cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns1rn8pph
title: Mixing genetically differentiated populations successfully boosts diversity of an endangered carnivore

description: Biodiversity decline and genetic erosion are among the most challenging
 conservation issues. Genetic admixture, the mixing of two or more
 genetically differentiated populations, can increase genetic diversity of
 admixed individuals. However, genetic admixture for conservation purposes
 is rare due to concerns over outbreeding depression, loss of local
 adaptations and scepticism regarding the benefits of mixing populations.
 We used an introduced population of Tasmanian devils (Sarcophilus
 harrisii) descended from two genetically differentiated source populations
 to illustrate the benefits of genetic admixture for translocation
 programs. Devils are endangered due to an infectious cancer causing 80%
 population declines across their range since disease emergence in 1996.
 Devil populations are known to be structured on an east-west cline across
 Tasmania. As part of their conservation management, devils were introduced
 to Maria Island, Tasmania in an assisted colonisation in 2012 with
 supplementations in 2013 and 2017. Of the released individuals (N = 34),
 23 were western (13M; 10F), four were eastern (4F), and seven were of
 mixed origin (2M; 5F). The genetic composition of devils born on Maria
 Island (N = 185) was examined using 927 SNP loci. Using a reconstructed
 pedigree for each individual, we examined the proportion of founding
 origin (east, west or mixed) and used Shannon’s Diversity Index to
 quantify the evenness of founder origin. Individuals with mixed origins (N
 = 102) had higher genetic diversity than purebred individuals (N = 83),
 and increased evenness of founder origin was positively correlated with
 genetic diversity. Increased genetic diversity had no influence on
 reproductive success. For a genetically depauperate species, mixing
 individuals descended from differentiated populations, resulted in
 increased diversity in subsequent generations. This finding permits
 conservation managers to select individuals for translocation that produce
 offspring with higher genetic diversity, creating high-diversity source
 populations that can be used when augmenting other declining wild
 populations.
description: This file contains 1) the genotypes of 290 Tasmanian devils
 generated using reduced representation sequencing, 2) the founder origins
 of 185 Tasmanian devils living on an offshore island including individual
 standardised heterozygosity calculated using the GenHet package for R, 3)
 the number of offspring produced by each resident Tasmanian devil on the
 island over their lifetime, 4) a binary response as to whether each devil
 bred in a given year on the island, and 5) the number of offpsring
 produced by each devil on the island annually.
DOI: 10.5061/dryad.cz8w9gj0n
title: Winter in water: differential responses and the maintenance of biodiversity

description: The ecological consequences of winter in freshwater systems are an
 understudied but rapidly emerging research area. Here, we argue that
 winter periods of reduced temperature and light (and potentially oxygen
 and resources) could play an underappreciated role in mediating the
 coexistence of species. This may be especially true for temperate and
 subarctic lakes, where seasonal changes in the thermal environment might
 fundamentally structure species interactions. With climate change already
 shortening ice-covered periods on temperate and polar lakes, consideration
 of how winter conditions shape biotic interactions is urgently needed.
 Using freshwater fishes in northern temperate lakes as a case study, we
 demonstrate how physiological trait differences (e.g., thermal preference,
 light sensitivity) drive differential behavioral responses to winter among
 competing species. Specifically, some species have a higher capacity for
 winter activity than others. Existing and new theory is presented to argue
 that such differential responses to winter can promote species
 coexistence. Importantly, if winter is a driver of niche differences that
 weaken competition between relative to within species, then shrinking
 winter periods could threaten coexistence by tipping the scales in favor
 of certain sets of species over others.
description: Data files include those used to generate Figs. 3, 4 and
 5: Alexie Lake - telemetry (positions and means), water
 temp and light profile Lake of Two Rivers - telemetry
 (positions and means), water temp profile ELA (lakes
 373, 224) lake trout individual growth data Full details of the dataset
 collection and processing are provided in the Supplemental Information
 file associated with the publication.
DOI: 10.5061/dryad.qv9s4mwb9
title: Data from: Simulating effects of fitness and dispersal on the use of Trojan sex chromosomes for invasive species management

description: The use of Trojan Y Chromosomes (TYC) for controlling invasive species
 involves manipulating the sex chromosomes of captive-raised individuals.
 Once released, the offspring of these individuals consist of only one sex,
 thereby skewing the sex-ratio of the invasive population and potentially
 leading to eradication. Simulation models are needed that can inform
 managers on how to maximize the likelihood of species eradication, since
 implementation of this novel management approach in the field is still
 rare. Here, we present the first spatially explicit, mechanistic
 simulation model of a real-world TYC program for invasive species
 eradication. Using a brook trout (Salvelinus fontinalis) system model, we
 investigated the effects of competitive and reproductive fitness of the
 captive-raised YY males, dispersal behavior upon their release, and
 landscape heterogeneity on eradication success. Likelihood of eradication
 was dependent on both the competitive and reproductive fitness of the
 Trojan individuals. Competitive fitness (i.e., survival) had a higher
 threshold for eradication, below which populations failed to be
 eradicated. Movement ecology of both the wild and YY male populations was
 important for eradication. Under a restricted dispersal scenario for YY
 males following their release, the wild population was not extirpated but
 maintained a stable, yet reduced, population size. In terms of landscape
 configuration, time to eradication of local patches increased with greater
 connectivity within the stream network. In addition to sex ratio
 distortion, density-dependent mortality resulting from outplantings made
 an important contribution to eradication and therefore may also affect
 native competitors. While our results indicate that eradication is
 possible, maximizing its likelihood requires an understanding of the
 fitness and movement ecology of both the wild and YY male populations of
 the invasive species. Both our model and the principles derived from this
 study related to fitness and behavioral landscape ecology can be broadly
 applied to other invaded species and systems.
description: These data include inputs and outputs to the program CDMetaPOP
 version 1.40 (https://github.com/ComputationalEcologyLab/CDMetaPOP). Summary files that describe model output are also included. An additional excel file is included that details results from the connectivity measures and their relationship with patch occupancy.
description: See readme files for explanations of each data set.
DOI: 10.6086/d1nq3b
title: Subspecies differentiation in an enigmatic chaparral shrub species

description: Delimiting biodiversity units is difficult in organisms in which
 differentiation is obscured by hybridization, plasticity, and other
 factors that blur phenotypic boundaries. Such work is more complicated
 when the focal units are subspecies, the definition of which has not been
 broadly explored in the era of modern genetic methods. Eastwood manzanita
 (Arctostaphylos glandulosa Eastw.) is a widely distributed and
 morphologically complex chaparral shrub species with much subspecific
 variation that has proven challenging to categorize. Currently ten
 subspecies are recognized, however, many of them are not geographically
 segregated, and morphological intermediates are common. Subspecies
 delimitation is of particular importance in this species, as two of the
 subspecies are rare. The goal of this study was to apply an evolutionary
 definition of subspecies to characterize structure within Eastwood
 manzanita. We used publicly-available geospatial environmental
 data and reduced-representation genome sequencing to characterize
 environmental and genetic differentiation among subspecies. In addition,
 we tested whether subspecies could be differentiated by
 environmentally-associated genetic variation. Our analyses do not
 show genetic differentiation among subspecies of Eastwood manzanita, with
 the exception of one of the two rare subspecies. In addition, our
 environmental analyses did not show ecological differentiation, though
 limitations of the analysis prevent strong conclusions. Genetic
 structure within Eastwood manzanita does not correspond to current
 subspecies circumscriptions but rather reflects geographic distribution.
 Our study suggests that subspecies concepts need to be reconsidered in
 long-lived plant species, especially in the age of next generation
 sequencing.
DOI: 10.5061/dryad.p8cz8w9m6
title: Examination of sample size determination in integration studies based on the coefficient of variation (ICV)

description: Although there are various indices available for calculating morphological
 integration, the integration coefficient of variation (ICV) is most suited
 for assessing magnitudes of integration within and between morphological
 variance/covariance (V/CV) matrices. However, it is currently not known
 what the effects of varying sample sizes are on the reliable estimation of
 distributions of ICV scores. In this regard, the effects of varying sample
 size on ICV was examined by simulating parameter V/CV matrices with
 varying underlying magnitudes of average trait correlation (r2). ICV
 distributions were generated using a trait resampling protocol for various
 sample sizes (11 through 150) within various parameter r2 values. Next,
 empirical r2 values were calculated based on data from 22 skeletal
 elements of 40 Macaca fascicularis specimens to examine whether the
 results from the simulation corresponded to real biological data. Mean ICV
 scores of various sample sizes were compared using Mann-Whitney U tests to
 examine which minimum sample sizes are required to reliably calculate mean
 ICV. Mann-Whitney U test results based on the simulated data showed that a
 sample size of 51 may be sufficient even for relatively low r2 values of
 0.05. The empirical macaque data showed that 30‒40 individuals may be
 sufficient to reliably calculate mean ICV scores across skeletal elements.
 Our results correspond closely with previous assessments by Cheverud and
 colleagues that argued that a sample size of 40 is necessary to accurately
 estimate the structure of V/CV matrices.
description: Skeletal elements were scanned using a HDI-120 and a Macro R5X
 structured-light scanner (LMI technologies INC., Vancouver, Canada). 18
 wild specimens of <i>M. fascicularis</i> were from the Museum
 of Comparative Zoology at Harvard University and 22 captive specimens were
 from the Department of Anthropology of University at Buffalo, SUNY. For
 the limb bones (scapula, humerus, radius, os coxa, femur, tibia), only 35
 specimens (18 wild and 17 captive) out of total 40 specimens were
 available. The following 22 skeletal elements were quantified: cranium,
 mandible, 13 elements of the vertebral column (C1, C2, C3, C5, C7, T1, T4,
 T7, T10, T12, L1, L4, L7), sacrum, scapula, humerus, radius, os coxa,
 femur, and tibia (there were 3 specimens with T13 as the last thoracic
 vertebra, 4 specimens with L6 as the last lumbar vertebra, and 1 specimen
 with 4 sacral vertebrae). In the case of bilateral elements, the left side
 was landmarked. When the left side was damaged, the right side was
 landmarked instead. All landmarks were digitized using the software
 <i>Landmark</i> (Wiley et al. 2005) on the 3D scanned skeletal
 elements. Descriptions of the landmarking protocol for each skeletal
 element can be found in supplementary data (Supplementary Table 1-10).
 Traits were generated for each skeletal element by calculating all
 possible Euclidean distances between pairs of landmarks on each
 bone.
DOI: 10.15468/dl.257gj2
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Astragalus inversus"
 ]
}

 The dataset includes 99 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002259-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rjdfn2z79
title: Diversity and ecology of aphyllophoroid fungi on driftwood logs on the shores of the Baltic Sea

description: Driftwood is woody debris that is floating on the sea or brought onto the
 shore by the sea. It can have a natural origin but often it originates
 from human activities. Driftwood has a significant ecological role as a
 microhabitat for a large range of species. Dead-wood-associated
 aphyllophoroid fungi on driftwood have been studied rather little
 globally, and there are hardly any studies conducted in the Baltic Sea. We
 studied the diversity and ecology of polypores and corticioids growing on
 driftwood (man-made logs) on the shores of Finnish SW-archipelago. In
 total, 394 driftwood logs were surveyed for visible fungal sporocarps. We
 found altogether 145 species (1023 records) of which approximately
 three-fourths were corticioids. The driftwood logs hosted several rare and
 noteworthy species, such as one new corticioid species, 16 nationally rare
 species, and 40 new species to the region. The five most common species
 accounted for one-third of all observations, whereas 82 species (11 % of
 all records) were recorded only once or twice. Larger logs hosted, on
 average, more species compared to small-diameter logs. The mean number of
 species increased significantly when comparing the logs in the first and
 the middle stages of decay. Our results show that driftwood logs can host
 a wide variety of species and they provide an important substrate for many
 dead-wood-associated fungi, including species of conservation concern and
 species with restricted ecological requirements. Driftwood hosted several
 species that have not been previously found in the archipelago forests,
 and the logs clearly enrich the fungal diversity in the area. Our results
 encourage to increase dead wood for fungi in coastal forests where it has
 been dramatically decreased as a result of strong hemeroby.
description: This data was collected in the field work 2015-2016 in the
 Archipelago Sea, SW Finland. The survey based on sporocarp inventory and
 collected specimens were identified microscopically.
DOI: 10.5061/dryad.18931zcsw
title: Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments

description: Multipartite viruses have two or more genome segments, and package
 different segments into different particle types. Although multipartition
 is thought to have a cost for virus transmission, its benefits are not
 clear. Recent experimental work has shown that the equilibrium frequency
 of viral genome segments, the setpoint genome formula (SGF), can be
 unbalanced and host-species dependent. These observations have
 reinvigorated the hypothesis that changes in genome-segment frequencies
 can lead to changes in virus-gene expression that might be adaptive. Here
 we explore this hypothesis by developing models of bipartite virus
 infection, leading to a threefold contribution. First, we show that the
 SGF depends on the cellular multiplicity of infection (MOI), when the
 requirements for infection clash with optimizing the SGF for
 virus-particle yield per cell. Second, we find that convergence on the SGF
 is very rapid, often occurring within a few cellular rounds of infection.
 Low and intermediate MOIs lead to faster convergence on the SGF. For low
 MOIs this effect occurs because of the requirements for infection, whereas
 for intermediate MOIs this effect is also due to the high levels of
 variation generated in the genome formula. Third, we explored the
 conditions under which a bipartite virus could outcompete a monopartite
 one. As the heterogeneity between environments and specificity of
 gene-expression requirements for each environment increased, the bipartite
 virus was more likely to outcompete the monopartite virus. Under some
 conditions changes in the genome formula helped to exclude the monopartite
 competitor, highlighting the versatility of the genome formula. Our
 results show the inextricable relationship between MOI and the SGF, and
 suggest that under some conditions the cost of multipartition can be
 outweighed by its benefits for the rapid tuning of viral gene expression.
description: This submission contains all the R code used for numerical
 predictions and simulations presented in the paper. Selected simulation
 results are also included, to allow the reader quick access to results
 without having to run some of these (computationally intensive)
 scripts.
description: The R code and simulation results are organized according to the
 figures presented in the data, to help easily find the relevant
 code.
DOI: 10.6084/m9.figshare.23987826
title: Functional redundancy and dissimilarity of bacterial communities and global bacterial genomes from GTDB

description: This datasets contains files (mostly taxa-by-trait matrices) that were used for the analysis of the functional redundancy and dissimilarity of bacterial communities from freshwater (microcosms) and from bacterial genomes accessed from the Genome Taxonomy Database (GTDB). The codes used for the analysis is also shared.MAGs_KO_input_alpha.csv: taxa-by-trait matrix for alpha diversityMAGs_ab_input_alpha.csv: taxa x abundance matrix for alpha diversitypMAGs_KO_input_beta.csv:taxa-by-trait matrix for beta diversitypMAGs_ab_input_beta.csv: taxa x abundance matrix for beta diversityMAGs_KO_input_gamma.csv: taxa-by-trait matrix for regional pool diversity (122 MAGs)df_GTDB.txt: taxa-by-trait matrix of 28 714 genomes from the GDTB88_taxa_alizee_gtdb-C10_renamed.treefile: Phylogenetic tree to assess beta MNTDmodified_Rao.Rlist_fun_2025.rds : List of KOs in each functional category (R version)List_functions_2025.csv: List of KOs in each functional category (as a dataframe)Code_Part1.R: Code to explore alpha, beta and overall taxa pool functional diversityCode_Part2.R: Code to explore GTDB genomes functional diversity and comparison with the MAGs from the experimental communities.<br>
DOI: 10.6084/m9.figshare.23987826.v3
title: Functional redundancy and dissimilarity of bacterial communities and global bacterial genomes from GTDB

description: This datasets contains files (mostly taxa-by-trait matrices) that were used for the analysis of the functional redundancy and dissimilarity of bacterial communities from freshwater (microcosms) and from bacterial genomes accessed from the Genome Taxonomy Database (GTDB). The codes used for the analysis is also shared.MAGs_KO_input_alpha.csv: taxa-by-trait matrix for alpha diversityMAGs_ab_input_alpha.csv: taxa x abundance matrix for alpha diversitypMAGs_KO_input_beta.csv:taxa-by-trait matrix for beta diversitypMAGs_ab_input_beta.csv: taxa x abundance matrix for beta diversityMAGs_KO_input_gamma.csv: taxa-by-trait matrix for regional pool diversity (122 MAGs)df_GTDB.txt: taxa-by-trait matrix of 28 714 genomes from the GDTB88_taxa_alizee_gtdb-C10_renamed.treefile: Phylogenetic tree to assess beta MNTDmodified_Rao.Rlist_fun_2025.rds : List of KOs in each functional category (R version)List_functions_2025.csv: List of KOs in each functional category (as a dataframe)Code_Part1.R: Code to explore alpha, beta and overall taxa pool functional diversityCode_Part2.R: Code to explore GTDB genomes functional diversity and comparison with the MAGs from the experimental communities.<br>
DOI: 10.5061/dryad.fxpnvx0nt
title: Experimental infection of bumble bees with honey bee associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts

description: Pathogen spill-over represents an important cause of biodiversity decline.
 For wild bee species such as bumble bees, many of which are in decline,
 correlational data point toward viral spill-over from naged honey bees as
 a potential cause. Yet impacts of honey bee viruses on wild bees are
 rarely evaluated. Here, in a series of highly controlled laboratory
 infection assays with well characterised viral inocula, we show that three
 viral types isolated from honey bees (Deformed wing virus genotype A,
 Deformed wing virus genotype B and Black queen cell virus) readily
 replicate within hosts of the bumble bee Bombus terrestris. Impacts of
 these honey bee-derived viruses – either injected or fed – on the
 mortality of B. terrestris workers were, however, negligible and likely
 dependent on host condition. Our results highlight the potential threat of
 viral spill-over from honey bees to novel wild bee species, though they
 also underscore the importance of additional studies on this and other
 non- bee species under field-realistic conditions to evaluate whether
 pathogen spill-over has a negative impact on wild bee individuals and
 population fitness.
DOI: 10.6084/m9.figshare.23987826.v2
title: Functional redundancy and dissimilarity of bacterial communities and global bacterial genomes from GTDB

description: This datasets contains files (mostly taxa-by-trait matrices) that were used for the analysis of the functional redundancy and dissimilarity of bacterial communities from freshwater (microcosms) and from bacterial genomes accessed from the Genome Taxonomy Database (GTDB). The codes used for the analysis is also shared.MAGs_KO_input_alpha.csv: taxa-by-trait matrix for alpha diversityMAGs_ab_input_alpha.csv: taxa x abundance matrix for alpha diversitypMAGs_KO_input_beta.csv:taxa-by-trait matrix for beta diversitypMAGs_ab_input_beta.csv: taxa x abundance matrix for beta diversityMAGs_KO_input_gamma.csv: taxa-by-trait matrix for regional pool diversity (122 MAGs)df_GTDB.txt: taxa-by-trait matrix of 28 714 genomes from the GDTB88_taxa_alizee_gtdb-C10_renamed.treefile: Phylogenetic tree to assess beta MNTDmodified_Rao.Rlist_fun_2025.rds : List of KOs in each functional category (R version)List_functions_2025.csv: List of KOs in each functional category (as a dataframe)Code_Part1.R: Code to explore alpha, beta and regional pool functional diversityCode_Part2.R: Code to explore GTDB genomes functional diversity and comparison with the MAGs from the experimental communities.