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134 results for “Population Expansion”
Data from: Expansion history and environmental suitability shape effective population size in a plant invasion
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Population expansion, divergence, and persistence in western fence lizards (Sceloporus occidentalis) at the northern extreme of their distributional range
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The code used to simulate range expansion in "The effect of the recombination rate between adaptive loci on the capacity of a population to expand its range"
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Data from: Population structure, ancestral admixture, gene flow, and landscape association of blacklegged ticks during range expansion in the Midwestern U.S.
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Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge
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Weak founder effects but significant spatial genetic imprint of recent contraction and expansion of European beech populations.
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Ecological and behavioral mechanisms of density-dependent habitat expansion in a recovering African ungulate population
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Larger males facilitate population expansion in Ophraella communa
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Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time
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Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow
The demographic and phylogeographic histories of species provide insight into the processes responsible for generating biological diversity, and genomic datasets are now permitting the estimation of species histories with unprecedented accuracy. We used a genomic single nucleotide polymorphism (SNP) dataset generated using a RAD-Seq method to investigate the historical demography and phylogeography of a widespread lowland Neotropical bird (Xenops minutus). As expected, we found that prominent landscape features that act as dispersal barriers, such as Amazonian rivers and the Andes Mountains, are associated with the deepest phylogeographic breaks, and also that isolation by distance is limited in areas between these barriers. In addition, we inferred positive population growth for most populations and detected evidence of historical gene flow between populations that are now physically isolated. Although we were able to reconstruct the history of Xenops minutus with unprecedented resolution, we had difficulty conclusively relating this history to the landscape events implicated in many Neotropical diversification hypotheses. We suggest that even if many traditional diversification hypotheses remain untestable, investigations using genomic datasets will provide greater resolution of species histories in the Neotropics and elsewhere.
Data from: The population origins and expansion of feral cats in Australia
The historical literature suggests that in Australia, the domestic cat (Felis catus) had a European origin [~200 years before present (ybp)], but it is unclear if cats arrived from across the Asian land bridge contemporaneously with the dingo (4000 ybp), or perhaps immigrated ~40000 ybp in association with Aboriginal settlement from Asia. The origin of cats in Australia is important because the continent has a complex and ancient faunal assemblage that is dominated by endemic rodents and marsupials and lacks the large placental carnivores found on other large continents. Cats are now ubiquitous across the entire Australian continent and have been implicit in the range contraction or extinction of its small to medium sized (<3.5kg) mammals. We analyzed the population structure of 830 cats using 15 short tandem repeat (STR) genomic markers. Their origin appears to come exclusively from European founders. Feral cats in continental Australia exhibit high genetic diversity in comparison with the low diversity found in populations of feral cats living on islands. The genetic structure is consistent with a rapid westerly expansion from eastern Australia and a limited expansion in coastal Western Australia. Australian cats show modest if any population structure and a close genetic alignment with European feral cats as compared to cats from Asia, the Christmas and Cocos (Keeling) Islands (Indian Ocean), and European wildcats (F. silvestris silvestris).
Data from: How traffic facilitates population expansion of invasive species along roads: the case of common ragweed in Germany
1. Because common ragweed (Ambrosia artemisiifolia L., henceforth Ambrosia) has negative effects on human health, it is a common focus for management, which would benefit from a better understanding of the underlying mechanisms by which the species spreads. Road systems are known to be invasion corridors, but the conduit function of vehicles for the rapid spread of Ambrosia along roads and for population extension along roadside verges has not yet been demonstrated convincingly. 2. To quantify the effect of different traffic volumes on the dispersal and population extension of Ambrosia we used two approaches: First, by combining field experiments along roads with records of the seed rain around single plants, we simulated a combined dispersal kernel that revealed the interactions between primary dispersal and traffic-mediated secondary dispersal. Second, we recorded seedling recruitment around isolated roadside populations over two years to determine how traffic-related parameters affect population extension. 3. The longest traffic-mediated dispersal distances exceeded those of primary dispersal by about one order of magnitude. Traffic volume had a significant positive effect on dispersal distances and on the lateral deposition of seeds on the road verge. 4. Seedling recruitment around isolated roadside populations was significantly higher in the driving direction than against, but only at the distance where the major seed rain of traffic-mediated dispersal is to be expected according to the combined dispersal kernel (3-15 m). 5. Synthesis and applications: This study isolates effects of road traffic from confounding mechanisms (e.g. mowing machinery, propagule pressure from infested fields) on common ragweed (Ambrosia artemsiifolia L.) invasions. Results demonstrate traffic-mediated dispersal in Ambrosia invasions as a routine and predictable process that facilitates population extension in the direction of traffic along roadsides, depending on traffic volume. This highlights the importance of prioritizing mowing along high use roads and mowing of isolated populations to prevent seed abscission and further spread of common ragweed Ambrosia.
Data from: Homogenous population genetic structure of the non-native raccoon dog (Nyctereutes procyonoides) in Europe as a result of rapid population expansion
The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species' dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large 'central' population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations.
Data from: Loci under selection during multiple range expansions of an invasive plant are mostly population-specific, but patterns are associated with climate
Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate-related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene-level patterns of evolution may be population specific.
Data from: Long-term expansion of juniper populations in managed landscapes: patterns in space and time
1. Forest cover has increased world-wide over the last decade despite continuous forest fragmentation. However, a lack of long-term demographic data hinders our understanding of the spatial dynamics of colonization in remnant populations inhabiting recently protected areas or set-aside rural lands. 2. We investigated the population expansion of the Phoenician juniper (Juniperus phoenicea subsp. turbinata), which is an endozoochorous Mediterranean tree species inhabiting landscapes that have been managed for many centuries. By combining the photointerpretation of aerial photos that have been taken over the last 50 years with in situ sampling and spatial analyses of replicated plots, we estimated the population growth over the chronosequence; identified hotspots, coldspots and outliers of regeneration; and assessed the roles of key environmental factors in driving demographic expansion patterns, including elevation, initial density and distance to remnant forests. 3. Ecological factors leading to seed limitation, such as initial plant density, are expected to drive colonization patterns at the early stages. Factors mediating the competition for limiting resources, such as water availability, would prevail at later stages of expansion. We further expect that nucleated colonization patterns emerge driven by vertebrate seed dispersal. 4. The photointerpretation of aerial images in combination with in situ measurements has yielded reliable density data. Overall, our results show a marked demographic expansion during the first decade followed by a period of steady and heterogeneous population growth with signs of local population decline. We found evidence of nucleated establishment patterns as expected for an endozoochorous species. Hotspots and outliers of regeneration emerged throughout the study chronosequence, whereas coldspots of regeneration only appeared at advanced colonization stages. Factors influencing dispersal limitation had contrasting effects at different colonization stages, and the initial density influenced population growth at various spatial scales. 5. Synthesis. The photointerpretation of aerial images shows that the influence of dispersal limitation versus factors mediating competitive responses changes throughout colonization stages. Whereas dispersal limitation is the main factor influencing colonization at early stages, competition for local resources controls population growth at later stages. Therefore, long-term studies are required to capture the overall combined influence of key ecological factors in shaping long-term spatial demographic trends.
Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1–0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.
Data from: Impact of population expansion on genetic diversity and structure of river otters (Lontra canadensis) in central North America
Populations of North American river otters (Lontra canadensis) declined throughout large portions of the continent during the early 1900s due to habitat degradation and unregulated trapping. River otters had been extirpated in North Dakota (ND), but the Red River Valley has since been recolonized, with potential source populations including the neighboring states of Minnesota or South Dakota, or the Canadian province of Manitoba (MB). We genotyped 9 microsatellite loci in 121 samples to determine the source population of river otters in the Red River Valley of ND, as well as to assess population structure and diversity of river otters in central North America. Overall, genetic diversity was high, with an average observed heterozygosity of 0.58. Genetic differentiation was low (F ST < 0.05) between river otters in ND and those of Minnesota, suggesting that eastern ND was recolonized by river otters from Minnesota. River otters from MB were genetically distinct from all other sampled populations. Low genetic differentiation (F ST = 0.044) between South Dakota and Louisiana (LA) suggested that reintroductions using LA stock were successful. The genetic distinctiveness of river otters from different geographic regions should be considered when deciding on source populations for future translocations.
Data from: Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)
Genetic diversity, and thus the adaptive potential of invasive populations, is largely based on three factors: patterns of genetic diversity in the species' native range, the number and location of introductions, and the number of founding individuals per introduction. Specifically, reductions in genetic diversity ("founder effects") should be stronger for species with low within-population diversity in their native range and few introductions of few individuals to the invasive range. We test these predictions with Geranium carolinianum, a winter annual herb native to North America and invasive in China. We measure the extent of founder effects using allozymes and microsatellites, and ask whether this is consistent with its colonization history and patterns of diversity in the native range. In the native range, genetic diversity is higher and structure is lower than expected based on life-history traits. In China, our results provide evidence for multiple introductions near Nanjing, Jiangsu province, with subsequent range expansion to the west and south. Patterns of genetic diversity across China reveal weak founder effects that are driven largely by low- diversity populations at the expansion front, away from the introduction location. This suggests that reduced diversity in China has resulted from successive founder events during range expansion, and that the loss of genetic diversity in the Nanjing area was mitigated by multiple introductions from diverse source populations. This has implications for the future of G. carolinianum in China, as continued gene flow among populations should eventually increase genetic diversity within the more recently founded populations.
Data from: Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe
Even though populations of many large carnivores are expanding throughout Europe, the Eurasian lynx population in the Western Carpathians seems unable to spread beyond the western boundaries of its current distributional range. Many factors, both extrinsic and intrinsic, can influence the potential for range expansion: landscape fragmentation, natal philopatry, low natural fecundity and high mortality, and low and sex-biased dispersal rates. In this study we used non-invasive genetic sampling to determine population size fluctuation, sub-structuring and social organisation of the peripheral lynx population at the Czech-Slovak border. Even though the population size has been relatively stable over the period studied (2010-2016), the individual inbreeding coefficients of residents at the end of the study were much higher than those of founders at the beginning of the study. While non-resident individuals (predominantly males) occurred regularly in the study population, only resident individuals with well-established home ranges participated in breeding and produced offspring. Almost half the offspring detected in the study (predominantly females) settled in or near the natal area. Subsequent incestuous mating resulted in production of inbred individuals, reduction of effective population size of the population, and sub-structuring of the population through formation of two distinct family lineages. Our study illustrates how social constraints, such as territoriality, breeding of residents and natal philopatry of females lead to incestuous mating in small-sized populations, especially at the periphery of their distribution. This threat should be taken into account in planning of conservation and population recovery of species with similar social structure.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.
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