cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397729
title: Data from: A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree height measurements through ages 3–40 years permitted the testing of GS methods temporally. The genotyping-by-sequencing (GBS) platform was used for single nucleotide polymorphism (SNP) discovery in conjunction with three unordered imputation methods applied to a data set with 60% missing information. Further, three diverse GS models were evaluated based on predictive accuracy (PA), and their marker effects. Moderate levels of PA (0.31–0.55) were observed and were of sufficient capacity to deliver improved selection response over TS. Additionally, PA varied substantially through time accordingly with spatial competition among trees. As expected, temporal PA was well correlated with age-age genetic correlation (r=0.99), and decreased substantially with increasing difference in age between the training and validation populations (0.04–0.47). Moreover, our imputation comparisons indicate that k-nearest neighbor and singular value decomposition yielded a greater number of SNPs and gave higher predictive accuracies than imputing with the mean. Furthermore, the ridge regression (rrBLUP) and BayesCπ (BCπ) models both yielded equal, and better PA than the generalized ridge regression heteroscedastic effect model for the traits evaluated.
DOI: 10.14288/1.0397730
title: Data from: The origin and evolution of phototropins

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent duplications in most major land-plant lineages (mosses, lycophytes, ferns, and seed plants), but remained single-copy genes in liverworts and hornworts—an evolutionary pattern shared with another family of photoreceptors, the phytochromes. Following each major duplication event, the phototropins differentiated in parallel, resulting in two specialized, yet partially overlapping, functional forms that primarily mediate either low- or high-light responses. Our detailed phylogeny enables us to not only uncover new phototropin lineages, but also link our understanding of phototropin function in Arabidopsis with what is known in Adiantum and Physcomitrella (the major model organisms outside of flowering plants). We propose that the convergent functional divergences of phototropin paralogs likely contributed to the success of plants through time in adapting to habitats with diverse and heterogeneous light conditions.
DOI: 10.14288/1.0397732
title: Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906) and post-bottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n=25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón’s tortoise population has recovered through an ex situ head-start program in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old, and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples was very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (Ne) of 58 (95% CI = 50-69) for the post-bottleneck population; no pre-bottleneck Ne point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true Ne. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding program, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.
DOI: 10.14288/1.0397733
title: Data from: An experimental test of the effect of predation upon behaviour and trait correlations in threespine stickleback

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Benthic and limnetic threespine stickleback (Gasterosteus aculeatus) are a classic example of ecological speciation. Behavioural and armour divergence between these species has been predicted to be the result of divergent selection driven in part by differential predation from cutthroat trout (Oncorhynchus clarki). To experimentally test this prediction, we reared split families of benthic–limnetic hybrids in the presence or absence of trout predation. Our results show that the presence of trout had little effect upon stickleback behaviour. We then compared performance in behavioural assays among stickleback that varied in armour to test if armour morphology correlates with behaviour. Our measurements revealed trait correlations between several behaviours and components of armour morphology. Trout predation did not result in an increased correlation between traits, therefore differential trout predation between benthics and limnetics is unlikely to be the cause of these correlations. The presence of trait correlations in advanced generation hybrids suggests that pleiotropy or linkage between genes underlying behaviour and armour morphology may be greater than previously appreciated.
DOI: 10.14288/1.0397734
title: Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now-extinct North American poplar.
DOI: 10.14288/1.0397735
title: Data from: The shortfall of sociality: group-living affects hunting performance of individual social spiders

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ineffective hunters in cooperative foraging groups may be shielded from natural selection by their more effective group mates, whereas those living solitarily would starve and thus be removed from the population. The problem may be exacerbated in large groups where it may be easier for individuals to withhold participation. Group foragers may thus be ineffective individual hunters or exhibit greater inter-individual variation in hunting abilities, in particular when living in large groups. We test these hypotheses in spider species of the genus Anelosimus that differ in their level of sociality and, among social species, in colonies of different sizes. We found that individuals from the more social species, and those from larger groups, reacted more slowly to prey than those from solitary species or small groups. Individuals from these categories also had greater inter-individual variation in reaction times. Individuals from large social groups also had lower prey capture success than those from small ones. These differences may have been driven by the size of the group from which the social individuals were taken, as those from small colonies behaved similarly to individuals of the two less social species. This finding suggests that hunting ability may develop as a phenotypically plastic trait.
DOI: 10.15468/dl.dtz8s7
title: Occurrence Download

description: A dataset containing 4408 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Colección Entomológica - Museo de Historia Natural UniLlanos"
 ]
}

 The dataset includes 4408 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000460-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0397737
title: Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.
DOI: 10.14288/1.0397739
title: Data from: Reproductive success is energetically linked to foraging efficiency in Antarctic fur seals

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The efficiency with which individuals extract energy from their environment defines their survival and reproductive success, and thus their selective contribution to the population. Individuals that forage more efficiently (i.e., when energy gained exceeds energy expended) are likely to be more successful at raising viable offspring than individuals that forage less efficiently. Our goal was to test this prediction in large long-lived mammals under free-ranging conditions. To do so, we equipped 20 lactating Antarctic fur seals (Arctocephalus gazella) breeding on the Kerguelen Island in the Southern Ocean with tags that recorded GPS locations, depth and tri-axial acceleration to determine at-sea behaviours and detailed time-activity budgets during their foraging trips. We also simultaneously measured energy spent at sea using the doubly-labeled water (DLW) method, and estimated the energy acquired while foraging from 1) type and energy content of prey species present in scat remains, and 2) numbers of prey capture attempts determined from head acceleration. Finally, we followed the growth of 36 pups from birth until weaning (of which 20 were the offspring of our 20 tracked mothers), and used the relative differences in body mass of pups at weaning as an index of first year survival and thus the reproductive success of their mothers. Our results show that females with greater foraging efficiencies produced relatively bigger pups at weaning. These mothers achieved greater foraging efficiency by extracting more energy per minute of diving rather than by reducing energy expenditure. This strategy also resulted in the females spending less time diving and less time overall at sea, which allowed them to deliver higher quality milk to their pups, or allowed their pups to suckle more frequently, or both. The linkage we demonstrate between reproductive success and the quality of individuals as foragers provides an individual-based quantitative framework to investigate how changes in the availability and accessibility of prey can affect fitness of animals.
DOI: 10.14288/1.0397741
title: Data from: Making pore choices: repeated regime shifts in stomatal ratio

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Ecologically important traits do not evolve without limits. Instead, evolution is constrained by the set of available and viable phenotypes. In particular, natural selection may only favour a narrow range of adaptive optima constrained within selective regimes. Here, I integrate data with theory to test whether selection explains phenotypic constraint. A global database of 599 plant species from 94 families shows that stomatal ratio, a trait affecting photosynthesis and defence against pathogens, is highly constrained. Most plants have their stomata on the lower leaf surface (hypostomy), but species with half their stomata on each surface (amphistomy) form a distinct mode in the trait distribution. A model based on a trade-off between maximizing photosynthesis and a fitness cost of upper stomata predicts a limited number of adaptive solutions, leading to a multimodal trait distribution. Phylogenetic comparisons show that amphistomy is the most common among fast-growing species, supporting the view that CO2 diffusion is under strong selection. These results indicate that selective optima stay within a relatively stable set of selective regimes over macroevolutionary time.
DOI: 10.14288/1.0397742
title: Data from: Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge-feeding

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Rorqual whales (crown Balaenopteridae) are unique among aquatic vertebrates in their ability to lunge-feed. During a single lunge, rorquals rapidly engulf a large volume of prey-laden water at high speed, which they then filter to capture suspended prey. Engulfment biomechanics are mostly governed by the coordinated opening and closing of the mandibles at large gape angles, which differentially exposes the floor of the oral cavity to oncoming flow. Mouth area in rorquals is delimited by unfused bony mandibles that form kinetic linkages to each other and with the skull. The relative scale and morphology of these skeletal elements have profound consequences for the energetic efficiency of foraging in these gigantic predators. Here we performed a morphometric study of rorqual mandibles using a dataset derived from a survey of museum specimens. Across adult specimens of extant balaenopterids, mandibles range in size from ~1-6 m in length, and at their upper limit they represent the single largest osteological element of any vertebrate, living or extinct. Our analyses determined that rorqual mandibles exhibit positive allometry, whereby the relative size of these mandibles becomes greater with increasing body size. These robust scaling relationships allowed us to predict mandible length for fragmentary remains (e.g., incomplete and/or fossil specimens), as we demonstrated for two partial mandibles from the latest Miocene of California, U.S.A., and for mandibles from previously described fossil balaenopterids. Furthermore, we showed the allometry of mandible length to body size in extant mysticetes, which hints at fundamental developmental constraints in mysticetes despite their ecomorphologic differences in the feeding styles. Lastly, we outlined how our findings can be used to test hypotheses about the antiquity and evolution of lunge-feeding.
DOI: 10.14288/1.0397743
title: Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an approximate Bayesian computation (ABC) framework to test which scenario best fit the observed genetic data. Simulations indicated that phylogeographic and multilocus population-level sampling both could differentiate among refugial scenarios, although inferences made using mitochondrial data were less accurate when a longer coalescence time was assumed. Furthermore, all empirical genetic datasets were most consistent with expansion from a single refugium based on ABC. Our results indicate a stronger role for post-glacial range expansion, rather than isolation in allopatric refugia followed by range expansion, in structuring diversity in this species. To distinguish among complex historical scenarios, we recommend explicitly modeling the effects of range expansion and evaluating alternate refugial scenarios for wide-ranging taxa.
DOI: 10.14288/1.0397744
title: Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
DOI: 10.14288/1.0397745
title: Data from: Weak habitat isolation in a threespine stickleback (Gasterosteus spp.) species pair

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Reproductive isolation is central to the study of speciation. Multiple isolating barriers may prevent species from hybridizing, although their individual strength and the interactions between them are rarely measured. We quantified habitat isolation in a recently diverged threespine stickleback species pair (Gasterosteus aculeatus complex) and controlled for any such interactions. Using enclosures in an outdoor pond, we confirm that males of the two species strongly prefer different nesting habitats: limnetic males build nests in open habitats, whereas benthic males nest under vegetation. However, forcing males to nest in their nonpreferred habitat did not reduce the probability of spawning by females. As a result, habitat isolation between the species is estimated to be weak. We compared the strength of habitat isolation estimated in the present study with estimates of other behavioural barriers using previously published data. We discovered that, although total mating isolation between the species is strong, the contributions of differences in body size and male nuptial colour are similarly individually weak. Instead, interactions with other, undetermined species-specific traits were responsible for most of the isolation resulting from differences in body size and, in benthics, colour. This is one of the first attempts to estimate individual isolating barriers at the same time as controlling for interactions.