cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs85242
title: Data from: Selection on VPS13A linked to migration in a songbird

description: Animal migration demands an interconnected suite of adaptations for
 individuals to navigate over long distances. This trait complex is crucial
 for small birds whose migratory behaviors—such as directionality—are more
 likely innate, rather than being learned as in many longer-lived birds.
 Identifying causal genes has been a central goal of migration ecology, and
 this endeavor has been furthered by genome-scale comparisons. However,
 even the most successful studies of migration genetics have achieved low
 resolution associations, identifying large chromosomal regions that
 encompass hundreds of genes, one or more of which might be causal. Here we
 leverage the genomic similarity among golden-winged (Vermivora
 chrysoptera) and blue-winged warblers (V. cyanoptera) to identify a single
 gene—Vacuolar Protein Sorting 13A (VPS13A)—that is associated with
 distinct differences in migration to Central American (CA) or South
 American (SA) wintering areas. We find reduced sequence variation in this
 gene-region for SA wintering birds, and show this is the likely result of
 natural selection on this locus. In humans, variants of VPS13A are linked
 to the neurodegenerative disorder chorea-acanthocytosis. This new
 association provides one of the strongest gene-level associations with
 avian migration differences.
description: Supplementary Sample
 InformationSupplementary Sample
 Information as well as SRA accession numbers.supplementary_table_sample_info_v3_FINAL.xlsxAdditional MethodsDescription of additional details for sampling, sequencing, and bioinformatic analyses.dryad_methods.docx
DOI: 10.5061/dryad.06rd3fm
title: Data from: Diversity of bat astroviruses in Lao PDR and Cambodia

description: Astroviruses are known to infect humans and a wide range of animal
 species, and can cause gastroenteritis in their hosts. Recent studies have
 reported astroviruses in bats in Europe and in several locations in China.
 We sampled 1876 bats from 17 genera at 45 sites from 14 and 13 provinces
 in Cambodia and Lao PDR respectively, and tested them for astroviruses.
 Our study revealed a high diversity of astroviruses among various
 Yangochiroptera and Yinpterochiroptera bats. Evidence for varying degrees
 of host restriction for astroviruses in bats was found. Furthermore,
 additional Pteropodid hosts were detected. The astroviruses formed
 distinct phylogenetic clusters within the genus Mamastrovirus, most
 closely related to other known bat astroviruses. The astrovirus sequences
 were found to be highly saturated indicating that phylogenetic
 relationships should be interpreted carefully. An astrovirus clustering in
 a group with other viruses from diverse hosts, including from ungulates
 and porcupines, was found in a Rousettus bat. These findings suggest that
 diverse astroviruses can be found in many species of mammals, including
 bats.
description: P1 Cambodia bats
 Astrovirus data_2019Aug16_1658Data pertaining to bats
 sampled in Cambodia for which Astrovirus family testing was
 performedP1 Laos bats Astrovirus
 Data_2019Aug16_1656Data pertaining to bats
 sampled in Lao PDR for which Astrovirus family testing was
 performed
DOI: 10.5061/dryad.fh8mr62
title: Data from: Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

description: South-East Asia is a hot spot for emerging zoonotic diseases, and bats
 have been recognized as hosts for a large number of zoonotic viruses such
 as Severe Acute Respiratory Syndrome (SARS), responsible for acute
 respiratory syndrome outbreaks. Thus, it is important to expand our
 knowledge of the presence of viruses in bats which could represent a risk
 to humans. Coronaviruses (CoVs) have been reported in bat species from
 Thailand, China, Indonesia, Taiwan and the Philippines. However no such
 work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965
 bats were therefore sampled at interfaces with human populations in these
 two countries. They were tested for the presence of coronavirus by
 consensus reverse transcription-PCR assay. A total of 93 samples (4.7%)
 from 17 genera of bats tested positive. Sequence analysis revealed the
 presence of potentially 37 and 56 coronavirus belonging to
 alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs
 group is known to include some coronaviruses highly pathogenic to human,
 such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from
 frugivorous bats (family Pteropodidae) (n=55) clustered with other bat
 βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra
 fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs
 were all detected in various genera of insectivorous bats and clustered
 with diverse bat αCoV sequences previously published. A closely related
 strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was
 detected in 2 Myotis bats. We highlighted the presence and the high
 diversity of coronaviruses circulating in bats from Cambodia and Lao PDR.
 Three new bat genera and species were newly identified as host of
 coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis
 horsfieldii.
description: P1 Cambodia bats
 Coronavirus data_2019Aug16_1658Data associated with
 bats sampled in Cambodia and tested for CoronavirusesP1 Laos bats Coronavirus
 Data_2019Aug16_1656Data associated with
 bats sampled in Lao PDR and tested for Coronaviruses
DOI: 10.5061/dryad.2646vp0
title: Data from: Metatranscriptomics yields new genomic resources and sensitive detection of infections for diverse blood parasites

description: Metatranscriptomics is a powerful method for studying the composition and
 function of complex microbial communities. The application of
 metatranscriptomics to multi-species parasite infections is of particular
 interest, as research on parasite evolution and diversification has been
 hampered by technical challenges to genome-scale DNA sequencing. In
 particular, blood parasites of vertebrates are abundant and diverse though
 they often occur at low infection intensities and exist as multi-species
 infections, rendering the isolation of genomic sequence data challenging.
 Here, we use birds and their diverse haemosporidian parasites to
 illustrate the potential for metatranscriptome sequencing to generate
 large quantities of genome-wide sequence data from multiple blood parasite
 species simultaneously. We used RNA-Seq on 24 blood samples from songbirds
 in North America to show that metatranscriptomes can yield large
 proportions of haemosporidian protein-coding gene repertoires even when
 infections are low-intensity (&lt;0.1% red blood cells infected) and
 consist of multiple parasite taxa. By bioinformatically separating host
 and parasite transcripts and assigning them to the haemosporidian genus of
 origin, we found that transcriptomes detected ~23% more total parasite
 infections across all samples than were identified using microscopy and
 DNA barcoding. For single-species infections, we obtained data for upwards
 of 1,300 loci from samples with as low as 0.03% parasitemia, with the
 number of loci increasing with infection intensity. In total, we provide
 data for 1,502 single-copy orthologous loci from a
 phylogenetically-diverse set of 33 haemosporidian mitochondrial lineages.
 The metatranscriptomic approach described here has the potential to
 accelerate ecological and evolutionary research on haemosporidians and
 other diverse parasites.
description: All_AppendicesExcel file containing Appendices 1 (data summary by sample), Appendix 2 (RNA extraction results), and 3 (list of contigs that were identified as contaminants).Galen_2019_R_codeR script containing code needed to replicate analyses from the study (multiple correspondence analysis, multiple regression, and quantification of infections from transcriptomes).Presence/absence matrix of orthogroups across samplesThis matrix was used for the multiple correspondence analysis from the studyorthogroup_pres_ab.txtOutput of ContamFinder pipelineThis directory contains the output of the ContamFinder pipeline that was run on each of the transcriptomes sequenced in this study.contamfinder_output.zipOutput of genus assignment analysisThis directory contains the FASTA file output of the genus assignment analysis for each orthogroup that was identified using OrthoMCL (1,502 orthogroups in total).genus_assignment_51pct_cutoff_output.zipgenus_assignment_output_RAxML_gene_treesThis directory contains the gene trees that correspond to the output of the genus assignment analysis
DOI: 10.5061/dryad.8041f4r
title: Data from: Interaction between extreme weather events and mega‐dams increases tree mortality and alters functional status of Amazonian forests

description: 1. Forest responses to changes in drought frequency is a critical unknown
 for the future of Amazon forests under climate change, but equally
 important is the much less studied response to large floods, which may
 also increase tree mortality and change forest functionality. Further,
 forest vulnerability to flood is being exacerbated by large hydroelectric
 dams on Amazon rivers that put upland environments not adapted to flood at
 unique risk. 2. To address this critical knowledge gap, we evaluated the
 synergistic effects of the extreme 2014 rainfall coupled with the newly
 constructed Jirau hydroelectric dam on tree survival and forest
 functionality, in the upper Madeira River basin. We used surveys of
 campinarana white-sand forests (stems &gt;1 cm in seven 1 ha plots)
 conducted before and after the extreme flood to test trait-based
 ecological theory predictions of the impact of drought on overall
 community function. 3. We found that flooding increased mortality by
 nearly five-fold (from 3.2% to 15.1%), mostly in smaller trees. This large
 mortality induced significant and consistent shifts in community function,
 towards species with conservative life strategies: direct comparison of
 trait differences between surviving and dying trees showed that survivors
 had smaller, high density stomata, and higher leaf dry matter content,
 wood density and root tissue density. Size and density of stomata and root
 tissue density were the most important predictors of species mortality
 rates. 4. Synthesis and applications. Although focused on a single event
 in one type of forest, this work highlights the general importance, and
 need for further study, of synergism between climate change and
 development in Amazon forests. In particular, we expect that continued
 expansion of hydroelectric dams in Amazonia will likely intensify the
 impact of large floods on forests made newly vulnerable by these dams,
 with substantial effect on future forest functionality in expanded
 floodplain areas across the Basin.16-Aug-2019
description: BD_funcional_Moser_etal_JAEFunctional data, plot numbers, indivudal numbers, species names
DOI: 10.5061/dryad.5kt172j
title: Data from: Assessing the Function of Geophagy in a Malagasy Rainforest Lemur

description: Geophagy has been observed in nearly every long-term study of folivorous
 primates. Yet despite frequent observations of this behavior, conclusive
 explanations for soil consumption remain ambiguous. This study tests the
 most frequently proposed hypotheses for geophagy using data collected on
 the geophagic behavior of the Milne-Edwards’ sifaka (Propithecus edwardsi)
 living in two forests with varying levels of disturbance within Ranomafana
 National Park, Madagascar. Field data were collected from December 2002 to
 November 2003, during which time soil samples were collected for mineral
 analyses from 102 sites selected for geophagy and 42 control sites at
 which no geophagy was recorded. Results indicate that control soils differ
 significantly between the two study sites, and that this difference is
 primarily attributable to varying levels of habitat disturbance. The
 frequency of soil consumption also does not vary significantly by sex or
 between logged and unlogged habitats. Soil consumption significantly
 correlated with fruit/seed consumption overall, but to a lesser degree in
 logged compared to unlogged sites. Clay minerals found in soils likely
 prevent absorption of dietary toxins in the gut and/or may mediate gut pH.
 This provides strong evidence for the protection hypothesis for geophagy,
 which may be especially important in areas where logging, or other forms
 of habitat disturbance, have been experienced.
description: Semel et al _ Geophagy
 in sifakas at RNPData file consists of
 three worksheets (standard soil tests, specific ions tests and soil
 composition), containing the raw data summarized in Table 2 and used in
 subsequent analyses.
DOI: 10.5061/dryad.p1s7r7g
title: Data from: Trophic rewilding establishes a landscape of fear: Tasmanian devil introduction increases risk-sensitive foraging in a key prey species

description: Global declines of large carnivores have reduced the ‘landscape of fear’
 that constrains the behaviour of other species. In recent years, active
 and passive trophic rewilding have potentially begun restoring these lost
 top-down controls. The Tasmanian devil (Sarcophilus harrisii) has declined
 severely due to a novel transmissible cancer. In response to extinction
 fears, devils were introduced to the devil-free Maria Island, where their
 abundance rapidly increased. We tested how this introduction influenced
 risk-sensitive foraging in the common brushtail possum (Trichosurus
 vulpecula), a major prey species for devils, using giving-up densities
 (GUDs). Before the introduction of devils, possum GUDs on Maria Island
 were indistinguishable from the long-diseased region of Tasmania, where
 devils have been rare since ~2000. Three years after devil introduction,
 GUDs were 64% higher on Maria Island than the control region,
 demonstrating that after an initial period of high mortality, possums
 quickly adopted risk-sensitive foraging behaviours. Devil activity across
 Maria Island was variable, leading to a heterogeneous landscape of fear
 and highlighting that top predators must be at functional densities to
 elicit behavioural responses from prey. Our study provides strong evidence
 that top predators modify the behaviour of prey by instilling fear,
 causing rapid ecological change following recoveries.
description: GUDdata_mBACIThis study investigated how the introduction of an apex predator, the Tasmanian devil, influenced the risk-sensitive foraging of a major prey species, the common brushtail possum. Data comes from a before-after control-impact giving-up densities foraging experiment. Please cite the published paper in Ecography (DOI: 10.1111/ecog.04635) as well as the data files on Dryad.GUDdata_secondAnalysis_AFTERonlyThis study investigated how the introduction of an apex predator, the Tasmanian devil, influenced the risk-sensitive foraging of a major prey species, the common brushtail possum. This data comes from the "after" period of a before-after control-impact giving-up densities foraging experiment. We used this part of the data to assess how the local activity of Tasmanian devils recorded on remote cameras influenced possum foraging behaviour. Please cite the published paper in Ecography (DOI: 10.1111/ecog.04635) as well as the data files on Dryad.
DOI: 10.5061/dryad.9tb689h
title: Data from: The evolution of egg trading in simultaneous hermaphrodites

description: Egg trading, whereby simultaneous hermaphrodites exchange each
 other's eggs for fertilization, constitutes one of the few rigorously
 documented and most widely cited examples of direct reciprocity among
 unrelated individuals. Yet how egg trading may initially invade a
 population of non-trading simultaneous hermaphrodites is still unresolved.
 Here, we address this question with an analytical model that considers
 mate encounter rates and costs of egg production in a population that may
 include traders (who provide eggs for fertilization only if their partners
 also have eggs to reciprocate), providers (who provide eggs regardless of
 whether their partners have eggs to reciprocate), and withholders
 ("cheaters" who only mate in the male role and just use their
 eggs to elicit egg release from traders). Our results indicate that a
 combination of intermediate mate encounter rates, sufficiently high costs
 of egg production, and a sufficiently high probability that traders detect
 withholders (in which case eggs are not provided) is conducive to the
 evolution of egg trading. Under these conditions traders can invade—and
 resist invasion from—providers and withholders alike. The prediction that
 egg trading evolves only under these specific conditions is consistent
 with the rare occurrence of this mating system among simultaneous
 hermaphrodites.
description: Code to reproduce
 figuresJupyter notebook with
 Python code to produce the figures of the paper.eggtrading.ipynb
DOI: 10.5061/dryad.67fs3bs
title: Data from: A new echimyid genus (Rodentia, Caviomorpha) in Central Argentina: uncovered diversity of a Brazilian group of mammals in the Pleistocene

description: We describe a new extinct spiny rat, Proclinodontomys dondasi n. gen. n.
 sp. (Rodentia, Caviomorpha, Echimyidae), represented by a
 noteworthy-preserved skull and mandible from the early-middle Pleistocene
 outcrops at the coastal cliffs of southeastern Buenos Aires Province
 (Central Argentina). Phylogenetic analyses allow us to propose that the
 new species described here and the already known Eurzygomatomys mordax
 (Winge), represent a new genus closely related to the living
 Euryzygomatomys spinosus and Clyomys laticeps. The new genus differs from
 Euryzygomatomys and Clyomys by having much more procumbent upper incisors,
 a more developed fossa for the M. temporalis, more flared and laterally
 expanded zygomatic arches, frontal less markedly expanded posteriorly,
 jugals much deeper anteriorly than posteriorly, with the dorsal border
 descending more abruptly posteriorly, smaller orbital cavity, and external
 auditory meatus relatively smaller and slanted upward and backward.
 Several features of the new species reflect a higher degree of adaptation
 to semifossorial habits than those of E. spinosus. The origin of the
 semifossorial ecomorphotype within echimyids may have been triggered by
 the expansion of relatively open and arid environments that arose near the
 Miocene-Pliocene boundary. The record of this new echimyid in Central
 Argentina indicates that during the early Pleistocene, the southern limit
 of the geographic range of extinct representatives of the Brazilian
 lineage of semifossorial echimyids extended further south than that of
 their living members.
description: S1_Morphological data
 matrix TNT fileS1 [Morphological data
 matrix TNT file] Morphological data matrix for cladistic analysis in TNT,
 composed by 62 characters evaluated in 26 Echimyid taxa. S2 [Combined data
 matrix TNT file] Combined data matrix for cladistic analysis in TNT of 30
 Echimyid taxa. Data set is composed both 62 morphological and 5303 DNA
 characters from the first portion of the protein-coding cytochrome b gene,
 12S ribosomal RNA, growth hormone receptor exon 10, recombination
 activating gene 1, and the v von Willebrand factor exon 28. S3 [Combined
 data matrix Nexus file] Nexus file of combined data matrix for the
 Bayesian analysis. Detail of the matrix composition is indicated in
 Supplemental Material S2. S4 [Common synapomorphies and autapomorphies]
 List of common synapomorphies and autapomorphies of three most
 parsimonious morphological trees obtained in the TNT cladistics analysis
 of equal weights.Candela et al-Supplementary
 Data.zip
DOI: 10.6084/m9.figshare.31161244
title: CVH database

description: CVH composite and demographic/behavioral variables
DOI: 10.6084/m9.figshare.31161244.v1
title: CVH database

description: CVH composite and demographic/behavioral variables
DOI: 10.5061/dryad.bm008d2
title: Data from: Evolution of mating types in finite populations: the precarious advantage of being rare

description: Sexually reproducing populations with self-incompatibility bear the cost
 of limiting potential mates to individuals of a different type. Rare
 mating types escape this cost since they are unlikely to encounter
 incompatible partners, leading to the deterministic prediction of
 continuous invasion by new mutants and an ever increasing number of types.
 However, rare types are also at an increased risk of being lost by random
 drift. Calculating the number of mating types that a population can
 maintain requires consideration of both the deterministic advantages and
 the stochastic risks. By comparing the relative importance of selection
 and drift, we show that a population of size N can maintain a maximum of
 approximately N1/3 mating types for intermediate population sizes while
 for large N we derive a formal estimate. Although the number of mating
 types in a population is quite stable, the rare type advantage promotes
 turnover of types. We derive explicit formulas for both the invasion and
 turnover probabilities in finite populations.
description: Codes to generate the
 data and figuresThe c++ code, the
 generated data and the python files to produce the plots in Figure 4 and
 Figure 5b of the manuscript. The python files are the ones producing the
 actual figures, the c++ code generates the data.Figures.tar.gz
DOI: 10.5061/dryad.2t64448
title: Data from: Spatio-temporal responses of predators to hyperabundant geese affect risk of predation for sympatric-nesting species

description: The Arctic is undergoing rapid changes, with anthropogenic shifts in
 climate having important and well-documented impacts on habitat.
 Populations of predators and their prey are affected by changing climate
 and other anthropogenic factors, and these changing trophic interactions
 could have profound effects on breeding populations of Arctic birds.
 Variable abundance of lemmings (a primary prey of generalist Arctic
 predators) and increasing abundance of light geese (Lesser Snow and Ross’
 Geese; a secondary prey) could have negative consequences for numerous
 sympatric shorebirds (an incidental prey). Using 16 years of predator-prey
 observations and 13-years of shorebird nest survival data at a site near a
 goose colony we identify relationships among geese, lemmings, and their
 shared predators and then relate predator indices to shorebird risk of
 nest predation. During two years, we also placed time-lapse cameras and
 artificial shorebird nests at increasing distances from a goose colony to
 document spatial trends in predators and their effect on risk of
 predation. In the long-term data, yearly indices of light geese positively
 influenced indices of gulls and jaegers, and shorebird nest predation rate
 was negatively correlated with jaeger and fox indices. All three predator
 indices were highest near the goose colony and artificial nest predation
 probability was negatively correlated with distance from goose colony, but
 these effects were less apparent during the second year. Combined, these
 results highlight the variation in predator-mediated interactions between
 geese and shorebirds and outline one mechanism by which hyperabundant
 geese may be contributing to local or regional declines in Arctic-nesting
 shorebird populations.
description: artificial nest survival
 dataArtificial nest survival
 data for 2015 and 2016 at East Bay Mainland and Coats
 Island.artificial nest
 survival.xlsCamera predator
 observationsPredator observations on
 trail cameras at East Bay Mainland and Coats Island in 2015 and
 2016.Camera
 indices.xlsYearly observation
 indicesObservations of
 lemmings, predators, and geese per 8-hour observer day at East Bay
 Mainland.