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opencc-by-4.0Mar 2008View details →

Fig. 6 in Population structure, growth and fishery yield of Leporinus acutidens (Valenciennes, 1837) (Teleostei: Anostomidae) in Yacyretá Reservoir (Argentina)

Fig. 6. Monthly average condition factor (K) by sex for L. acutidens.

opencc-by-4.0Sep 2005View details →

Fig. 5 in Reproductive and population dynamics of the Bay whiff Citharichthys spilopterus Günther, 1862 (Pleuronectiformes: Paralichthyidae) in the Mamanguá Inlet, Rio de Janeiro, Brazil

Fig. 5. Analyses of the sex ratio of C. spilopterus: a) by length groups and b) by months.

opencc-zeroSep 2021View details →

Larger males facilitate population expansion in Ophraella communa

<div class="WordSection1"> <ol> <li>One of the most intriguing concepts in animal ecology is the reproductive advantages offered by larger body size, and the females prefer to mate with larger males in order to gain reproductive advantage. </li> <li>Currently, it is not clear how females recognize signs of male "quality" and what mechanisms are involved in producing offspring with direct or indirect benefits. Our study aims to assess the preferences of females for males in Ophraella communa, determine the reproductive benefits and reveal the underlying mechanism behind this advantage.</li> <li>We demonstrate that male body size is an important determinant in the evolutionary process of O. communa, affecting female mate choice. Moreover, our study establishes that females prefer males with a larger body size, and this could further improve the developmental and reproductive fitness of their offspring. Finally, we focus on the seminal fluid proteins (SFPs) in O. communa, determine differentially expressed genes (i.e., OcACE, OcCBP and OcSFP) by analyzing their proteomes and transcriptomes, and define the role of these SFPs-related genes through RNAi. </li> <li>Our study proved that the reproductive benefit of large males may be regulated by biased expression of crucial SFPs genes. The present study advances our understanding of the biological significance of preferential mating.</li> </ol> </div>

opencc-zeroSep 2021View details →

Data from: Decreased selectivity during mate choice in a small-sized population of a long-lived seabird

As biparental care is crucial for breeding success in Procellariiformes seabirds (i.e., albatrosses and petrels), these species are expected to be choosy during pair formation. However, the choice of partners is limited in small-sized populations, which might lead to random pairing. In Procellariiformes, the consequences of such limitations for mating strategies have been examined in a single species. Here, we studied mate choice in another Procellariiforme, Bulwer's petrel Bulweria bulwerii, in the Azores (ca 70 breeding pairs), where the species has suffered a dramatic population decline. We based our approach on both a 11-year demographic survey (capture-mark-recapture) and a genetic approach (microsatellites, n = 127 individuals). The genetic data suggest that this small population is not inbred and did not experience a genetic bottleneck. Moreover, pairing occurred randomly with respect to genetic relatedness, we detected no extrapair parentage (n = 35 offspring), and pair fecundity was unrelated to relatedness between partners. From our demographic survey, we detected no assortative mating with respect to body measurements and breeding experience and observed very few divorces, most of which were probably forced. This contrasts with the pattern previously observed in the much larger population from the Selvagens archipelago (assortative mating with respect to bill size and high divorce rate). We suggest that the Bulwer's petrels from the Azores pair with any available partner and retain it as long as possible despite the fact that reproductive performance did not improve with pair common experience, possibly to avoid skipping breeding years in case of divorce. We recommend determining whether decreased choosiness during mate choice also occurs in reduced populations of other Procellariiform species. This might have implications for the conservation of small threatened seabird populations.

opencc-zeroSep 2021View details →

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the results of, to our knowledge, the first meta-analysis to examine within-species variation in thermal plasticity, using results from 20 studies (19 species) that quantified thermal acclimation capacities across 78 populations. We used meta-regression to evaluate two leading hypotheses. The climate variability hypothesis predicts that populations from more thermally variable habitats will have greater plasticity, while the trade-off hypothesis predicts that populations with the lowest heat tolerance will have the greatest plasticity. Our analysis indicates strong support for the trade-off hypothesis because populations with greater thermal tolerance had reduced plasticity. These results advance our understanding of variation in populations' susceptibility to climate change and imply that populations with the highest thermal tolerance may have limited phenotypic plasticity to adjust to ongoing climate warming.

opencc-by-4.0Sep 2021View details →

Reproduction package for the paper "Multi-dimensional population modelling using frbpoppy: Magnetars can produce the observed fast radio burst sky"

This is a basic reproduction package for the paper "Multi-dimensional population modelling using frbpoppy: Magnetars can produce the observed fast radio burst sky" by David Gardenier & Joeri van Leeuwen (2021). * arXiv: <a href="https://arxiv.org/abs/2012.06396">arXiv:2012.06396</a> * DOI:  <a href="https://doi.org/10.1051/0004-6361/202040119">10.1051/0004-6361/202040119</a>

Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

"Synthetic recombinant" populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.

Population assignment tests uncover rare long-distance larval dispersal events

Long-distance dispersal (LDD) is consequential to metapopulation ecology and evolution. In systems where dispersal is undertaken by small propagules, such as larvae in the ocean, documenting LDD is especially challenging. Genetic parentage analysis has gained traction as a method for measuring larval dispersal, but such studies are generally spatially limited, leaving LDD understudied in marine species. We addressed this knowledge gap by uncovering LDD with population assignment tests in the coral reef fish Elacatinus lori—a species whose short-distance dispersal has been well-characterized by parentage analysis. When adults (n = 931) collected throughout the species' range were categorized into three source populations, assignment accuracy exceeded 99%, demonstrating low rates of connectivity between populations in the adult generation. After establishing high assignment confidence, we assigned settlers (n = 3,828) to source populations. Within the settler cohort, < 0.1% of individuals were identified as long-distance dispersers from other populations. These results demonstrate an exceptionally low level of connectivity between E. lori populations, despite the potential for ocean currents to facilitate LDD. More broadly, these findings illustrate the value of combining genetic parentage analysis and population assignment tests to uncover short- and long-distance dispersal, respectively.

Environmental change reduces body condition, but not population growth, in a high-arctic herbivore

Environmental change influences fitness-related traits and demographic rates, which in herbivores are often linked to resource-driven variation in body condition. Coupled body condition-demographic responses may therefore be important for herbivore population dynamics in fluctuating environments, such as the Arctic. We applied a transient Life-Table Response Experiment ('transient-LTRE') to demographic data from Svalbard barnacle geese (Branta leucopsis), to quantify their population-dynamic responses to changes in body mass. We partitioned contributions from direct and delayed demographic and body condition-mediated processes to variation in population growth. Declines in body condition (1980-2017), which positively affected reproduction and fledgling survival, had negligible consequences for population growth. Instead, population growth rates were largely reproduction-driven, in part through positive responses to rapidly advancing spring phenology. The virtual lack of body condition-mediated effects indicates that herbivore population dynamics may be more resilient to changing body condition than previously expected, with implications for their persistence under environmental change.

Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)

Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (Eumops floridanus) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome b sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (FST = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., Ne < 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as Eumops ferox from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.

Population genetics under the Massenerhebung effect: the influence of topography on the demography of Acer morrisonense (Sapindaceae)

Aim: The Massenerhebung effect (Mass elevation effect) refers to heat or wind-driven altitudinal distribution patterns of temperature-dependent parameters among massifs with narrower range and lower elevation around peripheral and isolated mountains compared to core and continuous ones. Although common in ecology, this effect is rarely discussed in population genetics. Here, we use genetic markers to reveal population genetic patterns and also test the mountain- and sky-barrier hypotheses relevant to the Massenerhebung distribution pattern of Acer morrisonense in Taiwan's rugged topography and varied local climates. Location: The alpine and cloud forest of Taiwan. Taxon: Acer morrisonense Hayata Methods: Two chloroplast DNA (cpDNA) fragments and 17 expressed sequence tag-simple sequence repeat (EST-SSR) loci respectively from 200 and 286 individuals were used to elucidate the phylogeographic pattern of pollen and seed dispersal of A. morrisonense. These data were combined with ecological niche modeling (ENM) to infer distribution range shifts and refugia. We also correlated the genetic-divergence indices with spatial factors to clarify latitudinal and altitudinal effects on genetic diversity. Results: The incongruent phylogeographic patterns of genetic distributions between nuclear and cpDNA markers indicate unhindered pollen flow but spatially constrained seed dispersal. Taken together with ENM, the genetic pattern further reflects historical colonization from central-mountain refugia to edges since the Holocene. The Massenerhebung reduces the gene flow by the surrounding mountains and also causes lower genetic diversity compared to central alpine populations. Main conclusions: This study is the first to reveal the influence of Massenerhebung effect on cpDNA genetic structure of montane trees and reflect the spatial trends of seed dispersal. This population genetic pattern can also be attributed to the demography-related range shifts with paleoclimate fluctuations under complex mountain topography, supporting the mountain-barrier hypothesis. The results have important implications for conserving the genetic diversity of species with a wide altitudinal distribution range.

Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination

Polymorphisms can lead to speciation if there is differential mating success among conspecifics divergent for a trait. Polymorphism for sex determining system might be particularly expected to isolate gene pools, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). We investigated this question using a rare example of a species exhibiting polymorphism for sex determination: the viviparous snow skink Carinascincus ocellatus. While a coparatively high elevation population has entirely genotypic sex determination, in a lower elevation population there is an additional environmental component to sex determination. These systems also exhibit minor differences in sex-linked genotypes. Using 'Isolation with Migration' analysis of neutral loci, we estimated that these populations and their sex determining systems diverged in the absence of gene flow, across multiple periods of geographic proximity during Pleistocene glaciations. Our analysis suggests that populations of C. ocellatus with divergent sex determining systems are likely reproductively isolated, even though they are presently underlined by only subtle DNA differences. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.

opencc-zeroOct 2022View details →

Dataset 2 for Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly

Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographical areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the West may result from (1) admixture of different western refuges, (2) more recent demographic changes, or (3) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow and selection in a region that is expected to be particularly vulnerable to climate change.

opencc-by-4.0Dec 2022View details →

VCFs of fly population Virginia + Others

Find information of this dataset on: https://github.com/Jcbnunez/Cville-Seasonality-2016-2019

opencc-zeroOct 2022View details →

Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys

Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we use genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this polyphagous pest. Our analysis demonstrated that BMSB exhibits spatial structure but admixture rates are high among introduced populations, resulting in similar levels of genomic diversity across native and introduced populations. These spatial genomic patterns suggest a complex invasion scenario, potentially with multiple bridgehead events, posing a challenge for accurately assigning BMSB incursions to their source using reduced-representation genomic data. By associating allele frequencies with the invasion status of BMSB populations, we found significantly differentiated SNPs located in close proximity to genes for insecticide resistance and olfaction. Comparing variations in allele frequencies among populations for outlier SNPs suggests that BMSB invasion success has likely evolved from standing genetic variation. In addition to being a major nuisance of households, BMSB has caused significant economic losses to agriculture in recent years and continues to expand its range. Despite no record of BMSB insecticide resistance to date, our results show high capacity for potential evolution of such characters, highlighting the need for future sustainable and targeted management strategies.

opencc-zeroOct 2022View details →

Data from: Resource availability affects seasonal trajectories of population-level learning

Environmental effects on learning are well known, such as cognition that is mediated by nutritional consumption. Less known is how seasonally variable environments affect phenological trajectories of learning. Here, we test the hypothesis that nutritional availability affects seasonal trajectories of population-level learning in species with developmentally plastic cognition. We test this in bumble bees (Apidae: Bombus), a clade of eusocial insects that produce individuals at different time points across their reproductive season and exhibit organ developmental plasticity in response to nutritional consumption. To accomplish this, we develop a theoretical model that simulates learning development across a reproductive season for a colony parameterized with observed life history data. Our model finds two qualitative seasonal trajectories of learning: (1) an increase in learning across the season and (2) no change in learning across the season. We also find these two qualitative trajectories revealed by empirical learning data; the proportion of workers successfully completing a learning test increases across a season for two bumble bee species (Bombus auricomus, Bombus pensylvanicus), but does not change for another three (Bombus bimaculatus, Bombus griseocollis, Bombus impatiens). This study supports the novel consideration that resources affect seasonal trajectories of population-level learning in species with developmentally plastic cognition.

opencc-by-4.0Nov 2022View details →

Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population

This repository holds the datasets and R code files needed to run the models in: Brandell et al., 2022. Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population. PLOS ONE. Excel files have associated KEYs for each data column; CSVs are analyzed with their associated R code.

opencc-by-4.0Sep 2022View details →

Data - Attack of the clones: population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Colletotrichum lupini, causing lupin anthracnose, is one of the worst pathogens to lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the genetic diversity, evolutionary dynamics and molecular basis of host-speciation of this notorious lupin pathogen. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction-site associated DNA sequencing (3D-RADseq), resulting in a dataset of unparalleled resolution. Phylogenetic and structural analysis could distinguish four (I – IV) independent lineages. The strong population structure, low recombination rate and slow linkage decay strongly indicate that C. lupini reproduces clonally. Different morphologies and virulence patterns on white and Andean lupin were observed between and within clonal lineages. Lineage II  isolates were shown to have a mini chromosome which was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this mini-chromosome could indicate a function related to virulence or host-speciation. All four lineages were present in the South American Andes region, which is concluded to be the center of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seed-borne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.

opencc-by-4.0Dec 2022View details →

Figures 1–2 in Reanalysis of the Yunnan population of Scorpiops kubani with a description of a new species, Scorpiops lowei sp. n. (Scorpiones: Scorpiopidae)

Figures 1–2: Scorpiops kubani, male paratype, dorsal (1) and ventral (2) views.