cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7g2h4
title: Data from: Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone

description: Ecological speciation involves the evolution of reproductive isolation and
 niche divergence in the absence of a physical barrier to gene flow. The
 process is one of the most controversial topics of the speciation debate,
 particularly in tropical regions. Here, we investigate ecologically based
 divergence across an Amazonian ecotone in the electric fish, Steatogenys
 elegans. We combine phylogenetics, genome scans, and population genetics
 with a recently developed individual-based evolutionary landscape genetics
 approach that incorporates selection. This framework is used to assess the
 relative contributions of geography and divergent natural selection
 between environments as biodiversity drivers. We report on two closely
 related and sympatric lineages that exemplify how divergent selection
 across a major Amazonian aquatic ecotone (i.e., between rivers with
 markedly different hydrochemical properties) may result in replicated
 ecologically mediated speciation. The results link selection across an
 ecological gradient with reproductive isolation and we propose that
 assortative mating based on water color may be driving the divergence.
 Divergence resulting from ecologically driven selection highlights the
 importance of considering environmental heterogeneity in studies of
 speciation in tropical regions. Furthermore, we show that framing
 ecological speciation in a spatially explicit evolutionary landscape
 genetics framework provides an important first step in exploring a wide
 range of the potential effects of spatial dependence in natural selection.
description: AFLP
 dataAFLP data for
 Steatogenys elegans cryptic species 1 and 2 including sampling
 locations.DRYAD
 Data.xlsx
DOI: 10.5061/dryad.h6t17
title: Data from: Both male and female novel traits promote the correlated evolution of genitalia between the sexes in an arthropod

description: The correlated evolution of genitalia between sexes has been demonstrated
 in many taxa. However, it remains unclear whether female rather than male
 genitalia can play a key role in the correlated evolution of male and
 female genitalia. We conducted an extensive cross-population analysis of
 the divergence patterns of genital structures, weights of whole genital
 organs and the bodies of both sexes, and male genital length in a group of
 xystodesmid millipedes showing diverse genital morphologies. We
 demonstrate that the correlated evolution of male and female genitalia
 toward exaggerated states has occurred in the millipedes, which have
 evolved novel traits in both males (forceps-like gonopods) and females
 (retractable bellows). Enlargement and elongation of forceps-like gonopods
 may be advantageous in sperm competition, whereas enlargement and
 elongation of the bellows may facilitate acceptance/rejection of
 insemination for ensuring the female's fitness. These male and female
 genital parts have affected the correlated evolution in the opposite sex,
 resulting in diversification and exaggeration of genital morphology. Our
 study suggests that evolutionary novel traits in not only males but also
 in females could play an important role in the correlated evolution of
 genitalia between the sexes.
description: Genital binary data of
 xystodesmid millipedesThe data were collected
 based on observations of specimens.Table_S2.docxContinuous data of body and genitalia of xystodesmid millipedesThe data were collected based on measurements of specimens.Table_S3.docx
DOI: 10.5061/dryad.r1h4h
title: Data from: The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples

description: The mode in which sexual organisms choose mates is a key evolutionary
 process, as it can have a profound impact on fitness and speciation. One
 way to study mate choice in the wild is by measuring trait correlation
 between mates. Positive assortative mating is inferred when individuals of
 a mating pair display traits that are more similar than those expected
 under random mating while negative assortative mating is the opposite. A
 recent review of 1134 trait correlations found that positive estimates of
 assortative mating were more frequent and larger in magnitude than
 negative estimates. Here we describe the scale-of-choice effect (SCE),
 which occurs when mate choice exists at a smaller scale than that of the
 investigator's sampling, while simultaneously the trait is
 heterogeneously distributed at the true scale-of-choice. We demonstrate
 the SCE by Monte Carlo simulations and estimate it in two organisms
 showing positive (Littorina saxatilis) and negative (L. fabalis)
 assortative mating. Our results show that both positive and negative
 estimates are biased by the SCE by different magnitudes, typically towards
 positive values. Therefore, the low frequency of negative assortative
 mating observed in the literature may be due to the SCE's impact on
 correlation estimates, which demands new experimental evaluation.
description: Simulations
 DataWe assayed different
 values for the number of populations N = {10, 100}, number of mating pairs
 K={20, 500}, coefficient of variation CV (0 to 1 with increments of 0.1),
 intrapopulation standard deviation σw = {0.1, 0.3, 0.45} and choice C (-1
 to 1 with increments of 0.1), giving a total of 2,772
 combinations.Rolán-Alvarez et al 2015.
 Simulations Data.xlsxhttp://acraaj.webs.uvigo.es/software/sourcemicroA.zip
DOI: 10.5061/dryad.gh317
title: Data from: Species delimitation and phylogeny in the genus Nasutitermes (Termitidae: Nasutitermitinae) in French Guiana

description: Species delimitation and identification can be arduous for taxa whose
 morphologic characters are easily confused, which can hamper global
 biodiversity assessments and pest species management. Exploratory methods
 of species delimitation that use DNA sequence as their primary information
 source to establish group membership and estimate putative species
 boundaries are useful approaches, complementary to traditional taxonomy.
 Termites of the genus Nasutitermes make interesting models for the
 application of such methods. They are dominant in Neotropical primary
 forests but also represent major agricultural and structural pests.
 Despite the prevalence, pivotal ecological role and economical impact of
 this group, the taxonomy of Nasutitermes species mainly depends on
 unreliable characters of soldier external morphology. Here, we generated
 robust species hypotheses for 79 Nasutitermes colonies sampled throughout
 French Guiana without any a priori knowledge of species affiliation.
 Sequence analysis of the mitochondrial cytochrome oxidase II gene was
 coupled with exploratory species-delimitation tools, using the automatic
 barcode gap discovery method (ABGD) and a generalized mixed
 Yule-coalescent model (GMYC) to propose primary species hypotheses (PSHs).
 PSHs were revaluated using phylogenetic analyses of two more loci
 (mitochondrial 16S rDNA and nuclear internal transcribed spacer 2) leading
 to 16 retained secondary species hypotheses (RSSH). Seven RSSHs,
 represented by 44/79 of the sampled colonies, were morphologically
 affiliated to species recognized as pests in the Neotropics, where they
 represent a real invasive pest potential in the context of growing
 ecosystem anthropization. Multigenic phylogenies based on combined
 alignments (1426–1784 bp) were also reconstructed to identify ancestral
 ecological niches and major-pest lineages, revealing that Guyanese pest
 species do not form monophyletic groups.
description: Nasutitermes and
 outgroup COII haplotypesCytochrome oxidase II
 (COII) unique haplotypes for Nasutitermes samples and two outgroups.
 Genbank Accession Numbers and putative species are
 indicated.COIIhaplotypes.fasNasutitermes and outgroup 16S haplotypes16S rDNA (16S) unique haplotypes for Nasutitermes samples and two outgroups. Genbank Accession Numbers and putative species are indicated.16Shaplotypes.FASNasutitermes and outgroup ITS2 sequencesInternal Transcribed Spacers 2 (ITS2) sequences for Nasutitermes samples and two outgroups. Genbank Accession Numbers and putative species are indicated.ITS2_uipacconsensus.FASTotal combined alignment (COII/16S/ITS2)Total combined alignment (1784bp) for COII, 16rDNA and ITS2 sequences. Samples with at least one missing locus were discarded from the analyses, resulting in datasets of 64 Nasutitermes and two outgroup samples.CONCATALL.fasMorphological datasetTaxonomic notes on the identification of the Nasutitermes speciesmorpho.docx
DOI: 10.5061/dryad.b9q73
title: Data from: Population differentiation of 2 forms of Bryde’s whales in the Indian and Pacific Oceans

description: Accurate identification of units for conservation is particularly
 challenging for marine species as obvious barriers to gene flow are
 generally lacking. Bryde’s whales (Balaenoptera spp.) are subject to
 multiple human-mediated stressors, including fisheries bycatch, ship
 strikes, and scientific whaling by Japan. For effective management, a
 clear understanding of how populations of each Bryde’s whale
 species/subspecies are genetically structured across their range is
 required. We conducted a population-level analysis of mtDNA control region
 sequences with 56 new samples from Oman, Maldives, and Bangladesh, plus
 published sequences from off Java and the Northwest Pacific. Nine
 diagnostic characters in the mitochondrial control region and a maximum
 parsimony phylogenetic analysis identified 2 genetically recognized
 subspecies of Bryde’s whale: the larger, offshore form, B. edeni brydei,
 and the smaller, coastal form, B. e. edeni. Genetic diversity and
 differentiation indices, combined with a reconstructed maximum parsimony
 haplotype network, indicate strong differences in the genetic diversity
 and population structure within each subspecies. Discrete population units
 are identified for B. e. brydei in the Maldives, Java, and the Northwest
 Pacific, and for B. e. edeni between the Northern Indian Ocean (Oman and
 Bangladesh) and the coastal waters of Japan.
description: Kershawetal_TableS1_SampleInformationTable S1: Details of new Bryde’s whale samples. Sample ID corresponds to original field sample code as managed by the American Museum of Natural History. Taxon was designated as a result of the phylogenetic analysis carried out in the current study. Sampling sites are as follows: BAN, Swatch-of-No-Ground, Bangladesh; BAN (CB), Cox’s Bazaar, Bangladesh; MAL, Maldives; OMA, Oman. Latitude and Longitude are in decimal degrees; N, North; E, East. Body length is given in meters or, if this information wasn’t available, as life history stage. Sex is coded as: M, male; F, female. ND, no data.Kershawetal_TableS2_HaplotypeInformationTable S2: Table of corresponding accession (ACCN) numbers for haplotypes H01-H49 included in the study. From the 299 bp mitochondrial consensus sequence (bp position 15545-15843 in the mtDNA genome of B. e. edeni [ACCN: AB201258]), H01-H45 were identified as B. e. brydei, and H46-H48 were identified as B. e. edeni. The B. e. edeni haplotype H49 was identified from the 407 bp consensus sequence (bp position 15500-15906 in the mtDNA genome of B. e. edeni [ACCN: AB201258]). The total number of individuals (N) for each haplotype is shown and, when two accession numbers are listed, the number of individuals represented by each is indicated in parentheses. * indicates the five new haplotypes described by the current study. The remaining forty-four haplotypes have been previously described and published (Kanda et al. 2007; Yoshida & Kato 1999). For details of haplotype frequencies across sampling locations, see Figure 2 of the main article.
DOI: 10.5061/dryad.dt115
title: Data from: Evolution of mutation rates in hypermutable populations of Escherichia coli propagated at very small effective population size

description: Mutation is the ultimate source of the genetic variation—including
 variation for mutation rate itself—that fuels evolution. Natural selection
 can raise or lower the genomic mutation rate of a population by changing
 the frequencies of mutation rate modifier alleles associated with
 beneficial and deleterious mutations. Existing theory and observations
 suggest that where selection is minimized, rapid systematic evolution of
 mutation rate either up or down is unlikely. Here, we report systematic
 evolution of higher and lower mutation rates in replicate hypermutable
 Escherichia coli populations experimentally propagated at very small
 effective size—a circumstance under which selection is greatly reduced.
 Several populations went extinct during this experiment, and these
 populations tended to evolve elevated mutation rates. In contrast,
 populations that survived to the end of the experiment tended to evolve
 decreased mutation rates. We discuss the relevance of our results to
 current ideas about the evolution, maintenance and consequences of high
 mutation rates.
description: Fitness data for both LB
 and Minimal Glucose surviving populationsThis file contains the
 final density, maximum growth rate, and Colony Forming Unit data for all
 the surviving population from both LB and minimal glucose
 lines.LB+MG
 fitness data .xlsxMaximum likelihood
 mutation rate estimatesThis file contains the
 maximum likelihood estimates of mutation rates obtained by using the
 fluctuation analysis approach for both the LB and minima glucose
 populations that survived, as well as, the populations that went
 extinct.maximum likelihood mutation
 rate estimates .xlsxVariance in measures of
 fitness over timeThis file contains the
 variance in the the two measures of fitness (final density and maximum
 growth rate), measured over time, for both the LB and the minimal glucose
 population.variance in fitness data
 .xlsxCorellatin between
 streptomycin and nalidixic acid mutation ratesThis file describes the
 correlation between the maximum likelihood estimates of the streptomycin
 rates and the nalidixic acid rates for both the LB and the MG
 populationsEffect of tetracycline
 on mutation rate
DOI: 10.5061/dryad.s13rt
title: Data from: How the zebra got its stripes: a problem with too many solutions

description: The adaptive significance of zebra stripes has thus far eluded
 understanding. Many explanations have been suggested, including social
 cohesion, thermoregulation, predation evasion and avoidance of biting
 flies. Identifying the associations between phenotypic and environmental
 factors is essential for testing these hypotheses and substantiating
 existing experimental evidence. Plains zebra striping pattern varies
 regionally, from heavy black and white striping over the entire body in
 some areas to reduced stripe coverage with thinner and lighter stripes in
 others. We examined how well 29 environmental variables predict the
 variation in stripe characteristics of plains zebra across their range in
 Africa. In contrast to recent findings, we found no evidence that striping
 may have evolved to escape predators or avoid biting flies. Instead, we
 found that temperature successfully predicts a substantial amount of the
 stripe pattern variation observed in plains zebra. As this association
 between striping and temperature may be indicative of multiple biological
 processes, we suggest that the selective agents driving zebra striping are
 probably multifarious and complex.
description: zebra_phenotypesenvironmental_data
DOI: 10.5061/dryad.9054
title: Data from: No relationship between canalization and developmental stability in the skull of a natural population of Mastomys natalensis (Rodentia: Muridae)

description: The aim of the present work was to investigate the relationship between
 canalization and developmental stability under varying environmental
 conditions. Three different cohorts of Mastomys natalensis (Rodentia,
 Muridae), displaying different growth trajectories, were analyzed by means
 of Geometric morphometrics. A set of 23 landmarks was digitalized on the
 dorsal skull of 292 specimens from Morogoro (Tanzania). Patterns of among-
 and within-individual (measured as fluctuating asymmetry) variation were
 assessed and compared among and within the three groups in order to test
 for the presence of a common mechanism between canalization and
 developmental stability. Results showed that there was no congruence
 between canalization and developmental stability: 1) levels of FA and
 among-individual variation varied in a discordant fashion, 2) no
 correspondence between variance-covariance matrix of among- and within
 individual variation was found, 3) environmental effects were able to
 alter the covariance structure of among- individual variation living
 patterns associated with fluctuating asymmetry unaffected. These findings
 support the view of multiple mechanisms underlying developmental buffering
 of shape variation.
description: Landmarks23 landmarks of the dorsal view of the skull in 2D. 2 replicates per individual
DOI: 10.5061/dryad.3bc74
title: Data from: Competition during thermoregulation altered the body temperatures and hormone levels of lizards

description: Every organism must thermoregulate to maximize its performance, but
 competing organisms limit access to preferred microclimates. Such
 competition often creates hierarchies in which dominant individuals have
 more access to limited resources than subordinate individuals. To assess
 the costs of competition during thermoregulation, we measured
 thermoregulation, movement, and hormones of male lizards (Sceloporus
 jarrovi) when alone and when paired with a smaller or larger conspecific.
 Large males were 31% closer to the heat source when paired than when
 alone, resulting in a higher mean body temperature (35.7°C vs. 33.9°C).
 Conversely, small males were 40% farther from the heat source when paired,
 resulting in lower mean body temperature (32.1°C vs. 33.6°C). When paired,
 large and small males to circulate 26% and 44% more corticosterone,
 respectively. Conversely, large males circulated 26% more testosterone
 when paired, while small males circulated 26% less testosterone. Both
 dominant and subordinate males incurred costs when paired, including
 poorer thermoregulation, more movement, and greater physiological stress.
 Thus, competition for thermal resources should feature more prominently in
 ecological and evolutionary models of thermoregulation.
description: Data_for_Dryad_RuschExcel
DOI: 10.5061/dryad.v5v3k
title: Data from: Host effects on microbiota community assembly

description: 1. To what extent host-associated microbiota assembly is driven by host
 selection or simply by happenstance remains an open question in microbiome
 research. 2. Here, we take a first step towards elucidating the relative
 importance of host selection on the establishing gut microbial community
 in an ecologically relevant organism. 3. We presented germ-free bumblebee,
 Bombus terrestris, workers from ten colonies with a “global” microbial
 species pool comprised of an equal mixture of the gut microbiota of all
 colonies. 4. By means of 16S amplicon sequencing, we found that while
 overall microbiota community composition was generally shifted between
 pool-exposed workers compared to workers that naturally acquired their gut
 microbiota, but that the specific composition of the established
 microbiota also depended on colony identity (e.g. genetic background). 5.
 Because the microbiota is protective against parasite infection in this
 system, variation in the filtering of a beneficial microbial community can
 have important consequences for host resistance and eventual co-evolution
 with parasites.
description: Sample
 MetadataSample
 informationE11_SampleMetadata.txtCrithidia bombi Infection DataData of infection outcome seven days post parasite exposure.E11_CrithidiaInfectionData.txtOTU Count TableOTU count table based on 97% sequence identityE11_OTUTable.txtOTU TaxonomyTaxonomic information for each OTU based on RDP v16 and SILVA database v128.E11_OTUTaxonomy.txtOTU Centroid SequencesReference sequence for each OTU.E11_OTUCentroidSequences.fa
DOI: 10.5061/dryad.hh2g4s48
title: Data from: Modeling intraspecific adaptation of Abies sachalinensis to local altitude and responses to global warming, based on a 36-year reciprocal transplant experiment

description: Intraspecific adaptation in Abies sachalinensis was examined using models
 based on long-term monitoring data gathered during a reciprocal transplant
 experiment with eight seed source populations and six transplantation
 sites along an altitudinal gradient. The consequence of local adaptation
 was evaluated by testing the home-site advantage for upslope and downslope
 transplants at five ages. The populations’ fitness-linked trait was set as
 their productivity (tree height ×survival rate) at each age. The effects
 of global warming were evaluated on the basis of the 36-year performance
 of downslope transplants. Evidence was found for adaptive genetic
 variation affecting both height and survival from an early age. Increasing
 the distance between seed source and planting site significantly reduced
 productivity for both upslope and downslope transplantation, demonstrating
 the existence of a significant home-site advantage. The decrease in
 productivity was most distinct for upslope transplantations, indicating
 strong local adaptation to high altitudes. Global warming is predicted to
 increase the productivity of high-altitude populations. However, due to
 their existing local adaptation, all tested populations exhibited lower
 productivity under warming than demes that were optimal for the new
 climate. These negative predictions should be considered when planning the
 management of locally-adapted plant species such as A. sachalinensis.
description: Ishizuka_Abies_H,SurviveSee read-me file.Ishizuka_Abies_productivitySee read-me file.