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opencc-zeroJan 2022View details →

Role of individual dispersal in genetic resilience in fluctuating populations of the gray-sided vole Myodes rufocanus

Population densities of the grey-sided vole Myodes rufocanus fluctuate greatly within and across years in Japan. Here, to investigate the role of individual dispersal in maintaining population genetic diversity, we examined how genetic diversity varied during fluctuations in density by analyzing eight microsatellite loci in voles sampled three times per year for 5 years, using two fixed trapping grids (approximately 0.5 ha each). At each trapping session, all captured voles at each trapping grid were removed. The STRUCTURE program was used to analyze serially collected samples to examine how population crashes were related to temporal variability, based on local-scale genetic compositions in each population. In total, 461 and 527 voles were captured at each trapping grid during this study. The number of voles captured during each trapping session (i.e., vole density) varied considerably at both grids. Although patterns in fluctuations were not synchronized between grids, the peak densities were similar. At both grids, the mean allele number recorded at each trapping session was strongly, positively, and non-linearly correlated with density. STRUCTURE analyses revealed that the proportions of cluster compositions among individuals at each grid differed markedly before and after the crash phase, implying the long-distance dispersal of voles from remote areas at periods of low density. The present results suggest that, in grey-sided vole populations, genetic diversity varies with density largely at the local scale; in contrast, genetic variation in a metapopulation is well-preserved at the regional scale due to the density-dependent dispersal behaviors of individuals. By influencing the dispersal patterns of individuals, fluctuations in density affect metapopulation structure spatially and temporally, while the levels of genetic diversity are preserved in a metapopulation.

opencc-zeroFeb 2022View details →

Genetic data and niche differences suggest that disjunct populations of Diglossa brunneiventris are not sister lineages

Disjunct distributions within a species are of great interest in systematics and biogeography. This separation can function as a barrier to gene flow when the distance among populations exceeds the dispersal capacity of individuals, and depending on the duration of the barrier, it may eventually lead to speciation. Here we describe patterns of geographic differentiation of two disjunct populations of Diglossa brunneiventris separated by approximately 1000 km along the Andes. Diglossa brunneiventris vuilleumieri is isolated in northern Colombia, while Diglossa brunneiventris brunneiventris has a seemingly continuous distribution across Peru, Bolivia, and Chile. We sequenced mitochondrial and nuclear DNA of the two Diglossa brunneiventris subspecies to evaluate whether they form a monophyletic clade, while including the other three species within the carbonaria complex (D. gloriosa, D. humeralis and D. carbonaria). We also constructed ecological niche models for each Diglossa brunneiventris subspecies to compare their climatic niches. We found that when using all available molecular data, the two D. brunneiventris subspecies are not sister lineages. In fact, each subspecies is more closely related to other species in the carbonaria complex. Our niche modeling analyses showed that the subspecies are occupying almost entirely different climatic niches. An additional, and not expected result was that the carbonaria complex might encompass more cryptic species than previously considered. We suggest reevaluating the taxonomic status of these brunneiventris populations, especially the northern subspecies, given its highly restricted range and potential threatened status.

opencc-zeroFeb 2022View details →

Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations

An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.

The population genetics of adaptation through copy-number variation in a fungal plant pathogen

Supplementary Tables S1-S8 for the manuscript "The population genetics of adaptation through copy-number variation in a fungal plant pathogen"

Data from: Ecological genetics of Juglans nigra: differences in early growth patterns of natural populations

Many boreal and temperate forest tree species distributed across large geographic ranges are composed of populations adapted to the climate they inhabit. Forestry provenance studies and common gardens provide evidence of local adaptation to climate when associations between fitness traits and the populations' home climates are observed. Most studies that evaluate tree height as a fitness trait do so at a specific point in time. In this study, we elucidate differences in early growth patterns in black walnut (Juglans nigra L.) populations by modeling height growth from seed up to age 11. The data comprise tree height measurements between ages 2 to 11 for 52 natural populations of black walnut collected through its geographic range and planted in one or more of 3 common gardens. We use the Chapman-Richards growth model in a mixed-effects framework and test whether populations differ in growth patterns by incorporating populations' home climate into the model. In addition, we evaluate differences in populations' absolute growth and relative growth based on the fitted model. Models indicated that populations from warmer climates had the highest cumulative growth through time, with differences in average tree height between populations from home climates with a mean annual temperature (MAT) of 13 °C and of 7 °C estimated to be as high as 80% at age 3. Populations from warmer climates were also estimated to have higher and earlier maximum absolute growth rate than populations from colder climates. In addition, populations from warm climates were predicted to have higher relative growth rates at any given tree size. Results indicate that natural selection may shape early growth patterns of populations within a tree species, suggesting that fast early growth rates are likely selected for in relatively mild environments where competition rather than tolerance to environmental stressors becomes the dominant selection pressure.

Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China

Inreasing damage of pests in agriculture and forestry can arise both as a consequence of changes in local species and through the introduction of alien species. In this study, we used population genetics approaches to examine population processes of two pests of the tree-of-heaven trunk weevil (TTW), Eucryptorrhynchus brandti (Harold) and the tree-of-heaven root weevil (TRW), E. scrobiculatus (Motschulsky) on the tree-of-heaven across their native range of China. We analyzed the population genetics of the two weevils based on ten highly polymorphic microsatellite markers. Population genetic diversity analysis showed strong population differentiation among populations of each species, with FST ranges from 0.0197 to 0.6650 and from -0.0724 to 0.6845, respectively. Populations from the same geographical areas can be divided into different genetic clusters, and the same genetic cluster contained populations from different geographical populations, pointing to dispersal of the weevils possibly being human-mediated. Redundancy analysis showed that the independent effects of environment and geography could account for 93.94% and 29.70% of the explained genetic variance in TTW, and 41.90% and 55.73% of the explained genetic variance in TRW, respectively, indicating possible impacts of local climates on population genetic differentiation. Our study helps to uncover population genetic processes of these local pest species with relevance to control methods.

opencc-by-4.0Apr 2022View details →

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

The sweet chestnut orchards (Castanea sativa Mill.) are traditionally planted in the northern Adriatic region. This study investigates their population structure, as well as the genetic background of three toponymous clonal varieties. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this study. We have identified five closely related clones, which represent a singular, polyclonal marron variety, found in all three cultivation areas, acompanied by many hybrids, resulting from the breeding between cultivated and wild chestnuts.

Fig. 3 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 3. Polyclonal structure of studied Eusomus ovlulum samples inUkraine.

Fig. 2 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 2. The electrophoretic spectra of the esterases in the Eusomus ovulum specimens.

Fig. 1 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation

Fig. 1. Geographic localization of Eusomus ovulum samples.

Lack of spatial and temporal genetic structure of Japanese eel (Anguilla japonica) populations

Japanese eel (Anguilla japonica) is an important food source in East Asia whose population has dramatically declined since the 1970s. Despite past analysis with DNA sequencing, microsatellite and isozyme methods, management decisions remain hampered by contradictory findings. For example, it remains unresolved whether Japanese eels are a single panmictic population or whether they harbor significant substructure. Accurate assessment of population genetic substructure, both spatial and temporal, is essential for determining the relevant number of distinct management units appropriate for this species. In the present study, we assayed genetic variation genome-wide using Restriction Site Associated DNA Sequencing (RAD-seq) technology to analyze the population genetic structure of Japanese eels. For analysis of temporal isolation, five "cohort" samples were collected yearly from 2005 to 2009 in the Yangtze River Estuary. For analysis of spatial structure, five "arrival wave" samples were collected in China in 2009, and two arrival wave samples were collected in Japan in 2001. In each cohort of each arrival wave, five individuals were collected for a total of 55 eels sampled. In total, 214,210 loci were identified from these individuals, 106,652 of which satisfied quality checks and were retained for further analysis. There was relatively little population differentiation between arrival waves and cohorts collected either at different locations during the same year (Fst = 0.077) or at the same location collected over subsequent years (Fst = 0.082), and locations displayed no consistent isolation-by-distance.

Data from: Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affects behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour - a locomotor response used to measure e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared to locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4. Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.

Data from: Tracking population genetic signatures of local extinction with herbarium specimens

Background and Aims Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. Methods We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex-situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. Key Results Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as powerful predictor of functional connectivity which may promote decision making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. Conclusions Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex-situ population and a germination trial underscores the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

opencc-zeroMay 2022View details →

Population changes in a whale breeding ground revealed by citizen science noninvasive genetics unique microsatellite profiles of southern right whales

Historical exploitation, and a combination of current anthropogenic impacts, such as climate change and habitat degradation, impact the population dynamics of marine mammalian megafauna. Right whales (Eubalaena spp.) are large cetaceans recovering from hunting, whose reproductive and population growth rate appear to be impacted by climate change. We apply noninvasive genetic methods to monitor southern right whale (E. australis, SRW) and test the application of noninvasive genetics to minimise the observer effects on the population. Our aim is to describe population structure, and interdecadal and interannual changes to assess species status in the Great Acceleration period of Anthropocene. As a basis for population genetic analyses, we collected samples from sloughed skin during post-migration epidermal moult. Considering the exploration-exploitation dilemma, we collaborated with whale-watching companies, as part of a citizen science approach and to reduce ad hoc logistic operations and biopsy equipment. We used mitochondrial and microsatellite data and population genetic tools. We report for the first time the genetic composition and differentiation of the Namibian portion of the range. Population genetic parameters suggest that South Africa hosts the largest population. This corresponds with higher estimates of current gene flow from Africa compared to older samples. We have observed considerable interannual variation in population density at the breeding ground and an interdecadal shift in genetic variability, evidenced by an increase in the point estimate inbreeding. Clustering analyses confirmed differentiation between the Atlantic and Indo-Pacific, presumably originating during the ice ages. We show that population monitoring of large whales, essential for their conservation management, is feasible using noninvasive sampling within non-scientific platforms. Observed patterns are concurrent to changes of movement ecology and decline in reproductive success of the South African population, probably reflecting a large-scale restructuring of pelagic marine food webs.

opencc-zeroMay 2022View details →

Population genetics and biogeography of the lungwort lichen in North America support distinct Eastern and Western gene pools

Populations of species with large spatial distributions are shaped by complex forces that differ throughout their ranges. To maintain the genetic diversity of species, genepool-based subsets of widespread species must be considered in conservation assessments. In this study, the population genetics of the lichenized fungus Lobaria pulmonaria and its algal partner, Symbiochloris reticulata , were investigated to determine population structure, genetic diversity, and degree of congruency in eastern and western North America. Data loggers measuring temperature and humidity were deployed at selected populations in eastern North America to test for climatic adaptation. To better understand the role Pleistocene glaciations played in shaping population patterns, a North American, range-wide species distribution model was constructed and hindcast to 22,000 years before present and at 500-year time slices from then to the present. The presence of two gene pools with minimal admixture was supported, one in the Pacific Northwest and one in eastern North America. Western populations were significantly more genetically diverse than eastern populations. There was no evidence for climatic adaptation among eastern populations, though there was evidence for range-wide adaptation to evapotranspiration rates. Hindcast distribution models suggest that observed genetic diversity may be due to a drastic Pleistocene range restriction in eastern North America, whereas a substantial coastal refugial area is inferred in the west. Taken together the results show different, complex population histories of L. pulmonaria in eastern and western North America, and suggest that conservation planning for each gene pool should be considered separately.

opencc-zeroMay 2022View details →

Population structure and genetic variance among local populations of an non-native earthworm species in Minnesota, USA

A variety of human activities have been identified as driving factors for the release and spread of invasive earthworm species in North America. Population genetic markers can help to identify locally relevant anthropogenic vectors and provide insights into the processes of population dispersal and establishment. We sampled the invasive European earthworm species Lumbricus terrestris at nine sites and several bait shops within the metropolitan area of Minneapolis-St. Paul in Minnesota, USA. We used microsatellite markers to infer genetic diversity and population structure, and 16S rDNA to address multiple introduction events, including bait dumping, which is a common source of L. terrestris introductions into the wild. Our results indicate multiple introductions but not from current bait dumping. Overall, genetic structure was low and earthworms >5000 m apart were genetically differentiated, except for one sampling location, indicating jump-dispersal followed by population establishment. Further, earthworms at one location north of Minneapolis established from one or few founder individuals, suggesting that earthworm invasions are ongoing. We therefore encourage further monitoring of earthworm populations using molecular markers, in order to disentangle the different human-related vectors contributing to the spread of earthworms and their establishment, which is essential to develop adequate management strategies.

opencc-zeroJun 2022View details →

Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the U.S. was evaluated in four ways: 1) using genetic relationships from pedigree data [(n=64,310 animals recorded in the U.S. National Sheep Improvement Program (NSIP)]; 2) using molecular data (n=304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n=109) and Irish (n=55) Suffolk sheep to those in the U.S. using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n=18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the U.S. population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in U.S. Suffolk sheep engaged in NSIP was proposed.

opencc-zeroJun 2022View details →

Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout (Oncorhynchus clarkii) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.

opencc-zeroJun 2022View details →

A genetically isolated dingo population in western Victoria, Australia, reveals greater structuring of the Australian dingo

The Australian dingo is a relatively recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed genetic data using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual levels. Upon finding low genetic diversity in western Victoria, we tested for a recent genetic bottleneck. The broader southern Australia sample (n=1,138) comprised mostly hybrid animals, with ~30% dingoes. All western Victorian individuals (n= 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and no recent bottleneck. Based upon our characterisation of this unusual mainland population, we sound caution for future studies assuming homogeneity of dingoes across the continent.