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2,445 results for “Genetics: population”
Data from: Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis
Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that H. axyridis native area most likely consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate: (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete, (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Data from: Genetic variation and structure of Diaphorina citri (Hemiptera:Liviidae) in populations from México
The Asian citrus psyllid, Diaphorina citri Kuwayama, is native to Asia but has recently invaded North America. Asian citrus psyllid is a significant pest of citrus crops by its direct feeding but, more importantly, as the vector of the bacterium 'Candidatus Liberibacter asiaticus', which causes Huanglongbing disease. Asian citrus psyllid was first found in México in 2001 and 2002 and, since then, has spread quickly across the country, suggesting rapid adaptation to new environments. Yet, we lack information on the genetic variation and structure that could facilitate or inhibit adaptation. Using six microsatellite markers, we analyzed genetic variation and structure among six localities in México: three in western states near the Pacific coast and two in the Yucatán Peninsula near the Gulf of México. We found low genetic diversity (no more than three alleles per locus) and intermediate differentiation between all populations. Asian citrus psyllid populations clustered into two genetic groups, but, surprisingly, these clusters were present in western populations. The first group included El Arenal, and the second group included Autlán de Navarro, Colima, and Tecomán. Interestingly, both of the Yucatán populations shared variation from the two clusters, suggesting admixture. We infer that reproductive isolation, barriers to gene flow, local selection, and the possibility of multiple invasions have influenced the current genetic structure of Asian citrus psyllid in México.
Data from: The genetic underpinnings of population cyclicity: establishing expectations for the genetic anatomy of cycling populations
Despite extensive research into the mechanisms underlying population cyclicity, we have little understanding of the impacts of numerical fluctuations on the genetic variation of cycling populations. Thus, the potential implications of natural and anthropogenically-driven variation in population cycle dynamics on the diversity and evolutionary potential of cyclic populations is unclear. Here, we use Canada lynx Lynx canadensis matrix population models, set up in a linear stepping-stone, to generate demographic replicates of biologically realistic cycling populations. Overall, increasing cycle amplitude predictably reduced genetic diversity and increased genetic differentiation, with cyclic effects increased by population synchrony. Modest dispersal rates (1–3% of the population) between high and low amplitude cyclic populations did not diminish these effects suggesting that spatial variation in cyclic amplitude should be reflected in patterns of genetic diversity and differentiation at these rates. At high dispersal rates (6%) groups containing only high amplitude cyclic populations had higher diversity and lower differentiation than those mixed with low amplitude cyclic populations. Negative density-dependent dispersal did not impact genetic diversity, but did homogenize populations by reducing differentiation and patterns of isolation by distance. Surprisingly, temporal changes in diversity and differentiation throughout a cycle were not always consistent with population size. In particular, negative density-dependent dispersal simultaneously decreased differences in genetic diversity while increasing differences in genetic differentiation between numerical peaks and nadirs. Combined, our findings suggest demographic changes at fine temporal scales can impact genetic variation of interacting populations and provide testable predictions relating population cyclicty to genetic variation. Further, our results suggest that including realistic demographic and dispersal parameters in population genetic models and using information from temporal changes in genetic variation could help to discern complex demographic scenarios and illuminate population dynamics at fine temporal scales.
Data from: Sex-biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon
An approach frequently used to demonstrate a genetic basis to population-level phenotypic differences is to employ common garden rearing designs, where observed differences are assumed to be attributable to primarily additive genetic effects. Here, in two common garden experiments, we employed factorial breeding designs between wild and domestic, and among wild populations of Chinook salmon (Oncorhynchus tshawytscha). We measured the contribution of additive (VA) and maternal (VM) effects to the observed population differences for 17 life history and fitness-related traits. Our results show that, in general, maternal effects contribute more to phenotypic differences among populations than additive genetic effects. These results suggest that maternal effects are important in population phenotypic differentiation, and also signify that the inclusion of the maternal source of variation is critical when employing models to test population differences in salmon, such as in local adaptation studies.
Data From: Genetic structure of recently fragmented suburban populations of European stag beetle
<p>Habitat loss and fragmentation due to urbanisation can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (<i>Lucanus cervus</i> L.) populations in a suburban context using samples collected in three locations and during the period 2002-2016. The sampling area has seen recent landscape changes which resulted in population declines. Through the use of a suite of FST, clustering analysis, individual assignment, and relatedness analysis we assessed fine scale spatiotemporal genetic variation within and among habitat patches using 283 individuals successfully genotyped at 17 microsatellites. Our findings suggested the three locations to hold demographically independent populations, at least over time scales of relevance to conservation, though with higher levels of gene flow in the past. Contrary to expectation from tagging studies, dispersal appeared to be mainly female-biased. Although the life cycle of stag beetle suggests its generations to be discrete, no clear temporal structure was identified, which could be attributed to the varying duration of larval development. Since population bottlenecks were detected and estimates of effective number of breeders were low, conservation actions are eminent which should include the establishment of suitable dead wood for oviposition on both local and regional scales to increase (re)colonisation success and connectivity among current populations.</p>
Data from: Population genetic analysis of a parasitic mycovirus to infer the invasion history of its fungal host
Hymenoscyphus fraxineus mitovirus 1 (HfMV1) occurs in the fungus Hymenoscyphus fraxineus, an introduced plant pathogen responsible for the devastating ash dieback epidemic in Europe. Here, we explored the prevalence and genetic structure of HfMV1 in order to elucidate the invasion history of both the virus and the fungal host. A total of 1298 H. fraxineus isolates (181 from Japan and 1117 from Europe) were screened for the presence of this RNA virus and 301 virus-positive isolates subjected to partial sequence analysis of the viral RNA polymerase gene. Our results indicate a high mean prevalence (78.7%) of HfMV1 across European H. fraxineus isolates, which is supported by the observed high transmission rate (average 83.8%) of the mitovirus into sexual spores of its host. In accordance with an expected founder effect in the introduced population in Europe, only 1.1% of the Japanese isolates were tested virus positive. In Europe, HfMV1 shows low nucleotide diversity but a high number of haplotypes, which seem to be subjected to strong purifying selection. Phylogenetic and clustering analysis detected two genetically distinct HfMV1 groups, both present throughout Europe. This pattern supports the hypothesis that only two (mitovirus-carrying) H. fraxineus individuals were introduced into Europe as previously suggested from the bi-allelic nature of the fungus. Moreover, our data points to reciprocal mating events between the two introduced individuals, which presumably initiated the ash dieback epidemic in Europe.
Data from: How obstacles perturb population fronts and alter their genetic structure
As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from complex environments with many obstacles.
Data from: Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus
Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake (Sistrurus catenatus). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates less than 50. Heterozygosity-fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model-based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.
Genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations
<p>Rufiji tilapia (<em>Oreochromis urolepis urolepis</em>) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth-rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (<em>Oreochromis niloticus</em>). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices.</p>
Figure 1 in Effects of fragmentation on genetic variation in populations of the terrestrial earthworm Drawida japonica Michaelsen, 1892 (Oligochaeta, Moniligastridae) in Shandong and Liaodong peninsulas, China
Figure 1. Map of collection sites in Shandong (SD) and Liaodong (LD) peninsulas of China.
Intra-population genetic variation in the level and rhythm of daily activity in Drosophila immigrans
<p>Genetic diversity within a population, such as polymorphisms and personality, is considered to improve population performance because such intraspecific variations have the potential to alleviate the competition for a limited resource or the risk of predation and sexual harassment at a population-level. Variation in the level and rhythm of daily activity in a population could also affect population performance by directly altering ecological, social, and sexual interactions among individuals. However, it remains to be elucidated whether such intra-population variation in the level and rhythms of daily activity exists in a natural population. Here, we investigated the genetic variation in daily activity within a single natural population of Drosophila immigrans. We established 21 isofemale lines from a single natural population, and measured larval activity level and the level and daily pattern of adult activity over a 24 h period. Larval activity level significantly varied among isofemale lines. Likewise, the activity level in the adult stage significantly varied among lines. The significant variation was also found in the daily pattern of adult activity; some lines showed greater activity level in the daytime, and others showed greater activity level in the night. Our results consistently suggest that there is a genetic variation in behavioral activity in a natural population, probably contributing to shaping the population performance.</p>
Figure 2 in Genetic, ecological and morphological differences among populations of the cactophilic Drosophila mojavensis from southwestern USA and northwestern Mexico, with descriptions of two new subspecies
Figure 2. Lateral view of abdominal pattern in Drosophila m. mojavensis. (A) Male; (B) female.
Figure 2 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 2 Phylogenetic trees of the mtDNA control region haplotypes in C. guichenoti reconstructed with Bayesian inference. Numbers at nodes represent Bayesian posterior probabilities and neighbor-joining tree. At the right side of the figure, the numbers represent the total of individuals from different sampling locations in each haplotype.
Figure 3 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 3 Median-joining network of the mtDNA control region haplotypes of C. guichenoti. The size of each circle indicates the relative frequency of the corresponding haplotype in the whole data set.
Supplementary material 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Tables S1, S2, Figures S1, S2
Figure 4 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 4 Isolation by distance (IBD) relationship among C. guichenoti wild populations in five populations collected in 2009 a and seven populations collected in 2019 b.
Figure 1 from: Liu D, Lan F, Xie S, Diao Y, Zheng Y, Gong J (2021) Dynamic genetic diversity and population structure of Coreius guichenoti. ZooKeys 1055: 135-148. https://doi.org/10.3897/zookeys.1055.70117
Figure 1 Sampling localities of China (solid triangles indicate sites in 2009; solid circle indicate sites in 2019) of C. guichenoti. For full names of populations, see Table 1.
Figure 2 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions
Figure 2. Neighbor-joining (Saitou and Nei 1987) cladogram, based on the net nucleotide divergence.
Fig. 17. Habitats N in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 17. Habitats N of Steins, near the central transect (tables 2, 3; figs. 3, 5; appendix 1), 23 August 1990. Top. Looking N (from low hill behind allelemobile in fig. 16, top) across the grassland that separates site 16 (marmoratus) and site 12 (largely punctilinealis; figs. 3, 49). Bottom. Looking NE at grassland and alkali flats, from same place as the top photograph.
Fig. 2. Site 49 in Hybridization Among Western Whiptail Lizards (Cnemidophorus Tigris) In Southwestern New Mexico: Population Genetics, Morphology, And Ecology In Three Contact Zones
Fig. 2. Site 49 (appendix 2). Huerfano Butte (E side), Pima County, Arizona, about 43 km SSE Tucson, showing dramatic change in vegetation (desertification) in less than 70 years (based on Lowe et al., 1970a; their fig. 2). Top. About 1902, courtesy of Walter S. Phillips, University of Arizona Bottom. 16 March 1969.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.