cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h18931zm7
title: Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution

description: Garter snakes (Thamnophis) are a successful group of natricines endemic to
 North America.  They have become important natural models for
 ecological and evolutionary research, yet prior efforts to resolve
 phylogenetic relationships have resulted in conflicting topologies and
 weak support for certain relationships.  Here, we use
 phylogenomic data generated with a reduced representation double-digest
 RADseq approach to reassess the evolutionary relationships across
 Thamnophis.  We then use the resulting phylogeny to better
 understand how biogeography and feeding ecology have influenced lineage
 diversification and morphological evolution.  We recovered highly
 congruent and strongly supported topologies from maximum likelihood and
 Bayesian inference analyses, but some discordance with a multispecies
 coalescent approach.  All phylogenomic estimates split Thamnophis
 into two clades largely defined by northern and southern North American
 species.  Divergence time estimates and biogeographic analyses
 indicate a mid-Miocene origin of Thamnophis in Mexico.  In
 addition, historical vicariant events thought to explain biogeographic
 patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain
 Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns
 of diversification in Thamnophis as well.  Analyses of
 morphological traits associated with feeding ecology showed degrees of
 phylogenetic signal, and ancestral state reconstruction suggested some
 association between head morphology and diet composition.  Our
 new estimate of Thamnophis phylogeny yields an improved understanding of
 the biogeographic history and morphological evolution of garter snakes,
 and provides a robust framework for future research on these snakes.
description: <em>Thamnophis</em>_fastqs<br>Directory
 containing .fastq files for all <em>Thamnophis  </em>and
 outgourp individuals analyzed in the paper. This directory has been
 compressed as a tar archive. To uncompress from the command line:$ tar
 -zxvf Thamnophis_fastqs.tar.gz
 specimen_information This text file
 contains information on each specimen analyzed with ddRAD data.  This file
 contains identification numbers for voucher specimens and their
 corresponding barcode identification.  
 ddRAD_subsample_loci_beast_script R
 script modified from Villaverdea et al., 2021 to randomly subsample ddRAD
 loci
DOI: 10.5061/dryad.4f4qrfjcp
title: Data from: Litter decomposition affected by bamboo expansion is modulated by litter-mixing and microbial composition

description: Litter decomposition is a key ecosystem process that drives carbon (C) and
 nutrient cycling, which could be affected by shifts in plant community
 composition caused by plant invasion or expansion. However, how changes in
 leaf litter composition (e.g., litter-mixing effect) and soil microbial
 community induced by shift in plant community composition affect
 decomposition remains elusive. Here, by deploying 432 litterbags (50-μm
 mesh screen), we treated leaf litter of bamboo (Phyllostachys edulis­) and
 tree species (in a mixture or alone) and decomposed them in forest sites
 expanded or not expanded by bamboo at three regions, to assess the effects
 of bamboo expansion on decomposition, microbial community structure and
 function. Bamboo expansion reduced microbial C to nitrogen (N) ratio and
 nutritional stress indicator (cy/pre), which was very likely ascribed to
 elevated N availability as a result of accelerated litter N release. The N
 loss of bamboo litter (28.1 ± 03%) was more than double of tree species
 litter (13.2 ± 3.1%), and decomposing litter of bamboo and tree species in
 a mixture increased litter N loss from 15.3± 3.1% to 25.9± 3.1% (by 69%).
 However, no consistent effect of litter type and litter treatment on C
 loss was observed. The non-additive litter-mixing effect is attributable
 to increased microbial nutrient use efficiency, which is illustrated by
 the interactive effect between litter treatment and cy/pre on
 decomposition. Moreover, the forest type interactively affected
 decomposition with cy/pre as ignoring litter treatment, where higher decay
 rate and litter N loss at bamboo expanded than non-expanded sites would be
 expected when both sites having comparable cy/pre, but the reality is that
 bamboo expansion tends to have lower cy/pre. These results imply a
 trade-off between introduced litter and nutrient use efficiency of local
 microbial community to drive decomposition. Our results demonstrate that
 litter decomposition affected by bamboo expansion was jointly modulated by
 litter-mixing and microbial composition, which sheds new insights on
 predicting changes in soil C and nutrient cycling induced by shifts in
 plant community composition.
DOI: 10.5061/dryad.ttdz08kzt
title: List of known SNP positions (based on SNP chip data) for base quality score recalibration of alignments for whole-genome resequencing and whole-genome bisulfite sequencing data from great tits (Parus major)

description: The profiling of epigenetic marks like DNA methylation has become a
 central aspect of studies in evolution and ecology. Bisulfite sequencing
 is commonly used for assessing genome-wide DNA methylation at single
 nucleotide resolution but these data can also provide information on
 genetic variants like single nucleotide polymorphisms (SNPs). However,
 bisulfite conversion causes unmethylated cytosines to appear as thymines,
 complicating the alignment and subsequent SNP calling. Several tools have
 been developed to overcome this challenge, but there is no independent
 evaluation of such tools for non-model species, which often lack genomic
 references. Here, we used whole-genome bisulfite sequencing (WGBS) data
 from four female great tits (Parus major) to evaluate the performance of
 seven tools for SNP calling from bisulfite sequencing data. We used SNPs
 from whole-genome resequencing data of the same samples as baseline SNPs
 to assess common performance metrics like sensitivity, precision, and the
 number of true positive, false positive, and false negative SNPs for the
 full range of variant and genotype quality values. We found clear
 differences between the tools in either optimizing precision (Bis-SNP),
 sensitivity (biscuit), or a compromise between both (all other tools).
 Overall, the choice of SNP caller strongly depends on which performance
 parameter should be maximized and whether ascertainment bias should be
 minimized to optimize downstream analysis, highlighting the need for
 studies that assess such differences.
description: A total of 2015 female great tits were genotyped using a custom
 made Affymetrix great tit 650K SNP chip (Kim et al. 2018) at Edinburgh
 Genomics (Edinburgh, United Kingdom). Axiom Analysis Suite 1.1 was used
 for SNP calling following the Affymetrix best practices
 workflow. Kim, J. M.,
 A. W. Santure, H. J. Barton, J. L. Quinn, E. F. Cole, Great Tit HapMap
 Consortium, M. E. Visser, et al. 2018. “A High-Density SNP Chip for
 Genotyping Great Tit ( <i>Parus Major</i> ) Populations and
 Its Application to Studying the Genetic Architecture of Exploration
 Behaviour.” <i>Molecular Ecology Resources</i> 18 (4): 877–91.
 https://doi.org/10.1111/1755-0998.12778.
DOI: 10.5061/dryad.4qrfj6qb1
title: Persistence of plant-mediated microbial soil legacy effects in soil and inside roots

description: Plant-soil feedbacks are shaped by microbial legacies that plants leave in
 the soil. We tested the persistence of these legacies after subsequent
 colonization by the same or other plant species. Soil fungal legacies were
 detectable for months, but the current plant effect on fungi amplified in
 time. Contrary, in bacterial communities, legacies faded away rapidly and
 bacteria communities were influenced strongly by the current plant.
 However, both fungal and bacterial legacies were conserved inside the
 roots of the current plant species and their composition significantly
 correlated with plant growth. Hence, microbial soil legacies present at
 the time of plant establishment play a vital role in shaping plant growth
 even when these legacies have faded away in the soil due the growth of the
 current plant species. We conclude that soil microbiome legacies are
 reversible and versatile, but that they can create plant-soil feedbacks
 via altering the endophytic community acquired during early ontogeny.
description: PSF experiment was conducted by growing 6 plant species (3
 Poaceae and 3 Asteraceae) in outside mesocosms for a year. Subsequently
 all plants were grown in all soils for 5 more months to investigae the
 effects of growing in own soil vs other soils on soil microbes and plant
 biomass. Here plant biomass (below-ground and above-ground) data is
 reported after 5 months of growth in these soils with different plant
 legacies.
DOI: 10.5061/dryad.8kprr4xp5
title: Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily-conserved ribosomal DNA

description: Crustaceans are notoriously difficult to age because of their
 indeterminate growth and the moulting of their exoskeleton throughout
 life. The poor knowledge of population age structure in crustaceans
 therefore hampers accurate assessment of population dynamics and
 consequently sustainable fisheries management. Quantification of DNA
 methylation of the evolutionarily-conserved ribosomal DNA (rDNA) may allow
 for age prediction across diverse species. However, the rDNA epigenetic
 clock remains to be tested in crustaceans, despite its potential to inform
 both ecological and evolutionary understanding, as well as conservation
 and management practices. Here, patterns of rDNA methylation with age were
 measured across 5,154 bp of rDNA corresponding to 355 quality filtered
 loci in the economically-important European lobster (Hommarus gammarus).
 Across 0–51 month-old lobsters (n = 155) there was a significant linear
 relationship between age and percentage rDNA methylation in claw tissue at
 60% of quality-filtered loci (n = 214). An Elastic Net regression model
 using 46 loci allowed for the accurate and precise age estimation of
 individuals (R2 = 0.98, standard deviation = 1.6 months). Applying this
 ageing model to antennal DNA from wild lobsters of unknown age (n = 38)
 resulted in predicted ages that are concordant with estimates of minimum
 size-at-age in the wild, with a mean age of 40.07 months (range 32.8 -
 55.65 months).  Overall, the rDNA epigenetic clock shows
 potential as a novel, non-lethal ageing technique for European
 lobsters.  However, further validation is required across a wider
 range of known-age individuals and tissue types before the model can be
 used in an applied scenario.
description: see manuscript
DOI: 10.5061/dryad.59zw3r27w
title: Social and abiotic factors differentially affect plumage ornamentation of young and old males in an Australian songbird

description: Both abiotic environmental conditions and variation in social environment
 are known to impact the acquisition of sexual signals. However, the
 influences of abiotic environmental and social factors are rarely compared
 to each other. Here we test the relative importance of these factors in
 determining whether and when male red-backed fairywrens (Malurus
 melanocephalus) moult into a known sexual signal, ornamented breeding
 plumage. One-year-old male red-backed fairywrens vary in whether or not
 they acquire ornamentation, whereas males age two and older vary in their
 timing of ornament acquisition. It is unclear whether these processes are
 determined by the same or different factors and we examine both events
 using a combination of long-term breeding records and non-breeding social
 networks. We found that one-year-old males that paired prior to the start
 of the breeding season were more likely to acquire ornamented plumage, but
 rainfall did not influence whether one-year-old males acquired ornamented
 plumage. Thus, for young individuals, social cues appear to play a larger
 role than abiotic environmental factors in determining ornament
 acquisition. For older males, timing of ornamented plumage acquisition was
 constrained by rainfall, with drier non-breeding seasons leading to poorer
 physiological condition and later moult dates. Thus, sexual signal
 variation in older males appears to be a condition-dependent trait, driven
 by abiotic environmental and physiological factors rather than social
 cues. These findings reveal that factors influencing sexual signal
 expression can vary with age when age classes exhibit different forms of
 signal variation. Our results suggest that social environment may drive
 sexual signal variation in young individuals, whereas abiotic
 environmental variation may drive sexual signal variation in older
 individuals.
description: See README file for descriptions of each dataset and summaries of
 each R script. See annotated R code for instructions on how to run the
 analyses.
DOI: 10.5061/dryad.sj3tx965g
title: Evidence for niche conservatism in alpine beetles under a climate-driven species pump model

description: Aim Past glacial climate cycles have generated lineage diversity in alpine
 habitats, acting as a climate-driven species pump. It is not clear how
 much this process contributes to ecological diversification of alpine
 species. To examine this problem, we test patterns of genetic and
 phenotypic divergence in two co-distributed species complexes of
 flightless alpine ground beetles. Greater differentiation in
 ecologically-important functional traits would indicate that ecological
 selection is an outcome of oscillating climate change, whereas greater
 differentiation in non-ecological traits would indicate niche
 conservatism. Location The Cascades Range and Trinity Mountains of western
 North America. Taxon Members of the Nebria paradisi and N. vandykei
 species complexes (Insecta: Coleoptera: Carabidae: Nebriinae) Methods We
 generated genome-wide single nucleotide polymorphism data and
 mitochondrial sequence data, as well as morphological and physiological
 data, to compare populations spanning the range of both species.
 Phylogenetic and population genetic analyses were used to infer the
 relationships among taxa and populations within each species complex, as
 well as historical population demography. Support vector machines were
 used to test for classification of taxa and populations based on
 ecomorphological, ecophysiological, and male reproductive traits. Mantel
 tests were then used to assess statistical associations between phenotypic
 and genetic divergence among populations. Results The N. vandykei and N.
 paradisi species complexes are each comprised of genetically distinctive
 populations exhibiting long-term demographic declines. Each phylogeny
 supports multiple monophyletic groups with geographical cohesion. By
 examining phenotypic traits among populations in both species’ complexes,
 we show that reproductive trait divergence can discriminate species and
 population status more effectively than ecomorphological or
 ecophysiological traits. Reproductive and genetic divergence are
 significantly correlated in the N. vandykei species complex. Main
 Conclusions We found limited evidence of ecological selection acting on
 functional traits. Instead, reproductive and genetic divergence evolved
 among isolated populations in both species complexes, suggesting niche
 conservatism may be a common outcome in alpine species diversification.
DOI: 10.5061/dryad.02v6wwq3s
title: Optimal Stopover Model: a state dependent habitat selection model for staging passerines during migration

description: 1. During their seasonal migration, birds stage in areas comprising
 stopover sites of varying quality. Given that migrating birds have a
 limited information about their environments, they may land at a
 low-quality stopover site in which their fuel deposition rate (FDR) is
 low. Birds landing at such sites, should decide either to extend their
 stopover duration or to quickly depart in search for a better site. These
 decisions, however, strongly depend on their body condition upon landing.
 2. To understand the decision-making process of passerines within a
 stopover area, comprising stopover sites of varying quality, prior to the
 crossing of a large ecological barrier, we constructed a state-dependent
 habitat selection model. The model assumes that even if migrating birds
 have an expectation of encountered area quality, they cannot control for
 their initial landing site. Once landing, movement between a low to high
 quality stopover site will occur only if the body condition of these birds
 is high to the extent that they can entail the energetic cost of movement.
 Birds in the model aim to maximize their fuel load at the end of the
 stopover period, to suffice for successfully crossing a large ecological
 barrier. 3. The model is based on empirical data on autumn migrating
 Blackcaps (Sylvia atricapilla), collected at two important stopover sites
 in the Negev desert of Israel. Migrating passerines staging at these two
 sites differ in their fuel deposition rate and body condition. The model
 shows that the optimal behavior when arriving at a low-quality stopover
 site is to abandon it quickly. However, as lean individuals cannot entail
 the costs of searching for an alternative site, they have no other choice
 but to stay there even if their chances to successfully cross the Sahara
 Desert ahead are low. 4. Our model can be applied to other ecological
 systems. Proper use of this model may allow good assessment of stopover
 site quality, as indicated by the bird’s fuel deposition rate, regardless
 of specific site characteristics. Hence it can help applying targeted
 management decisions regarding the maintenance of stopover sites or
 establishment of new ones.
DOI: 10.5061/dryad.pzgmsbcmw
title: Amaranthus palmeri EPSPS copy number and glyphosate resistance variation

description: Gene copy number variation (CNV) has been increasingly associated with
 organismal responses to environmental stress, but we know little about the
 quantitative relation between CNV and phenotypic variation. In this study
 we quantify the relation between variation in EPSPS
 (5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital
 drop PCR and variation in phenotypic glyphosate resistance in 22
 populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding
 agricultural weed. Overall, we detected a significant positive relation
 between population mean copy number and resistance. The majority of
 populations exhibited high glyphosate resistance yet maintained
 low-resistance individuals, resulting in bimodality in many populations.
 We also investigated threshold models for the relation between copy number
 and resistance, and found evidence for a threshold of ~15 EPSPS copies:
 there was a steep increase in resistance below the threshold, followed by
 a much shallower increase. Across 924 individuals, as copy number
 increases the range of variation in resistance decreases, yielding an
 increasing frequency of high phenotypic resistance individuals. Among
 populations we detected a decline in variation (s.d.) as mean phenotypic
 resistance increased from moderate to high, consistent with the prediction
 that as phenotypic resistance increases in populations, stabilizing
 selection decreases variation in the trait. Our study demonstrates that
 populations of A. palmeri can harbour wide variation in EPSPS copy number
 and phenotypic glyphosate resistance, reflecting the history of, and
 template for future, resistance evolution.
description: Phenotypic glyphosate resistance data was collected under
 experimental conditions at the University of Guelph.
 Copy number variation (CNV) of the target gene EPSPS and
 reference gene ALS were collected using digital drop PCR (BioRad QX200
 platform).
description: Please see attached ReadMe file for details on the data files and
 how they correspond to component of the paper "Defense by
 duplication: The relation between phenotypic glyphosate resistance
 and <i>EPSPS</i> gene copy number variation in
 <i>Amaranthus palmeri".</i>
DOI: 10.5061/dryad.hdr7sqvjg
title: Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard

description: Hybridization is among the evolutionary mechanisms most frequently
 hypothesized to drive the success of invasive species, in part because
 hybrids are common in invasive populations. One explanation for this
 pattern is that biological invasions coincide with a change in selection
 pressures that limit hybridization in the native range. To investigate
 this possibility, we studied the introduction of the brown anole (Anolis
 sagrei) in the southeastern United States. We find that native populations
 are highly genetically structured. In contrast, all invasive populations
 show evidence of hybridization among native-range lineages. Temporal
 sampling in the invasive range spanning 15 years showed that invasive
 genetic structure has stabilized, indicating that large-scale contemporary
 gene flow is limited among invasive populations and that hybrid ancestry
 is maintained. Additionally, our results are consistent with hybrid
 persistence in invasive populations resulting from changes in natural
 selection that occurred during invasion. Specifically, we identify a
 large-effect X chromosome locus associated with variation in limb length,
 a well-known adaptive trait in anoles, and show that this locus is often
 under selection in the native range, but rarely so in the invasive range.
 Moreover, we find that the effect size of alleles at this locus on limb
 length is much reduced in hybrids among divergent lineages, consistent
 with epistatic interactions. Thus, in the native range, epistasis
 manifested in hybrids can strengthen extrinsic post-mating isolation.
 Together, our findings show how a change in natural selection can
 contribute to an increase in hybridization in invasive populations.
description: These data were obtained from multiple populations across the
 range of A. sagrei (including Cuba, Bahamas, Florida and Southern
 Georgia), and consist of genomic and morphological data. The genomic
 data were obtained using double-digest RAD-seq. The VCF files included in
 this archive have been filtered using methods described in Bock et al.
 (2021). The scripts needed to perform these filtering steps are also
 included in the data archive. The raw reads used at the beginning of the
 analyses have been deposited on the NCBI SRA (accession numbers are given
 in Dataset S1 of Bock et al. 2021). The morphological data (also included
 in Dataset S2 of Bock et al. 2021) were obtained from X-ray images. The
 specimens used to collect these morphological data along with
 associated X-ray images have been deposited in the Herpetological
 Collection of the Harvard Museum of Comparative Zoology (MCZ; museum
 identification codes are given in Dataset S1 of Bock et al. 2021). Backup
 tail tip tissue for these specimens is maintained in the cryogenic
 collection at MCZ.