cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1fp853q
title: Data from: Functional trait evolution in Sphagnum peat mosses and its relationship to niche construction

description: Species in the genus Sphagnum create, maintain, and dominate boreal
 peatlands through ‘extended phenotypes’ that allow these organisms to
 engineer peatland ecosystems and thereby impact global biogeochemical
 cycles. One such phenotype is the production of peat, or incompletely
 decomposed biomass, that accumulates when rates of growth exceed
 decomposition. Interspecific variation in peat production is thought to be
 responsible for the establishment and maintenance of ecological gradients,
 such as the microtopographic hummock-hollow gradient, along which
 sympatric species sort within communities. This study investigated the
 mode and tempo of functional trait evolution across 15 species of Sphagnum
 using data from the most extensive studies of Sphagnum functional traits
 to date and phylogenetic comparative methods. We found evidence for
 phylogenetic conservatism of the niche descriptor height-above-water-table
 and of traits related to growth, decay, and litter quality. However, we
 fail to detect the influence of phylogeny on interspecific variation in
 other traits such as shoot density and suggest that environmental context
 can obscure phylogenetic signal. Trait correlations indicate possible
 adaptive syndromes that may relate niche and its construction. This study
 is the first to formally test the extent to which functional trait
 variation among Sphagnum species is a result of shared evolutionary
 history.
description: BEAST2 Configuration
 FileAn XML file used in
 BEAST2 to infer phylogenetic relationships. The file contains the DNA
 sequence alignment, data partitions, and parameter information used for
 BEAST2 analyses.Piatkowski&Shaw_2019_BEAST2_configuration.xmlMaximum clade credibility treeThe maximum clade credibility tree used for phylogenetic analyses in Nexus format. The TreeAnnotator package within the BEAST2 toolkit was used to summarize the posterior tree distribution with median node heights.Piatkowski&Shaw_2019_MCC_Tree.nexTrees from Bayesian posterior distributionA set of 1,000 trees randomly drawn from the concatenated posterior distribution of three independent BEAST2 runs after 10% burn-in.Piatkowski&Shaw_2019_1K_Posterior_Trees.nex
DOI: 10.5061/dryad.h825302
title: Data from: Re-imagining maize inbred potential: identifying breeding crosses using genetic variance of simulated progeny

description: Proper choice of parents for breeding populations is essential in
 developing new maize (Zea mays L.) inbreds for improved hybrid
 performance. Breeders have frequently chosen parental combinations based
 on mid-parent (MP) value, or predicted progeny mean, to combine favorable
 traits from the two parents. When two breeding populations have the same
 MP value, an accurate prediction of progeny variance may reveal which
 population has a greater potential for genetic gain. In this study we used
 available inbred genotypes and new hybrid phenotypes from 246 inbreds with
 expired Plant Variety Protection certificates and 39 historically
 important North American dent inbreds, all test crossed to Iodent inbred
 PHP02. We used the R package ‘PopVar’ to simulate bi-parental populations
 and perform genome-wide prediction to predict the progeny mean, genetic
 variance, and superior progeny mean for grain yield, grain moisture, and
 test weight within each virtual population. Breeding crosses were ranked
 based on the mean grain yield of superior progeny and correlated trait
 responses for test weight and moisture. Results show that combining
 germplasm from different proprietors in new breeding crosses can produce
 inbreds with improved performance in a hybrid test cross. The simulation
 and prediction model presented in this study may help breeders to identify
 parental pairs with the greatest potential for genetic gain in hybrid crop
 breeding programs.
description: Geno_allGenotype data for this publication.Parent_keyKey to identify the inbred name from parental designation in the genotype file.PhenoPhenotypic data for ex-PVP inbreds testcrossed to three testers. Statistical analysis was done as described in the publication.
DOI: 10.5061/dryad.qp59ck8
title: Data from: Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow

description: A lack of optimal gene combinations, as well as low levels of genetic
 diversity are often associated with the formation of species range
 margins. Conservation efforts rely on predictive modelling using abiotic
 variables and assessments of genetic diversity to determine target species
 and populations for controlled breeding, germplasm conservation and
 assisted migration. Biotic factors such as interspecific competition and
 hybridization, however, are largely ignored, despite their prevalence
 across diverse taxa and their role as key evolutionary forces.
 Hybridization between species with well developed barriers to reproductive
 isolation often results in the production of offspring with lower fitness.
 Generation of novel allelic combinations through hybridization, however,
 can also generate positive fitness consequences. Despite this possibility,
 hybridization-mediated introgression is often considered a threat to
 biodiversity because it can blur species boundaries. The contribution of
 hybridization towards increasing genetic diversity of populations at range
 margins has only recently gathered attention in conservation studies. We
 assessed the extent to which hybridization contributes towards range
 dynamics by tracking spatio-temporal changes in the central location of a
 hybrid zone between two recently diverged species of pines: Pinus
 strobiformis and P. flexilis. By comparing geographic cline centre
 estimates for global admixture coefficient with morphological traits
 associated with reproductive output we demonstrate a northward shift in
 the hybrid zone. Using a combination of spatially explicit,
 individual-based simulations and linkage disequilibrium variance
 partitioning we note a significant contribution of adaptive introgression
 towards this northward movement, despite the potential for differences in
 regional population size to aid hybrid zone movement. Overall, our study
 demonstrates that hybridization between recently diverged species can
 increase genetic diversity and generate novel allelic combinations. These
 novel combinations may allow range margin populations to track favourable
 climatic conditions or facilitate adaptive evolution to on-going and
 future climate change.
description: Sims.tar
DOI: 10.5061/dryad.n3s0p79
title: Data from: Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China

description: The origin and evolution of polyploid organisms have been extensively
 studied in plants, but this topic remains only partially understood in
 vertebrates, where polyploidy is relatively rare. In this study, we used
 Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in
 nature, as a model animal to improve our understanding of biogeographic
 history and evolution of polyploid vertebrates. After collecting samples
 from different geographical populations in China, their ploidy levels were
 determined using flow cytometry. Two mitochondrial markers (cytb and CR)
 were then used for phylogeographic analyses to unravel the possible
 origins of diploids and tetraploids in China. The results showed that
 different ploidy specimens were not evenly distributed: diploids had wider
 geographic distribution than tetraploids and triploids. There was no clear
 allopatric geographical range or boundary to divide diploid and polyploid
 populations. Rather, the analysis of mtDNA sequences indicated that
 tetraploids were autopolyploids, with lower genetic diversity than
 diploids. The results suggest that tetraploids originated from sympatric
 diploids via multiple polyploidization events. The genetic structure
 showed similar patterns between diploids and tetraploids, whereas complex
 genetic differentiation was found among regions. The potential origin of
 M. anguillicaudatus was deduced to be in the Pearl River basin, which
 exhibited the highest nucleotide diversity and genetic differentiation.
 These findings provide insights into the evolution of polyploidy in
 vertebrates.
description: Misgurnus
 anguillicaudatus CR and cytbThe partial sequences of
 CR (control region) an cyt b (cytochrome b) of Misgurnus anguillicaudatus
 collected in the field of major seven rivers in China. All nucleotide
 sequences were initially aligned using CLUSTALW implemented in MEGA
 6.0.Misgurnus anguillicaudatus CR
 cytb.fas
DOI: 10.5061/dryad.rj2gf5j
title: Data from: Spatiotemporal variations of vegetation and its determinants in the National Key Ecological Function Area on Loess Plateau between 2000 and 2015

description: China defined twenty-five National Key Ecological Function Areas in 2010,
 and adopted various measures to support ecosystem restoration in these
 areas. During the process of environment policymaking, it is important to
 observe the variation of vegetation and its driving factors. In this
 paper, we chose the National Key Ecological Function Area (NKEFA) on Loess
 Plateau as the study area. Based on MODIS-NDVI data between 2000 and 2015,
 the trend analysis was used to depict the change of NDVI and the stepwise
 regression analysis method was used to quantitatively assess its
 determinants. The results show that: (1) The vegetation coverage in study
 area was low in the northwest and high in the southeast, corresponding to
 the distribution of precipitation and temperature. (2) NDVI in the growing
 season increased remarkably from 0.2841 in 2000 to 0.4199 in 2015 with a
 linear tendency of 0.085/10a. 71.22% of the study area experienced an
 extremely significant increasing of NDVI, while only 0.03% of the total
 area suffered from significant decreasing of NDVI. (3) Compared to
 climatic factors, ecosystem conservation policies and labor transfer
 contributed more to the vegetation changes in the study area. In order to
 ensure ecological security and sustainable development in these areas, it
 is necessary to maintain the continuity of ecological compensation policy.
 Moreover, developing targeted eco-compensation policies and encouraging
 farmers to participate in non-farm employment are effective ways to reach
 a win-win outcome of reducing the ecosystem pressure and improving the
 welfare of rural households.
description: Raw data for Hao et al.,
 Ecology and EvolutionRaw data for Hao et al.,
 Ecology and evolution. File includes two data tables describing vegetation
 cover, temperature and precipitation change. Other figures have also been
 put in the data file.ECE-2018-09-01072.zip
DOI: 10.5061/dryad.2gm8348
title: Data from: The use of cattle Bos taurus for restoring and maintaining holarctic landscapes: conclusions from a long-term study (1946-2017) in northern England

description: Cattle Bos taurus can perform valuable ecological functions in the
 maintenance of high nature value (HNV) pastoral systems. They have also
 attracted attention as potentially filling the ecological niches of
 megaherbivores, notably the extinct aurochs Bos primigenius, in rewilding
 initiatives. Native cattle breeds are recognized under the 1992 Rio
 Convention as components of biodiversity. They are used in HNV settings,
 but their conservation as breeds has rarely been an important
 consideration for their management in these contexts. The Chillingham herd
 has been kept under minimal management in Chillingham Park (northern
 England) for several centuries. Chillingham Park is not a rewilding
 scenario, but the long‐term study of the cattle can be informative for the
 design of rewilding schemes that involve cattle as megaherbivores. The
 pastures of the park are species‐rich seminatural grasslands. To 2004,
 pasture management was influenced by the need to provide herbage for a
 flock of sheep that was under separate ownership, as well as for the
 cattle. Surveys of the vegetation conducted in 1979 and 2006–2008 showed a
 decline of plant species richness (species per 100 m2 quadrat) from 33.8
 in 1979 to 22.6 in 2006–2008. This was acceptable as the conservation
 priority has always been the cattle herd. With removal of the sheep from
 2004, it became possible to include recovery of plant diversity as a
 management goal. In 2017, the cattle numbered 111 (64 in 1979). Plant
 species richness in 2017 had increased to 26.3 species per quadrat. It has
 therefore been possible at Chillingham both to conserve the cattle herd
 and to improve plant diversity. While providing basic information of
 relevance to the management of cattle in free‐ranging situations, this
 study also suggests a general principle, that the management of pastoral
 landscapes by native breeds of cattle, can deliver multiple conservation
 benefits.
description: Chillers total veg
 archive revised 2017Plant species
 occurrenceChillers veg archive
 1979-2006-2007-2008
DOI: 10.5061/dryad.4rn1q84
title: Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences

description: The timing and tempo of the processes involved in community assembly are
 of substantial concern to community ecologists and conservation managers.
 The fossil record is a valuable source of data for studying past changes
 in community composition, but it is not always detailed enough to allow
 the process of community assembly to be resolved at regional or site
 scales while tracing the trajectories of known species with associated
 known traits. We present a three‐step framework for studying present‐day
 species accumulation through time: DNA sampling from multiple individuals
 from multiple species within a community; estimates of coalescence times
 for each species using molecular dating methods; and plotting the
 accumulation of present‐day species through time using the inferred
 population ages. Our approach is illustrated using whole chloroplast
 genomes from plants from three rainforest communities in eastern
 Australia. Expected times to coalescence for multiple species in each
 community were inferred from pooled high‐throughput sequence libraries.
 Local assemblage accumulation curves for each community were constructed.
 We also explored the variation in assemblage accumulation curves of
 species with different functional traits. Models of equilibrium species
 richness informed our null hypothesis and largely explained the shape of
 the assemblage accumulation curves and indicated that the complexities of
 the accumulation process should be explored with additional parameters,
 for example allowing species classes with different extinction rates. The
 assemblage accumulation curves for the study sites showed evidence of
 recent population expansions within each of the communities. This signal
 of recent accumulation is consistent with the increase in suitable
 rainforest habitat that followed the Last Glacial Maximum. Our method of
 constructing assemblage accumulation curves provides a simple approach for
 visualizing species‐accumulation data. It can be used to test hypotheses
 such as the relative survival potential of species‐specific ecological
 attributes. Although our example used single‐nucleotide polymorphisms
 derived from whole‐chloroplast sequencing, this framework can be applied
 to mitochondrial genomes and to communities of other organisms.
description: AAC_branchrate
 estimate_chloroplast168A fasta files containing
 concatenated chloroplast genesestimatingtimetocoalescenceAn .xlsx file containing the data and calculations used for building the AAC curves presented in the mansucriptsimulationsSeveral files containing code and data for simulations for assemblage accumulation curves. readme file included in the zip folder
DOI: 10.5061/dryad.rc7bh42
title: Data from: Plant competition as a mechanism of invasion on islands: revisiting the conclusions of Kuebbing and Nuñez (2016)

description: Identifying the mechanisms underlying invasive plant establishment and
 native plant decline remains a central goal in ecology, particularly for
 biodiversity hotspots such as islands. We re-analyzed a previously
 published meta-dataset to test the prediction that neighbor effects are
 stronger on islands vs. continents because island plants are weaker
 competitors. Although we detected marginally stronger neighbor effects on
 islands than continents, this was due, at least in part, to stronger
 competition among native species. An absence of studies testing neighbor
 effects between native vs. invasive plants on islands prevents a rigorous
 test for competition effects on islands, highlighting an important
 knowledge gap.
description: Barton_Wong_Island_CompetitionEffect size data for neighbor effect sizes from islands.
DOI: 10.5061/dryad.dg70f0j
title: Data from: Rate of inter-sex interactions affects injury likelihood in Tasmanian devil contact networks

description: Identifying the types of contacts that result in disease transmission is
 important for accurately modelling and predicting transmission dynamics
 and disease spread in wild populations. We investigated contacts within a
 population of adult Tasmanian devils (Sarcophilus harrisii) over a
 six-month period and tested whether individual-level contact patterns were
 correlated with accumulation of bite wounds. Bite wounds are important in
 the spread of devil facial tumour disease (DFTD), a clonal cancer cell
 line transmitted through direct inoculation of tumour cells when
 susceptible and infected individuals bite each other. We used multi-model
 inference and network autocorrelation models to investigate the effects of
 individual-level contact patterns, identities of interacting partners, and
 position within the social network on the propensity to be involved in
 bite-inducing contacts. We found that males were more likely to receive
 potentially disease-transmitting bite wounds than females, particularly
 during the mating season when males spend extended periods mate-guarding
 females. The number of bite wounds individuals received during the mating
 season was unrelated to any of the network metrics examined. Our approach
 illustrates the necessity for understanding which contact types spread
 disease in different systems to assist the management of this and other
 infectious wildlife diseases.
description: Tasmanian devil
 interactionsRates of interactions of
 an adult population of Tasmanian devils collected over a 6 month period in
 2015.ArthurRiver_data_2015.csv
DOI: 10.5061/dryad.k2t648q
title: Data from: Sex- and tissue-specific differences in telomere length in a reptile

description: The usage of telomere length (TL) in blood as a proxy for the TL of other
 tissues relies on the assumption that telomere dynamics across all tissues
 are similar. However, telomere attrition can be caused by reactive oxygen
 species (ROS) which may vary with metabolic rate, which itself varies
 across organs depending upon the life history strategy of an organism.
 Thus we chose to measure the telomeres of various cell types in juvenile
 painted dragon lizards, Ctenophorus pictus, given their unusual life
 history strategy. Individuals typically only experience a single mating
 season. We measured the TL of male and female dragons using qPCR and
 observed that TL varied with tissue type and sex. Telomeres of blood cells
 were longer than those of liver, heart, brain, and spleen, and females had
 longer telomeres than males. Brain telomeres in males were approximately
 half the length of those in females. Telomeric attrition in the male brain
 may be due to the need for rapid learning of reproductive tactics
 (territory patrol and defence, mate-finding). Significant correlations
 between the TL of tissue types suggest that blood TL may be a useful proxy
 for the TL of other tissues. Our comparison of organ-specific telomere
 dynamics, the first in a reptile, suggests that the usage of blood TL as a
 proxy requires careful consideration of the life history strategy of the
 organism.
description: Egg, morphometric and
 telomeric data for all Ctenophorus pictus individualsData of lab hatched and
 raised painted dragons, generated in Excel. ID refers to individual
 hatchlings used in the experiment, SVL = snout-vent length, TL = total
 length, RelTel = relative telomere length, telb = telomere primers, 18S =
 reference gene, run no refers to the qpcr run number the samples were
 amplified indryad
 data.xlsx
DOI: 10.5061/dryad.s88fv55
title: Data from: Juvenile plumage whiteness is associated with the evolution of clutch size in passerines

description: The offspring of many animals are conspicuous during parental dependence,
 despite juveniles generally suffering from high predation risk. However,
 to date, it is unclear whether offspring structural ornaments play a role
 in intra-family communication. This is the case of conspicuous plumage in
 young birds, which is worn unchanged during a long period after fledging,
 when they still depend on their parents. If plumage color facilitates
 intra-family interactions, its role should be more important in
 large-brooded species, where the strength of intra-family conflict is
 potentially stronger. We therefore performed a comparative study in 210
 passerine bird species to test whether an offspring structural trait,
 white plumage, evolves more frequently in lineages with larger clutches.
 We also explored the number of broods raised per year as another source of
 intra-family conflict. First, we found that juvenile whiteness was more
 frequent in open-nesting species. Moreover, in agreement with our
 prediction, the presence of juvenile white tail/wing patches was strongly
 and positively associated with clutch size. This relationship was not due
 to the strong resemblance between offspring and adult plumage, which was
 controlled for in the statistical analyses. Moreover, the association
 remained significant after taking into account predation risk, for which
 there was information for a subset of species. In contrast, juvenile
 whiteness was not associated with the number of broods raised per year.
 These results may suggest that the evolution of juvenile conspicuousness
 is favored in species with potentially stronger intra-brood sibling
 conflict.
description: Table
 S1The
 table includes data of juvenile whiteness (ventral and tail/wing
 whiteness), average clutch size, the species body mass, the number of
 broods and predation rate.treesThis file includes 100
 trees downloaded from Birdtree.org for the 210 bird species used in the
 main analyses.
DOI: 10.15468/dl.bwapp7
title: Occurrence Download

description: A dataset containing 82038 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Procambarus clarkii"
 ]
}

 The dataset includes 82038 records from 551 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001630-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.