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opencc-zeroJun 2021View details →

Run and output files from: Holocene population expansion of a tropical bee coincides with early human colonisation of Fiji rather than climate change

There is substantial debate about the relative roles of climate change and human activities on biodiversity and species demographies over the Holocene. In some cases, these two factors can be resolved using fossil data, but for many taxa such data are not available. Inferring historical demographies of taxa has become common, but the methodologies are mostly recent and their shortcomings often unexplored. The bee genus Homalictus is developing into a tractable model system for understanding how native bee populations in tropical islands have responded to past climate change. We greatly expand on previous studies using sequences of the mitochondrial gene COI from 474 specimens and between 171 and 3,928 autosomal (DArTSeq) SNP loci from 19 specimens of the native Fijian bee, Homalictus fijiensis (Perkins & Cheesman, 1928), to explore its historical demography using coalescent and mismatch analyses. We ask whether past changes in demography were human- or climate-driven, while considering analytical assumptions. We show that inferred changes in population sizes are too recent to be explained by past climate change. Instead we find that a dramatic increase in population size for the main island of Viti Levu coincides with increasing occupation by humans and their modification of the environment. We found no corresponding change in bee population size for another major island, Kadavu, where human populations and agricultural activities have been historically very low. Our analyses indicate that molecular approaches can be used to disentangle the impacts of humans and climate change on a major tropical pollinator and that stringent analytical approaches are required for reliable interpretation of results.

FIG. 5. Correlation between the spatial distribution index and population density. A in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 5. Correlation between the spatial distribution index and population density. A. For Brephulopsis cylindrica and Xeropicta derbentina at 160 plots for three years. B. For Harmozica ravergiensis in nine sites×20 plots for two years. РИС. 5. Корреляция меЖду индексом пространственного распределения и плотностью популяции. А. Для Brephulopsis cylindrica и Xeropicta derbentina на 160 плоЩадках За три года. В. Для Harmozica ravergiensis на девяти участках по 20 плоЩадок За два года.

FIG. 4 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 4. Boxplots for estimating the density of different age classes in the Xeropicta derbentina population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 4. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Xeropicta derbentina в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 3 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 3. Boxplots for estimating the density of different age classes in the Brephulopsis cylindrica population in warm months of 2017, 2019, and 2020 for 160 test plots. Adult snails are represented by red boxes; juvenile snails are represented by blue boxes. РИС. 3. Боксплоты для оценок плотности раЗличных воЗрастных классов в популяции Brephulopsis cylindrica в раЗные теплые месяцы 2017, 2019 и 2020 гг. для 160 пробных плоЩадок. ВЗрослые особи покаЗаны красным цветом, ювенильные особи покаЗаны голубым цветом.

FIG. 2 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 2. Scheme of plots in a regular grid. A. Study site. B. Brephulopsis cylindrica and Xeropicta derbentina in the field. C. Scheme of plots in a regular grid. РИС. 2. Регулярная сетка плоЩадок. A. РасполоЖение исследуемого участка. B. Brephulopsis cylindrica и Xeropicta derbentina в месте обитания. C. Схема регулярной сетки плоЩадок.

opencc-by-4.0Jun 2019View details →

SNP call data for: The current epidemic of the barley pathogen Ramularia collo-cygni derives from a recent population expansion and shows global admixture

Ramularia Leaf Spot is becoming an ever increasing problem in main barley growing regions since the 1980s, causing up to 70% yield loss in extreme cases. Yet, the causal agent Ramularia collo-cygni, remains poorly studied. The diversity of the pathogen in the field thus far remains unknown. Furthermore, it is unknown to which extend the pathogen has a sexual reproductive cycle. To date, the teleomorph of R. collo-cygni has not been observed. To study the genetic diversity of R. collo-cygni and to get more insights into its biology, we sequenced the genomes of 19 R. collo-cygni isolates from multiple geographic locations and diverse hosts. Here we share the SNP call data as well as the reference genome. The reference genome files and assembly can be found on ENI: GCA_900074925.1 https://www.ebi.ac.uk/ena/data/view/GCA_900074925.1 The raw sequence data is also available through ENI: ERX2296228 https://www.ebi.ac.uk/ena/data/view/ERX2296228

opencc-zeroNov 2022View details →

Data for: Population niche width is driven by within-individual niche expansion and individual specialization in introduced brook trout in mountain lakes

The width of a population's resource use niche is determined by individual diet breadth ("within-individual component") and the degree of niche partitioning between individuals ("between-individual component"). The balance between these two factors affects ecological stability and evolutionary trajectories, and may shift as ecological opportunity permits broader population niches. Lakes in California's Sierra Nevada Mountains vary in resource diversity for introduced brook trout (Salvelinus fontinalis) due to elevation, lake morphometry, and watershed features. We compared the relative contributions of within- and between-individual niche components to two measures of the dietary niches of thirteen populations of brook trout: prey taxonomic composition and prey size distribution. For both taxonomic and size diversity of fish diets, population niche width was positively related to both the within- and between-individual components. For taxonomic diversity, the two components increased in parallel, while for size diversity, the between-individual component became more important relative to the within-individual component in populations with the greatest niche widths. Our results support the Niche Variation Hypothesis that populations with broader niches are more heterogeneous among individuals and show that individual niche width and individual specialization can operate in parallel to expand the population niche.

opencc-zeroDec 2022View details →

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum

Pleistocene climate cycles are well known to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; ~21,000 years ago) have been surmised to lead to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of twenty co-distributed boreal-breeding bird species of North America from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to deglaciation during the middle Wisconsin period (~45,000 years ago) whereas genetic diversity was maintained throughout the LGM despite shifts in geographic range. We conclude that earlier glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these high-latitude species. We did not find differences in historic population dynamics between species differing in migratory behaviour, contributing to growing evidence that major switches in migratory strategy during the Last Glacial Maximum are unnecessary to explain contemporary migratory patterns.

publicJun 2021View details →

Run and output files from: Holocene population expansion of a tropical bee coincides with early human colonisation of Fiji rather than climate change

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publicDec 2022View details →

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum

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publicNov 2022View details →

Data for: Population niche width is driven by within-individual niche expansion and individual specialization in introduced brook trout in mountain lakes

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opencc-zeroOct 2020View details →

Weak founder effects but significant spatial genetic imprint of recent contraction and expansion of European beech populations.

Understanding the ecological and evolutionary processes occurring during species range shifts is important in the current context of global change. Here, we investigate the interplay between recent expansion, gene flow and genetic drift, and their consequences for genetic diversity and structure at landscape and local scales in European beech (Fagus sylvatica L.) On Mont Ventoux, South-Eastern France, we located beech forest refugia at the time of the most recent population minimum, approximately 150 years ago, and sampled 71 populations (2042 trees) in both refugia and expanding populations over an area of 15,000 ha. We inferred patterns of gene flow and genetic structure using 12 microsatellite markers. We identified six plots as originating from planting, rather than natural establishment, mostly from local genetic material. Comparing genetic diversity and structure in refugia versus recent populations did not support the existence of founder effects: heterozygosity (He = 0.667) and allelic richness (Ar = 4.298) were similar, and FST was low (0.031 overall). Still, significant spatial evidence of colonization was detected, with He increasing along the expansion front, while genetic differentiation from the entire pool (βWT) decreased. Isolation by distance was found in refugia but not in recently expanding populations. Our study indicates that beech capacities for colonization and gene flow were sufficient to preserve genetic diversity despite recent forest contraction and expansion. Because beech has long distance pollen and seed dispersal, these results illustrate a 'best case scenario' for the maintenance of high genetic diversity and adaptive potential under climate-change related range change.

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FIG. 1 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 1. Map of study sites. РИС. 1. Карта раЗмеЩения исследуемых участков.

opencc-zeroJun 2022View details →

Population expansion, divergence, and persistence in western fence lizards (Sceloporus occidentalis) at the northern extreme of their distributional range

Population dynamics within species at the edge of their distributional range, including the formation of genetic structure during range expansion, are difficult to study when they have had limited time to evolve. Western Fence Lizards (Sceloporus occidentalis) have a patchy distribution at the northern edge of their range around the Puget Sound, Washington, where they almost exclusively occur on imperiled coastal habitats. The entire region was covered by Pleistocene glaciation as recently as 16,000 years ago, suggesting that populations must have colonized these habitats relatively recently. We tested for population differentiation across this landscape using genome-wide SNPs and morphological data. A time-calibrated species tree supports the hypothesis of a post-glacial establishment and subsequent population expansion into the region. Despite a strong signal for fine-scale population genetic structure across the Puget Sound with as many as 8–10 distinct subpopulations supported by the SNP data, there is minimal evidence for morphological differentiation at this same spatiotemporal scale. Historical demographic analyses suggest that populations expanded and diverged across the region as the Cordilleran Ice Sheet receded. Population isolation, lack of dispersal corridors, and strict habitat requirements are the key drivers of population divergence in this system. These same factors may prove detrimental to the future persistence of populations as they cope with increasing shoreline development associated with urbanization.

opencc-zeroAug 2022View details →

Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

opencc-zeroDec 2020View details →

Parental population range expansion before secondary contact promotes heterosis

Population genomic analysis of hybrid zones is instrumental to our understanding of the evolution of reproductive isolation. Many temperate hybrid zones are formed by the secondary contact between two parental populations that have undergone post-glacial range expansion. Here we show that explicitly accounting for historical parental isolation followed by range expansion prior to secondary contact is fundamental for explaining genetic and fitness patterns in these hybrid zones. Specifically, ancestral population expansion can result in allele surfing where neutral or slightly deleterious mutations drift to high frequency at the expansion front. If these surfed deleterious alleles are recessive, they can contribute to substantial heterosis in hybrids produced at secondary contact, counteracting negative effects of Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening reproductive isolation. When BDMIs are linked to such recessive deleterious alleles the fitness benefit of introgression at these loci can facilitate introgression at the BDMIs. The extent to which this occurs depends on the strength of selection against the linked deleterious alleles and the distribution of recombination across the chromosome. Finally, surfing of neutral loci can alter the expected pattern of population ancestry, thus accounting for historical population expansion is necessary to develop accurate null genomic models of secondary-contact hybrid zones.

opencc-zeroSep 2021View details →

Larger males facilitate population expansion in Ophraella communa

<div class="WordSection1"> <ol> <li>One of the most intriguing concepts in animal ecology is the reproductive advantages offered by larger body size, and the females prefer to mate with larger males in order to gain reproductive advantage. </li> <li>Currently, it is not clear how females recognize signs of male "quality" and what mechanisms are involved in producing offspring with direct or indirect benefits. Our study aims to assess the preferences of females for males in Ophraella communa, determine the reproductive benefits and reveal the underlying mechanism behind this advantage.</li> <li>We demonstrate that male body size is an important determinant in the evolutionary process of O. communa, affecting female mate choice. Moreover, our study establishes that females prefer males with a larger body size, and this could further improve the developmental and reproductive fitness of their offspring. Finally, we focus on the seminal fluid proteins (SFPs) in O. communa, determine differentially expressed genes (i.e., OcACE, OcCBP and OcSFP) by analyzing their proteomes and transcriptomes, and define the role of these SFPs-related genes through RNAi. </li> <li>Our study proved that the reproductive benefit of large males may be regulated by biased expression of crucial SFPs genes. The present study advances our understanding of the biological significance of preferential mating.</li> </ol> </div>

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A digital GIS update to the classic Ulbrich 1930 map of muskrat (Undatra zibethica) population range expansion in Central Europe

This dataset is a digital version of a seminal dispersal data set of muskrat spread in Central Europe. We obtained and scanned an original copy of Ulbrich (1930), creating a digital image file, which we then geo-referenced in Arc Gis 10.2. The data herein contains metadata explaining the conversion process, necessary images to geo-reference the map, reference points used to "fix" the dispersal map to a map of present-day Europe, intermediate files (points and polygons produced when tracing the population ranges), and the final spatial dataset.   Reference to the original data:  Ulbrich, Johannes.  1930.  Die Bisamratte; lebenweise, gang ihrer ausbreitung in Europa, wirtschaftliche bedeutung und bekampfung.  Heinrich, Dresden.

opencc-by-4.0Mar 2023View details →

opencc-zeroSep 2023View details →

Sequencing data for: Chronosequence of invasion reveals minimal losses of population genomic diversity, niche expansion, and trait divergence in the polyploid, leafy spurge

Rapid evolution may play an important role in the range expansion of invasive species and modify forecasts of invasion, which are the backbone of land management strategies. However, losses of genetic variation associated with colonization bottlenecks may constrain trait and niche divergence at leading range edges, thereby impacting management decisions that anticipate future range expansion. The spatial and temporal scales over which adaptation contributes to invasion dynamics remain unresolved. We leveraged detailed records of the ~130-year invasion history of the invasive polyploid plant, leafy spurge (Euphorbia virgata), across ~500km in Minnesota, U.S.A. We examined the consequences of range expansion for population genomic diversity, niche breadth, and the evolution of germination behavior. Using genotyping-by-sequencing, we found some population structure in the range core, where introduction occurred, but panmixia among all other populations. Range expansion was accompanied by only modest losses in sequence diversity, with small, isolated populations at the leading edge harboring similar levels of diversity to those in the range core. The climatic niche expanded during most of the range expansion, and the niche of the range core was largely non-overlapping with the invasion front. Ecological niche models indicated that mean temperature of the warmest quarter was the strongest determinant of habitat suitability and that populations at the leading edge had the lowest habitat suitability. Guided by these findings, we tested for rapid evolution in germination behavior over the time course of range expansion using a common garden experiment and temperature manipulations. Germination behavior diverged from early to late phases of the invasion, with populations from later phases having higher dormancy at lower temperatures. Our results suggest that trait evolution may have contributed to niche expansion during invasion and that distribution models, which inform future management planning, may underestimate invasion potential without accounting for evolution.