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Fig. 4 in Population structure, growth and fishery yield of Leporinus acutidens (Valenciennes, 1837) (Teleostei: Anostomidae) in Yacyretá Reservoir (Argentina)

Fig. 4. Age structure of L. acutidens compared by study period.

Fig. 5 in Population structure, growth and fishery yield of Leporinus acutidens (Valenciennes, 1837) (Teleostei: Anostomidae) in Yacyretá Reservoir (Argentina)

Fig. 5. Relationship of the condition factor (K) by standard length class and sex for L. acutidens.

Fig. 1. Sampling area. 1 in Population structure, growth and fishery yield of Leporinus acutidens (Valenciennes, 1837) (Teleostei: Anostomidae) in Yacyretá Reservoir (Argentina)

Fig. 1. Sampling area. 1- Yabebiry Stream; 2- Nemesio Parma; 3- Puerto Valle, 4- Puerto Júpiter.

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-zeroOct 2021View details →

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.

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-zeroJan 2023View details →

Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population

The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise FST-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average HE = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (FIS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (A. brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

opencc-zeroFeb 2023View details →

Different waves of postglacial recolonisation and genomic structure of bank vole population in NE Poland

Previous studies indicated that in some species phylogeographic patterns obtained in analyses of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check if there was any discordance between mitochondrial and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in analyses of other genetic markers and functional genes. However, genome-wide SNP analyses revealed a more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as previously recognised in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for an insufficient amount of time to develop significant genetic differentiation.

opencc-zeroMar 2023View details →

Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data

New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between Bos indicus (Brahman and Gyr) and B. taurus breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.

opencc-by-4.0Mar 2023View details →

Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs

Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.

opencc-zeroMar 2023View details →

Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests

Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The pre-human extent of these grasslands is a topic of vigorous debate, with conventional wisdom holding that they are anthropogenic in nature and emerging evidence supporting that grasslands were a component of the pre-human Central Highlands vegetation. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, which makes them a valuable indicator species. Population divergences among forest-dwelling mammals can serve as a proxy for habitat fragmentation and patterns of post-divergence gene flow can reveal potential migration corridors consistent with a wooded grassland mosiac. We used RADseq data to infer phylogenetic relationships, population structure, demographic models of post-divergence gene flow, and population size change through time. These analyses offer evidence that open habitats are an ancient component of the Central Highlands, and that wide-spread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Notably, though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may be more vulnerable from paleoclimatic changes.

opencc-zeroMay 2023View details →

Quantifying the age-structure of free-ranging delphinid populations: testing the accuracy of Unoccupied Aerial System-photogrammetry

Understanding the population health status of long-lived and slow-reproducing species is critical for their management. However, it can take decades with traditional monitoring techniques to detect population-level changes in demographic parameters. Early detection of the effects of environmental and anthropogenic stressors on vital rates would aid in forecasting changes in population dynamics and therefore inform management efforts. Changes in vital rates strongly correlate with deviations in population growth, highlighting the need for novel approaches that can provide early warning signs of population decline (e.g., changes in age-structure). We tested a novel and frequentist approach, using Unoccupied Aerial System- (UAS) photogrammetry, to assess the population age-structure of small delphinids. First, we measured the precision and accuracy of UAS-photogrammetry in estimating total body length (TL) of trained bottlenose dolphins (Tursiops truncatus). Using a log-transformed linear model, we estimated TL using the blowhole-to-dorsal-fin-distance (BHDF) for surfacing animals. To test the performance of UAS-photogrammetry to age-classify individuals, we then used length measurements from a 35-year dataset from a free-ranging bottlenose dolphin community to simulate UAS-estimates of BHDF and TL. We tested five age-classifiers and determined where young individuals (<10 years) were assigned when misclassified. Finally, we tested whether UAS-simulated BHDF only or the associated TL estimates provided better classifications. TL of surfacing dolphins was overestimated by 3.3% ±3.1% based on UAS-estimated BHDF. Our age-classifiers performed best in predicting age-class when using broader and fewer (two and three) age-class bins with ~80% and ~72% assignment performance, respectively. Overall, 72.5-93% of the individuals were correctly classified within two years of their actual age-class bin. Similar classification performances were obtained using both proxies. UAS-photogrammetry is a non-invasive, inexpensive, and effective method to estimate TL and age-class of free-swimming dolphins. UAS-photogrammetry can facilitate the detection of early signs of population changes, which can provide important insights for timely management decisions.

opencc-zeroMay 2023View details →

Social network and fitness data from age-structured populations of forked fungus beetles

We investigated the relationships between age, social behavior, and fitness at three levels of organization: the individual, the local social environment, and the population. Replicate groups of forked fungus beetles (Bolitotherus cornutus) were engineered to have either young- or old- biased age structures, and both social and reproductive behaviors were recorded.

opencc-zeroMay 2023View details →

Axiom canine microarray data from Australian dingoes and domestic dogs for admixture and population structure analysis

Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to inter-specific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. There has been concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here we apply genome-wide single nucleotide polymorphism (SNP) genotyping to a set of 385 wild and captive dingoes from across Australia and then carry out comparisons to domestic dogs, and perform ancestry modelling and biogeographic analyses to characterize population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes, challenging previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in southeastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policy makers to assess and inform dingo management policy and legislation moving forwards.

opencc-by-4.0Jul 2020View details →

Figure 5 in The spatial structure of а snow leopard population (Panthera uncia, Felidae, Carnivora) in east Kyrgyzstan

Figure 5. Spatial distribution of snow leopards in the Sarychat–Ertash Reserve.

Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units

Understanding the patterns and processes driving population structure is crucial for conservation planning. Spatial conservation units (CUs) for one or more species have been defined using similarities in communities, habitats, and resource management concerns. Additionally, CU boundaries can be informed by population genetic structure. Here, we determined the population structure of the Bobolink (Dolichonyx oryzivorus), a migratory grassland bird. Its breeding range spans longitudinally across most of North America in the northern U.S. and southern Canada, and its population has declined by 59% from 1971 to 2014. We sampled blood from Bobolinks at seven breeding sites and used a ddRAD sequencing approach to identify 3236 SNPs for population genetic analyses. Using the Bayesian clustering approach, STRUCTURE, we found low levels of genetic differentiation across the breeding range. F st values ranged from 0.002 to 0.036 among all population pairs, and genetic structure followed an isolation-by-distance model. Despite low levels of genetic differentiation, we found evidence for four genetic groupings— breeding populations in Oregon and British Columbia were distinct from each other as well as from Central and eastern North American breeding populations. Investigating the demographic history of the populations using approximate Bayesian computation, we found evidence that western Bobolink populations are not relict populations but instead were founded during a recent westward range expansion, possibly enabled by agricultural expansion. We identify four genetics-based CUs that may serve as a complementary spatial framework, broader in scale compared to the commonly-used Bird Conservation Regions, for defining and achieving population objectives.

Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.

Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)

Microsatellite dataset of 322 hare samples from five species: 76 samples from the broom hare (Lepus castroviejoi); 81 for the European hare (L. europaeus); 68 for the Iberian hare (L. granatensis); 77 for the mountain hare (L. timidus); and 20 for the Italian hare (L. corsicanus).

Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature

Pathogen life history theory assumes a positive relationship between pathogen load in host tissues and pathogen transmission. Empirical evidence for this relationship is surprisingly rare due to the difficulty of measuring transmission for many pathogens. The comparative method, where a common host is experimentally infected with a set of pathogen strains, is a powerful approach for investigating the relationships between pathogen load and transmission. The validity of such experimental estimates of strain-specific transmission is greatly enhanced if they can predict the pathogen population strain structure in nature. Borrelia burgdorferi is a multi-strain, tick-borne spirochete that causes Lyme disease in North America. This study used 11 field-collected strains of B. burgdorferi, a rodent host (Mus musculus, C3H/HeJ) and its tick vector (Ixodes scapularis) to determine the relationship between pathogen load in host tissues and lifetime host-to-tick transmission (HTT). Mice were experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT was measured by infesting mice with I. scapularis larval ticks on 3 separate occasions. The prevalence and abundance of the strains in the mouse tissues and the ticks were determined by qPCR. We used published databases to obtain estimates of the frequencies of these strains in wild I. scapularis populations. Spirochete loads in ticks and lifetime HTT varied significantly among the 11 strains of B. burgdorferi. Strains with higher spirochete loads in the host tissues were more likely to infect feeding larvae, which molted into nymphs with a higher probability of B. burgdorferi infection (i.e., higher HTT). Our laboratory-based estimates of lifetime HTT were predictive of the frequencies of these strains in wild I. scapularis populations. For B. burgdorferi, the strains that establish high abundance in host tissues and that have high lifetime transmission are the strains that are most common in nature.

Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales

Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.