cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397929
title: Data from: Resource selection and landscape change reveal mechanisms suppressing population recovery for the world's most endangered antelope

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Understanding how bottom-up and top-down forces affect resource selection can inform restoration efforts. With a global population size of &lt;500 individuals, the hirola Beatragus hunteri is the world's most endangered antelope, with a declining population since the 1970s. While the underlying mechanisms are unclear, some combination of habitat loss and predation are thought to be responsible for low abundances of contemporary populations. Efforts to conserve hirola are hindered by a lack of understanding as to why population density remains low, despite eradication of the viral disease, rinderpest. To elucidate factors underlying chronically low numbers, we examined resource selection and landscape change within the hirola's native range. Because hirola are grazers, we hypothesized that the availability of open areas would be linked both to forage and safety from predators. We quantified: (1) changes in tree cover across the hirola's historical range in eastern Kenya over the past 27 years; (2) how tree cover has influenced resource selection by hirola; and (3) interactions between tree cover and predation. Between 1985 and 2012, tree cover increased by 251% across the historical range of hirola. Tree encroachment was associated with a 98% decline of hirola and elephant Loxodonta africana populations, a 74% decline in cattle Bos indicus, an increase in browsing livestock by 327%, and a reduction in rainfall. Although hirola avoided tree cover, we found no evidence that predation on hirola increased with increasing tree cover. Synthesis and applications. Hirola may qualify as a refugee species, in which contemporary populations are restricted to suboptimal habitat and exhibit low survival, reproduction, or both. The extinction of hirola would be the first of a mammalian genus on the African continent in modern history. We conclude that contemporary low numbers of hirola are due at least partly to habitat loss via tree encroachment, triggered by some combination of elephant extirpation, overgrazing, drought, and perhaps fire suppression. We recommend a combination of rangeland restoration efforts (including conservation of elephants, manual clearing of trees, and grass seeding), increased enforcement of an existing protected area (Arawale National Reserve), and reintroductions to enhance recovery for this endangered species. These efforts will rely on enhanced support from the international conservation community and the cooperation of pastoralist communities with which the hirola coexist.
DOI: 10.14288/1.0397930
title: Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We used a Bayesian clustering analysis method to detect potential hybridization between glacial lineages. Results: Two highly divergent mtDNA lineages were identified in the Arctic region with distinct but overlapping geographic distributions: one in Beringia and the other over the entire Arctic Archipelago and coastal mainland east of Alaska. The microsatellite data also implied the existence of these two lineages. Evidence of hybridization was detected between the Arctic lineage and an Atlantic lineage in eastern North America. Main conclusions: Our data suggested survival and recolonization from two northern glacial refugia: one in Beringia and another in a smaller refugium, perhaps in the Arctic Archipelago itself or a separate refugium within Beringia. Patterns of hybridization detected supported the presence of a secondary contact zone between glacial lineages in the eastern Canadian Arctic.
DOI: 10.14288/1.0397932
title: Data from: Using fuzzy logic to determine the vulnerability of marine species to climate change

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Marine species are being impacted by climate change and ocean acidification, although their level of vulnerability varies due to differences in species' sensitivity, adaptive capacity and exposure to climate hazards. Due to limited data on the biological and ecological attributes of many marine species, as well as inherent uncertainties in the assessment process, climate change vulnerability assessments in the marine environment frequently focus on a limited number of taxa or geographic ranges. As climate change is already impacting marine biodiversity and fisheries, there is an urgent need to expand vulnerability assessment to cover a large number of species and areas. Here, we develop a modelling approach to synthesize data on species-specific estimates of exposure, and ecological and biological traits to undertake an assessment of vulnerability (sensitivity and adaptive capacity) and risk of impacts (combining exposure to hazards and vulnerability) of climate change (including ocean acidification) for global marine fishes and invertebrates. We use a fuzzy logic approach to accommodate the variability in data availability and uncertainties associated with inferring vulnerability levels from climate projections and species' traits. Applying the approach to estimate the relative vulnerability and risk of impacts of climate change in 1074 exploited marine species globally, we estimated their index of vulnerability and risk of impacts to be on average 52 ± 19 SD and 66 ± 11 SD, scaling from 1 to 100, with 100 being the most vulnerable and highest risk, respectively, under the ‘business-as-usual' greenhouse gas emission scenario (Representative Concentration Pathway 8.5). We identified 157 species to be highly vulnerable while 294 species are identified as being at high risk of impacts. Species that are most vulnerable tend to be large-bodied endemic species. This study suggests that the fuzzy logic framework can help estimate climate vulnerabilities and risks of exploited marine species using publicly and readily available information.
DOI: 10.14288/1.0397935
title: Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Although there is no known general explanation as to why sexual populations resist asexual invasion, previous work has shown that sexuals can outcompete asexuals in structured populations. However, it is currently unknown whether costly sex can be maintained with the weak structure that is commonly observed in nature. We investigate the conditions under which obligate sexuals resist asexual invasion in structured populations subject to recurrent mutation. We determine the level of population structure needed to disfavour asexuals, as calculated using the average Fst between all pairs of demes. We show that the critical Fst needed to maintain sex decreases as the population size increases, and approaches modest levels as observed in many natural populations. Sex is maintained with lower Fst if there are both advantageous and deleterious mutation, if mutation rates are sufficiently high, and if deleterious mutants have intermediate selective strengths, which maximises the effect of Muller's Ratchet. Additionally, the critical Fst needed to maintain sex is lower when there are a large number of subpopulations. Lower Fst values are needed to maintain sex when demes vary substantially in their pairwise distances (e.g., when arrayed along one dimension), although this effect is often modest, especially if some long-distance dispersal is present.
DOI: 10.14288/1.0397938
title: Data from: Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesised to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesised to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra-pair reproduction and male within-pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate non-zero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modelled as direct and associative genetic effects on offspring paternity respectively, in free-living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, while substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra-pair reproduction is facilitated by genetic covariance with male within-pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.
DOI: 10.14288/1.0397940
title: Data from: Spatial variation in herbivory, climate and isolation predict plant height and fruit phenotype in Plectritis congesta island populations

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Climate and herbivory can each drive natural selection on plant traits, but may interact to give rise to different patterns in trait distributions when surveyed across island populations. These different patterns may arise because the occurrence of ungulate herbivores often varies across archipelagos, potentially leading to strong and abrupt spatial heterogeneity in the direction or intensity of natural selection. In contrast, climate tends to vary gradually and thus is more likely to lead to gradual clines in trait values. Population isolation may also affect trait values, given that random genetic drift may fix alleles or traits in the absence of gene flow, or because gene flow between populations with similar or opposing selection pressures may augment or swamp the effects of selection. Here, we estimate the independent and interactive effects of deer, climate and isolation on fruit phenotype and plant height in 285 Plectritis congesta populations at 77 island and 44 mainland sites in western North America. Plectritis congesta is a palatable winter annual with two fruit phenotypes based on a simple Mendelian locus with clear dominance, and heritable variation in height as a polygenic trait. Fruit phenotype and plant height were well-predicted by deer occurrence; plants in populations with resident deer were short (15.0 ± 1.1 cm) and mainly expressed wingless fruits (73.0 ± 4.0 %), whereas plants in populations without deer were 2.6 times taller (38.9 ± 5.3 cm) and only 9.0 ± 1.6 % expressed wingless fruits. Wingless fruits were less common in populations experiencing wetter conditions with more seasonal variability in temperatures, particularly in the absence of deer. In contrast, population isolation was unrelated to fruit phenotype, except in populations rarely exposed to deer, where plants expressed phenotypes more like those in populations without deer as isolation increased. Our results are consistent with the hypothesis that spatial variation in browsing by deer, or other factors correlated with it, contributes to population-level variation in fruit phenotype and plant height in P. congesta, and that climate leads to a modest spatial gradient in plant height.
DOI: 10.15468/dl.tmkf5a
title: Occurrence Download

description: A dataset containing 4371 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección de mamíferos de la Universidad del Valle"
 ]
}

 The dataset includes 4371 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000466-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0397941
title: Data from: Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (Ne) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ~100 generations, ~2500 years) and deep (pre-Holocene, &gt;10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical Ne of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary Ne were very small (i.e., &lt; 50). On the basis of the comparison of these genetic estimates with published census size data, Ne generally represented ~0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
DOI: 10.14288/1.0397942
title: Data from: Individual dispersal decisions in a cooperative breeder: ecological constraints, the benefits of philopatry, and the social queue for dominance

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Delayed dispersal is a key step in the evolution of familial animal societies and cooperative breeding. However, no consensus has been reached on the ecological and social circumstances driving delayed dispersal. 2. Here we test predictions from the ecological constraints and benefits of philopatry hypotheses as well as the recently-proposed dual benefits hypothesis to better understand the evolution of group-living and cooperative breeding. Furthermore, we consider how individual social circumstances within groups affect dispersal decisions. 3. We examine 11 years of life-history information on a wild population of cooperatively breeding southern pied babblers (Turdoides bicolor). We investigate the effects of ecological conditions, natal-group membership and individual social context on male and female dispersal delays, disperser survival and acquisition of dominance. 4. Female dispersal decisions are generally unconstrained by ecological or social circumstances. In contrast, males disperse in response to relaxed ecological constraints, decreases in nepotistic tolerance, or when low social rank in the queue for dominance decreases their likelihood of gaining a dominant breeding position. Early dispersal by end-of-queue males often leads to a head-of-queue subordinate position in a non-natal group, thereby increasing access to dominant breeding positions. However, males and females remaining in natal groups gain benefits of philopatry via increased survival and, for head-of-queue males, very high likelihood of acquisition of a breeding position. 5. Overall, predictions from the dual benefits hypothesis best describe these results, while some predictions from each of the ecological constraints and benefits of philopatry hypotheses were supported. The benefits of living and working together (collective action benefits) in large stable groups are of central importance in shaping dispersal delays in southern pied babbler societies. In addition, position in the subordinate social queue for dominance is key in determining access to reproduction, particularly for males. This research highlights the importance of considering the costs and benefits of individual social circumstances in dispersal decisions and illustrates how the dual benefits hypothesis offers new perspectives in understanding delayed dispersal.
DOI: 10.14288/1.0397946
title: Data from: A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.
DOI: 10.14288/1.0397947
title: Data from: Urbanization drives the evolution of parallel clines in plant populations

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Urban ecosystems are an increasingly dominant feature of terrestrial landscapes. While evidence that species can adapt to urban environments is accumulating, the mechanisms through which urbanization imposes natural selection on populations are poorly understood. The identification of adaptive phenotypic changes (i.e. clines) along urbanization gradients would facilitate our understanding of the selective factors driving adaptation in cities. Here, we test for phenotypic clines in urban ecosystems by sampling the frequency of a Mendelian-inherited trait—cyanogenesis—in white clover (Trifolium repens L.) populations along urbanization gradients in four cities. Cyanogenesis protects plants from herbivores, but reduces tolerance to freezing temperatures. We found that the frequency of cyanogenic plants within populations decreased towards the urban centre in three of four cities. A field experiment indicated that spatial variation in herbivory is unlikely to explain these clines. Rather, colder minimum winter ground temperatures in urban areas compared with non-urban areas, caused by reduced snow cover in cities, may select against cyanogenesis. In the city with no cline, high snow cover might protect plants from freezing damage in the city centre. Our study suggests that populations are adapting to urbanization gradients, but regional climatic patterns may ultimately determine whether adaptation occurs.
DOI: 10.14288/1.0397948
title: Data from: Effects of gene action, marker density, and time since selection on the performance of landscape genomic scans of local adaptation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Genomic “scans” to identify loci that contribute to local adaptation are becoming increasingly common. Many methods used for such studies have assumed that local adaptation is created by loci experiencing antagonistic pleiotropy and that the selected locus itself is assayed, and few consider how signals of selection change through time. However, most empirical data sets have marker density too low to assume that a selected locus itself is assayed, researchers seldom know when selection was first imposed, and many locally adapted loci likely experience not antagonistic pleiotropy but conditional neutrality. We simulated data to evaluate how these factors affect the performance of tests for genotype-environment association. We found that three types of regression-based analyses (linear models, mixed linear models, and latent factor mixed models) and an implementation of BayEnv all performed well, with high rates of true positives and low rates of false positives, when the selected locus experienced antagonistic pleiotropy, and when the selected locus was assayed directly. However, all tests had reduced power to detect loci experiencing conditional neutrality, and the probability of detecting associations was sharply reduced when physically linked rather than causative loci were sampled. Antagonistic pleiotropy also maintained detectable genotype-environment associations much longer than conditional neutrality. Our analyses suggest that if local adaptation is often driven by loci experiencing conditional neutrality, genome-scan methods will have limited capacity to find loci responsible for local adaptation.