cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0p6bj53
title: Data from: Habitat preference differentiates the Holocene range dynamics but not barrier effects on two sympatric, congeneric trees (Tristaniopsis, Myrtaceae).

description: Niche partitioning can lead to differences in the range dynamics of plant
 species through its impacts on habitat availability, dispersal, or
 selection for traits that affect colonization and persistence. We
 investigated whether niche partitioning into upland and riparian habitats
 differentiates the range dynamics of two closely related and sympatric
 eastern Australian trees: the mountain water gum (Tristaniopsis collina)
 and the water gum (T. laurina). Using genomic data from SNP genotyping of
 480 samples, we assessed the impact of biogeographic barriers and tested
 for signals of range expansion. Circuit theory was used to model
 isolation-by-resistance across three palaeo-environment scenarios: the
 Last Glacial Maximum, the Holocene Climate Optimum and present-day
 (1950-2014). Both trees showed similar genetic structure across
 historically dry barriers, despite evidence of significant environmental
 niche differentiation and different post-glacial habitat shifts.
 Tristaniopsis collina exhibits the signature of serial founder effects
 consistent with recent or rapid range expansion, whilst T. laurina has
 genetic patterns consistent with long-term persistence in geographically
 isolated populations despite occupying a broader bioclimatic niche. We
 found the minor influence of isolation-by-resistance on both species,
 though other unknown factors appear to shape genetic variation. We
 postulate that specialized recruitment traits (adapted to
 flood-disturbance regimes) rather than habitat availability limited
 post-glacial range expansion in T. laurina. Our findings indicate that
 niche breadth does not always facilitate range expansion through
 colonization and migration across barriers, though it can promote
 long-term persistence in situ.
description: SNP dataset for
 georeferenced samples of Tristaniopsis collina, T.
 laurinaSingle line SNP markers
 (0,1,2) for 238 samples of Tristaniopsis collina and 301 T. laurina
 samples collected in the field. SNP calling performed by Diversity Arrays
 Technology, Canberra. See website for details
 (https://www.diversityarrays.com/). Geolocation data for samples in
 separate files.Tristaniopsis-raw-data.zip
DOI: 10.5281/zenodo.18262138
title: Data supporting "Does the public value ecosystem services secured by pine savanna restoration and bobwhite management on private lands?", published in Forest Policy and Economics

description: Data supporting: Nimlos N.M., Pienaar E.F., Martin J.A. (2026) Does the public value ecosystem services secured by pine savanna restoration and bobwhite management on private lands? Forest Policy and Economics, 184: 103711. https://doi.org/10.1016/j.forpol.2026.103711
DOI: 10.5281/zenodo.18262137
title: Data supporting "Does the public value ecosystem services secured by pine savanna restoration and bobwhite management on private lands?", published in Forest Policy and Economics

description: Data supporting: Nimlos N.M., Pienaar E.F., Martin J.A. (2026) Does the public value ecosystem services secured by pine savanna restoration and bobwhite management on private lands? Forest Policy and Economics, 184: 103711. https://doi.org/10.1016/j.forpol.2026.103711
DOI: 10.5061/dryad.j3t420p
title: Data from: Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

description: The estimation of origination and extinction rates and their temporal
 variation is central to understanding diversity patterns and the
 evolutionary history of clades. The fossil record provides the only direct
 evidence of extinction and biodiversity changes through time and has long
 been used to infer the dynamics of diversity changes in deep time. The
 software PyRate implements a Bayesian framework to analyze fossil
 occurrence data to estimate the rates of preservation, origination and
 extinction while incorporating several sources of uncertainty. Building
 upon this framework, we present a suite of methodological advances
 including more complex and realistic models of preservation and the first
 likelihood-based test to compare the fit across different models. Further,
 we develop a new reversible jump Markov chain Monte Carlo algorithm to
 estimate origination and extinction rates and their temporal variation,
 which provides more reliable results and includes an explicit estimation
 of the number and temporal placement of statistically significant rate
 changes. Finally, we implement a new C++ library which speeds up the
 analyses by orders of magnitude, therefore facilitating the application of
 PyRate to large datasets. We demonstrate the new functionalities through
 extensive simulations and with the analysis of a large dataset of Cenozoic
 marine mammals. We compare our analytical framework against two
 alternative methods to infer origination and extinction rates revealing
 that PyRate decisively outperforms them across a range of simulated
 datasets. Our analyses indicate that explicit statistical model testing,
 which is often neglected in fossil-based macroevolutionary analyses, is
 crucial to obtain accurate and robust results.
description: Empirical_dataFossil dataset and input files to reproduce the analysis of marine mammals shown in the paperSilvestro_et_al_2019_Paleobiology_SISupporting information, including analysis protocol to reproduce empirical results, supplementary tables and figures.
DOI: 10.5061/dryad.r901kb6
title: Data from: Loss of functional connectivity in migration networks induces population decline in migratory birds

description: Migratory birds rely on a habitat network along their migration routes by
 temporarily occupying stopover sites between breeding and non-breeding
 grounds. Removal or degradation of stopover sites in a network might
 impede movement, and thereby reduce migration success and survival. The
 extent to which the breakdown of migration networks, due to changes in
 land use, impacts the population sizes of migratory birds is poorly
 understood. We measured the functional connectivity of migration networks
 of waterfowl species that migrate over the East Asian-Australasian Flyway
 from 1992-2015. We analysed the relationship between changes in
 non-breeding population sizes and changes in functional connectivity,
 while taking into account other commonly-considered species traits, using
 a Phylogenetic Linear Mixed Model. We found that population sizes
 significantly declined with a reduction in the functional connectivity of
 migration networks; no other predictor variables were important. We
 conclude that the current decrease in functional connectivity, due to
 habitat loss and degradation in migration networks, can negatively and
 crucially impact population sizes of migratory birds. Our findings provide
 new insights into the underlying mechanisms that affect population trends
 of migratory birds under environmental changes. Establishment of
 international agreements leading to the creation of systematic
 conservation networks associated with migratory species’ distributions and
 stopover sites may safeguard migratory bird populations.
description: Population trends of the
 study speciesSpecies names are
 abbreviated: ts - tundra swan (Cygnus columbianus); sg - swan goose (Anser
 cygnoid); bg - bean goose (Anser fabalis); gwfg - greater white-fronted
 goose (Anser albifrons); lwfg - lesser white-fronted goose (Anser
 erythropus); glg - greylag goose (Anser anser); ct - common teal (Anas
 crecca); np - northern pintail (Anas acuta).yearlypop.csvChanges in functional connectivityCFC is changes in functional connectivity. The unit for the data is square kilometre (sqkm). Species names are abbreviated: ts - tundra swan (Cygnus columbianus); sg - swan goose (Anser cygnoid); bg - bean goose (Anser fabalis); gwfg - greater white-fronted goose (Anser albifrons); lwfg - lesser white-fronted goose (Anser erythropus); glg - greylag goose (Anser anser); ct - common teal (Anas crecca); np - northern pintail (Anas acuta).connectivity.csvSpecies traitsSpecies names are abbreviated: ts - tundra swan (Cygnus columbianus); sg - swan goose (Anser cygnoid); bg - bean goose (Anser fabalis); gwfg - greater white-fronted goose (Anser albifrons); lwfg - lesser white-fronted goose (Anser erythropus); glg - greylag goose (Anser anser); ct - common teal (Anas crecca); np - northern pintail (Anas acuta).speciestraits.csv
DOI: 10.5061/dryad.s7h937n
title: Data from: Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

description: Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800
 species distributed throughout Southeast Asia and the Pacific Islands. On
 the Hawaiian Islands, 60 named species and over 89 putative hybrids exist,
 most of which are identified on the basis of morphology. Despite many
 previous studies on the Hawaiian Cyrtandra lineage, questions regarding
 the reconciliation of morphology and genetics remain, many of which can be
 attributed to the relatively young age and evidence of hybridization
 between species. We utilized targeted enrichment, high-throughput
 sequencing, and modern phylogenomics tools to test 33 Hawaiian Cyrtandra
 samples for species relationships and hybridization in the presence of
 incomplete lineage sorting (ILS). Both concatenated and species-tree
 methods were used to reconstruct species relationships, and network
 analyses were conducted to test for hybridization. We expected to see high
 levels of ILS and putative hybrids intermediate to their parent species.
 Phylogenies reconstructed from the concatenated and species-tree methods
 were highly incongruent, most likely due to high levels of incomplete
 lineage sorting. Network analyses inferred gene flow within this lineage,
 but not always between taxa that we expected. Multiple hybridizations were
 inferred, but many were on deeper branches of the island lineages
 suggesting a long history of hybridization. We demonstrated the utility of
 high-throughput sequencing and a phylogenomic approach to understanding
 species relationships and gene flow in the presence of ILS.
description: Supplementary
 DataThis supplemental zip
 folder contains: 1) Assembled sequences after Hyb-Seq enrichment, 2)
 Sequences trimmed using 0.5 occupancy, 3) Gene trees for trimmed
 sequences, 4) Gene trees with nodes collapsed if bootstrap support &lt;
 30, 5) Bootstrap trees for each gene tree, 6) RAxML output files, 7)
 ASTRAL output files, 8) Gene trees for introgression analyses on
 Kaua'i, 9) Gene trees for introgression analyses on Maui-Nui, 10)
 Gene trees for introgression analyses on O'ahu.JSE_Dryad.zip
DOI: 10.5061/dryad.5d2nv88
title: Data from: Geography best explains global patterns of genetic diversity and post-glacial co-expansion in marine turtles

description: For many species, climate oscillations drove cycles of population
 contraction during cool glacial periods followed by expansion during
 interglacials. Some groups, however, show evidence of uniform and
 synchronous expansion while others display differences in the timing and
 extent of demographic change. We compared demographic histories inferred
 from genetic data across marine turtle species to identify responses to
 post-glacial warming shared across taxa and to examine drivers of past
 demographic change at the global scale. Using coalescent simulations and
 approximate Bayesian computation (ABC), we estimated demographic
 parameters, including the likelihood of past population expansion, from a
 mitochondrial dataset encompassing 23 previously identified lineages from
 all 7 marine turtle species. For lineages with a high posterior
 probability of expansion, we conducted a hierarchical ABC analysis to
 estimate the proportion of lineages expanding synchronously and the timing
 of synchronous expansion. We used Bayesian Model Averaging to identify
 variables associated with expansion and genetic diversity. Approximately
 60% of extant marine turtle lineages showed evidence of expansion, with
 the rest mainly exhibiting patterns of genetic diversity most consistent
 with population stability. For lineages showing expansion, there was a
 strong signal of synchronous expansion after the Last Glacial Maximum.
 Expansion and genetic diversity were best explained by ocean basin and the
 degree of endemism for a given lineage. Geographic differences in
 sensitivity to climate change have implications for prioritizing
 conservation actions in marine turtles as well as for identifying areas of
 past demographic stability and potential resilience to future climate
 change for broadly distributed taxa.
description: Complete FASTA files for
 each lineage and script for subsampling filesThis ZIP file contains
 the 23 FASTA files used for each of the marine turtle lineages included in
 this study. These files include each sequence at its observed frequency
 based on the previous studies. An R script is also included that can be
 used to subsample these FASTA files to 200 sequences as done in the
 publication.marineturtle_fastas.zip
DOI: 10.5061/dryad.mq427sp
title: Data from: Male and female Rufous-and-white Wrens do not match song types with same-sex rivals during simulated territorial intrusions

description: In birds with song repertoires, song-type matching occurs when an
 individual responds to another individual’s song by producing the same
 song type. Song-type matching has been described in multiple bird species
 and a growing body of evidence suggests that song-type matching may serve
 as a conventional signal of aggression, particularly in male birds in the
 temperate zone. Few studies have investigated song-type matching in
 tropical birds or female birds, in spite of the fact that avian
 biodiversity is highest in the tropics, that female song is widespread in
 the tropics, and that female song is the ancestral state among songbirds.
 In this study of rufous-and-white wrens (Thryophilus rufalbus), a resident
 neotropical songbird where both sexes sing, we presented territorial males
 and females with playback that simulated a territorial rival producing
 shared and unshared songs. In response, both males and females sang
 matched song types at levels statistically equal to levels expected by
 chance. Furthermore, males and females exhibited similar levels of
 aggression and similar vocal behaviours in response to playback of both
 shared and unshared songs. These results indicate that rufous-and-white
 wrens do not use song-type matching in territorial conflicts as a
 conventional signal of aggression. We discuss alternative hypotheses for
 the function of song-type sharing in tropical birds. In particular, we
 point out that shared songs may play an important role in intra-pair
 communication, especially for birds where males and females combine their
 songs in vocal duets, and this may supersede the function of song-type
 matching in some tropical birds.
description: Rufous-and-white Wren
 Song Matching DataMale and female wren
 responses to playback of shared and unshared songs.RWWR Data for dryad
 Final.csv
DOI: 10.5061/dryad.r79k7sc
title: Data from: Climate‐driven shifts in the distribution of koala browse species from the Last Interglacial to the near future

description: The koala's (Phascolarctos cinereus) distribution is currently
 restricted to eastern and south‐eastern Australia. However, fossil records
 dating from 70 ± 4 ka (ka = 103 years) from south‐western Australia and
 the Nullarbor Plain are evidence of subpopulation extinctions in the
 southwest at least after the Last Interglacial (128‐116 ka). We
 hypothesize that koala sub‐population extinctions resulted from the
 eastward retraction of the koala's main browse species in response to
 unsuitable climatic conditions. We further posit a general reduction in
 the distribution of main koala‐browse trees in the near future in response
 climate change. We modelled 60 koala‐browse species and constructed a set
 of correlative species distribution models for five time periods: Last
 Interglacial (128‐116 ka), Last Glacial Maximum (~ 23‐19 ka), Mid‐Holocene
 (~ 7‐5 ka), present (interpolations of observed data, representative of
 1960‐1990), and 2070. We based our projections on five hindcasts and one
 forecast of climatic variables extracted from WorldClim based on two
 general circulation models (considering the most pessimistic scenario of
 high greenhouse‐gas emissions) and topsoil clay fraction. We used 17 dates
 of koala fossil specimens identified as reliable from 70 (± 4) to 535 (±
 49) ka, with the last appearance of koalas at 151 ka in the southwest. The
 main simulated koala‐browse species were at their greatest modelled extent
 of suitability during the Last Glacial Maximum, with the greatest loss of
 koala habitat occurring between the Mid‐Holocene and the present. We
 predict a similar habitat loss between the present and 2070. The spatial
 patterns of habitat change support our hypothesis that koala extinctions
 in the southwest, Nullarbor Plain, and central South Australia resulted
 from the eastward retraction of the dominant koala‐browse species in
 response to long‐term climate changes. Future climate patterns will likely
 increase the extinction risk of koalas in their remaining eastern ranges.
description: Dryad_DATAclimatic_past, climatic_present, continental areas data, nonclimatic_clay data. We also provided four README files for each data.
DOI: 10.5061/dryad.k0512c7
title: Data from: Local adaptation for enhanced salt tolerance reduces non-adaptive plasticity caused by osmotic stress

description: Organisms often respond to environmental change via phenotypic plasticity,
 where an individual modulates its phenotype according to the environment.
 Highly variable or changing environments can exceed physiological limits
 and generate maladapted plastic phenotypes, which is termed non-adaptive
 plasticity. In some cases, selection may reduce the negative or disruptive
 impacts of environmental stress and produce locally adapted populations.
 Salt is an increasingly prevalent contaminant of freshwater systems and
 can induce non-adaptive plastic phenotypes for freshwater organisms like
 amphibians. Hyla cinerea is a frog species with populations inhabiting
 brackish, coastal habitats, so we use this species to test whether coastal
 populations are locally adapted to tolerate saltwater by determining how
 salt exposure during the embryonic and larval stages alters mortality and
 plastic developmental and metamorphic phenotypes of coastal and inland
 populations. Coastal frogs have higher survival, faster growth rates, and
 metamorphose sooner than inland frogs across salinities. Coastal frogs
 also metamorphose smaller (likely a consequence of earlier metamorphosis)
 yet maintain constant size, while higher salinities reduce metamorphic
 size for inland frogs. Coastal frogs evolved to minimize non-adaptive and
 disruptive impacts of saltwater during larval development and accelerate
 the larval period to reduce time spent in a stressful environment.
description: Albecker&McCoy2019_DataFile1This file contains information for survivorship, time to metamorphosis, and size at metamorphosis.mortality2017.xlsxTad_Growth_origThis data file contains the weekly growth measurements.Analyses_Evolution_AlbeckerMcCoy2019Code used to analyze data
DOI: 10.5061/dryad.rb0qk13
title: Data from: Cold adaptation in the Asian tiger mosquito’s native range precedes its invasion success in temperate regions

description: Adaptation to environmental conditions within the native range of exotic
 species can condition the invasion success of these species outside their
 range. The striking success of the Asian tiger mosquito, Aedes albopictus,
 to invade temperate regions has been attributed to the winter survival of
 diapause eggs in cold environments. In this study, we evaluate genetic
 polymorphisms (SNPs) and wing morphometric variation among three
 biogeographical regions of the native range of A. albopictus.
 Reconstructed demographic histories of populations show an initial
 expansion in Southeast Asia and suggest that marine regression during late
 Pleistocene and climate warming after the last glacial period favored
 expansion of populations in southern and northern regions respectively.
 Searching for genomic signatures of selection, we identified significantly
 differentiated SNPs among which several are located in or within 20kb
 distance from candidate genes for cold adaptation. These genes involve
 cellular and metabolic processes and several of them have been shown to be
 differentially expressed under diapausing conditions. The three
 biogeographical regions also differ for wing size and shape, and wing size
 increases with latitude supporting Bergmann’s rule. Adaptive genetic and
 morphometric variation observed along the climatic gradient of A.
 albopictus native range suggests that colonization of northern latitudes
 promoted adaptation to cold environments prior to its worldwide invasion.
description: ddRADseq SNP dataset
 used for genetic analysesThe dataset comprises
 36,512 SPNs (imputed genotypes). The SFS for each population was estimated
 from the 36,512 SNPs after removing monomorphic loci. Removing minor
 allele count results in 10,483 SNPs (detection of selection). The position
 (CHROM), loci (LOCI ID), position (POS), reference allele (REF) and
 alternative allele (ALT) are given for each SNP. The genotypes are encoded
 as 0: homozygote REF; 1: heterozygote; 2: homozygote ALT. This dataset was
 obtained from double digest restriction associated DNA sequencing
 (ddRADseq). Genomic data have been published in Sherpa et al. 2019,
 Molecular Ecology, DOI: 10.1111/mec.15071. The raw sequences analyzed in
 the study are available in the European Nucleotide Archive repository
 (http://www.ebi.ac.uk/ena), and accessible under study accession number
 PRJEB31109.ddRADseq_SNP_dataset.xlsxWing geometric morphometrics dataMorphometric data in the form of the coordinates of the 20 morphometric landmarks (LM) for each used individual. Shape: Procruste coordinates with coordinates 1 and 2 for each LM. CS: centroid size (in mm). Digitalized pictures of wings are freely available upon request from S. Sherpa.Wing_geometric_morphometrics_data.xlsxEuropean Nucleotide Archive (ENA) study PRJEB31109