cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hhmgqnkdw
title: Demographic History and Genomic Targets of Positive Selection in Giant Gough Mice

description: A key challenge in understanding how natural selection operates is to
 identify the mutations and genes that make it possible. Positive selection
 on beneficial mutations distorts linked variation by altering the site
 frequency spectrum, the configuration of haplotypes, and population
 differentiation. By comparing patterns of sequence variation to neutral
 predictions across genomes, the targets of positive selection can be
 located. We applied this logic to an unusual population of house mice that
 shows phenotypic and ecological hallmarks of selection. Mice from Gough
 Island are twice the body size of mainland mice, eat live seabirds,
 maintain a very high population density, and inhabit an environment
 without predators or humans. We used massively parallel short-read
 sequencing to survey the genomes of 14 Gough Island mice. We computed a
 set of summary statistics to capture diverse aspects of variation across
 these genome sequences, used approximate Bayesian computation to
 reconstruct a null demographic model, and then applied machine learning to
 estimate the posterior probability of positive selection in each region of
 the genome. We conducted parallel analyses on genome sequences from 8 mice
 from Germany, treating them as representatives of a mainland reference
 population. A few thousand 5kb windows show strong evidence for positive
 selection in Gough Island mice but not in German mice. Genic regions and
 the X chromosome contain disproportionate shares of these selection
 windows. Over-represented gene ontologies in selection windows emphasize
 neurological themes. Inspection of genomic regions harboring many
 selection windows with high posterior probabilities pointed to genes with
 known effects on exploratory behavior and body size as potential targets.
 Some genes in these regions have missense mutations and/or putative
 regulatory mutations with large differences between Gough Island mice and
 German/French mice in the frequency of the derived allele; these are
 candidates for adaptive variants. Our results provide a genomic portrait
 of adaptation to island conditions and position Gough Island mice as a
 powerful system for understanding the genetic component of natural
 selection.
description: SNP vcf files. Summary statistics used for ABC
 inference and selection scan.
DOI: 10.5061/dryad.sxksn0310
title: fMRI/fPACT 3D image stacks and analysis codes for function

description: Functional human brain imaging is mainly based on
 blood-oxygen-level-dependent (BOLD) functional magnetic resonance
 imaging (fMRI), which is a mature technology with recognized constraints
 in certain clinical and research applications. Photoacoustic computed
 tomography (PACT) is a promising complementary modality to fMRI as it does
 not involve magnetic fields and allows quantification of deoxyhemoglobin
 and oxyhemoglobin concentrations, convertible to oxygen saturation and
 blood volume. Here, we demonstrate PACT of the human brain. 3D
 functional image stacks of fMRI and PACT as well as the customized
 codes for functional analysis are included.
 'Data/fMRI data/' includes the image stacks of fMRI
 acquisition. The fMRI brain function can be extracted by loading the
 parameter scripts in 'Data/fMRI script/' into
 SPM12. 'Data/fPACT data/' includes the image stacks of
 PACT acquisition. The PACT brain function can be
 extracted by
 running 'Code/fPACT script/run_function_recon.m'.
DOI: 10.5061/dryad.8w9ghx3jp
title: Detritus decorations as the extended phenotype deflect avian predator attack increasing fitness in an orb‐web spider

description: A number of strategies that divert attacks of visually guided predators,
 such as birds, have evolved multiple times in animals. Detritus web
 decorations built by certain orb-web spider species are thought to deflect
 avian predator attacks away from spiders and towards their web
 decorations. Still, empirical evidence for this function and its adaptive
 significance is lacking. The orb-web spider, Cyclosa monticola, adorns its
 web using a linear detritus decoration consisting of moults, egg sacs,
 prey remains, and leaf litters. In the present study, we investigated
 whether detritus decorations constructed by C. monticola spiders divert
 attacks of avian predators away from spiders. We first employed colour
 modelling to compare spider bodies and detritus decoration colouration
 from the perspective of domestic chicks and blue tits. We then
 experimentally tested the deflection hypothesis in the laboratory using
 naïve chicks as predators. We put the chicks in a cage containing a web
 either with (S+) or without (S-) a spider and either with (D+) or without
 (D-) detritus decoration (a total of four types of webs: S+D+, S+D-, S-D+,
 and S-D-) under both natural habitat background and white background. We
 found that the colour of C. monticola spiders is indistinguishable from
 that of their detritus decorations for both chicks and blue tits with both
 backgrounds. Laboratory predation experiments showed that with both
 backgrounds, chicks attacked the spiders much less frequently when their
 decorations were present on the webs (S+D+; natural habitat: 20%, white
 background: 30%) than when their decorations were absent (S+D-; natural
 habitat: 95%, white background: 85%), resulting in greater spider survival
 advantage. We also found that the rate of attack of spiders and their
 decorations was not random; the decorations were more likely to be
 attacked than spiders, regardless of the ratio of surface area of
 decorations to spider bodies when both spiders and decorations were
 presented (S+D+). Therefore, our results support a deflection, rather than
 concealment hypothesis for web decorations. In conclusion, our study
 provides evidence that the extended phenotypes beyond the animal bodies,
 can divert avian predator attacks, therefore, may improve the fitness of
 animals.
DOI: 10.5061/dryad.59zw3r257
title: Phoca Vitulina Diet Summary

description: This data set summarizes the molecular diet data collected from Phoca
 Vitulina scat throught out the Salish Sea. The collection methods and
 analysis details are descripted in "Large scale molecular barcoding
 of prey DNA reveals predictors of intrapopulation feeding diversity in a
 marine predator", published in Ecology and Evolution.
DOI: 10.5061/dryad.rn8pk0p78
title: Stan code from: Simulation modeling reveals the evolutionary role of landscape shape and species dispersal on genetic variation within a metapopulation

description: Different shapes of landscape boundaries can affect the habitat networks
 within them and consequently the spatial genetic-patterns of a
 metapopulation. In this study, we used a mechanistic framework to evaluate
 the effects of landscape shape, through watershed elongation, on genetic
 divergence among populations at the metapopulation scale. Empirical
 genetic data from four, sympatric stream-macroinvertebrates having aerial
 adults were collected from streams in Japan to determine the roles of
 species-specific dispersal strategies on metapopulation genetics.
 Simulation results indicated that watershed elongation allows the
 formation of river networks with fewer branches and larger topographic
 constraints. This results in decreased interpopulation connectivity but a
 lower level of spatial isolation of distal populations (e.g., those found
 in headwaters) occurring in the landscapes examined. Distal populations
 had higher genetic divergence when their downstream-biased dispersal
 (relative to upstream- and/or overland-biased dispersal) was high. This
 underscores the importance of distal populations influencing genetic
 divergence at the metapopulation scale for species having
 downstream-biased dispersal. In turn, lower genetic divergence was
 observed under watershed elongation when the genetic isolation of distal
 populations was decreased in such species. This strong association between
 landscape shape and evolutionary processes highlights the importance of
 natural, spatial architecture in assessing the effectiveness of
 conservation and management strategies.
DOI: 10.5061/dryad.pvmcvdnj1
title: Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

description: Background: Homologous sex chromosomes can differentiate over time because
 recombination is suppressed in the region of the sex determining locus,
 leading to the accumulation of repeats, progressive loss of genes that
 lack differential influence on the sexes and sequence divergence on the
 hemizygous homolog. Divergence in the non-recombining regions leads to the
 accumulation of Y or W specific sequence useful for developing sex-linked
 markers. Here we use in silico whole-genome subtraction to identify
 putative sex-linked sequences in the scincid lizard Bassiana duperreyi
 which has heteromorphic XY sex chromosomes. Results: We
 generated  96.7 x 109 150 bp paired-end genomic sequence reads
 from a XY male and 81.4  x 109 paired-end reads from an XX female
 for in silico whole genome subtraction to yield Y enriched contigs. We
 identified 7 reliable markers which were validated as Y chromosome
 specific by polymerase chain reaction (PCR) against a panel of 20 males
 and 20 females. Conclusions: The sex of B. duperreyi can be reversed by
 low temperatures (XX genotype reversed to a male phenotype). We have
 developed sex-specific markers to identify the underlying genotypic sex
 and its concordance or discordance with phenotypic sex in wild populations
 of B. duperreyi. Our pipeline can be applied to isolate Y or W
 chromosome-specific sequences of any organism and is not restricted to
 sequence residing within single-copy genes. This study greatly improves
 our knowledge of the Y chromosome in B. duperreyi and will enhance future
 studies of reptile sex determination and sex chromosome evolution.
description: Reads
 from a focal male and a focal female were analysed independently as
 follows. First, reads were decomposed into k-mers of 27 bp using Jellyfish
 2.0. Unique k-mers were counted, again using Jellyfish 2.0 and k-mers in
 common between the male and female sets were removed from the male set.
 This yielded a (subtracted) k-mer set that was enriched for Y chromosome
 sequence. The Y enriched k-mers were then reassembled into contigs using
 an inchworm assembler (kassemble.cgi uploaded here) with stringent
 extension criteria. Briefly, the assembler initially took a focal k-mer at
 random and searched for other k-mers that matched exactly k-1 bp of the
 focal k-mer. If this second k-mer was unique, then the focal k-mer was
 extended by one bp, and the process was repeated. If the k-mer was not
 unique, then the extension process was terminated. The extension occurred
 to both the left and the right, yielding relatively short contigs (up to
 ca 1400 bp) that contain sequence unique to the male individual.
 The
 resultant contigs were selected on length and used to develop primers for
 screening individuals of known sex. PCR validation on 20 males and 20
 females was the basis for selecting a final set of primer pairs for a
 definitive sex test.
description: Refer to the README file.
DOI: 10.5061/dryad.v6wwpzgst
title: Diatom defence: Grazer induction and cost of shell-thickening

description: 1. Diatoms account for 40 % of the ocean primary production and play a key
 role in the oceans’ ability to sequester carbon. The evolutionary success
 of diatoms and their role in ocean biogeochemistry are related to the
 siliceous shell that provide partial protection against grazing. 2. The
 structure and function of phytoplankton communities are governed by
 environmental constraints and organismal trade-offs. Defence mechanisms
 may help explain the high diversity of phytoplankton (incl. diatoms) in
 the ocean, but only if the defence comes at a cost. Defence costs have
 been notoriously difficult to demonstrate and quantify in marine
 phytoplankton. 3. Here, we demonstrate for seven species of planktonic
 diatoms that their shell thickens and their growth rate declines when
 cells are exposed to chemical cues from copepods, important predators of
 diatoms. The responses are proportional to the concentration of grazer
 cues, but are also highly variable, both between and within species. 4. At
 our standard experimental condition, the typical decline in growth rate is
 10 %, and the typical increase in cellular biogenic silica is 16 %. The
 latter value corresponds to a decline in grazing mortality due to small
 copepods of 11 %. Thus, silification in response to grazers is exactly
 warranted. 5. The similar magnitude of the costs and benefits of
 silification suggests a flat fitness landscape along the
 competition-defence axis. This may help explain the high diversity of
 coexisting diatoms in the ocean. 6. The significant but variable
 contribution of diatoms to the downward flux of organic carbon in the
 ocean depends to a large extent on the silica content of the cells. This
 is due less to the ballasting effect of silica, but mainly to the
 different life histories of more or less defended cells that are governed
 by evolutionary adaptations and – as demonstrated here - plastic responses
 to grazers.
DOI: 10.5061/dryad.18931zctr
title: Data from: Sexual and ecological selection on a sexual conflict gene

description: Sexual selection and conflict can act on genes with important metabolic
 functions, potentially shaping standing genetic variance in such genes,
 and thus evolutionary potential of populations. Here, using experimental
 evolution, we show how reproductive competition intensity and thermal
 environment affect selection on phosphogluconate dehydrogenase (6Pgdh) – a
 metabolic gene involved in sexual selection and conflict in the bulb mite.
 The S allele of 6Pgdh increases male success in reproductive competition,
 but is detrimental to S-bearing males’ partners. We found that the rate of
 the S allele spread increased with the proportion of males in the
 experimental populations, illustrating that harm to females is more easily
 compensated for males under more intense sexual competition. Furthermore,
 we found that under equal sex ratio, the S allele spreads faster at higher
 temperature. While the direction of selection on 6Pgdh was not reversed in
 any of the conditions we tested, which would be required for environmental
 heterogeneity to maintain polymorphism at this locus, our study highlights
 that ecological and sexual selection can jointly affect selection on
 important metabolic enzymes.
description: Munbers of S and F alleles assessed based on genotyping a random
 sample of 30 individuals per population after generations 1, 5 and 10 of
 experimental evolution at diferent temperatures and sex rations.
DOI: 10.15468/dl.2hj5x9
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bolusanthus speciosus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 158 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002449-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ht76hdrck
title: Data from: A shift towards the annual habit in selfing Arabidopsis lyrata

description: The annual life history is often associated with the ability to
 self-fertilize. However, it is unknown which, of selfing or the annual
 habit, evolves first during the speciation process. Using a two-year
 common garden, we asked if the evolution of selfing in the normally
 perennial Arabidopsis lyrata was accompanied by a shift towards the annual
 habit. Despite their very recent divergence from obligately outcrossing
 populations, selfing plants exhibited a 39% decrease in over-winter
 survival after the first year as compared to outcrossing plants.
 Reproductive investment in the first year did not explain this difference
 in survival. We conclude that the evolutionary transition to selfing in
 perennial A. lyrata has been accompanied by a shift towards the annual
 habit. Because the shift does not appear to be due to reproductive
 trade-offs, its drivers require further investigation.
DOI: 10.5061/dryad.jm63xsj7q
title: Hedgehog signaling is necessary and sufficient to mediate craniofacial plasticity in teleosts

description: Phenotypic plasticity, the ability of a single genotype to produce
 multiple phenotypes under different environmental conditions, is critical
 for the origins and maintenance of biodiversity; however, the genetic
 mechanisms underlying plasticity as well as how variation in those
 mechanisms can drive evolutionary change remain poorly understood. Here,
 we examine the cichlid feeding apparatus, an icon of both prodigious
 evolutionary divergence and adaptive phenotypic plasticity. We first
 provide a tissue-level mechanism for plasticity in craniofacial shape by
 measuring rates of bone deposition within functionally salient elements of
 the feeding apparatus in fishes forced to employ alternate foraging modes.
 We show that levels and patterns of phenotypic plasticity are distinct
 among closely related cichlid species, underscoring the evolutionary
 potential of this trait. Next, we demonstrate that hedgehog (Hh)
 signaling, which has been implicated in the evolutionary divergence of
 cichlid feeding architecture, is associated with environmentally induced
 rates of bone deposition. Finally, to demonstrate that Hh levels are the
 cause of the plastic response and not simply the consequence of producing
 more bone, we use transgenic zebrafish in which Hh levels could be
 experimentally manipulated under different foraging conditions. Notably,
 we find that the ability to modulate bone deposition rates in different
 environments is dampened when Hh levels are reduced, whereas the
 sensitivity of bone deposition to different mechanical demands increases
 with elevated Hh levels. These data advance a mechanistic understanding of
 phenotypic plasticity in the teleost feeding apparatus and in doing so
 contribute key insights into the origins of adaptive morphological
 radiations.
description: Bone deposition rate data were collected via dual fluorochrome
 labeling, followed by fluorescence microscopy. All bone deposition data
 were analyzed in R. See methods section in the associated article for
 additional details. Gene expression data were collected
 via RT-qPCR and quantified in R. See methods section in the associated
 article for additional details, including primer sequences. 
description: Missing values are denoted as NA in the datasets.
DOI: 10.5061/dryad.1rn8pk0r8
title: Data from: 200 million years of anuran body size evolution in relation to geography, ecology, and life history

description: Surprisingly little is known about body-size evolution within the most
 diverse amphibian order, anurans (frogs and toads), despite known effects
 of body size on the physiological, ecological, and life-history traits of
 animals more generally. Here we examined anuran body-size evolution among
 2434 species with over 200 million years of shared evolutionary history.
 We found clade-specific evolutionary shifts to new body-size optima along
 with numerous independent transitions to gigantic and miniature body
 sizes, despite the upper limits of anuran body size remaining quite
 consistent throughout the fossil record. We found a weak, positive
 correlation between a species’ body size and maximum latitude and
 elevation, including a dearth of small species at higher elevations and
 broader latitudinal and elevational ranges in larger anurans. Although we
 found modest differences in mean anuran body size among microhabitats,
 there was extensive overlap in the range of body sizes across
 microhabitats. Finally, we found that larger anurans are more likely to
 consume vertebrate prey than smaller anurans are, and that species with a
 free-swimming larval phase during development are larger on average than
 those in which development into a froglet occurs within the egg. Overall,
 anuran body size does not conform to geographic and ecological patterns
 observed in other tetrapods but is perhaps more notable for variation in
 body size within geographic regions, ecologies, and life-histories. Here
 we document this variation and propose target clades for detailed studies
 aimed at disentangling how and why variation in body size was generated
 and is maintained in anurans.
description: All data was collected from the literature and sources are cited
 in the data table. Data types without references in the data table are all
 from single sources that are stated in the publication's
 methods. 
description: Data types without references in the data table are all from
 single sources that are stated in the publication's
 methods.
DOI: 10.15468/dl.s4g9tn
title: Occurrence Download

description: A dataset containing 63379 records in GBIF matching the query:
SELECT
 '435' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -69.23837900975829
 AND decimalLongitude &lt;= -59.94074752362532
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 63379 records were derived from 220 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002433-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2v6wwpzjx
title: Data from: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)

description: Extant species in the order Crocodylia are remnants of an ancient lineage
 of large-bodied archosaur reptiles. Despite decades of systematic studies,
 phylogenetic relationships among members of the genus Crocodylus (true
 crocodiles) in the Neotropics are poorly understood. Here we estimated
 phylogenomic relationships among the four extant Crocodylus species in the
 Americas. Species-tree reconstructions using genotypic data from 17,538
 SNPs collected for 33 individuals spanning six Crocodylus species (four
 ingroup and two outgroup) revealed novel relationships for all Neotropical
 species. For the first time, C. acutus, the American crocodile, was
 recovered as monophyletic when individuals from Antillean and continental
 populations were analyzed together. Our results also contradict previous
 inferences based on mitochondrial DNA data and a limited number of nuclear
 markers by robustly grouping Morelet's crocodile (C. moreletii) as
 the sister species to C. acutus., suggesting a novel phylogeographic
 hypothesis for the group. The present study punctuates the importance of
 using nuclear genome-wide information and representative sampling for
 resolving phylogenetic relationships, especially in broadly distributed
 species and those with complex evolutionary histories.
description: nextRAD genotyping-by-sequencing libraries were constructed by
 SNPsaurus, LLC following Russello et al. (2015) <em>PeerJ
 </em>(https://doi.org/10.7717/peerj.1106)