cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.30bj3
title: Data from: Complex mitonuclear interactions and metabolic costs of mating in male seed beetles

description: The lack of evolutionary response to selection on mitochondrial genes
 through males predicts the evolution of nuclear genetic influence on
 male-specific mitochondrial function, for example by gene duplication and
 evolution of sex-specific expression of paralogs involved in metabolic
 pathways. Intergenomic epistasis may therefore be a prevalent feature of
 the genetic architecture of male-specific organismal function. Here, we
 assess the role of mitonuclear genetic variation for male metabolic
 phenotypes [metabolic rate and respiratory quotient (RQ)] associated with
 ejaculate renewal, in the seed beetle Callosobruchus maculatus, by
 assaying lines with crossed combinations of distinct mitochondrial
 haplotypes and nuclear lineages. We found a significant increase in
 metabolic rate following mating relative to virgin males. Moreover,
 processes associated with ejaculate renewal showed variation in metabolic
 rate that was affected by mitonuclear interactions. Mitochondrial
 haplotype influenced mating-related changes in RQ, but this pattern varied
 over time. Mitonuclear genotype and the energy spent during ejaculate
 production affected the weight of the ejaculate, but the strength of this
 effect varied across mitochondrial haplotypes showing that the genetic
 architecture of male-specific reproductive function is complex. Our
 findings unveil hitherto underappreciated metabolic costs of mating and
 ejaculate renewal, and provide the first empirical demonstration of
 mitonuclear epistasis on male reproductive metabolic processes.
description: Beetle metabolic rate
 dataThis dataset contains
 metabolic rate, respiratory quotient, body weight and ejaculate weight
 data from seed beetles with different mitonuclear
 genotypes.BeetleMetabolicRate_Dryad.txt
DOI: 10.5061/dryad.mt5sj
title: Data from: Molecular footprints of the Holocene retreat of dwarf birch in Britain

description: Past reproductive interactions among incompletely isolated species may
 leave behind a trail of introgressed alleles, shedding light on historical
 range movements. Betula pubescens is a widespread native tetraploid tree
 species in Britain, occupying habitats intermediate to those of its native
 diploid relatives, B. pendula and B. nana. Genotyping 1134 trees from the
 three species at 12 microsatellite loci we found evidence of introgression
 from both diploid species into B. pubescens, despite the ploidy
 difference. Surprisingly, introgression from B. nana, a dwarf species
 whose present range is highly restricted in northern, high-altitude peat
 bogs, was greater than introgression from B. pendula, which is
 morphologically similar to B. pubescens and has a substantially
 overlapping range. A cline of introgression from B. nana was found
 extending into B. pubescens populations far to the south of the current B.
 nana range. We suggest that this genetic pattern is a footprint of a
 historical decline and/or northwards shift in the range of B. nana
 populations due to climate warming in the Holocene. This is consistent
 with pollen records that show a broader, more southerly distribution of B.
 nana in the past. Ecological niche modelling predicts that B. nana is
 adapted to a larger range than it currently occupies, suggesting
 additional factors such as grazing and hybridisation may have exacerbated
 its decline. We found very little introgression between B. nana and B.
 pendula, despite both being diploid, perhaps because their distributions
 in the past have rarely overlapped. Future conservation of B. nana may
 partly depend on minimisation of hybridisation with B. pubescens, and
 avoidance of planting B. pendula near B. nana populations.
description: Microsatellite genotype
 dataMicrosatellite genotype
 datamicrosatellite
 data.xlsxR
 scriptsR scripts used in data
 analyses and making of figures
DOI: 10.5061/dryad.968k6
title: Data from: Depth as an organizing force in Pocillopora damicornis: intra-reef genetic architecture

description: Relative to terrestrial plants, and despite similarities in life history
 characteristics, the potential for corals to exhibit intra-reef local
 adaptation in the form of genetic differentiation along an environmental
 gradient has received little attention. The potential for natural
 selection to act on such small scales is likely increased by the ability
 of coral larval dispersal and settlement to be influenced by environmental
 cues. Here, we combine genetic, spatial, and environmental data for a
 single patch reef in Kāne‘ohe Bay, O‘ahu, Hawai‘i, USA in a landscape
 genetics framework to uncover environmental drivers of intra-reef genetic
 structuring. The genetic dataset consists of near-exhaustive sampling (n =
 2352) of the coral, Pocillopora damicornis at our study site and six
 microsatellite genotypes. In addition, three environmental parameters –
 depth and two depth-independent temperature indices – were collected on a
 4 m grid across 85 locations throughout the reef. We use ordinary kriging
 to spatially interpolate our environmental data and estimate the three
 environmental parameters for each colony. Partial Mantel tests indicate a
 significant correlation between genetic relatedness and depth while
 controlling for space. These results are also supported by multi-model
 inference. Furthermore, spatial Principle Component Analysis indicates a
 statistically significant genetic cline along a depth gradient. Binning
 the genetic dataset based on size-class revealed that the correlation
 between genetic relatedness and depth was significant for new recruits and
 increased for larger size classes, suggesting a possible role of larval
 habitat selection as well as selective mortality in structuring intra-reef
 genetic diversity. That both pre- and post-recruitment processes may be
 involved points to the adaptive role of larval habitat selection in
 increasing adult survival. The conservation importance of uncovering
 intra-reef patterns of genetic diversity is discussed.
description: Gorospe_Karl_dataThis file contains location information, depth, hothour, and hotspot temperature data for all corals in the study. The temperatures were taken at 85 locations across a single reef and interpolated temperatures were assigned to each colonyGorospe_Karl_logger_dataThis file contains the actual reading of temperature at the 85 locations across a single reef. They were used to assign interpolated values to each coral colony on the reef.
DOI: 10.5061/dryad.gs94r
title: Data from: Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

description: We investigated the biogeographic history of antelope squirrels, genus
 Ammospermophilus, which are widely distributed across the deserts and
 other arid lands of western North America. We combined range-wide sampling
 of all currently recognized species of Ammospermophilus with a multilocus
 data set to infer phylogenetic relationships. We then estimated divergence
 times within identified clades of Ammospermophilus using fossil-calibrated
 and rate-calibrated molecular clocks. Lastly, we explored generalized
 distributional changes of Ammospermophilus since the last glacial maximum
 using species distribution models, and assessed responses to Quaternary
 climate change by generating demographic parameter estimates for the three
 wide-ranging clades of A. leucurus. From our phylogenetic estimates we
 inferred strong phylogeographic structure within Ammospermophilus and the
 presence of three well-supported major clades. Initial patterns of
 historical divergence were coincident with dynamic alterations in the
 landscape of western North America, and the formation of regional deserts
 during the Late Miocene and Pliocene. Species distribution models and
 demographic parameter estimates revealed patterns of recent population
 expansion in response to glacial retreat. When combined with evidence from
 co-distributed taxa, the historical biogeography of Ammospermophilus
 provides additional insight into the mechanisms that impacted
 diversification of arid-adapted taxa across the arid lands of western
 North America. We propose species recognition of populations of the
 southern Baja California peninsula to best represent our current
 understanding of evolutionary relationships among genetic units of
 Ammospermophilus.
description: Ammospermophilus
 mutlilocus datasetNexus file with aligned
 sequences for 7 genes generated from 23 samples. See ReadMe file to match
 sample names with voucher specimens.Ammo_multilocus.TXTAmmospermophilus mtDNA datasetNexus file with aligned sequences for 2 mtDNA genes generated from 88 samples. See ReadMe file to match sample names with voucher specimens.AmmoCO3_CR.txt
DOI: 10.5061/dryad.7sj4t8h
title: Data from: Species richness and phylogenetic diversity of seed plants across vegetation zones of Mount Kenya, East Africa

description: Mount Kenya is of ecological importance in tropical east Africa due to the
 dramatic gradient in vegetation types that can be observed from low to
 high elevation zones. However, species richness and phylogenetic diversity
 of this mountain have not been well studied. Here, we surveyed
 distribution patterns for a total of 1,335 seed plants of this mountain
 and calculated species richness and phylogenetic diversity across seven
 vegetation zones. We also measured phylogenetic structure using the net
 relatedness index (NRI) and the nearest species index (NTI). Our results
 show that lower montane wet forest has the highest level of species
 richness, density, and phylogenetic diversity of woody plants, while lower
 montane dry forest has the highest level of species richness, density, and
 phylogenetic diversity in herbaceous plants. In total plants, NRI and NTI
 of four forest zones were smaller than three alpine zones. In woody
 plants, lower montane wet forest and upper montane forest have
 overdispersed phylogenetic structures. In herbaceous plants, NRI of
 Afro‐alpine zone and nival zone are smaller than those of bamboo zone,
 upper montane forest, and heath zone. We suggest that compared to open dry
 forest, humid forest has fewer herbaceous plants because of the closed
 canopy of woody plants. Woody plants may have climate‐dominated niches,
 whereas herbaceous plants may have edaphic and microhabitat‐dominated
 niches. We also proposed lower and upper montane forests with high species
 richness or overdispersed phylogenetic structures as the priority areas in
 conservation of Mount Kenya and other high mountains in the Eastern
 Afro‐montane biodiversity hotspot regions.
description: A checklist of seed
 plants of Mount Kenya, East AfricaThis is a comprehensive
 checklist of seed plants based on data from various scientific expeditions
 to Mount Kenya since the 1900s. These data sources include published
 floras and field guides such as Flora of Tropical East Africa, Upland
 Kenya Wild Flowers and Ferns, Wild Flowers of East Africa and Kenya Trees
 Shrubs and Lianas, data of specimens from East African Herbarium, Nairobi,
 Kenya (EA) and Global Biodiversity Information Facility (GBIF,
 https://www.gbif.org/), and data from our own scientific expedition from
 2009 to 2016 (specimens were stored at Herbarium of Wuhan Botanical
 Garden, Wuhan, China, HIB). Species were assigned to vegetation zones
 according to the sampling locations and habitat descriptions described in
 the monographs. Growth forms of species were classified as either woody or
 herbaceous plants.Seed plants of Mt.
 Kenya_Data.xls
DOI: 10.5061/dryad.q5570
title: Data from: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins

description: Over the last few decades, advances in molecular techniques have led to
 the detection of strong geographic population structure and cryptic
 speciation in many benthic marine taxa, even those with long-lived pelagic
 larval stages. Polychaete annelids, in particular, generally show a high
 degree of population divergence, especially in mitochondrial genes. Rarely
 have molecular studies confirmed the presence of ‘cosmopolitan’ species.
 The amphinomid polychaete Hermodice carunculata was long considered the
 sole species within its genus, with a reported distribution throughout the
 Atlantic and adjacent basins. However, recent studies have indicated
 morphological differences, primarily in the number of branchial filaments,
 between the East and West Atlantic populations; these differences were
 invoked to re-instate Hermodice nigrolineata, formerly considered a junior
 synonym of H. carunculata. We utilized sequence data from two
 mitochondrial (cytochrome c oxidase subunit I, 16S rDNA) markers and one
 nuclear (internal transcribed spacer) marker to examine the genetic
 diversity of Hermodice throughout its distribution range in the Atlantic
 Ocean, including the Mediterranean Sea, the Caribbean Sea, the Gulf of
 Mexico and the Gulf of Guinea. Our analyses revealed generally low genetic
 divergences among collecting localities and between the East and West
 Atlantic, although phylogenetic trees based on mitochondrial data indicate
 the presence of a private lineage in the Mediterranean Sea. A
 re-evaluation of the number of branchial filaments confirmed differences
 between East and West Atlantic populations; however, the differences were
 not diagnostic and did not reflect the observed genetic population
 structure. Rather, we suspect that the number of branchial filaments is a
 function of oxygen saturation in the environment. Our results do not
 support the distinction between H. carunculata in the West Atlantic and H.
 nigrolineata in the East Atlantic. Instead, they re-affirm the older
 notion that H. carunculata is a cohesive species with a broad distribution
 across the Atlantic Ocean.
description: COI and 16s combined
 alignedConcatenated sequence
 alignments of COI and 16S, respectively. Used in AMOVA and Phylogenetic
 analyses.Final combined
 aligned.fasCOI
 alignment16S
 alignmentHermodice specimen
 information 1-9-2013
DOI: 10.5061/dryad.m07t1
title: Data from: Convergent evolution in social swallows (Aves: Hirundinidae)

description: Behavioral shifts can initiate morphological evolution by pushing lineages
 into new adaptive zones. This has primarily been examined in ecological
 behaviors, such as foraging, but social behaviors may also alter
 morphology. Swallows and martins (Hirundinidae) are aerial insectivores
 that exhibit a range of social behaviors, from solitary to colonial
 breeding and foraging. Using a well-resolved phylogenetic tree, a database
 of social behaviors, and morphological measurements, we ask how shifts
 from solitary to social breeding and foraging have affected morphological
 evolution in the Hirundinidae. Using a threshold model of discrete state
 evolution, we find that shifts in both breeding and foraging social
 behavior are common across the phylogeny of swallows. Solitary swallows
 have highly variable morphology, while social swallows show much less
 absolute variance in all morphological traits. Metrics of convergence
 based on both the trajectory of social lineages through morphospace and
 the overall morphological distance between social species scaled by their
 phylogenetic distance indicate strong convergence in social swallows,
 especially socially foraging swallows. Smaller physical traits generally
 observed in social species suggest that social species benefit from a
 distinctive flight style, likely increasing maneuverability and foraging
 success and reducing in-flight collisions within large flocks. These
 results highlight the importance of sociality in species evolution, a link
 that had previously been examined only in eusocial insects and primates.
description: Hirundinidae Dryad data
 and R scriptZip file contains
 behavioral, morphological, and phylogenetic data utilized in this paper,
 as well as citations for behavioral data and R scripts for analyses
 used.
DOI: 10.15468/dl.ssnbnm
title: Occurrence Download

description: A dataset containing 360621 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Allan Herbarium (CHR)"
 ]
}

 The dataset includes 360621 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000632-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2r6r4
title: Data from: Interactions between parental traits, environmental harshness and growth rate in determining telomere length in wild juvenile salmon

description: A larger body size confers many benefits, such as increased reproductive
 success, ability to evade predators and increased competitive ability and
 social status. However, individuals rarely maximize their growth rates,
 suggesting that this carries costs. One such cost could be faster
 attrition of the telomeres that cap the ends of eukaryotic chromosomes and
 play an important role in chromosome protection. A relatively short
 telomere length is indicative of poor biological state, including poorer
 tissue and organ performance, reduced potential longevity and increased
 disease susceptibility. Telomere loss during growth may also be
 accelerated by environmental factors, but these have rarely been subjected
 to experimental manipulation in the natural environment. Using a wild
 system involving experimental manipulations of juvenile Atlantic salmon
 Salmo salar in Scottish streams, we found that telomere length in juvenile
 fish was influenced by parental traits and by direct environmental
 effects. We found that faster-growing fish had shorter telomeres and there
 was a greater cost (in terms of reduced telomere length) if the growth
 occurred in a harsher environment. We also found a positive association
 between offspring telomere length and the growth history of their fathers
 (but not mothers), represented by the number of years fathers had spent at
 sea. This suggests that there may be long-term consequences of growth
 conditions and parental life history for individual longevity.
description: Fry weight
 LMMData contained in this
 spreadsheet relates to the linear mixed-effect model explaining variation
 in fry weight (g).Fry survival
 LMMData contained in this
 spreadsheet relates to the linear mixed-effect model explaining variation
 in fry survival.Embryo RTL
 LMMData contained in this
 spreadsheet relates to the linear mixed-effect model explaining variation
 in embryo telomere length.Fry RTL
 LMMData contained in this
 spreadsheet relates to the linear mixed-effect model explaining variation
 in fry telomere length.
DOI: 10.5061/dryad.5nt3r
title: Data from: Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in Phrynosomatid lizards

description: The evolution of viviparity is a key life-history transition in
 vertebrates, but the selective forces favoring its evolution are not fully
 understood. With &gt;100 origins of viviparity, squamate reptiles
 (lizards and snakes) are ideal for addressing this issue. Some evidence
 from field and laboratory studies supports the “cold-climate” hypothesis,
 wherein viviparity provides an advantage in cold environments by allowing
 mothers to maintain higher temperatures for developing embryos.
 Surprisingly, the cold-climate hypothesis has not been tested using both
 climatic data and phylogenetic comparative methods. Here, we investigate
 the evolution of viviparity in the lizard family Phrynosomatidae using
 GIS-based environmental data, an extensive phylogeny (117 species), and
 recently developed comparative methods. We find significant relationships
 between viviparity and lower temperatures during the warmest (egg-laying)
 season, strongly supporting the cold-climate hypothesis. Remarkably, we
 also find that viviparity tends to evolve more frequently at tropical
 latitudes, despite its association with cooler climates. Our results help
 explain this and two related patterns that seemingly contradict the
 cold-climate hypothesis: the presence of viviparous species restricted to
 low-elevation tropical regions and the paucity of viviparous species at
 high latitudes. Finally, we examine whether viviparous taxa may be at
 higher risk of extinction from anthropogenic climate change.
description: rawdataraw data for all independent variables used (latitude, altitude, bio1, bio10, bio12)
DOI: 10.5061/dryad.765gr
title: Data from: Individual-based analyses reveal limited functional overlap in a coral reef fish community.

description: 1.Detailed knowledge of a species’ functional niche is crucial for the
 study of ecological communities and processes. The extent of niche
 overlap, functional redundancy and functional complementarity are of
 particular importance if we are to understand ecosystem processes and
 their vulnerability to disturbances. 2.Coral reefs are among the most
 threatened marine systems, and anthropogenic activity is changing the
 functional composition of reefs. The loss of herbivorous fishes is
 particularly concerning as the removal of algae is crucial for the growth
 and survival of corals. Yet, the foraging patterns of the various
 herbivorous fish species are poorly understood. 3.Using a multidimensional
 framework, we present novel individual-based analyses of species’ realized
 functional niches, which we apply to a herbivorous coral reef fish
 community. In calculating niche volumes for 21 species, based on their
 microhabitat utilization patterns during foraging, and computing
 functional overlaps, we provide a measurement of functional redundancy or
 complementarity. Complementarity is the inverse of redundancy and is
 defined as less than 50% overlap in niche volumes. 4.The analyses reveal
 extensive complementarity with an average functional overlap of just
 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two
 broad groups. The first group (predominantly surgeonfishes and
 parrotfishes) comprises species feeding on exposed surfaces and
 predominantly open reef matrix or sandy substrata, resulting in small
 niche volumes and extensive complementarity. In contrast, the second group
 consists of species (predominantly rabbitfishes) that feed over a wider
 range of microhabitats, penetrating the reef matrix to exploit concealed
 surfaces of various substratum types. These species show high variation
 among individuals, leading to large niche volumes, more overlap and less
 complementarity. 5.These results may have crucial consequences for our
 understanding of herbivorous processes on coral reefs, as algal removal
 appears to depend strongly on species-specific microhabitat utilization
 patterns of herbivores. Furthermore, the results emphasize the capacity of
 the individual-based analyses to reveal variation in the functional niches
 of species, even in high diversity systems such as coral reefs,
 demonstrating its potential applicability to other high-diversity
 ecosystems.
description: Raw_data_niche_overlapThe data characterizes the choice of microhabitats by herbivorous coral reef fishes during their foraging activity. The columns specify the id (species plus individual number), the surface orientation, the underlying substratum, the extent to which an individual penetrated the substratum with its body or snout and the number of bites taken.