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227 results for “demographic history”
Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species
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Data from: Demographic history and genomic diversity and divergence in blue tit populations across heterogeneous environments
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Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon
<p class="17"><span>A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (<i><span>Oncorhynchus kisutch</span></i>) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.</span></p>
A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data
<p>A common goal of population genomics and molecular ecology is to reconstruct the demographic history of a species of interest. A pair of powerful tools based on the sequentially Markovian coalescent have been developed to infer past population sizes using genome sequences. These methods are most useful when sequences are available for only a limited number of genomes and when the aim is to study ancient demographic events. The results of these analyses can be difficult to interpret accurately, because doing so requires some understanding of their theoretical basis and of their sensitivity to confounding factors. In this practical review, we explain some of the key concepts underpinning the pairwise and multiple sequentially Markovian coalescent methods (PSMC and MSMC, respectively). We relate these concepts to the use and interpretation of these methods, and we explain how the choice of different parameter values by the user can affect the accuracy and precision of the inferences. Based on our survey of 100 PSMC studies and 30 MSMC studies, we describe how the two methods are used in practice. Readers of this article will become familiar with the principles, practice, and interpretation of the sequentially Markovian coalescent for inferring demographic history.</p>
Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged fairywren
<p>The existence of distinct traits in island versus mainland populations offers opportunities to gain insights into how eco-evolutionary processes operate under natural conditions. We used two island colonization events in the white-winged fairywren (<i>Malurus </i><i>leucopterus</i>) to investigate the genomic and demographic origin of melanic plumage. This avian species is distributed across most of Australia, and males of the mainland subspecies (<i>M. l. leuconotus</i>) exhibit a blue nuptial plumage in contrast to males of two island subspecies – <i>M. l. leucopterus </i>on Dirk Hartog Island<i> </i>and <i>M. l. edouardi</i>on Barrow Island – that exhibit a black nuptial plumage. We used reduced-representation sequencing to explore differentiation and demographic history in this species and found clear patterns of divergence between mainland and island populations, with additional substructuring on the mainland. Divergence between the mainland and Dirk Hartog was approximately 10 times more recent than the split between the mainland and Barrow Island, supporting two independent colonizations. In both cases, estimated gene flow between the mainland and the islands was low, contributing to signals of divergence among subspecies. Our results present demographic reconstructions of mainland-island dynamics and associated plumage variation in white-winged fairywrens, with broader implications regarding our understanding of convergent evolution in insular populations.</p>
Data from: Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?
Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male-male competition within a species selects for capability to reproductively interfere with a closely related species. Here we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of C. chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, C. maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually-selected traits on interspecific competitive dynamics.
Data from: The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an under-appreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.
Data from: The demographic and life history costs of fear: trait-mediated effects of threat of predation on Aedes triseriatus
1. Predators alter prey populations via direct lethality (density-mediated effects), but in many taxa the indirect nonlethal threat of predation may be almost as strong an effect, altering phenotypically plastic traits such as prey morphology, behaviour, and life history (trait-mediated effects). There are costs to anti-predator defences and the strength of prey responses to cues of predation likely depends on both the perceived level of risk and food availability. 2. The goal of this study was to test the hypothesis that the costs of nonlethal trait-mediated interactions impacting larvae can have carryover effects that alter life history traits, adult characteristics, and ultimately population dynamics. 3. The effects of Toxorhynchites rutilus kairomones and chemical alarm cues on Aedes triseriatus were assessed in a two-level factorial design manipulating nutrient level (low or high) and chemical cues of predation (present or absent). 4. Nonlethal chemical cues of predation significantly decreased female survivorship, and significantly decreased female size. Females emerged as adults significantly earlier when exposed to predation cues when there was high nutrient availability. When raised in the low nutrient treatment and exposed to predator cues adult females had 2.1 times the hazard of death compared to high nutrient-no predator cues. Females raised in the high nutrient and predator cue treatment blood fed sooner than did females from other combinations. 5. Fear of predation can substantially alter prey life history traits and behaviour, which can cascade into dramatic population, community, and ecosystem effects. Exposure to predator cues significantly decreased estimated cohort rate of increase, potentially altering the expected population density of the next generation.
Data from: Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions
Drosophila subobscura presents a rich and complex chromosomal inversion polymorphism. It can thus be considered a model system i) to study the mechanisms originating inversions and how inversions affect the levels and patterns of variation in the inverted regions, and ii) to study adaptation at both the single-gene and chromosomal inversion levels. It is therefore important to infer its demographic history since previous information indicated that its nucleotide variation is not at mutation-drift equilibrium. For that purpose, we sequenced 16 non-coding regions distributed across those parts of the J chromosome not affected by inversions in the studied population and possibly either by other selective events. The pattern of variation detected in these 16 regions is similar to that previously reported within different chromosomal arrangements, suggesting that the latter results would, thus, mainly reflect recent demographic events rather than the partial selective sweep imposed by the origin and frequency increase of inversions. Among the simple demographic models considered in our ABC analysis of variation at the 16 regions, the model best supported by the data implies a population size expansion soon after the penultimate glacial period. This model constitutes a better null model and it is therefore an important resource for subsequent studies aiming among others to uncover selective events across the species genome. Our results also highlight the importance of introducing the possibility of multiple hits in the coalescent simulations with an outgroup.
Data from: Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas
Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.
Figure 5 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 5 Bayesian Skyline Plots based on the mtDNA partial control region sequences of Odontamblyopus lacepedii.
Figure 2 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 2 Maximum Likelihood tree is shown based on the control region haplotypes of Odontamblyopus lacepedii. The species of O. rebecca was used as the outgroup.
Figure 4 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 4 Mismatch distribution for demographic expansion based on mtDNA partial control region sequences of Odontamblyopus lacepedii.
Supplementary material 1 from: Liu X, Zhou Y, Ouyang S, Wu X (2019) Phylogeographic patterns and demographic history of Pomacea canaliculata and Pomacea maculata from different countries (Ampullariidae, Gastropoda, Mollusca). Nature Conservation 36: 71-92. https://doi.org/10.3897/natureconservation.36.35045
: Data type: molecular data
Data from: Evaluation of demographic history and neutral parameterization on the performance of Fst outlier tests
FST outlier tests are a potentially powerful way to detect genetic loci under spatially divergent selection. Unfortunately, the extent to which these tests are robust to non-equilibrium demographic histories has been under-studied. We developed a landscape-genetics simulator to test the effects of isolation by distance (IBD) and range expansion on FST outlier methods. We evaluated the two most commonly used methods for the identification of FST outliers (FDIST2 and BayeScan, which assume samples are evolutionarily independent) and two recent methods (FLK and Bayenv2, which estimate and account for evolutionary non-independence). Parameterization with a set of neutral loci ("neutral parameterization") always improved the performance of FLK and Bayenv2, while neutral parameterization caused FDIST2 to actually perform worse in the cases of IBD or range expansion. BayeScan was improved when the prior odds on neutrality was increased, regardless of the true odds in the data. On their best performance, however, the widely-used methods had high false-positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary non-independence. In addition, default settings in FDIST2 and BayeScan resulted in many false positives under balancing selection. However, all methods did very well if a large set of neutral loci is available to create empirical p-values. We conclude that in species that exhibit IBD or have undergone range expansion, many of the published FST outliers based on FDIST2 and BayeScan are probably false positives, but FLK and Bayenv2 show great promise for accurately identifying loci under spatially-divergent selection.
Figure 2 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 2. Mismatch distribution of Dugesia japonica from Taihang Mountains based on mitochondrial COI.
Demographic inferences and climatic niche modeling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale
<p>Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within 'sky islands.</p> <p>Here we studied the genetic structure of the Apollo butterfly in five such alpine islands (above 1000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly defavorable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya versus 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a non-equilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely inter-connected populations over time according to a 'metapopulation-pulsar' functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale.</p>
A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data
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Data from: Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas
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Demographic inferences and climatic niche modeling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale
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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.
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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.