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1,068 results for “demographic”
Data from: Post-Pleistocene demographic history of the North Atlantic endemic Irish moss Chondrus crispus: glacial survival, spatial expansion and gene flow
Range expansions and gene flow as micro-evolutionary processes played a leading role in the population demographic history of marine organisms. Herein, we sequenced partial mtDNA Cox1 gene from 26 assigned geographic populations in order to understand how Irish moss (Chondrus crispus) responded to severe climatic oscillations during the Pleistocene glaciations and contemporary forces such as gene flow. Phylogeographic patterns indicated that haplotype frequency distributions were strongly skewed, with nearly half found only in single samples and thus restricted to a single population. Analysis of molecular variance revealed that most of the variation was within populations with no significant genetic structuring on either side of the Atlantic. Demographic analyses indicated that ISI (Irish Sea and Ireland) and NS (the North Sea) areas experienced a slight trend of increase in population size over time, whereas EC (the English Channel) area experienced expansion beginning approximately 170,000-360,000 BP. The observed complex genetic pattern of C. crispus is consistent with a scenario of multiple unrelated founding events by survival of this species in at least three putative Pleistocene refugia along the European coastline, and subsequent trans-Atlantic dispersal combined with contiguous northward population expansion predating the LGM and geographically gene flow.
Data from: Genetic diversity, demographical history and conservation aspects of the endangered yew tree Taxus contorta (syn. Taxus fuana) in Pakistan
Western Himalayan yew (Taxus contorta Griffith, synonym T. fuana Nan Li & R.R. Mill), one of the highly prized tree species for its anticancer properties is experiencing severe reduction in populations across its range in Pakistan. We examined a chloroplast DNA region (trnL-F) and ten nuclear microsatellite loci variations among seven populations to investigate the levels of genetic diversity and demographical history of T. contorta in Pakistan. Low haplotype diversity (HT = 0.182), moderate level of microsatellite diversity (HE = 0.526 ± 0.034), significant population differentiation (FST = 0.106) and high level of inbreeding (FIS = 0.222-0.418) was found in T. contorta compared with its congeners. Results of mismatch distribution analysis, neutrality tests and data on glacial chronologies of western Himalaya indicated that demographic expansion of T. contorta in Pakistan predates extensive glaciations that occurred during late Pleistocene (140.06 thousand years ago (kya), and the spatial expansion most likely happened very recently in the Holocene (6.71 kya). An unprecedented level of habitat disturbances since past few decades coupled with the severe historic climate may have played an important role on an extant population structure of T. contorta. We have discussed a range of sustainable management measures for the ecological restoration of remnant populations as well as to exploit high economic benefits that can be obtained from this species.
Data from: Demographic responses of a site-faithful and territorial predator to its fluctuating prey: long-tailed skuas and arctic lemmings
1. Environmental variability, through interannual variation in food availability or climatic variables, is usually detrimental to population growth. It can even select for constancy in key life-history traits, though some exceptions are known. Changes in the level of environmental variability are therefore important to predict population growth or life-history evolution. Recently, several cyclic vole and lemming populations have shown large dynamical changes, that might affect rodent predator demography or life histories. 2. Skuas constitute an important case study among rodent predators, because of their strongly saturating breeding productivity (they lay only two eggs) and high degree of site fidelity, in which they differ from nomadic predators raising large broods in good rodent years. This suggests that they cannot capitalize on lemming peaks to the same extent as nomadic predators, and might be more vulnerable to collapses of rodent cycles. 3. We develop a model for the population dynamics of long-tailed skuas feeding on lemmings to assess the demographic consequences of such variable and nonstationary prey dynamics, based on data collected in NE Greenland. The model shows that populations of long-tailed skua sustain well changes in lemming dynamics, including temporary collapses (e.g. 10 years). A high floater-to-breeder ratio emerges from rigid territorial behaviour and a long life expectancy, which buffers the impact of adult abundance's decrease on the population reproductive output. 4. The size of the floater compartment is affected by changes in both mean and coefficient of variation of lemming densities (but not cycle amplitude and periodicity per se). In Greenland, the average lemming density is below the threshold density required for successful breeding (including during normally cyclic periods). Due to Jensen's inequality, skuas therefore benefit from lemming variability; a positive effect of environmental variation. 5. Long-tailed skua populations are strongly adapted to fluctuating lemming populations, an instance of demographic lability in the reproduction rate. They are also little affected by poor lemming periods, if there are enough floaters, or juveniles disperse to neighbouring populations. The status of Greenland skua populations therefore strongly depends upon floater numbers and juvenile movements, which are not known. This reveals a need to intensify colour-ringing efforts on the long-tailed skua at a circumpolar scale.
Data from: Comparing genetic diversity and demographic history in co-distributed wild South American camelids
Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1,000 individuals. For vicuña this bottleneck is inferred to have taken place ~3,300 years ago, but to have occurred more recently for guanaco at ~2,000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.
Data from: Gene flow and demographic history of leopards (Panthera pardus) in the central Indian highlands
Gene flow is a critical ecological process that must be maintained in order to counteract the detrimental effects of genetic drift in sub-divided populations, with conservation benefits ranging from promoting the persistence of small populations to spreading adaptive traits in changing environments. We evaluated historical and contemporary gene flow and effective population sizes of leopards in a landscape in central India using non-invasive sampling. Despite the dramatic changes in land use patterns in this landscape through recent times, we did not detect any signs that the leopard populations have been through a genetic bottleneck and they appear to have maintained migration-drift equilibrium. We found that historical levels of gene flow (mean mh = 0.07) were significantly higher than contemporary levels (mean mc = 0.03) and populations with large effective population sizes (Satpura and Kanha Tiger Reserves) are the larger exporters of migrants at both time scales. The greatest decline in historical versus contemporary gene flow is between pairs of reserves that are currently not connected by forest corridors (i.e, Melghat-Pench mh-mc= 0.063; and Kanha-Satpura mh-mc= 0.054). We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries, and suggest protection of forest corridors to maintain gene flow in this landscape.
Data from: Can collective memories shape fish distributions? A test, linking space-time occurrence models and population demographics
Social learning can be fundamental to cohesive group living, and schooling fishes have proven ideal test subjects for recent work in this field. For many species, both demographic factors, and inter- (and intra-) generational information exchange are considered vital ingredients in how movement decisions are reached. Yet key information is often missing on the spatial outcomes of such decisions, and questions concerning how migratory traditions are influenced by collective memory, density-dependent and density-independent processes remain open. To explore these issues, we focused on Atlantic herring (Clupea harengus), a long-lived, dense-schooling species of high commercial importance, noted for its unpredictable shifts in winter distribution, and developed a series of Bayesian space-time occurrence models to investigate wintering dynamics over 23 years, using point-referenced fishery and survey records from Icelandic waters. We included covariates reflecting local-scale environmental factors, temporally-lagged prey biomass and recent fishing activity, and through an index capturing distributional persistence over time, derived two proxies for spatial memory of past wintering sites. The previous winter's occurrence pattern was a strong predictor of the present pattern, its influence increasing with adult population size. Although the mechanistic underpinnings of this result remain uncertain, we suggest that a 'wisdom of the crowd' dynamic may be at play, by which navigational accuracy towards traditional wintering sites improves in larger and/or denser, better synchronized schools. Wintering herring also preferred warmer, fresher, moderately stratified waters of lower velocity, close to hotspots of summer zooplankton biomass, our results indicative of heightened environmental sensitivity in younger cohorts. Incorporating spatiotemporal correlation structure and time-varying regression coefficients improved model performance, and validation tests on independent observations one-year ahead illustrate the potential of uniting demographic information and non-stationary models to quantify both the strength of collective memory in animal groups and its relevance for the spatial management of populations.
Data from: Demographic plasticity facilitates ecological and economic resilience in a commercially important reef fish
1. Variation in life-history characteristics is evident within and across animal populations. Such variation is mediated by environmental gradients and reflects metabolic constraints or trade-offs that enhance reproductive outputs. While generalizations of life-history relationships across species provide a framework for predicting vulnerability to overexploitation, deciphering patterns of intraspecific variation may also enable recognition of peculiar features of populations that facilitate ecological resilience. 2. This study combines age-based biological data from geographically disparate populations of bluespine unicornfish (Naso unicornis)—the most commercially-valuable reef-associated species in the insular Indo-Pacific—to explore the magnitude and drivers of variation in life span and examine the mechanisms enabling peculiar mortality schedules. 3. Longevity and mortality schedules were investigated across eleven locations encompassing a range of latitudes and exploitation levels. The presence of different growth types was examined using back-calculated growth histories from otoliths. Growth-type dependent mortality (mortality rates associated with particular growth trajectories) was corroborated using population models that incorporated size-dependent competition. 4. We found a threefold geographic variation in life span that was strongly linked to temperature, but not to anthropogenic pressure or ocean productivity. All populations consistently displayed a two-phase mortality schedule, with higher than expected natural mortality rates in earlier stages of post-settlement life. Reconstructed growth histories and population models demonstrated that variable growth types within populations can yield this peculiar biphasic mortality schedule, where fast growers enjoy early reproductive outputs at the expense of greater mortality, and benefits for slow growers derive from extended reproductive outputs over a greater number of annual cycles. This promotes population resilience because individuals can take advantage of cycles of environmental change operating at both short and long-term scales. 5. Our results highlight a prevailing, fundamental misperception when comparing the life histories of long-lived tropical ectotherms: the seemingly incongruent combination of extended life spans with high mortality rates was enabled by coexistence of variable growth types in a population. Thus a demographic profile incorporating contrasting growth and mortality strategies obscures the demographic effects of harvest across space or time in N. unicornis and possibly other ectotherms with the combination of longevity and asymptotic growth.
Data from: Strong linkages between depth, longevity and demographic stability across marine sessile species
Understanding the role of the environment in shaping the evolution of life histories remains a major challenge in ecology and evolution. We synthesize longevity patterns of marine sessile species and find strong positive relationships between depth and maximum lifespan across multiple sessile marine taxa, including corals, bivalves, sponges and macroalgae. Using long-term demographic data on marine sessile and terrestrial plant species, we show that extreme longevity leads to strongly dampened population dynamics. We also used detailed analyses of Mediterranean red coral, with a maximum lifespan of 532 yr, to explore the life-history patterns of long-lived taxa and the vulnerability to external mortality sources that these characteristics can create. Depth-related environmental gradients – including light, food availability, temperature, and disturbance intensity –drive highly predictable distributions of life histories that, in turn, have predictable ecological consequences for the dynamics of natural populations.
Data from: Multi-DICE: R package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes
Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest, and composite likelihood optimization. Here, we introduce the R package Multi-DICE, a wrapper program that exploits existing simulation software for straight-forward and flexible execution of hierarchical model-based inference using the aSFS, which is derived from genomic-scale data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding event pulses, and specifying flexible hyperprior distributions. In sum, Multi-DICE provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a valuable tool for comparative phylogeography and population genomics.
Data from: Comparative genetic structure and demographic history in endemic Galápagos weevils
The challenge of maintaining genetic diversity within populations can be exacerbated for island endemics if they display population dynamics and behavioral attributes that expose them to genetic drift without the benefits of gene-flow. We assess patterns of genetic structure and demographic history in twenty seven populations of nine species of flightless endemic Galápagos weevils from nine of the islands and one winged introduced close relative. Analysis of mitochondrial DNA reveals significant population structure and moderately variable, though demographically stable, populations for lowland endemics (Fst= 0.094 to 0.541; π: 0.014 to 0.042; Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203), in contrast to signals of past contractions and expansions in highland specialists on two islands (Mismatch p=0.003 to 0.026 and D (Tajima)=-0.601to1.203). We interpret this series of variable and highly structured population groups as a system of long-established independently founded island units, where structuring could be a signal of micro-allopatric differentiation due to patchy host plant distribution and poor dispersal abilities. We suggest that the severe reduction and subsequent increase of suitably moist habitat that accompanied past climatic variation could have contributed to the observed population fluctuations in highland specialists. We propose the future exploration of hybridization between the introduced and highland endemic species on Santa Cruz, especially given the expansion of the introduced species into the highlands, the sensitivity to past climatic variation detected in highland populations and the potentially threatened state of single-island endemics.
Data from: Demographic responses of rare forest plants to multiple stressors: the role of deer, invasive species and nutrients
Forest ecosystems in eastern North America face multiple threats or stressors including plant and animal invasions and increased white-tailed deer (Odocoileus virginianus) herbivory. While each stressor may have independent detrimental effects on native biota, stressors often co-occur and are likely to have interactive effects. Despite recognition that concurrent processes drive plant demographic responses, few studies evaluate independent and combined effect of stressors. Using a network of 12 sites that varied in non-native plant cover and introduced earthworm density and biomass we experimentally assessed effects of deer exclusion (30 x 30 m paired plots), slug exclusion and nutrient addition on survival, growth and fecundity of four rare forest understorey plant species (Aristolochia serpentaria L., Agrimonia rostellata Wallr., Carex retroflexa Muhl. ex Willd, and Trillium erectum L). We found that single and combined effects of stressors were species-specific and varied according to plant stage and demographic parameter. Interactions were prevalent among all studied stressors and, for most cases, did not follow predicted responses. We found detrimental deer herbivory effects on reproductive A. rostellata and non-consumptive effects on A. serpentaria and T. erectum. Negative deer effects follow underlying predictions, and override effects of other stressors, even when other concurrent processes are at play. Contrary to expectations, we did not find negative effects of non-native plants. Earthworms had positive effects on A. rostellata and C. retroflexa (especially when deer were excluded), but negative effects on T. erectum. Slug effects were dependent on other stressors, especially on interactions with non-native plants and earthworms. Nutrient addition had a negative effect on survival of A. serpentaria and T. erectum, but positive effects on C. retroflexa and T. erectum growth. Synthesis: We found prevalent but unpredictable interactions among all study factors and plant species. Negative direct and indirect deer effects overrode impacts of all other stressors we investigated. A multi-factor approach is critical to predict plant responses to concurrent environmental forces. Assessment of combined effects should form an essential component of subsequent research on plant demography and management of declining species.
Data from: Effects of growth rate, size, and light availability on tree survival across life stages: a demographic analysis accounting for missing values and small sample sizes
Background: Plant survival is a key factor in forest dynamics and survival probabilities often vary across life stages. Studies specifically aimed at assessing tree survival are unusual and so data initially designed for other purposes often need to be used; such data are more likely to contain errors than data collected for this specific purpose. Results: We investigate the survival rates of ten tree species in a dataset designed to monitor growth rates. As some individuals were not included in the census at some time points we use capture-mark-recapture methods both to allow us to account for missing individuals, and to estimate relocation probabilities. Growth rates, size, and light availability were included as covariates in the model predicting survival rates. The study demonstrates that tree mortality is best described as constant between years and size-dependent at early life stages and size independent at later life stages for most species of UK hardwood. We have demonstrated that even with a twenty-year dataset it is possible to discern variability both between individuals and between species. Conclusions: Our work illustrates the potential utility of the method applied here for calculating plant population dynamics parameters in time replicated datasets with small sample sizes and missing individuals without any loss of sample size, and including explanatory covariates.
Data from: Long-term demographic surveys reveal a consistent relationship between average occupancy and abundance within local populations of a butterfly metapopulation
<p>Species distribution models are the tool of choice for large-scale population monitoring, environmental association studies, and predictions of range shifts under future environmental conditions. Available data and familiarity of the tools rather than the underlying population dynamics often dictate the choice of specific method — especially for the case of presence–absence data. Yet, for predictive purposes, the relationship between occupancy and abundance embodied in the models should reflect the actual population dynamics of the modelled species. To understand the relationship of occupancy and abundance in a heterogeneous landscape at the scale of local populations, we built a spatio-temporal regression model of populations of the Glanville fritillary butterfly (Melitaea cinxia) in a Baltic Sea archipelago. Our data comprised nineteen years of habitat surveys and snapshot data of land use in the region. We used variance partitioning to quantify relative contributions of land use, habitat quality, and metapopulation covariates. The model revealed a consistent and positive, but noisy relationship between average occupancy and mean abundance in local populations. Patterns of abundance were highly variable across years, with large uncorrelated random variation and strong local population stochasticity. In contrast, the spatio-temporal random effect, habitat quality, population connectivity, and patch size explained variation in occupancy, vindicating metapopulation theory as the basis for modelling occupancy patterns in fragmented landscapes. Previous abundance was an important predictor in the occupancy model, which points to a spillover of abundance into occupancy dynamics. While occupancy models can successfully model large-scale population structure and average occupancy, extinction probability estimates for local populations derived from occupancy-only models are overconfident, as extinction risk is dependent on actual, not average, abundance.</p>
Data from: The susceptibility of Echinacea angustifolia to a specialist aphid: eco-evolutionary perspective on genotypic variation and demographic consequences
1. Plants and their herbivores may influence each other's fitness and, hence, genetic dynamics, as well as their demography. Conversely, variation in fitness-related traits may influence the occurrence or intensity of the interaction. Disentangling the fitness consequences of an interaction in nature from the influence of fitness variation on it is challenging, but important to clarifying the ecological and evolutionary dynamics of plants with their herbivores. 2. As part of a larger effort to elucidate eco-evolutionary dynamics in a population of Echinacea angustifolia that is subject to severe fragmentation, we initiated an experiment in 2001 to evaluate differences in fitness among plants of three genotypic classes resulting from matings of plants from different remnant populations ('between', B), plants randomly chosen from the same remnant ('within', W) and maternal siblings ('inbreds', I). The experiment was planted into a field undergoing restoration to a prairie community. Fitness components of individual plants were recorded through 2012. During 2004–2010, each plant was also monitored for its load of Aphis echinaceae, a specialist insect herbivore. 3. Within a season, aphid-load depended consistently on a plant's location and on its load the previous season. Further, flowering individuals generally harboured more aphids than non-flowering plants. In analyses of overall plant fitness, within each genotypic class, fitness was greatest for plants with the greatest aphid-loads, consistent with the preference of aphids for flowering individuals. Inbreeding depression was severe, with I plants producing 60% fewer achenes than W or B plants, and varied with aphid-load. To distinguish the role of aphid choice from the effect of aphid herbivory in the relationship between plant fitness and aphid-load, we evaluated how components of fitness varied with prior aphid-load. Notably, genotype I plants with high aphid-loads the previous year produced far fewer achenes per flower head than those that carried fewer aphids. 4. Synthesis. Sibmating reduces individuals' demographic contribution by 60% over the first 12 years. Outbred individuals tolerate this aphid; each produces on average about 200 achenes per head in a year, despite a heavy aphid-load the previous year. However, inbreeding, which is greater in severely fragmented prairie habitat, results in poor tolerance. Aphid herbivory exacerbates inbreeding depression, further reducing the contribution of those individuals to population growth. This study illustrates an approach that helps to distinguish fitness-dependent attraction of herbivores from the effects of herbivory on plant fitness and demography, a goal that is critically important to eco-evolutionary understanding.
Data from: Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange, and distinct demographic histories
Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization timeframe suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.
Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling
We estimated the effective population sizes (Ne) and tested for short-term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D-loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean Ne estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake-level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro-endemics and populations in less favourable habitats have smaller Ne, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.
Data from: Tropical specialist versus climate generalist: diversification and demographic history of sister species of Carlia skinks from northwestern Australia
Species endemic to the tropical regions are expected to be vulnerable to future climate change due in part to their relatively narrow climatic niches. In addition, these species are more likely to have responded strongly to past climatic change, and this can be explored through phylogeographic analyses. To test the hypothesis that tropical specialists are more sensitive to climate change than climate generalists, we generated and analyze sequence data from mtDNA and ~2500 exons to compare scales of historical persistence and population fluctuation in two sister species of Australian rainbow skinks: the tropical specialist Carlia johnstonei and the climate generalist C. triacantha. We expect the tropical specialist species to have deeper and finer-scale phylogeographic structure and stronger demographic fluctuations relative to the closely related climate generalist species, which should have had more stable populations through periods of harsh climate in the late Quaternary. Within C. johnstonei, we find that populations from the northern Kimberley islands are highly divergent from mainland populations. In C. triacantha, one major clade occurs across the deserts and into the mesic Top End, and another occurs primarily in the Kimberley with scattered records eastwards. Where their ranges overlap in the Kimberley, both mitochondrial and nuclear DNA suggest stronger phylogeographic structure and range expansion within the tropical specialist, whereas the climate generalist has minimal structuring and no evidence of recent past range expansion. These results are consistent with the hypothesis that tropical specialists are more sensitive to past climatic change.
Data from: Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system
Habitat discontinuity, anthropogenic disturbance, and overharvesting have led to population fragmentation and declines worldwide. Preservation of remaining natural genetic diversity is crucial to avoid continued genetic erosion. Brown trout (Salmo trutta L.) is an ideal model species for studying anthropogenic influences on genetic integrity, as it has experienced significant genetic alterations throughout its natural distribution range due to habitat fragmentation, overexploitation, translocations, and stocking. The Pasvik River is a subarctic riverine system shared between Norway, Russia and Finland, subdivided by seven hydroelectric power dams that destroyed about 70% of natural spawning and nursing areas. Stocking is applied in certain river parts to support the natural brown trout population. Adjacent river segments with different management strategies (stocked versus not stocked) facilitated the simultaneous assessment of genetic impacts of dams and stocking based on analyses of 16 short tandem repeat loci. Dams were expected to increase genetic differentiation between and reduce genetic diversity within river sections. Contrastingly, stocking was predicted to promote genetic homogenization and diversity, but also potentially lead to loss of private alleles and to genetic erosion. Our results showed comparatively low heterozygosity and clear genetic differentiation between adjacent sections in non-stocked river parts, indicating that dams prevent migration and contribute to genetic isolation and loss of genetic diversity. Furthermore, genetic differentiation was low and heterozygosity relatively high across stocked sections. However, in stocked river sections, we found signatures of recent bottlenecks and reductions in private alleles, indicating that only a subset of individuals contribute to reproduction, potentially leading to divergence away from the natural genetic state. Taken together, these results indicate that stocking counteracts the negative fragmentation effects of dams, but also that stocking practices should be planned carefully in order to ensure long-term preservation of natural genetic diversity and integrity in brown trout and other species in regulated river systems.
Data from: Demographic history influences spatial patterns of genetic diversity in recently expanded coyote (Canis latrans) populations
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common. The southern and more recent expansion front occurred approximately 40 years later and across territory where gray wolves have been historically absent and remnant red wolves were extirpated in the 1970s. We conducted a genetic survey at 10 microsatellite loci of 482 coyotes originating from 11 eastern U.S. states to address how divergent demographic histories influence geographic patterns of genetic diversity. We found that population structure corresponded to a north-south divide, which is consistent with the two known expansion routes. Additionally, we observed extremely high genetic diversity, which is atypical of recently expanded populations and is likely the result of multiple complex demographic processes, in addition to hybridization with other Canis species. Finally, we considered the transition of allele frequencies across geographic space and suggest the mid-Atlantic states of North Carolina and Virginia as an emerging contact zone between these two distinct coyote expansion fronts.
Data from: Museum DNA reveals the demographic history of the endangered Seychelles warbler
The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.