cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cf223f4
title: Data from: Density-dependent offspring interactions do not explain macroevolutionary scaling of adult size and offspring size

description: Most lifeforms exhibit a correlated evolution of adult size (AS) and size
 at independence (SI), giving rise to AS-SI scaling relationships. Theory
 suggests that scaling arises because relatively large adults have
 relatively high reproductive output, resulting in strong density-dependent
 competition in early life, where large size at independence provides a
 competitive advantage to juveniles. The primary goal of our study is to
 test this Density Hypothesis, using large datasets that span the
 vertebrate tree of life (fishes, amphibians, reptiles, birds, and
 mammals). Our secondary goal is to motivate new hypotheses for AS-SI
 scaling, by exploring how subtle variation in life-histories among
 closely-related species is associated with variation in scaling. Our
 phylogenetically-informed comparisons do not support the Density
 Hypothesis. Instead, exploration of AS-SI scaling among life-history
 variants suggests that steeper AS-SI scaling slopes are associated with
 evolutionary increases in size at independence. We suggest that a positive
 association between size at independence and juvenile growth rate may
 represent an important mechanism underlying AS-SI scaling, a mechanism
 that has been underappreciated by theorists. If faster juvenile growth is
 a consequence of evolutionary increases in size at independence, this may
 help offset the cost of delayed maturation, leading to steeper AS-SI
 scaling slopes.
description: Anura Adult Size &
 Offspring SizeSpecies-mean adult size
 and egg size (g) for Anurans.Dryad.Anura.Data.xlsxCaudata Adult Size & Offspring SizeSpecies-mean adult size and egg size (g) for Caudata.Dryad.Caudata.Data.xlsxCyprinodontiformes Adult Size & Offspring SizeSpecies-mean adult size and egg size (g) for Caudata.Dryad.Cyprinodontiformes.Data.xlsxCyprinodontiformes Species & Reference ListList of references used to compile the size data for Cyprinodontiformes, with references listed for each species.Dryad.Cyprinodontiformes.Species&ReferenceList.xlsxPerciformes I Adult Size & Offspring SizeSpecies-mean adult size and offspring size (g) for "Perciformes I" datasetDryad.Perciformes.I.Data.xlsxPerciformes II Adult Size & Offspring SizeSpecies-mean adult size and offspring size (g) for "Perciformes II" datasetDryad.Perciformes.II.Data.xlsxPerciformes Species & Reference ListList of references used to compile size data for Perciformes, with references specific to each speciesDryad.Perciformes.Species&ReferenceList.xlsx
DOI: 10.5061/dryad.7d4t0g6
title: Data from: Annual temperature variation influences the vulnerability of montane bird communities to land-use change

description: Understanding how and why species respond to land-use change is one of the
 central challenges in conservation biology, yet the causes of variation in
 the responses of species to land-use change remain unclear. We tested
 whether adaptation to different abiotic environments influenced the
 vulnerability of bird communities to agricultural expansion in the
 Himalayan mountain range, which exhibits a strong east-west gradient in
 annual temperature variation. We did so by surveying bird communities in
 forest and agriculture at opposite ends of that gradient. We contrasted
 metrics of species richness, diversity, community composition, and forest
 dependency for species across land-use types and regions, and tested
 whether species’ thermal sensitivity influenced their response to the
 replacement of forest with agriculture. Agricultural land in the
 relatively aseasonal east harboured significantly fewer bird species than
 did forests, a pattern that is starkly reversed in the highly seasonal
 west. For species common to both regions, eastern populations used forest
 ~35% more than did western populations. While western species were less
 constrained by temperature than eastern species, western species with
 narrow thermal tolerances were also more forest dependent. Selection
 across a stark environmental gradient on a common species pool appears to
 have altered the vulnerability of Himalayan birds to forest loss, with
 communities in the relatively aseasonal east much more sensitive to forest
 conversion than those in the west. Adaptation to local environmental
 conditions appears to mediate species' responses to land use change,
 with thermal specialists more vulnerable to forest loss than species with
 greater thermal tolerances. Species' responses to global change may
 differ predictably along abiotic gradients even within a single region or
 biodiversity hotspot, and such variation must be addressed in conservation
 planning.
description: Forest and agricultural
 bird communities in the HimalayasThis dataset describes
 the species encountered on six transects each in agricultural and forest
 habits in the Himalayas. For each habitat (agriculture or forest), three
 transects were in the western Himalayas and three in the eastern
 Himalayas. The column headings represent: (1) region: whether western or
 eastern Himalayas; (2) habitat: whether agriculture or forest; (c)
 transect: the identity of the transect (which is the sampling unit); (d)
 rep: the replicate sample of each transect; (e and f): date and time of
 each observation; (g and h): the genus and species of each bird recorded;
 and (i) the group size of each bird record.forest and agricultural bird
 communities in the Himalayas.csv
DOI: 10.5061/dryad.34q91f0
title: Data from: Shared patterns of genome-wide differentiation are more strongly predicted by geography than by ecology.

description: Closely related populations often display similar patterns of genomic
 differentiation, yet it remains an open question which ecological and
 evolutionary forces generate these patterns. The leading hypothesis is
 that this similarity in divergence is driven by parallel natural
 selection. However, several recent studies have suggested that these
 patterns may instead be a product of the depletion of genetic variation
 that occurs as result of background selection (i.e. linked negative
 selection). To date, there have been few direct tests of these competing
 hypotheses. To determine the relative contributions of background
 selection and parallel selection to patterns of repeated differentiation,
 we examined 24 independently derived populations of freshwater stickleback
 occupying a variety of niches and estimated genomic patterns of
 differentiation in each relative to their common marine ancestor. Patterns
 of genetic differentiation were strongly correlated across pairs of
 freshwater populations adapting to the same ecological niche, supporting a
 role for parallel natural selection. In contrast to other recent work, by
 examining populations adapting to the same niche we did not find evidence
 that similar patterns of genomic differentiation are generated by
 background selection. We also found that overall patterns of genetic
 differentiation were considerably more similar for populations found in
 closer geographic proximity. In fact, the effect of geography on the
 repeatability of differentiation was greater than that of parallel
 selection. Our results suggest that shared selective landscapes and
 ancestral variation are the key drivers of repeated patterns of
 differentiation in systems that have recently colonized novel
 environments.
description: lake lake control fst
 correlation analysis and permutationmantel_inputmantel_qual_results.Rmdmantel_quant_results.Rmdmarine freshwater fst correlation estimation and permutationmrm_stick_qualmrm_stick_quantREADMEstats_150k_combined_mar26_2017stats_150k_fresh_fresh
DOI: 10.5061/dryad.7m07n0r
title: Data from: Bony labyrinth morphometry reveals hidden diversity in lungless salamanders (Family Plethodontidae): structural correlates of ecology, development, and vision in the inner ear

description: Lungless salamanders (Family Plethodontidae) form a highly speciose group
 that has undergone spectacular adaptive radiation to colonize a multitude
 of habitats. Substantial morphological variation in the otic region
 coupled with great ecological diversity within this clade make
 plethodontids an excellent model for exploring the ecomorphology of the
 inner ear. We examined the influence of habitat, development, and vision
 on inner ear morphology in 53 plethodontid species. We collected
 traditional and 3D geometric morphometric measurements to characterize
 variation in size and shape of the otic endocast and peripheral structures
 of the salamander ear. Phylogenetic comparative analyses demonstrate
 structural convergence in the inner ear across ecologically similar
 species. Species that dwell in spatially-complex microhabitats exhibit
 robust, highly curved semicircular canals suggesting enhanced vestibular
 sense, whereas species with reduced visual systems demonstrate reduced
 canal curvature indicative of relaxed selection on the vestibulo-ocular
 reflex. Cave specialists show parallel enlargement of auditory-associated
 structures. The morphological correlates of ecology among diverse species
 reveal underlying evidence of habitat specialization in the inner ear and
 suggest that there exists physiological variation in the function of the
 salamander ear even in the apparent absence of selective pressures on the
 auditory system to support acoustic behavior.
description: Supplementary_table_1Supplementary table S1. Museum specimen catalog numbers, micro-CT scanning parameters, GenBank accession numbers, and Procrustes coordinatestree_nexusA phylogenetic tree of 53 species generated using maximum likelihood method of estimation and based on a concatenated sequence of 9 nuclear genes and 4 mitochondrial genes obtained from GenBank (see supplementary table S1).
DOI: 10.5061/dryad.26sm738
title: Data from: An assessment of the immune costs associated with meiotic drive chromosomes in Drosophila

description: Most organisms are constantly adapting to pathogens and parasites that
 exploit their host for their own benefit. Less studied, but perhaps more
 ubiquitous, are intragenomic parasites or selfish genetic elements. These
 include transposable elements, selfish B chromosomes and meiotic drivers
 that promote their own replication without regard to fitness effects on
 hosts. Therefore, intragenomic parasites are also a constant evolutionary
 pressure on hosts. Gamete-killing meiotic drive elements are often
 associated with large chromosomal inversions that reduce recombination
 between the drive and wildtype chromosomes. This reduced recombination is
 thought to reduce the efficacy of selection on the drive chromosome and
 allow for the accumulation of deleterious mutations. We tested whether
 gamete-killing meiotic drive chromosomes were associated with reduced
 immune defense against two bacterial pathogens in three species of
 Drosophila. We found little evidence of reduced immune defense in lines
 with meiotic drive. One line carrying the Drosophila melanogaster
 autosomal Segregation Distorter did show reduced defense, but we were
 unable to attribute that reduced defense to either genotype or immune gene
 expression differences. Our results suggest that though gamete-killing
 meiotic drive chromosomes likely accumulate deleterious mutations, those
 mutations do not result in reduced capacity for immune defense.
description: qPCR data for D.
 melanogaster genotypes AMP expression after infectionFor each sample, we
 provide the plate ID, Well#, Fluorophore, Target, Sample name (Line ID, 0
 or 8 hour time point, PR for Providencia rettgeri and replicate), Cq
 value.qPCR.data.csv
DOI: 10.5061/dryad.v732vb1
title: Data from: Direct and indirect effects of sexual signal loss on female reproduction in the Pacific field cricket (Teleogryllus oceanicus)

description: Sexual signal evolution may present fitness consequences for the
 non-signaling sex due to shared genes and altered social conditions, but
 this is rarely studied in natural populations. On the Hawaiian Island of
 Kauai, most male Teleogryllus oceanicus (Pacific field crickets) lack the
 ability to sing because of a novel wing mutation (flatwing) that arose and
 spread in &lt;20 generations. Obligately silent flatwing males have
 been highly successful because they avoid detection by a deadly,
 acoustically-orienting parasitoid fly. Little is known about how the
 flatwing mutation and resulting song-less acoustic environment affects
 female fitness. We found that Kauai females carrying the flatwing allele
 invested less in reproductive tissues and experienced more instances of
 mating failure than normal-wing-carrying females, though total offspring
 production did not differ between female genotypes. Females from Oahu (HI,
 where the parasitoid and flatwing also occur) and Mangaia (an island in
 the Cook Islands which harbors neither the parasitoid nor flatwing)
 invested less in reproductive tissues when reared in a song-less acoustic
 environment. Kauai females did not exhibit this plasticity, perhaps
 because they have experienced nearly song-less conditions for the past ~15
 years following the establishment of flatwing. We show that female T.
 oceanicus experience a mix of costly and beneficial effects of sexual
 signal loss, which should help maintain the wing polymorphism in the wild.
 Our results demonstrate that the non-signaling sex can experience a
 nuanced set of phenotypic consequences resulting from signal evolution,
 which can further shape dynamics of sexual signal evolution.
description: Data for Heinen-Kay et
 al. Sexual signal loss and female reproductionData for (1) comparison
 of flatwing and normal-wing homozygous female reproductive tissue, (2)
 offspring production of flatwing and normal-wing females, and (3)
 reproductive tissue comparison between populations and acoustic
 treatments
DOI: 10.5061/dryad.4nd8448
title: Data from: High and dry: trade-off in arboreal calling in a treefrog mediated by local environment

description: Trade-offs shaping behavioral variation are often influenced by the
 environment. We investigated the role that the environment plays in
 mediating trade-offs using a widespread frog with a conspicuous mating
 display, Pseudacris crucifer. We first demonstrated, using playback and
 desiccation experiments, that calling site selection involves a trade-off
 between sound transmission and desiccation. We then determined the
 influence of local environmental conditions on the intensity of the
 trade-off by examining range-wide behavioral and environmental data. We
 showed that the benefit of improved call transmission is positively
 influenced by vegetation density and ground cover. Behavioral data are
 consistent with this relationship: sites with a greater transmission
 benefit have increased prevalence of arboreally-calling males. We also
 found that the prevalence of arboreal calling behavior increases with
 relative humidity and air temperature, suggesting an influence of these
 environmental variables on the desiccation cost of arboreal calling. This
 study provides a clear example of the role of the environment in mediating
 trade-off intensities and shaping critical behavioral traits.
description: Datafrom_HighandDry_Trade-offinarborealcallinginatreefrogmediatedbylocalenvironmentThis zip file contains all data files used for this publication as well as a README.txt file with further information.
DOI: 10.5061/dryad.gc0586g
title: Data from: Costs and benefits of giant sperm and sperm storage organs in Drosophila melanogaster

description: In Drosophila, long sperm are favoured in sperm competition based on the
 length of the female’s primary sperm storage organ, the seminal receptacle
 (SR). This sperm-SR interaction, together with a genetic correlation
 between the traits, suggests that the coevolution of exaggerated sperm and
 SR lengths may be driven by Fisherian runaway selection. Here, we explore
 the costs and benefits of long sperm and SR genotypes, both in the sex
 that carries them and in the sex that does not. We measured male and
 female fitness in inbred lines of D. melanogaster derived from four
 populations previously selected for long sperm, short sperm, long SRs, or
 short SRs. We specifically asked: what are the costs and benefits of long
 sperm in males and long SRs in females? Furthermore, do genotypes that
 generate long sperm in males or long SRs in females impose a fitness cost
 on the opposite sex? Answers to these questions will address whether long
 sperm are an honest indicator of male fitness, if male post-copulatory
 success is associated with male pre-copulatory success, if female choice
 benefits females or is costly, and whether intra-genomic conflict could
 influence evolution of these traits. We found that both sexes have
 increased longevity in long sperm and long SR genotypes. Males, but not
 females, from long SR lines had higher fecundity. Our results suggest that
 sperm-SR coevolution is facilitated by both increased viability and
 indirect benefits of long sperm and SRs in both sexes.
description: ReproductiveTraitLengthCompiled data sheet on measured sperm cells and SR lengthsMaleReprodSuccessSubsets of offspring produced, from up to 2 successfully mated males from each vialMatingTrialsBehavioural Observations of Mating behaviour every weekFemaleReprodSuccesscontains weekly counts of offspring numbers producedsurvivalAge for "survival cohorts"ReadMe
DOI: 10.5061/dryad.f735q5p
title: Data from: Predicting biodiversity loss in island and countryside ecosystems through the lens of taxonomic and functional biogeography

description: We investigate how variation in patch area and forest cover quantified for
 three different spatial scales (buffer size of 500, 1500 and 3000 m
 radius) affects species richness and functional diversity of bat
 assemblages in two ecosystems differing in fragment-matrix contrast: a
 landbridge island system in Panama and a countryside ecosystem in the
 Brazilian Amazon. Bats were sampled on 11 islands and the adjacent
 mainland in Panama, and in eight forest fragments and nearby continuous
 forest in Brazil. Species–area relationships (SAR) were assessed based on
 Chao1 species richness estimates, and functional diversity–area
 relationships (FAR) were quantified using Chao1 functional diversity
 estimates measured as the total branch length of a trait dendrogram. FARs
 were calculated using three trait sets: considering five species
 functional traits (FARALL), and trait subsets reflecting “diet breadth”
 (FARDIET) and “dispersal ability” (FARDISPERSAL). We found that in both
 study systems, FARALL was less sensitive to habitat loss than SAR, in the
 sense that an equal reduction in habitat loss led to a disproportionately
 smaller loss of functional diversity compared to species richness.
 However, the inhospitable and static aquatic matrix in the island
 ecosystem resulted in more pronounced species loss with increasing loss of
 habitat compared to the countryside ecosystem. Moreover, while we found a
 significant FARDISPERSAL for the island ecosystem in relation to forest
 cover within 500 m landscape buffers, FARDIET and FARDISPERSAL were not
 significant for the countryside ecosystem. Our findings highlight that
 species richness and functional diversity in island and countryside
 ecosystems scale fundamentally differently with habitat loss, and suggest
 that key bat ecological functions, such as pollination, seed dispersal,
 and arthropod suppression, may be maintained in fragments despite a
 reduction in species richness. Our study reinforces the importance of
 increasing habitat availability for decreasing the chances of losing
 species richness in smaller fragments.
description: Bat capture
 data_Panama&Brazil
DOI: 10.5061/dryad.02gr10f
title: Data from: Gene flow and genetic drift in urban environments

description: Evidence is growing that human modification of landscapes has dramatically
 altered evolutionary processes. In urban population genetic studies,
 urbanization is typically predicted to act as a barrier that isolates
 populations of species, leading to increased genetic drift within
 populations and reduced gene flow between populations. However,
 urbanization may also facilitate dispersal among populations, leading to
 higher genetic diversity within and lower differentiation between urban
 populations. We reviewed the literature on non-adaptive urban evolution to
 evaluate the support for each of these urbanse urban fragmentation and
 facilitation models. In a review of the literature with supporting
 quantitative analyses of 167 published urban population genetics studies,
 we found a weak signature of reduced within-population genetic diversity,
 and no evidence of consistently increased between-population genetic
 differentiation associated with urbanization. In addition, we found that
 urban landscape features act as barriers or conduits to gene flow,
 depending on the species and city in question. Thus, we speculate that
 dispersal ability of species and environmental heterogeneity between
 cities contribute to the variation exhibited in our results. However,
 greater than 90% of published studies reviewed here showed an association
 of urbanization with genetic drift or gene flow, highlighting the strong
 impact of urbanization on non-adaptive evolution. It is clear that
 organism biology and city heterogeneity obscure patterns of genetic drift
 and gene flow in a quantitative analysis. Thus, we suggest that future
 research makes comparisons of multiple cities and nonurban habitats, and
 takes into consideration species’ natural history, environmental
 variation, spatial modelling, and marker selection.
description: Dryad archived
 dataRaw data file that
 contains the literature reviewed and analyzed as well as the variables
 extracted from the publications used in our analyses.