecosystem. Here we undertook a population genetic analysis of G.
 natalis using a combination of 11 microsatellite markers and sequencing of
 the mitochondrial cytochrome oxidase subunit I gene from samples collected
 on Christmas Island as well as a single location from North Keeling Island
 (located approximately 900 km west of Christmas Island). The genetic
 results indicate that G. natalis is a single panmictic population on
 Christmas Island, with no spatial genetic structure or restricted gene
 flow apparent between sampled locations. Further, G. natalis from North
 Keeling Island are not genetically distinct and are recent immigrants from
 Christmas Island. The effective population size of G. natalis has likely
 remained large and stable on Christmas Island throughout its evolutionary
 history with relatively moderate to high levels of genetic diversity in
 microsatellite loci and mitochondrial haplotypes assessed in this study.
 For management purposes G. natalis can be considered a single panmictic
 population, which should simplify conservation efforts for the genetic
 management of this iconic island species.
description: Genetic data used to
 assess population structure of G. natalisMolecular data
 (microsatellite and mtDNA) used in the analysis of the population genetic
 structure of G. natalis on Christmas and North Keeling Island. There are
 three spreadsheets in the file, containing separate data used to analyse
 (1) small scale spatial structure (Spatial Autocorrel Analysis), (2)
 contemporary population genetic structure on Christmas Island and North
 Keeling Island (Population Genetic Analysis), and (3) mtDNA haplotype
 diversity and structure (mtDNA Analysis). Each spreadsheet has individual
 IDs, with cross over between samples found in (2) and (3). Spreadsheets
 'Spatial Autocorrel Analysis' and 'Population Genetic
 Analysis' also have sample location data (UTMs).DataFileDryad.xlsx
DOI: 10.5061/dryad.fb67t
title: Data from: Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds

description: The Canary Islands were settled in the first millennium AD by colonizers
 likely originating from North Africa. The settlers developed a farming
 economy with barley as the main crop. Archaeological evidence suggests the
 islands then remained isolated until European sea-travellers discovered
 and colonized them during the 14th and 15th centuries. Here we report a
 population study of ancient DNA from twenty-one archaeobotanical barley
 grains from Gran Canaria dating from 1050 to 1440 cal AD. The material
 showed exceptional DNA preservation and genotyping was carried out for 99
 single nucleotide markers. In addition 101 extant landrace accessions from
 the Canary Islands and the western Mediterranean were genotyped. The
 archaeological material showed high genetic similarity to extant landraces
 from the Canary Islands. In contrast, accessions from the Canary Islands
 were highly differentiated from both Iberian and North African mainland
 barley. Within the Canary Islands, landraces from the easternmost islands
 were genetically differentiated from landraces from the western islands,
 corroborating the presence of pre-Hispanic barley cultivation on
 Lanzarote. The results demonstrate the potential of population genetic
 analyses of ancient DNA. They support the hypothesis of an original
 colonization, possibly from present day Morocco, and subsequent isolation
 of the islands and reveal a farmer fidelity to the local barley that has
 lasted for centuries.
description: Barley SNP
 genotypesGenotyping results of
 archaeological and extant barley from the Canary Islands and extant barley
 from North Africa and the Mediterranean.CanaryBarley.csv
DOI: 10.5061/dryad.c2n12
title: Data from: Differences in greeting behaviour towards humans with varying levels of familiarity in hand-reared wolves (Canis lupus)

description: Socialized wolves' relationship with humans is a much debated, but
 important question in light of dog domestication. Earlier findings
 reported no attachment to the caretaker at four months of age in a Strange
 Situation Test, while recently attachment to the caretaker was reported at
 a few weeks of age in a similar paradigm. To explore wolf–human
 relationship, we analysed behaviours of hand reared, extensively
 socialized wolves towards four visitor types: foster-parents, close
 acquaintances, persons met once before, and complete strangers during a
 greeting episode. As hypothesized, in the greeting context subjects showed
 more intense and friendly behaviour towards foster-parents, than other
 visitor types, which may reflect familiarity and affinity. However,
 differences were more pronounced in the group situation (at six months of
 age) than in the individual situation (at 12 and 24 months), suggesting
 that unique status of foster parents may become less distinct as wolves
 get older, while exploration of novel social agents is expressed more with
 older age. Fear related behaviour patterns were only found in the
 individual situation, mainly displayed towards strangers. We showed that,
 in case of extensively socialized wolves, distinctive affiliation and
 affinity towards the foster parent prevails into adulthood.
description: GreetingSTATdataTableWolf greeting experiments, raw dataGroupDataEXP1Raw data EXP1IndividualDataEXP2Raw data, EXp 2
DOI: 10.5061/dryad.c7638
title: Data from: Influences of APOA5 variants on plasma triglyceride levels in Uyghur population

description: Objective: Single nucleotide polymorphisms (SNPs) in apolipoprotein A5
 (APOA5) gene are associated with triglyceride (TG) levels. However, the
 minor allele frequencies and linkage disequilibriums (LDs) of the SNPs in
 addition to their effects on TG levels vary greatly between Caucasians and
 East Asians. The distributions of the SNPs/haplotypes and their
 associations with TG levels in Uyghur population, an admixture population
 of Caucasians and East Asians, have not been reported to date. Here, we
 performed a cross-sectional study to address these. Methods: Genotyping of
 four SNPs in APOA5 (rs662799, rs3135506, rs2075291, and rs2266788) was
 performed in 1174 unrelated Uyghur subjects. SNP/haplotype and TG
 association analyses were conducted. Results: The frequencies of the SNPs
 in Uyghurs were in between those in Caucasians and East Asians. The LD
 between rs662799 and rs2266788 in Uyghurs was stronger than that in East
 Asians but weaker than that in Caucasians, and the four SNPs resulted in
 four haplotypes (TGGT, CGGC, TCGT, and CGTT arranged in the order of
 rs662799, rs3135506, rs2075291, and rs2266788) representing 99.2% of the
 population. All the four SNPs were significantly associated with TG
 levels. Compared with non-carriers, carriers of rs662799-C, rs3135506-C,
 rs2075291-T, and rs2266788-C alleles had 16.0%, 15.1%, 17.1%, and 12.4%
 higher TG levels, respectively. When haplotype TGGT was defined as the
 reference, the haplotypes CGGC, TCGT, and CGTT resulted in 16.1%, 19.0%,
 and 19.8% higher TG levels, respectively. The proportions of variance in
 TG explained by APOA5 locus were 2.5%, 0.3%, 0.4%, and 1.9% for single SNP
 rs662799, rs3135506, rs2075291, and rs2266788, respectively, and 3.0% for
 the haplotypes constructed by them. Conclusions: The association profiles
 between the SNPs and haplotypes at APOA5 locus and TG levels in this
 admixture population differed from those in Caucasians and East Asians.
 The functions of these SNPs and haplotypes need to be elucidated
 comprehensively.
description: Data from: Influences of
 APOA5 variants on plasma triglyceride levels in Uyghur
 populationoriginal
 datadata to
 plos one.xlsx
DOI: 10.5281/zenodo.18382533
title: Model outputs presented in the JAMES paper: Modelling sub-grid peatland vegetation dynamics in the ORCHIDEE-PEAT land surface model

description: Simulated areal fraction, gross primary productivity, and leaf area index of peatland plant functional types (PFTs) using the ORCHIDEE-PEAT land surface model.

Variables in each file include:VEGET_COV_MAX: areal fraction (per unit of total grid-cell area) of peatland plant functional types (PFTs);GPP: gross primary productivity of peatland PFTs;LAI: leaf area index of peatland PFTs.

The peatland PFTs include veget16-C3 graminoids (sedges and grasses), veget17-bryophytes (mosses), veget18-boreal broadleaf deciduous shrubs, veget19-boreal needleleaf evergreen trees, veget20-tropical evergreen trees, and veget21-tropical raingreen trees.
DOI: 10.5281/zenodo.18382534
title: Model outputs presented in the JAMES paper: Modelling sub-grid peatland vegetation dynamics in the ORCHIDEE-PEAT land surface model

description: Simulated areal fraction, gross primary productivity, and leaf area index of peatland plant functional types (PFTs) using the ORCHIDEE-PEAT land surface model.

Variables in each file include:VEGET_COV_MAX: areal fraction (per unit of total grid-cell area) of peatland plant functional types (PFTs);GPP: gross primary productivity of peatland PFTs;LAI: leaf area index of peatland PFTs.

The peatland PFTs include veget16-C3 graminoids (sedges and grasses), veget17-bryophytes (mosses), veget18-boreal broadleaf deciduous shrubs, veget19-boreal needleleaf evergreen trees, veget20-tropical evergreen trees, and veget21-tropical raingreen trees.
DOI: 10.5061/dryad.659016k
title: Data from: Below-ground resource partitioning alone cannot explain the biodiversity–ecosystem function relationship: a field test using multiple tracers

description: 1. Belowground resource partitioning is among the most prominent
 hypotheses for driving the positive biodiversity-ecosystem function
 relationship. However, experimental tests of this hypothesis in
 biodiversity experiments are scarce, and the available evidence is not
 consistent. 2. We tested the hypothesis that resource partitioning in
 space, in time, or in both space and time combined drives the positive
 effect of diversity on both plant productivity and community resource
 uptake. At the community level, we predicted that total community resource
 uptake and biomass production above- and belowground will increase with
 increased species richness or functional group richness. We predicted that
 at the species level resource partition breadth will become narrower, and
 that overlap between the resource partitions of different species will
 become smaller with increasing species richness or functional group
 richness. 3. We applied multiple resource tracers (Li and Rb as potassium
 analogues, the water isotopologues - H218O and 2H2O, and 15N) in three
 seasons at two depths across a species and functional group richness
 gradient at a grassland biodiversity experiment. We used this
 multidimensional resource tracer study to test if plant species partition
 resources with increasing plant diversity across space, time, or both
 simultaneously. 4. At the community level, community resource uptake of
 nitrogen and potassium and above- and belowground biomass increased
 significantly with increasing species richness but not with increasing
 functional group richness. However, we found no evidence that resource
 partition breadth or resource partition overlap decreased with increasing
 species richness for any resource in space, time, or both space and time
 combined. Synthesis: These findings indicate that belowground resource
 partitioning may not drive the enhanced resource uptake or biomass
 production found here. Instead, other mechanisms such as facilitation,
 species-specific biotic feedback, or aboveground resource partitioning are
 likely necessary for enhanced overall ecosystem function.
description: Jesch.et.al-Resource
 partitioningThis data file has the
 required data and code to create all figures and tables in Jesch et al.
 Journal of Ecology. Read me files for each dataset are also
 included.
DOI: 10.5061/dryad.d4g94
title: Data from: Adaptive divergence in Darwin's small ground finch (Geospiza fuliginosa): divergent selection along a cline

description: We examine here, in a single year (2005), phenotypic divergence along a
 560-m elevation gradient in Darwin's small ground finch (Geospiza
 fuliginosa) in the Galápagos Islands. In this sample, four composite
 measures of phenotypic traits showed significant differences along the
 18-km geographical cline extending from lowlands to highlands. Compared
 with lowland birds, highland birds had larger and more pointed beaks, and
 thicker tarsi, but smaller feet and claws. Finches in an intervening
 agricultural zone had predominantly intermediate trait values. In a
 second, mark–recapture study we analyse selection on morphological traits
 among birds recaptured across years (2000–2005) in lowland and highland
 habitats. Birds were more likely to survive in the highlands and during
 the wet season, as well as if they had large beaks and bodies. In
 addition, highland birds exhibited higher survival rates if they had small
 feet and pointed beaks – attributes common to highland birds as a whole.
 Lowland birds were more likely to survive if they possessed the opposite
 traits. Selection therefore reinforced existing morphological divergence,
 which appears to reflect local adaptation to differing resources during
 the predominantly drought-ridden conditions that characterized the 5-year
 study. Alternative explanations – including genetic drift, matching
 habitat choice, deformation by parasites, and the effects of wear –
 received little or no support.
description: Morphological
 measurements of Galapagos finches (Geospiza fuliginosa),
 2000-2005See the ReadMe
 file.Sulloway&Kleindorfer_DryadDataSubmission_8May2013.dat