Find research datasets worth reusing

Data from: Population genetic structures of two ecologically distinct species Betula platyphylla and B. ermanii inferred based on nuclear and chloroplast DNA markers

Climatic oscillations during the last glacial maximum (LGM) significantly affected the distribution patterns and genetic structure of extant plants. Northeast China (NEC) is a major biodiversity center in East Asia, and the influence of historical climate change on NEC populations is critical for understanding species responses to future climate change. However, only a few phylogeographic studies of cool-temperate deciduous tree species have been conducted in the area, and results are inconsistent for species with different niches or distribution areas. We employed multiple chloroplast and nuclear markers to investigate the genetic structure of two ecologically contrasting species, Betula platyphylla and B. ermanii, in NEC. Rare haplotypes were identified in the chloroplast genome of these species, and both exhibited high levels of nucleotide diversity based on a fragment of the nuclear gene G3PDH and microsatellites. Moreover, significant phylogeographic structure was detected for B. platyphylla, suggesting that these populations had recolonized from independent glacial refuges, whereas no genetic structure was found for B. ermanii.

Data from: Evolutionary and plastic phenotypic change can be just as fast as changes in population densities

Evolution and plasticity can drive population-level phenotypic change (e.g., changes in the mean phenotype) on time scales comparable to changes in population densities. However, it is unclear if phenotypic change has the potential to be just as fast as changes in densities, or if comparable rates of change only occur when densities are changing slow enough for phenotypes to keep pace. Moreover, it is unclear if this depends on the mode of adaptation. Using scaling theory and fast-slow dynamical systems theory, we develop a method for comparing maximum rates of density and phenotypic change estimated from population-level time series data. We apply our method to 30 published empirical studies where changes in morphological traits are caused by evolution, plasticity, or an unknown combination. For every study, the maximum rate of phenotypic change was 0.5 to 2.5 times faster than the maximum rate of change in density. Moreover, there were no systematic differences between systems with different modes of adaptation. Our results show that plasticity and evolution can drive phenotypic change just as fast as changes in densities. We discuss the implications of our results in terms of the strengths of feedbacks between population densities and traits.

Data from: Exploring a Pool-seq only approach for gaining population genomic insights in non-model species

Developing genomic insights is challenging in non-model species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data is used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta); one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual based SNPs) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (FST) between the two introduced populations exceeds that of the naturally sympatric populations (FST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies but estimates of average genic diversity differ (π ≈0.002 and π ≈0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq only approach can be suitable for detecting and quantifying genome wide population differentiation, and for comparing genomic diversity in populations of non-model species where reference genomes are lacking.

Data from: GPS tracking and population genomics suggest itinerant breeding across drastically different habitats in the Phainopepla

Migratory birds generally divide the annual cycle between discrete breeding and non-breeding ranges. Itinerant breeders, however, reproduce twice at different geographic locations, migrating between them. This unusual flexibility in movement ecology and breeding biology suggests that some species can rapidly modulate the conflicting physiological and behavioral traits required for migration and reproduction. The Phainopepla (Phainopepla nitens), a songbird of the southwestern USA, has long been suspected to breed first in desert habitats in spring, then migrate to woodland habitats to breed again in summer. However, direct evaluation of movement and gene flow among individuals breeding in different locations has previously been logistically intractable. We deployed GPS tags on free-flying Phainopeplas in southern California, all of which migrated to hypothesized woodland breeding habitats after desert breeding (an average distance of 232 km). GPS data also revealed previously unknown fall and spring stopover sites. Population genomic analyses revealed no genetic differentiation among desert and woodland breeding populations, indicating significant movement and gene flow across the region. Finally, we used random forest analyses to quantify substantial environmental differences among temporal stages. Our results provide direct evidence that individual Phainopeplas do indeed move between two drastically different breeding habitats in the same year, representing a rare and extreme example of life-history flexibility.

Data from: Restricted connectivity and population genetic fragility in a globally endangered hammerhead shark

Vagile, large-bodied marine organisms frequently have wide range dispersion but also dependence on coastal habitats for part of their life-history. These characteristics may induce complex population genetic structure patterns, with resulting implications for the management of exploited populations. The scalloped hammerhead, Sphyrna lewini, is a cosmopolitan, migratory shark in tropical and warm temperate waters, inhabiting coastal bays during parturition and juvenile development and the open ocean as adults. Here, we investigated the genetic connectivity and diversity of S. lewini in the western Atlantic using large sample coverage (N=308), and data from whole mitochondrial control region (mtCR) sequences and ten nuclear microsatellite loci. We detected significant population genetic structure with both mtCR and microsatellites markers (mtCR: ΦST = 0.60; p < 0.001; microsatellites: Dest 0.0794, p = 0.001, FST = 0.046, p < 0.05), and isolation by distance (mtCR r = 0.363, p = 0.009; microsatellites r = 0.638, p = 0.007). The migration and gene flow patterns, based on mtCR and microsatellites were asymmetric, and female reproductive philopatry is postulated to explain such population subdivision patterns. The notable population differentiation at microsatellites markers indicates low-levels of male-mediated gene flow in the western Atlantic. The overall effective population size was estimated as 299 (215 – 412 Confidence Interval), and there was no evidence of strong or recent bottleneck effects. Findings of at least three management units, moderate genetic diversity, and low effective population size in the context of current overfishing calls for intensive management aimed at short and long-term conservation for this endangered species in the western Atlantic Ocean.

Data from: Framework for quantifying population responses to disturbance reveals that coastal birds are highly resilient to hurricanes

Changes in the frequency and severity of extreme weather may introduce new threats to species that are already under stress from gradual habitat loss and climate change. We provide a probabilistic framework that quantifies potential threats by applying concepts from ecological resilience to single populations. Our approach uses computation to compare disturbance-impacted projections to a population's normal range of variation, quantifying the full range of potential impacts. We illustrate this framework with projection models for coastal birds, which are commonly depicted as vulnerable to disturbances, especially hurricanes and oil spills. We found that populations of coastal specialists are resilient to extreme disturbances, with high resistance to the effects of short-term reductions in vital rates and recovery within 20 years. Applying the general framework presented here across disturbance-prone species and ecosystems would improve understanding of population resilience and generate specific projections of resilience that are needed for effective conservation planning.

Data from: Wintering grounds, population size and evolutionary history of a cryptic passerine species from isotopic and genetic data

Cryptic species pose a particular challenge to biologists in the context of life history investigations because of the difficulty in their field discrimination. Additionally, there is normally a lag in their widespread acceptance by the scientific community once they are formally recognised. These two factors might constrain our ability to properly assess the conservation status of the different species conforming a cryptic complex. In this study, we analysed isotopic and genetic data to shed light into the still unclear wintering grounds, population size and evolutionary history of the Iberian chiffchaff (Phylloscopus ibericus), a species included within the Common chiffchaff (Phylloscopus collybita) until two decades ago due to their phenotypic similarity. We used molecular methods to identify spring-migrating Phylloscopus species captured in northern Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips (δ2Hc; which would reflect the signatures of their wintering grounds), we detected that δ2Hc values of Iberian chiffchaffs were similar to Willow warblers (Phylloscopus trochilus; a renowned trans-Saharan migrant), and higher than Common chiffchaffs (mostly a pre-Saharan migrant). These results strongly support the idea that Iberian chiffchaffs winter in tropical Africa. We additionally reconstructed the phylogeny and evolutionary history of the Iberian chiffchaff's clade using mitochondrial and nuclear markers. Our results revealed relatively high values of nucleotide diversity (and, hence, high Ne) for the species that were greater than the values of the Common/Iberian most recent common ancestor. This suggests that the Iberian chiffchaff did not experience strong bottlenecks after diverging from the Common chiffchaff approximately one million years ago. Ultimately, our study provides another illustrative example of how isotopic and genetic analysis tools can help to enhance our understanding of avian ecology and evolution.

opencc-by-4.0Aug 2020View details →

zenodo32/100

Extended Data: Population structure of Salmonella serotype Mbandaka

This project contains supplementary figures associated with the project.

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Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations: data related to publication

Data related to the following publication: "Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations"

opencc-by-4.0Sep 2020View details →

Data from: Mortality, perception, and scale: understanding how predation shapes space use in a wild prey population

Attempts to assess behavioral responses of prey to predation risk are often confounded by depredation of prey. Moreover, the scale at which the response of prey is assessed has important implications for discovering how predation risk alters prey behavior. Herein, we assessed space use of wild Ring-necked Pheasants (Phasianus colchicus) in response to spatial and temporal variation in recreational hunting. We radio-marked pheasants and monitored space use at two spatial scales: short-term seasonal home range, and nightly resting locations. Additionally, we considered temporal variation in predation risk by monitoring space use prior to and during the pheasant hunting season. Although we found no change in nightly resting location, pheasants subjected to predation risk expanded their home range and shifted home range location even when invulnerable to predation. Home range formation was plastic, with home ranges expanding and contracting as risk fluctuated before and during the hunting season. Depredation reduced the measured response within the population, obscuring the potential importance of perceived predation risk in shaping prey communities, particularly when not measured at the appropriate scale. By assessing space use of a wild prey population at multiple scales, considering spatial and temporal variation in predation risk, we show that not only does predation risk affect space use, but that the effects at the population level may be challenging to assess when not measured at the appropriate ecological scale because of the direct effects of differential mortality on the same behaviors.

Data from: A strong east-west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated based on two nuclear and one plastid sequences. Variation from four plastid regions and 17 nuclear microsatellite loci were used to decipher genetic structure in the carob tree and to test coalescent-based models by an Approximate Bayesian Computation (ABC) approach. We assessed our hypotheses by examining palaeobotanical records and hindcasting the past distribution of the carob tree at the Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using species distribution modelling (SDM). Results: The split between C. oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence within C. siliqua at 1.3 Ma. After a presence since the Oligocene, Ceratonia was found in the Western and the Eastern Mediterranean in the fossil records during the Pleistocene. Plastid and nuclear markers, characterized by low allelic richness, revealed a strong west-east genetic structuring. Approximate Bayesian computation (ABC) analyses rejected the ERH. Main conclusions: Our study supports a severe population decline during LIG. The strong west-east divergence and the occurrence of four lineages within C. siliqua provided support for a new hypothesis of multiple domestications of the carob tree from native populations throughout the Mediterranean basin.

Data from: The effects of climate warming on the migratory status of early summer populations of Mythimna separata(Walker) moths: a case-study of enhanced corn damage in central-northern China, 1980 - 2016

Mythimna separata (Walker) moths captured in light-traps were monitored in Luohe, central-northern China, from 1980 to 2016. Annual average temperature recorded an increase of 0.298 oC/10 years in this region in the period. Our results indicate that a rising Apr and May avarage temprature and earlier occurrences of days recording the highest day temperature (30℃) caused an advanced peak and increasing proportion of high ovarian development levels of first generation females in earlier summers. Results using Johnson's formulation of 'oogenesis-flight syndrome' indicate that increasing sexual maturity proportion has resulted in more emigrant individuals in the local first generaton moth becoming residents, and then increased individuls repidly in the local second generation moth since 2006. Consequences of this action have a boom in corn damage since 2007 in this region. Advanced peak dates of the first and second generation moth revealed the same response to increasing average monthly temperatures in the monitoring period. Increasing temperatures, the avarage May temperature exceeds or equal to 22℃, during the early 2000's may represent a physiological threshold for M. separata development. Our results suggest that climate warming may impact M. separata migratory status and cause a problem of crop production in this region.

Data from: Contrasting patterns of population structure at large and fine scales in an avian disturbance specialist of braided river ecosystems

Aim: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black-fronted tern (Chlidonias albostriatus); a specialist of the spatially and temporally dynamic environments of braided rivers. Location: New Zealand Methods: We used a three-pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b / control region), and phenotypic data (head-bill length, bill depth, wing length, weight). We determined large-scale genetic structure throughout the whole breeding range (approx. 150,000 km2), calculated genetic divergence of breeding populations, and tested for isolation-by-distance between populations. We investigated the level of fine-scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding populations to test for underlying mechanisms of population differentiation. Results: Nuclear and mitochondrial DNA showed that across their range black-fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation-by-distance. However, at fine geographical scales black-fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. Main conclusions: Significant fine-scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonisation of suitable habitat. For black-fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.

Data from: Influence of climate change and post-delisting management on long-term population viability of the conservation-reliant Kirtland's warbler

Rapid global climate change is resulting in novel abiotic and biotic conditions and interactions. Identifying management strategies that maximize probability of long-term persistence requires an understanding of the vulnerability of species to environmental changes. We sought to quantify the vulnerability of Kirtland's Warbler (Setophaga kirtlandii), a rare Neotropical migratory songbird that breeds almost exclusively in the Lower Peninsula of Michigan and winters in the Bahamian Archipelago, to projected environmental changes on the breeding and wintering grounds. We developed a population-level simulation model that incorporates the influence of annual environmental conditions on the breeding and wintering grounds, and parameterized the model using empirical relationships. We simulated independent and additive effects of reduced breeding grounds habitat quantity and quality, and wintering grounds habitat quality, on population viability. Our results indicated the Kirtland's Warbler population is stable under current environmental and management conditions. Reduced breeding grounds habitat quantity resulted in reductions of the stable population size, but did not cause extinction under the scenarios we examined. In contrast, projected large reductions in wintering grounds precipitation caused the population to decline, with risk of extinction magnified when breeding habitat quantity or quality also decreased. Our study indicates that probability of long-term persistence for Kirtland's Warbler will depend on climate change impacts to wintering grounds habitat quality, and contributes to the growing literature documenting the importance of considering the full annual cycle for understanding population dynamics of migratory species.

Data from: Chloroplast population genetics reveals low levels of genetic variation and conformation to the central–marginal hypothesis in Taxus wallichiana var. mairei, an endangered conifer endemic to China

The central–marginal hypothesis predicts that geographically peripheral populations should exhibit reduced genetic diversity and increased genetic differentiation than central populations due to smaller effective population size and stronger geographical isolation. We evaluated these predictions in the endangered conifer Taxus wallichiana var. mairei. Eight plastid simple sequence repeats (cpSSRs) were used to investigate plastid genetic variation in 22 populations of Taxus wallichiana var. mairei, encompassing nearly its entire distribution range. Low levels of plastid genetic variation and differentiation were detected in the populations, and the findings were attributed to low mutation rates, small population sizes, habitat fragmentation and isolation, and effective pollen or seed dispersal. Hunan and Hubei were identified as major refugia based on the number of private haplotypes and species distribution modeling. Trends in plastid genetic diversity and genetic differentiation from central to peripheral populations supported the predictions of the central–marginal hypothesis. In scenarios wherein the future climate becomes warmer, we predict that some peripheral populations will disappear and southern and southeastern regions will become significantly less habitable. Factors that include the levels of precipitation during the driest month, annual precipitation level, and annual temperature range will be decisive in shaping the future distribution of these populations. This study provides a theoretical basis for the conservation of T. wallichiana var. mairei.

opencc-zeroOct 2020View details →

Data from: Drivers of spatiotemporal variation in survival in a flyway population: a multi-colony study

1. Spatio-temporal variation in population dynamics of migratory populations is shaped by exposure to different environments during the annual cycle. Hence, exposure to similar environments should translate into synchrony in vital rates. Despite a wide-ranging breeding population, the Baltic/Wadden Sea flyway population of eiders (Somateria m. mollissima) shares wintering grounds in the southern Baltic Sea, inner Danish waters and the Wadden Sea; different colonies within this flyway population are therefore likely to exhibit some degree of synchrony in vital rates. 2. Here we used capture-recapture-recovery data to investigate the impact of hunting, winter climate (the North-Atlantic Oscillation Index), winter temperature, nitrogen runoff, autumn-winter body condition of blue mussels Mytilus spp., natural predation and epidemic disease (avian cholera) on annual survival of adult females in ten study colonies distributed between the Netherlands and Finland. Moreover, we tested how the degree of similarity in spatial winter distributions affected the degree of similarity in annual survival among colonies. 3. None of the covariates universally affected female survival. While the quality of blue mussels in the wintering area explained almost 40 % of the variation in survival of eiders breeding on Christiansø in the south-western Baltic Sea, incidence of epidemic disease explained > 60 % in two affected colonies. Furthermore, the spatial winter distribution did not appreciably influence annual survival rates in these ten colonies. 4. The lack of universal effects of spatial winter distribution and winter conditions on survival suggests that local breeding conditions may be more important, and hence prime targets for conservation efforts. Better monitoring of e.g. food quality, predation pressure and epidemic disease at the time of breeding could be the key to better understand the population dynamics in this endangered flyway population.

opencc-zeroOct 2020View details →

Data from: Allometric scaling of eDNA production in stream-dwelling brook trout (Salvelinus fontinalis) inferred from population size structure

Environmental DNA (eDNA) concentration exhibits a positive correlation with organism abundance in nature, but modelling this relationship could be substantially improved by incorporating the biology of eDNA production. A recent model (Yates et al. 2020) extended models of physiological allometric scaling to eDNA production, hypothesizing that brook trout eDNA production scales non-linearly with mass as a power-function with scaling coefficients < 1 in lakes. To validate this hypothesis, we re-analysed data from Wilcox et al. (2016) that examined the correlation between eDNA concentration and brook trout abundance in streams. We found that allometrically scaled mass (ASM) (e.g. ∑(individual mass0.36) best described patterns of eDNA concentration across streams (r2 = 0.43). ASM exhibited substantially improved model fit relative to biomass (r2 = 0.31, ∆AIC = 5.19), indicating that eDNA production did not scale linearly with biomass. However, the explanatory power of ASM was comparable to density (r2 = 0.40, ∆AIC = 1.25). Additionally, the optimal scaling coefficient estimated from the data (0.36) was substantially lower than that found in Yates et al. (2020) (0.72). Discrepancies between datasets could be attributable to ecological differences between study habitats (streams vs lakes) or due to the exclusion of juveniles (i.e. individuals < 75 mm) that can be abundant in stream environments. Nevertheless, this study adds to the growing body of literature demonstrating that individual eDNA production does not scale linearly with biomass.

opencc-zeroOct 2020View details →

Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1053 P. americana and other Periplaneta species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the USA.

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Data from: An integrated population model for estimating the relative effects of natural and anthropogenic factors on a threatened population of steelhead trout

This collection includes data on the abundance, age composition, and harvest of adult steelhead trout, as well as the numbers of juveniles released from a hatchery, for steelhead trout (Oncorhyncus mykiss) from the Skagit River in Washington, USA. It also includes estimates of the marine survival of hatchery-origin steelhead.

opencc-by-4.0Oct 2020View details →