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opencc-by-4.0Feb 2022View details →

Ugric vocabulary (appendix to Grünthal et al. 2022: Drastic demographic events triggered the Uralic spread)

Ugric cognates  (Appendix to the paper Grünthal, R., Heyd, V., Holopainen, S., Janhunen, J., Khanina, O., Miestamo, M., Nichols, J., Saarikivi, J. & Sinnemäki, K.  2022: Drastic demographic events triggered the Uralic spread. – Diachronica. https://doi.org/10.1075/dia.20038.gru)   Words found only in Hungarian and Khanty and/or Mansi.   Further work on Ugric etymologies (with updates to the information on this table) will be published on https://sanat.csc.fi/wiki/Hungarian_Historical_Phonology

opencc-by-4.0Feb 2022View details →

Indo-Iranian loans in Uralic (Appendix to Grünthal et al. 2022: Drastic demographic events triggered the Uralic spread)

Early Indo-Iranian loanwords in Uralic and their distribution (assembled from Holopainen, Sampsa 2019: Indo-Iranian borrowings in Uralic. PhD thesis, University of Helsinki).

opencc-by-4.0Feb 2022View details →

Proto-Uralic cognates (Appendix to Grünthal et al. 2022: Drastic demographic events triggered the Uralic spread)

A selection of Uralic cognates and their distribution (Appendix to the paper Grünthal, R., Heyd, V., Holopainen, S., Janhunen, J., Khanina, O., Miestamo, M., Nichols, J., Saarikivi, J. & Sinnemäki, K.  2022: Drastic demographic events triggered the Uralic spread. – Diachronica. https://doi.org/10.1075/dia.20038.gru)

opencc-zeroFeb 2022View details →

Population structure, patterns of natal dispersal, and demographic history in a declining aerial insectivore, the purple martin Progne subis

Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow, and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin (Progne subis) is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (P. s. subis) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (P. s. subis, P. s. arboricola, P. s. hesperia) across their North American breeding range by estimating effective population sizes over time. We used next-generation sequencing strategies for genomic analyses, integrating whole-genome resequencing data with continent-wide band encounter records to examine natal dispersal. We documented population structure across P. s. subis, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation-by-distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western P. s. arboricola and P. s. hesperia compared to the eastern P. s. subis subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in P. s. subis, and elucidate the origin of subspecies differentiation, highlighting the importance to conserve populations across the range to maximize genetic diversity and adaptive potential in the purple martin.

opencc-by-4.0Mar 2022View details →

WIld boar demographic parameters extracted from the literature

This is the data extraction and description of  parameters of WB population dynamics, including general drivers, population demography, mortality, reproduction, and spatial behaviour.  The definition of the most relevant parameters that describe the wild boar (WB) population dynamics is essential to guide African swine fever (ASF) control policies. These parameters should be framed considering different contexts, such as geographic, ecological and management contexts, and gaps of data useful for the parameter definition should be identified. This information would allow better harmonized monitoring of WB populations and higher impact of ASF management actions, as well as better parametrizing population dynamics and epidemiological models, which is key to develop more efficient cost-benefit strategies. ENETwild is a project funded by EFSA, www.enetwild.com.

opencc-by-4.0Mar 2022View details →

FaVCI2D Face Verification with Challenging Imposters and Diversified Demographics

Face verification aims to distinguish between genuine and imposter pairs of faces, which include the same or different identities, respectively. The performance reported in recent years gives the impression that the task is practically solved. Here, we revisit the problem and argue that existing evaluation datasets were built using two oversimplifying design choices. First, the usual identity selection to form imposter pairs is not challenging enough because, in practice, verification is needed to detect challenging imposters. Second, the underlying demographics of existing datasets are often insufficient to account for the wide diversity of facial characteristics of people from across the world. To mitigate these limitations, we introduce the FaVCI2D dataset. Imposter pairs are challenging because they include visually similar faces selected from a large pool of demographically diversified identities. The dataset also includes metadata related to gender, country and age to facilitate fine-grained analysis of results. FaVCI2D is generated from freely distributable resources. Experiments with state-of-the-art deep models that provide nearly 100% performance on existing datasets show a significant performance drop for FaVCI2D, confirming our starting hypothesis. Equally important, we analyze legal and ethical challenges which appeared in recent years and hindered the development of face analysis research. We introduce a series of design choices which address these challenges and make the dataset constitution and usage more sustainable and fairer. FaVCI2D is available at https://github.com/AIMultimediaLab/FaVCI2D-Face-Verification-with-Challenging-Imposters-and-Diversified-Demographics

opencc-zeroMar 2022View details →

Data from: Demographic correction – a tool for inference from individuals to populations

Estimation of responses of organisms to their environment using experimental manipulations, and comparison of such responses across sets of species, is one of the primary tools in ecology research. The most common approach is to compare response of a single life stage of species to an environmental factor and use this information to draw conclusions about population dynamics of these species. Such approach ignores the fact that interspecific fitness differences measured at a single life stage are not directly comparable and cannot be extrapolated to lifetime fitness of individuals and thus species' population dynamics. Comparison of one life stage only while omitting demographic information can strongly bias conclusions, both in experimental studies with a few species, and in large comparative studies. We illustrate the effect of this omission using both an exaggerated fictitious example, and biological data on congeneric species differing in their demography. We are showing, taking simple assumptions, that different demography can completely revert conclusions reached by a comparison based on an experiment focusing on a single life stage. We show that a "demographic correction", namely translating observed effects into differences in outcomes of demographic models, is a solution to this problem. It requires turning the detected effects from the experiment into changes of transition probabilities of projection matrix models. Although such solution is limited by the low number of species with demographic data available, we believe that existing data (and data likely to be collected in the near future) permit at least approximate handling of this problem.

opencc-zeroMar 2022View details →

Demographic, physiological, and genetic factors linked to poleward range expansion along the shoreline of China

Distribution range expansion is one of the most significant consequences of climate change in the Anthropocene. During range expansion, the former biogeographic barrier can be broken and then a new biogeographic pattern might appear. A comprehensive study, including demographic pattern, physiological performance and genetic features, is crucial for understanding how the expanding population occupies and survives in the new habitat, within which it formerly did not occur. In the present study, we investigated the demographic, physiological, and genetic features of the intertidal gastropod Nerita yoldii, which has extended its northern limit by ~200 km into areas that are warming up faster than the historical distribution over the former biogeographic break of the Yangtze River Estuary (YRE) during recent decades. The neutral SNPs data showed that the new marginal populations formed a distinct cluster established by a few founders. Demographic modeling analysis revealed that the new marginal populations experienced strong genetic bottlenecks followed by recent demographic expansion. Successful expansion that overcomes the founder effect (reduced genetic variation) might be attributed to its high capacity of rapid population growth and multiple introductions. According to the non-neutral SNPs under diversifying selection, there were high levels of heterozygosity in the new marginal populations, which might be beneficial for adapting to the novel thermal conditions. The common garden experiment showed that the new marginal populations have evolved divergent transcriptomic and physiological responses to heat stress, allowing them to occupy and survive in the novel environment. Our study also reveals a fast loss of transcriptional plasticity in the new marginal populations, potentially contributing to local adaptation. These results suggest a new biogeographic pattern for the snail N. yoldii has formed with the occurrence of demographic, physiologic and genetic changes, and emphasize the roles of adaptation of marginal populations during distribution range expansion.

opencc-zeroApr 2022View details →

Data from: Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range - wild grapevine sampling locations, Maxent input files, morphological and microsatellite data

This dataset contains raw data described in the paper: "Rahimi O., Ohana-Levi N., Brauner H., Inbar N., Hübner S. and Drori E. (2021) "Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range", accepted for publication in "Ecology and Evolution". The spatial distribution of plants is constrained by demographic and eco-geographic factors that determine the range and abundance of the species. In this study, we performed genetic and morphological analyzes based on SSR and OIV datasets. In addition, according to the spatial distribution model performed by Maxent software we found that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V.v. sylvestris distribution at its southern distribution range. All raw data used for this study can be found in this deposit which contains a table with grapevine locations, Maxent input files, morphological and microsatellite data.

opencc-zeroMay 2022View details →

Demographic consequences of heterogeneity in conspecific density dependence among mast fruiting tropical trees

The role of conspecific density dependence (CDD) in the maintenance of species richness is a central focus of tropical forest ecology. However, tests of CDD often ignore the integrated effects of CDD over multiple life-stages and their long-term impacts on population demography. We combined a 10-year time series of seed production, seedling recruitment and sapling and tree demography of three dominant Southeast Asian tree species that adopt a mast fruiting phenology. We used these data to construct individual-based models that examine the effects of CDD on population growth rates (λ) across life-history stages. Recruitment was driven by positive CDD for all species, supporting the predator satiation hypothesis, while negative CDD affected seedling and sapling growth of two species, significantly reducing λ. This negative CDD on juvenile growth overshadowed the positive CDD of recruitment, suggesting the cumulative effects of CDD during seedling and sapling development has greater importance than the positive CDD during infrequent masting events. Overall, CDD varied between positive and negative across life-history stages for all species, suggesting that assessments of CDD on transitions between just two stages (e.g. seeds-seedlings or juveniles-mature trees) likely misrepresents the importance of CDD on population growth and stability.

opencc-zeroMay 2022View details →

Water availability dictates how plant traits predict demographic rates

A major goal in ecology is to make generalizable predictions of organism responses to environmental variation based on their traits. However, straightforward relationships between traits and fitness are rare and likely vary with environmental context. Characterizing how traits mediate demographic responses to the environment may enhance predictions of organism responses to global change. We synthesized 15 years of demographic data and species-level traits in a shortgrass steppe to determine whether the effects of leaf and root traits on growth and survival depend on seasonal water availability. We predicted that (1) species with drought-tolerant traits, such as lower leaf turgor loss point (TLP) and higher leaf and root dry matter content (LDMC and RDMC), would be more likely to survive and grow in drier years due to higher wilting resistance, (2) these traits would not predict fitness in wetter years, and (3) traits that more directly measure physiological mechanisms of water use such as TLP would best predict demographic responses. We found that graminoids with more negative TLP and higher LDMC and RDMC had higher survival rates in drier years. Forbs demonstrated similar yet more variable responses. Graminoids grew larger in wetter years, regardless of traits. However, in both wet and dry years, graminoids with more negative TLP and higher LDMC and RDMC grew larger than less negative TLP and low LDMC and RDMC species. Traits significantly mediated the impact of drought on survival, but not growth, suggesting survival could be a stronger driver of species' drought response in this system. TLP predicted survival in drier years, but easier-to-measure LDMC and RDMC were equal or better predictors. These results advance our understanding of the mechanisms by which drought drives population dynamics, and show that abiotic context determines how traits drive fitness.

Rare species biodiversity, socio-demographics and local and landscape characteristics in Northern California community urban gardens

Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments where human management and disturbance is minimized. We know little about what species are rare, how many species are rare, and what management practices promote rare species in urban environments. Here, we identified which plants and species of birds and bees that control pests and pollinate crops are rare in urban gardens and assessed how social, biophysical factors, and cross-taxonomic comparisons influence rare species richness. We found overwhelming numbers of rare species, with over 50% of plant cultivars observed classified as rare. Our results highlight the importance of women, older individuals, and gardeners who live closer to garden sites in increasing the number of rare plants within urban areas. Fewer rare plants were found in older gardens and gardens with more bare soil. There were more rare bird species in larger gardens and more rare bee species where canopy cover was higher. We also found that in some cases, rarity begets rarity, with positive correlations found between the number of rare plants and bee species and between bee and bird species. Overall, our results suggest that urban gardens include a high number of species existing at low frequency and that social and biophysical factors promoting rare, planned biodiversity can cascade down to promote rare, associated biodiversity.

The expression of demographic costs of reproduction varies among coexisting plants with different life history traits

1. Demographic costs of reproduction in flowering plants should depend on life history and reproductive effort, but how the expression of costs varies with life history traits is poorly understood. 2. We experimentally increased and reduced reproductive effort (fruit production) to quantify demographic costs of reproduction in four coexisting species with contrasting growth forms (clonal vs. nonclonal) and flower production (single- vs. multi-flowered). We repeated the experiment in three years, and measured demographic rates the year after treatment. In two years, we also quantified costs of flower maintenance by contrasting the performance of nonfruiting plants with intact flowers and plants with their flowers removed. 3. Costs varied among species, in both magnitude and demographic rate affected. Costs of natural reproduction were expressed as reductions in size and fecundity next year, whereas increased reproduction additionally reduced sprouting probability. The magnitude of demographic costs of both reproduction and flower maintenance was highest in the nonclonal, multi-flowered species, and costs were more frequently detected in the two multi-flowered species than in the single-flowered ones. This may be explained by higher biomass allocation to reproductive parts and a longer flowering period in the former. Demographic costs of reproduction did not depend on clone size. 4. These results document that demographic costs vary among coexisting species sharing similar niches, and are associated with divergence in life history traits. Such trait-dependent variation in costs may reduce competition among coexisting species and facilitate diversity.

Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China

Tianshan Mountain provides a model for studying biological evolution and speciation. Here we assess the evolutionary history of the Ostrinia furnacalis and Ostrinia nubilalis, which are sympatric in the Yili River Valley in Xinjiang, China. Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI & COII & Cytb) and four nuclear DNA (nuDNA, EF-1α & Wingless & RPS5 & CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan) and MNS (Manasi). Our results reveal that there is a strong asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggest the genetic divergence between the two species in this area may have occurred in the late-Pleistocene (0.003–0.0127 Mya). Neutrality tests (Tajima's D, Fu's Fs) and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past, which may follow the 'mountain isolation' hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are clustered together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear and there is no strong correspondence between haplotypes and their geographical pattern for both ACB and ECB, implying that there has been frequent gene flow among the geographic populations in the Tianshan Mountains. These findings confirm that geological factors play an important role in driving genetic patterns.

opencc-by-4.0Jun 2022View details →

Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans

Inferred ROH and IBD calls from Korunes et al (2022). bioRxiv DOI: https://doi.org/10.1101/2020.12.14.422766 Samples originally collected and analyzed in Beleza et al. 2013, PLoS Genetics. Inferred local ancestry information can be found at <a href="https://doi.org/10.5281/zenodo.4021277">https://doi.org/10.5281/zenodo.4021277</a> See README.txt in upload for more detailed information.

Population structure and demographic analyses of Acanthocybium solandri from the Indo-Pacific and Atlantic oceans

This repository contains scripts, data and results for a populaton genomics study of genetic structure and demography of wahoo, Acanthocybium solandri, published in Journal of Biogeography: Haro-Bilbao et al. (2021) Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. In this work, we generated population allele frequencies for wahoo sampled at 11 locations around the globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs, we demonstrated a significant (but subtle) genetic divide between wahoo from the Indo-Pacific and those from the Atlantic. This genetic differentiation likely occurs against a background of high gene glow throughout the evolutionary history of wahoo, as we inferred from demographic analysis of select population pairs within and between oceanic regions. Analyses contained in this repository are for: (1) Filtering pooled ezRAD allele counts (assembled with dDocent and imputed using poolne_estim); (2) Estimation of genetic differentiation among globally sampled wahoo populations; (3) Estimation of site frequency spectra from joint allele frequencies among select population pairs; (4) Inference of demographic parameters (using δaδi); and (5) Generations of demographic simulation summary statistics. Most of the analyses are performed in R and can be run directly from within the repository directory, this includes: allele filtering, estimation of genetic differentiation, estimaiton of site frequency spectra, and generation of demographic summary statistics. Demographic inference using δaδi requires setup of a Unix environment: input data files and execution scripts are provided, but their implementation needs to be customised.

opencc-zeroJul 2022View details →

Demographic modelling helps tracking the rapid and recent divergence of a conifer species pair from central Mexico

Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they can evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify those factors that may lead to putative reproductive isolation. We explored various competing hypotheses to account for the rapid divergence of a fir species complex (Abies flinckii - A. religiosa) distributed in 'sky-islands' across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and center), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1,147 SNPs, generated by GBS, across 23 populations, and compared multiple demographic scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 Ma. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly-evolving species complexes as they may account for the large tropical and subtropical diversity.

opencc-zeroJul 2022View details →

Demographic history shapes genomic ancestry in hybrid zones

Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries), as well as heterogenicity (the genomic proportion heterozygous for ancestry), are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.

opencc-zeroAug 2022View details →

Genomic and morphometric data used in a demographic study of Coragyps vultures

The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000-year-old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following the natural selection imposed by this new and extreme, high-elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution.