cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.37s7b
title: Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system

description: The evolution of migration in birds has fascinated biologists for
 centuries. In this study, we performed phylogenetic-based analyses of
 Catharus thrushes, a model genus in the study of avian migration, and
 their close relatives. For these analyses, we used both mitochondrial and
 nuclear genes, and the resulting phylogenies were used to trace migratory
 traits and biogeographic patterns. Our results provide the first robust
 assessment of relationships within Catharus and relatives and indicate
 that both mitochondrial and autosomal genes contribute to overall support
 of the phylogeny. Measures of phylogenetic informativeness indicated that
 mitochondrial genes provided more signal within Catharus than did nuclear
 genes, whereas nuclear loci provided more signal for relationships between
 Catharus and close relatives than did mitochondrial genes. Insertion and
 deletion events also contributed important support across the phylogeny.
 Across all taxa included in the study, and for Catharus, possession of
 long-distance migration is reconstructed as the ancestral condition, and a
 North American (north of Mexico) ancestral area is inferred. Within
 Catharus, sedentary behaviour evolved after the first speciation event in
 the genus and is geographically and temporally correlated with Central
 American distributions and the final closure of the Central American
 Seaway. Migratory behaviour subsequently evolved twice in Catharus and is
 geographically and temporally correlated with a recolonization of North
 America in the late Pleistocene. By temporally linking speciation events
 with changes in migratory condition and events in Earth history, we are
 able to show support for several competing hypotheses relating to the
 geographic origin of migration.
description: Catharus_SpTree_AllDataNew_200milAll data, species tree, Figtree fileCatharus_SpTree_New_nuDNA_200milnuclear data only, species tree, Figtree fileCatharus-SpTree_AllDataNew-Constrained_200milall data, constrained species tree, Figtree filecatharusNewick
DOI: 10.5061/dryad.k029v
title: Data from: Implications of fidelity and philopatry for the population structure of female black-tailed deer

description: Site fidelity and philopatry are behavioral adaptations found in many
 species and their fitness benefits are well documented. The combined
 population level consequences of site fidelity and philopatry, however,
 have received little attention despite their importance for understanding
 spatial patterns in connectivity and population dynamics. We used an
 integrative approach to explore consequences of fidelity and philopatry on
 the fine-scale genetic structure of black-tailed deer (Odocoileus hemionus
 columbianus). We assessed fidelity to seasonal home ranges based on
 location data from 64 female deer fitted with global positioning system
 (GPS) collars between 2004 and 2013. We assessed philopatry from
 mitochondrial DNA (mtDNA) haplotypes using DNA extracted from 48 deer.
 Results based on location data revealed very small movements and seasonal
 home ranges together with high site fidelity. Fidelity improved survival;
 every 1 km increase in mean interlocation distances between consecutive
 summers increased the risk of mortality by 56.5%. Results from mtDNA
 sequencing revealed high genetic differentiation (FST &gt; 0.30) and
 low haplotype sharing among geographic areas separated by as little as
 4–10 km. The high genetic differentiation indicated multigenerational
 periods of philopatric behavior in the matrilineage of black-tailed deer.
 Combined these results suggest that site fidelity together with strong
 sex-biased philopatry can create marked short- and long-term demographic
 isolation and trap matriarchal units as a subset of the larger population
 with locally determined vital rates. Where such fine-scale population
 structuring as a consequence of fidelity and philopatry occurs,
 matrilineal groups might in some cases best serve as the basic units of
 conservation and management.
description: Weekly location data
 deer fidelity analysisFile contains individual
 deer ID as well as date, latitude, longitude and allocated season of GPS
 locations used to determine site fidelity of black-tailed deer in the
 Mendocino National Forest, California, USA.deer_fidelity_data_corrected.csvFidelity_deer_summaryFile contains information on deer ID, age, area and period of time a deer was colalred, number of seasons (summer and winter) a deer was monitored, info on weather a deer was non-migratory (column N0 = 1) and status at the end of the monitoring period to estimate cox proportional hazards.
DOI: 10.5061/dryad.21rt0fp0
title: Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas

description: Evolutionary relationships of 120 root-nodulating bacteria isolated from
 the nodules of Pisum sativum cultivated at 22 different locations of the
 trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal
 Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR,
 sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source
 utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The
 results demonstrated that all isolates belonged to Rhizobium leguminosarum
 symbiovar viciae (Rlv). Isolates from the two valleys were clearly
 separated on the basis of ERIC fingerprints, carbon-source utilization
 pattern, and whole-cell fatty acid methyl esters. Phylogenetic analysis of
 atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti
 valley. Lahaul valley isolates were represented by 3 sequence types of
 atpD and recA genes, and four sequence types of nodC and nifH genes.
 Genotypes from the two valleys were completely distinct, except for two
 Lahaul isolates that shared nodC and nifH sequences with Spiti isolates
 but were otherwise more similar to other Lahaul isolates. Isolates from
 the two highest Spiti valley sites (above 4000m) had a distinctive
 whole-cell fatty acid profile. Spiti valley isolates are closely related
 to Rlv sublineages from Xinjiang and Shanxi provinces in China, while
 Lahaul valley isolates resemble cosmopolitan strains of the western world.
 The high mountain pass between these valleys represents a boundary between
 two distinct microbial populations.
description: Carbon source
 utilization pattern of pea root-nodulating bacteriawhole-cell fatty acid
 composition of pea root-nodulating bacteriaWhole-cell fatty acids
 of the isolates were extracted and derivatized to methyl esters employing
 Instant FAME Kit and analysed on gas chromatograph equipped with FID
 detector.Genbank accession
 linksGenbank accession
 links
DOI: 10.5061/dryad.27pf7680
title: Data from: Integration of molecular, ecological, morphological and endosymbiont data for species delimitation within the Pnigalio soemius complex (Hymenoptera: Eulophidae)

description: Integrative taxonomy is a recently developed approach that uses multiple
 lines of evidence such as molecular, morphological, ecological and
 geographical data to test species limits, and it stands as one of the most
 promising approaches to species delimitation in taxonomically difficult
 groups. The Pnigalio soemius complex (Hymenoptera: Eulophidae) represents
 an interesting taxonomical and ecological study case, as it is
 characterized by a lack of informative morphological characters, deep
 mitochondrial divergence, and is susceptible to infection by
 parthenogenesis-inducing Rickettsia. We tested the effectiveness of an
 integrative taxonomy approach in delimiting species within the P. soemius
 complex. We analysed two molecular markers (COI and ITS2) using different
 methods, performed multivariate analysis on morphometric data and
 exploited ecological data such as host–plant system associations,
 geographical separation, and the prevalence, type and effects of
 endosymbiont infection. The challenge of resolving different levels of
 resolution in the data was met by setting up a formal procedure of data
 integration within and between conflicting independent lines of evidence.
 An iterative corroboration process of multiple sources of data eventually
 indicated the existence of several cryptic species that can be treated as
 stable taxonomic hypotheses. Furthermore, the integrative approach
 confirmed a trend towards host specificity within the presumed polyphagous
 P. soemius and suggested that Rickettsia could have played a major role in
 the reproductive isolation and genetic diversification of at least two
 species.
description: COI_alignmentFasta file containing aligned COI sequencesITS2_alignmentFasta file containing ITS2 sequences aligned by using the MAFFT algorithm G-INS-iIndividual by individual infection statusPDF file containing Individual by individual infection status.individual.infection.status.pdf
DOI: 10.5061/dryad.t215b
title: Data from: Persistence in peripheral refugia promotes phenotypic divergence and speciation in a rainforest frog

description: It is well established from the fossil record and phylogeographic analyses
 that late Quaternary climate fluctuations led to substantial changes in
 species' distribution, but whether and how these fluctuations
 resulted in phenotypic divergence and speciation is less clear. This
 question can be addressed through detailed analysis of traits relevant to
 ecology and mating within and among intraspecific lineages that persisted
 in separate refugia. In a biogeographic system (the Australian Wet
 Tropics, AWT) with a well-established history of refugial isolation during
 Pleistocene glacial periods, we test whether climate-mediated changes in
 distribution drove genetic and phenotypic divergence in the rainforest
 frog, Cophixalus ornatus. We combine paleomodeling and multilocus genetics
 to demonstrate long-term persistence within, and isolation among, one
 central and two peripheral refugia. In contrast to other AWT vertebrates,
 the three major lineages differ in ecologically relevant morphology and in
 mating call, reflecting divergent selection and/or genetic drift in the
 peripheral isolates. Divergence in mating call, and contact zone analyses,
 suggest that the lineages now represent distinct species. The results show
 that climate shifts can promote genetic and phenotypic divergence, and
 potentially speciation, and direct attention towards incorporating
 adaptive traits into phylogeographic studies to better resolve the
 mechanisms of speciation.
description: Hoskin et al - Am Nat -
 MorphologyMorphology data,
 collected in the field. Column headings, abbreviations, units - Species;
 Sex: M=male; SVL: Snout-to-vent length, in mm; TL: Tarsus length, in mm;
 HW: Head width, in mm; DISC: Third finger-disc width, in mm; WT: Weight,
 in grams; Major Lineage: Major genetic lineages. H=Hinchinbrook Is.,
 N=northern, C=central; Site/Location; Altitude: elevation above sea level,
 in metres.Hoskin et al - Am Nat -
 CallCall data - collected in
 the field Column headings, abbreviations, units - Species; Sex: M=male;
 Major Lineage: Major genetic lineages. H=Hinchinbrook Is., N=northern,
 C=central; DUR: Call duration, in milliseconds; DF: Call dominant
 frequency, in kHz; PULSE: Call pulse rate, in pulses/second; Temperature:
 Air temperature in degrees Celsius; Site/Location; Altitude: elevation
 above sea level, in metres.Hoskin et al - Am Nat -
 Distribution pointsHoskin et al - Am Nat -
 Sequence data (Corn16)Hoskin et al - Am Nat -
 Sequence data (Corn53)
DOI: 10.5061/dryad.20g8r
title: Data from: Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages

description: Genetic subdivision within a species is a vital component of the evolution
 of biodiversity. In some species of Acropora corals in Western Australia,
 conspecific individuals spawn in two seasons 6 months apart, which has the
 potential to impede gene flow and result in genetic divergence. Genetic
 comparison of sympatric spring and autumn spawners of Acropora samoensis
 was conducted to assess the level of reproductive isolation and genetic
 divergence between the spawning groups based on multiple loci (13
 microsatellite loci, the mitochondrial control region and two nuclear
 introns). Bayesian clustering and principal coordinate analysis of the
 microsatellite loci showed a high level of genetic differentiation between
 the spawning groups (F’ST = 0.30; P &lt; 0.001), as did the sequence
 data from PaxC and Calmodulin (ΦST = 0.97 and 0.31, respectively). At the
 PaxC locus, the autumn and spring spawners were associated with two
 divergent lineages that were separated by an evolutionary distance of 1.7%
 and statistical tests indicate divergent selection in PaxC, suggesting
 this gene may play a role in coral spawning. This study indicates that the
 autumn and spring spawners represent two cryptic species, and highlights
 the importance of asynchronous spawning as a mechanism influencing
 speciation in corals.
description: Microsatellite data of
 Acropora samoensisThis is the raw data
 from the 13 microsatellites that were genotyped in 80 individuals of
 Acropora samoensis in this study.Microsatellite
 dataset.csvCalmodulin_alignnmentThis is a Nexus file of the aligned sequences of the nuclear gene "Calmodulin" that were sequenced in this study.mtDNA_CR_alignmentThis is a Nexus file of the aligned sequences of the mitochondrial gene "Control Region" that were sequenced in this study.PaxC_cds_alignmentThis is a Nexus file of the aligned sequences of an 882 bp fragment of the CODING REGION of the nuclear gene "PaxC" that were sequenced in this study.PaxC_intron_alignmentThis is a Nexus file of the aligned sequences of the nuclear "PaxC" INTRON that were sequenced in this study.S4-WAM & GenBank Accession NumbersLists all the GenBank accession numbers for voucher specimens.S4-WAM_GenBank_Accession_No.docx
DOI: 10.5061/dryad.87g80
title: Data from: Site-specific group selection drives locally adapted group compositions

description: Group selection may be defined as selection caused by the differential
 extinction or proliferation of groups. The socially polymorphic spider
 Anelosimus studiosus exhibits a behavioral polymorphism where females
 exhibit either a “docile” or “aggressive” behavioral phenotype. Natural
 colonies are composed of a mixture of related docile and aggressive
 individuals, and populations differ in colonies’ characteristic
 docile:aggressive ratios. Using experimentally-constructed colonies of
 known composition, we demonstrate that population-level divergence in
 docile:aggressive ratios is driven by site-specific selection at the group
 level: certain ratios yield high survivorship at some sites but not
 others. Our data also suggest that colonies responded to the risk of
 extinction: perturbed colonies tended to adjust their composition over 2
 generations to match the ratio characteristic of their native site, thus
 promoting their long-term survival in their natal habitat. However,
 colonies of displaced individuals continued to shift their compositions
 towards mixtures that would have promoted their survival, had they
 remained at their home sites, regardless of their contemporary
 environment. Thus, the regulatory mechanisms that colonies use to adjust
 their composition appear to be locally-adapted. Our data provide the best
 experimental evidence of group selection driving collective traits in wild
 populations.
description: Source data on colony
 survival, correlates of extinction, and demography of natural
 coloniesR3_DRYAD_submission.xlsxLong Term Census DataLong_Term_Census_Data.xlsx
DOI: 10.6084/m9.figshare.31160737
title: Data from: Fire modifies leaf phenotype through bud mortality in a Cerrado species

description: The datasets used for the paper Fire modifies leaf phenotype through bud mortality in a Cerrado species
DOI: 10.6084/m9.figshare.31160737.v1
title: Data from: Fire modifies leaf phenotype through bud mortality in a Cerrado species

description: The datasets used for the paper Fire modifies leaf phenotype through bud mortality in a Cerrado species
DOI: 10.5061/dryad.sr7m5
title: Data from: Intraspecific variation in climate-relevant traits in a tropical rainforest lizard

description: Aim The exceptionally rich biodiversity found in tropical rainforest is
 under threat from anthropogenic climate change. We recognize the threat,
 yet we have little knowledge of the capacity of tropical species to adjust
 their climate sensitivity in response to it. One indicator of a species’
 capacity to adjust to different climates is the amount of intraspecific
 variation observed in its climate-relevant traits; if a climate-relevant
 trait varies, and this variation is correlated with local climates, it
 suggests the species can adjust the trait to different conditions through
 either phenotypic plasticity or evolutionary adaptation. Here, we test for
 intraspecific variation in climate-relevant traits in a rainforest
 specialist to shed light on the capacity of such species to adjust to
 different climates. Location The Wet Tropics Bioregion, Australia. Methods
 We studied 12 populations of a lizard that is a tropical rainforest
 specialist, the rainforest sunskink (Lampropholis coggeri), testing for
 intraspecific variation in four traits that are potentially important in
 determining a species’ climate sensitivity. The measured traits were as
 follows: critical thermal minimum, critical thermal maximum, thermal
 optimum for sprinting, and desiccation rate. Results We found substantial
 variation both through time and across space in the measured traits,
 suggesting both strong plasticity and substantial geographic variation.
 Moreover, trait variation was correlated with local climate variables,
 suggesting variation reflects adjustment to local conditions. Main
 conclusions If physiological lability similar to that observed in
 rainforest sunskinks occurs in tropical rainforest species more generally,
 these taxa may not be as climatically specialized, and so not as
 vulnerable to climate change, as previously thought.
description: Intraspecific variation
 dataData on CTmin, CTmax,
 Topt and desiccation rate for rainforest sunskinks from numerous
 populations, as well as environmental variables for each
 population/collection groupDiversity and Distribution
 data.xls
DOI: 10.5061/dryad.v176m
title: Data from: Genotype reconstruction of paternity in European lobsters (Homarus gammarus)

description: Decapod crustaceans exhibit considerable variation in fertilisation
 strategies, ranging from pervasive single paternity to the near-ubiquitous
 presence of multiple paternity, and such knowledge of mating systems and
 behaviour are required for the informed management of
 commercially-exploited marine fisheries. We used genetic markers to assess
 the paternity of individual broods in the European lobster, Homarus
 gammarus, a species for which paternity structure is unknown. Using 13
 multiplexed microsatellite loci, three of which are newly described in
 this study, we genotyped 10 eggs from each of 34 females collected from an
 Atlantic peninsula in the south-western United Kingdom. Single
 reconstructed paternal genotypes explained all observed progeny genotypes
 in each of the 34 egg clutches, and each clutch was fertilised by a
 different male. Simulations indicated that the probability of detecting
 multiple paternity was in excess of 95% if secondary sires account for at
 least a quarter of the brood, and in excess of 99% where additional sire
 success was approximately equal. Our results show that multiple paternal
 fertilisations are either absent, unusual, or highly skewed in favour of a
 single male among H. gammarus in this area. Potential mechanisms upholding
 single paternal fertilisation are discussed, along with the prospective
 utility of parentage assignments in evaluations of hatchery stocking and
 other fishery conservation approaches in light of this finding.
description: Microsatellite genotypes
 of European lobstersGenotype data at up to
 15 microsatellite loci for 612 lobsters from 28 locations. The first 312
 samples at top comprise fine-scale samples all taken within Cornwall, UK,
 and have also been used to calculate regional allele frequencies in the
 2015 PLOS ONE publication by Ellis et al; Genotype Reconstruction of
 Paternity in European Lobsters (Homarus gammarus). The next 300
 individuals comprise broad-scale European population genetic
 samples.FULL.DATA_LOBSTER.GENETICS_15markers_28sites_612samples.xlsxEuropean lobster genotypic progeny arrays34 European lobster (Homarus gammarus) progeny arrays, 10 embryo and 1 maternal sample were genotyped at 15 microsatellite loci (2 of which were discarded from the analysis due to the presence of null alleles) to reconstruct the paternal genotype(s) present in each clutch.Ellis2015_DATA_genotypic_reconstruction_of_european_lobster_paternity.xlsx
DOI: 10.5061/dryad.90qb7
title: Data from: Effects of antibiotic resistance alleles on bacterial evolutionary responses to viral parasites

description: Antibiotic resistance has wide-ranging effects on bacterial phenotypes and
 evolution. However, the influence of antibiotic resistance on bacterial
 responses to parasitic viruses remains unclear, despite the ubiquity of
 such viruses in nature and current interest in therapeutic applications.
 We experimentally investigated this by exposing various Escherichia coli
 genotypes, including eight antibiotic-resistant genotypes and a mutator,
 to different viruses (lytic bacteriophages). Across 960 populations, we
 measured changes in population density and sensitivity to viruses, and
 tested whether variation among bacterial genotypes was explained by their
 relative growth in the absence of parasites, or mutation rate towards
 phage resistance measured by fluctuation tests for each phage. We found
 that antibiotic resistance had relatively weak effects on adaptation to
 phages, although some antibiotic-resistance alleles impeded the evolution
 of resistance to phages via growth costs. By contrast, a mutator allele,
 often found in antibiotic-resistant lineages in pathogenic populations,
 had a relatively large positive effect on phage-resistance evolution and
 population density under parasitism. This suggests costs of antibiotic
 resistance may modify the outcome of phage therapy against pathogenic
 populations previously exposed to antibiotics, but the effects of any
 co-occurring mutator alleles are likely to be stronger.
description: Arias_Hall_BiolLett_2016_dataThe Excel file contains population density, bacteriophage sensitivity and mutation rate estimate data. The ReadMe worksheet describes the contents in detail. ‘Main experiment’ gives population densities after 0h, 20h and 72h in the main experiment. ‘Table S1’ gives changes in bacterial sensitivity to phages in control populations against all three phages. ‘FT raw data’ gives colony counts and population sizes from fluctuation assays. ‘Falcor’ gives output from mutation rate estimation using Falcor before and after correction for partial plating (plating efficiency).Dryad_Arias_Hall_v3.xlsx
DOI: 10.48656/87j0-ks63
title: ALIS Open Data
title: ALIS Open Data
title: ALIS Open Data
title: ALIS Open Data
DOI: 10.48656/s9k2-hy36
title: ALIS Open Data
title: ALIS Open Data
title: ALIS Open Data
title: ALIS Open Data