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5,538 results for “Population data”
Data from: Rapid divergence of mussel populations despite incomplete barriers to dispersal
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and test relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked water bodies of similar age (6,000 – 10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest Restriction-site Associated DNA sequencing), we show strong genetic structuring across populations (range FST: 0.07 – 0.24), and find limited gene flow through admixture plots. At large spatial scales (>1400km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. No signatures of isolation-by-environment were found. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which our data potentially corroborates by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of evolution-mediated priority effects in shaping divergence.
Data from: Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico
Identifying genetic connectivity and discrete population boundaries is an important objective for man- agement of declining Caribbean reef-building corals. A double digest restriction-associated DNA sequencing pro- tocol was utilized to generate 321 single nucleotide poly- morphisms to estimate patterns of horizontal and vertical gene flow in the brooding Caribbean plate coral, Agaricia lamarcki. Individual colonies (n = 59) were sampled from eight locations throughout southwestern Puerto Rico from six shallow (* 10–20 m) and two mesophotic habitats (* 30–40 m). Descriptive summary statistics (Fixation index, FST), analysis of molecular variance, and analysis through landscape and ecological associations and dis- criminant analysis of principal components estimated high population connectivity with subtle subpopulation structure among all sampling localities.
Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single-nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome-wide differentiation of the red-banded (eastern) color form from both black-banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color-pattern evolution in B. bifarius and other polymorphic bumble bee species.
Data from: Whole genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection
The prevailing demographic model for Drosophila melanogaster suggests that the colonization of North America occurred very recently from a subset of European flies that rapidly expanded across the continent. This model implies a sudden population growth and range expansion consistent with very low or no population subdivision. As flies adapt to new environments, local adaptation events may be expected. To describe demographic and selective events during North American colonization, we have generated a data set of 35 individual whole-genome sequences from inbred lines of D. melanogaster from a west coast US population (Winters, California, USA) and compared them with a public genome data set from Raleigh (Raleigh, North Carolina, USA). We analysed nuclear and mitochondrial genomes and described levels of variation and divergence within and between these two North American D. melanogaster populations. Both populations exhibit negative values of Tajima's D across the genome, a common signature of demographic expansion. We also detected a low but significant level of genome-wide differentiation between the two populations, as well as multiple allele surfing events, which can be the result of gene drift in local subpopulations on the edge of an expansion wave. In contrast to this genome-wide pattern, we uncovered a 50-kilobase segment in chromosome arm 3L that showed all the hallmarks of a soft selective sweep in both populations. A comparison of allele frequencies within this divergent region among six populations from three continents allowed us to cluster these populations in two differentiated groups, providing evidence for the action of natural selection on a global scale.
Data from: Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA
Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.
Data from: Which species, how many, and from where: Integrating habitat suitability, population genomics, and abundance estimates into species reintroduction planning
Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multi-species approaches. We used an interdisciplinary, multi-species, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.
Data from: Incorporating capture heterogeneity in the estimation of autoregressive coefficients of animal population dynamics using capture-recapture data
<p>Population dynamics models combine density-dependence and environmental effects. Ignoring sampling uncertainty might lead to biased estimation of the strength of density-dependence. This is typically addressed using state-space model approaches, which integrate sampling error and population process estimates. Such models seldom include an explicit link between the sampling procedures and the true abundance, which is common in capture-recapture settings. However, many of the models proposed to estimate abundance in the presence of capture heterogeneity lead to incomplete likelihood functions and cannot be straightforwardly included in state-space models.</p> <p>We assessed the importance of estimating sampling error explicitly by taking an intermediate approach between ignoring uncertainty in abundance estimates and fully specified state-space models for density-dependence estimation based on autoregressive processes. First, we estimated individual capture probabilities based on a heterogeneity model, using a conditional multinomial likelihood, followed by a Horvitz-Thompson estimate for abundance. Second, we estimated coefficients of autoregressive models for the log abundance. Inference was performed using the methodology of integrated nested Laplace approximation (INLA). We performed an extensive simulation study to compare our approach with estimates disregarding capture history information, and using R-package VGAM, for different parameter specifications. The methods were then applied to a real dataset of gray-sided voles <em>Myodes rufocanus</em>from Northern Norway.</p> <p>We found that density-dependence estimation was improved when explicitly modelling sampling error in scenarios with low process variances, in which differences in coverage reached up to 8% in estimating the coefficients of the autoregressive processes. In this case, the bias also increased assuming a Poisson distribution in the observational model. For high process variances, the differences between methods were small and it appeared less important to model heterogeneity.</p>
Data from: Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp, Serranidae)
Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which i. local adaptation and the early stages of speciation can be clearly identified and distinguished, ii. the amount of genetic divergence driven by the two processes is similar, and iii. comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome-wide levels of divergence that are comparable among allopatric populations (Fst estimate = 0.0042) and sympatric species (Fst estimate = 0.0038). Population genetic, clustering and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (Fst estimate ≈ 0), a very small proportion of Fst outlier loci (0.05-0.07%), and remarkably few repeated outliers (1-3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective this process does not appear to differ fundamentally from the early stages of speciation.
Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel
<p>The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (<i>Procellaria aequinoctialis</i>) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and 1st domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.</p>
Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads
<p>Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (<i>Spea multiplicata</i>). <i>Spea</i> tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can alternatively develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 14 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.</p>
Data from: Differential proteomic responses of selectively bred and wild Sydney rock oyster populations exposed to elevated CO2
Previous work suggests that larvae from Sydney rock oysters that have been selectively bred for fast growth and disease resistance are more resilient to the impacts of ocean acidification than nonselected, wild-type oysters. In this study, we used proteomics to investigate the molecular differences between oyster populations in adult Sydney rock oysters and to identify whether these form the basis for observations seen in larvae. Adult oysters from a selective breeding line (B2) and nonselected wild types (WT) were exposed for 4 weeks to elevated pCO2 (856 μatm) before their proteomes were compared to those of oysters held under ambient conditions (375 μatm pCO2). Exposure to elevated pCO2 resulted in substantial changes in the proteomes of oysters from both the selectively bred and wild-type populations. When biological functions were assigned, these differential proteins fell into five broad, potentially interrelated categories of subcellular functions, in both oyster populations. These functional categories were energy production, cellular stress responses, the cytoskeleton, protein synthesis and cell signalling. In the wild-type population, proteins were predominantly upregulated. However, unexpectedly, these cellular systems were downregulated in the selectively bred oyster population, indicating cellular dysfunction. We argue that this reflects a trade-off, whereby an adaptive capacity for enhanced mitochondrial energy production in the selectively bred population may help to protect larvae from the effects of elevated CO2, whilst being deleterious to adult oysters.
Data from: Genomic reconstruction of 100 000-year grassland history in a forested country: population dynamics of specialist forbs
Grassland ecosystems worldwide have been extensively converted to other land uses and are globally imperiled. Because many grasslands have been maintained by human activities, understanding their origin and history is fundamentally important to better contemporary management. However, existing methods to reconstruct past vegetation can produce contrasting views on grassland history. Here, we inferred demographic histories of 40 populations of four grassland forb species throughout Japan using high-resolution genome sequences and model-flexible demographic simulation based on the site frequency spectrum. Although two species showed a slight decline in population size between 100 000–10 000 years ago, our results suggest that population sizes of studied species have been maintained within the range of 0.5–2.0 times the most recent estimates for at least 100 000 years across Japan. Our results suggest that greater than 90% declines in Japanese grasslands and subsequent losses of grassland species in the last 100 years are geologically and biologically important and will have substantial consequences for Japanese biota and culture. People have had critical roles in maintaining disturbance-dependent grassland ecosystems and biota in this warm and wet forested country. In these contexts, disturbances associated with forest harvesting and traditional extensive farming have the potential to maintain grassland ecosystems and can provide important opportunities to reconcile resource production and conservation of grassland biodiversity.
Data for spatial and temporal refugia for an insect population declining due to climate change
<p>Insect declines have been reported worldwide, although the particular causes of the declines may be complex and are poorly understood. Meadow spittlebugs were one of the most abundant insects in the coastal prairie along the California coast 40 years ago but have largely disappeared. Evidence links this decline to changing climatic conditions, which have reduced survival of eggs and neonates. We identified several refugia where meadow spittlebug populations have persisted amidst unfavorable conditions. Protection from desiccating winds was the common attribute of these refugia. Following a wet year, adult meadow spittlebugs were able to disperse from one refuge that we studied to recolonize coastal prairie habitats, although populations declined over the next two drier years. Because of their previous high abundance, loss of meadow spittlebugs is likely to affect the functioning of this widespread habitat, including energy transfer, their host plants, and their predators. In addition, meadow spittlebugs are unusual in having been the subject of extensive physiological and long-term ecological data, so they can serve as a bellwether species, indicating the effects of climate change.</p>
Data from: Long-term persistence of wildlife populations in a pastoral area
<p>Facilitating coexistence between people and wildlife is a major conservation challenge in East Africa. Some conservation models aim to balance the needs of people and wildlife, but the effectiveness of these models is rarely assessed. Using a case-study approach, we assessed the ecological performance of a pastoral area in northern Tanzania (Manyara Ranch) and established a long-term wildlife population monitoring programme (carried out intermittently from 2003-2008 and regularly from 2011-2019) embedded in a distance sampling framework. By comparing density estimates of the road-transect based long-term monitoring to estimates derived from systematically distributed transects, we found that the bias associated with non-random placement of transects was non-significant. Overall, cattle, and sheep and goat reached the greatest densities and several wildlife species occurred at densities similar (zebra, wildebeest, waterbuck, Kirk's dik-dik) or possibly even greater (giraffe, eland, lesser kudu, Grant's gazelle, Thomson's gazelle) than in adjacent national parks in the same ecosystem. Generalized linear mixed models suggested that most wildlife species (8 out of 14) reached greatest densities during the dry season, that wildlife population densities either remained constant or increased over the 17-year period, that herbivorous livestock species remained constant, while domestic dog population decreased over time. Cross-species correlations did not provide evidence for interference competition between grazing or mixed livestock species and wildlife species but indicate possible negative relationships between domestic dog and warthog populations. Overall, wildlife and livestock populations in Manyara Ranch appear to coexist over the 17-year span. Most likely, this is facilitated by existing connectivity to adjacent protected areas, effective anti-poaching efforts, spatio-temporal grazing restrictions, favourable environmental conditions of the ranch and spatial heterogeneity of surface water and habitats. This long-term case study illustrates the potential of rangelands to simultaneously support wildlife conservation and human livelihood goals if livestock grazing is restricted in space, time and numbers.</p>
Data from: Biosystematics of Platanthera bifolia s.l. (Orchidaceae): Inferences from analysis of Scandinavian population samples
<p>Over the years, various authors have (sub)divided the Eurasian moth pollinated Platanthera bifolia into several taxa. Advanced studies using multivariate morphometric analysis and/or genetic fingerprinting have all included regions where the situation appears particularly complex. With the aim to resolve variation patterns in a region where the situation seems less complex, we analysed morphometric and AFLP data from 13 Scandinavian populations using a range of uni- and multivariate statistical methods. Variation was largely continuous, though with (individuals from) short-spurred and long-spurred populations, respectively, forming loose groups. Provided that successful pollinator shifts usually occur between moth species with small difference in proboscis length, this pattern is congruent with the hypothesis that spur length in P. bifolia s.l. has mainly evolved through pollinator shifts followed by selection in response to proboscis length of the prevailing local pollinator species. Acknowledging an important adaptive role of spur length, observing that spur length was among the main contributors to morphological variation, and noting this pattern to be congruent with both AFLP patterns and habitat requirements, we advocate the formal distinction between a short-spurred and a long-spurred taxon. Adopting the operational definitions of species, subspecies and variety provided in Flora Nordica, the two taxa should be recognized as P. bifolia var. bifolia and P. bifolia var. latissima, respectively. A key to the varieties is provided.</p>
UK dogs data from: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci
<p>Background: <span>Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) </span><span>can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from </span><span><span>two</span></span><span> countries </span><span><span>(UK and Sweden)</span></span><span> to perform </span><span>genome-wide association stud</span><span>ies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the </span><i><span>Fédération Cynologique Internationale</span></i><span> (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. </span><span><span>In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations.</span></span><span> Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs.</span></p> <p>Results: <span><span>Multiple SNPs with genome-wide significant and suggestive</span></span><span><span> associations</span></span><span> </span><span><span>were detected in single-population GWAS and the meta-analysis.</span></span><span> Few of these SNPs overlapped between populations </span><span><span>or between single-population GWAS and the meta-analysis</span></span><span>, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. </span><i><span>MED13</span></i><span> (Chr 9) and </span><i><span>PLEKHA7</span></i><span> (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia.</span></p> <p>Conclusions: <span>Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, </span><span><span>most</span></span><span> of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.</span></p>
Data from: Distribution and biogeography of Sanguina snow algae: fine-scale sequence analyses reveal previously unknown population structure
It has been previously suggested that snow algal species within the genus Sanguina (S. nivaloides and S. aurantia) show no population structure despite being found globally (S. nivaloides) or throughout the Northern Hemisphere (S. aurantia). However, systematic biogeographic research into global distributions is lacking due to few genetic and no genomic resources for these snow algae. Here, using all publicly available and previously unpublished Sanguina sequences of the Internal Transcribed Spacer 2 region, we investigate if this purported lack of population structure within Sanguina species is supported by additional evidence. Using a minimum entropy decomposition (MED) approach to examine fine-scale genetic population structure, we find that these snow algae populations are largely distinct regionally and have some interesting biogeographic structuring. This is in opposition to the currently accepted idea that Sanguina species lack any observable population structure across their vast ranges and highlights the utility of fine-scale (sub-OTU) analytical tools to delineate geographic and genetic population structure. This work extends the known range of S. aurantia and emphasizes the need for development of genetic and genomic tools for additional studies on snow algae biogeography.
Data used in timing is everything: Dichogamy and pollen germinability underlie variation in autonomous selfing among populations
<p><i>Premise of the study:</i> The evolution of multiple floral traits often underlies the transition from outcrossing to selfing. Such traits can influence the ability to self, and the timing at which selfing occurs, which in turn affects the costs of selfing. Species that display variation in autonomous selfing provide an opportunity to dissect the phenotypic changes that contribute to variability in the mating system. </p> <p><i>Methods: </i>In a common garden, we measured dichogamy and herkogamy in 24 populations of the protandrous mixed-mating herb <i>Campanula americana,</i> and related these to autonomous fruit set (autonomy). We then measured the timing of self-pollen deposition and fruit production in populations with high and low autonomy, and determined whether pollen germinability across floral development contributes to variation in autonomy. </p> <p><i>Key Results:</i> Populations that transitioned more rapidly to female phase displayed elevated autonomous selfing, but herkogamy was unassociated with autonomous selfing. Selfing occurred more rapidly in highly-autonomous populations due to greater self-pollen deposition early in female phase. Pollen germinability in low-autonomy populations remained constant across floral development, but in high-autonomy populations it increased after floral anthesis and was highest near the onset of female phase. </p> <p><i>Conclusions</i>:<i> </i>Reduced dichogamy, elevated self-pollen deposition, and higher pollen germination late in male phase contribute to both earlier selfing and greater selfing. These traits vary among populations, likely reflecting past selection on the mating system. While delayed selfing bears fewer fitness costs, the evolution of earlier selfing may be favored if self-pollen availability decreases over floral development.</p>
Data and statistical code from: Population differences in the effect of context on personality in an invasive lizard
<p>Within populations, individuals often differ consistently in their average level of behavior (i.e. animal personality), as well as their response to environmental change (i.e. behavioral plasticity). Thus, changes in environmental conditions might be expected to mediate the structure of animal personality traits. However, it is currently not well understood how personality traits change in response to environmental conditions, and whether this effect is consistent across multiple populations within the same species. Accordingly, we investigated variation in personality traits across two ecological contexts in the invasive delicate skink (<i>Lampropholis delicata</i>). Specifically, lizards from three different populations were repeatedly measured for individual activity in group behavioral assays under differing levels of food availability. We found that environmental context had a clear effect on the structure of lizard personality, where activity rates were not repeatable in the absence of food, but were repeatable in the presence of food resources. The difference in repeatability of activity rates across contexts appeared to be largely driven by an increase in among-individual variance when tested in the presence of food resources. However, this was only true for one of the populations tested, with food context having no effect on the expression of personality traits in the other two populations. Our results highlight the important role of environmental context in mediating the structure of animal personality traits and suggest that this effect may vary among populations.</p>
Nonrandom missing data can bias PCA inference of population genetic structure
<p>Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the Principal Component Analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (<i>Eptesicus fuscus</i>) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to 1) plot PCA with a color gradient showing per sample missingness, 2) interpret samples close to the PCA origin with extra caution, 3) explore filtering parameters with and without the missingness-biased samples, and 4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.