scholarly journals Phylogeographic structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe

2019 ◽  
Author(s):  
Rodrigo Vega ◽  
Allan D. McDevitt ◽  
Joanna Stojak ◽  
Alina Mishta ◽  
Jan M. Wójcik ◽  
...  
Keyword(s):  
Demographic History ◽  
Population Expansion ◽  
Glacial Refugia ◽  
Intraspecific Diversity ◽  
Phylogeographic Structure ◽  
Evolutionary Potential ◽  
Early Diversification ◽  
Patterns And Processes ◽  
Sorex Minutus ◽  
Pygmy Shrew

ABSTRACTSouthern and northern glacial refugia are considered paradigms that explain the complex phylogeographic patterns and processes of European biota. Although the Eurasian pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae) has been used a model species to study geographic isolation and genetic diversification in Mediterranean peninsulas in the Last Glacial Maximum (LGM), and post-glacial population expansion from cryptic northern glacial refugia in Western and Central Europe, there has been incomplete knowledge about the phylogeographic structure, genetic differentiation and demographic history within these regions. Here, we provide a revisited statistical phylogeographic study of S. minutus with greater sampling coverage in terms of numbers of individuals and geographic range, making it the most comprehensive investigation of this species to date. The results showed support for genetically distinct and diverse phylogeographic groups consistent with southern and northern glacial refugia, as expected from previous studies, but also identified geographical barriers concordant with glaciated mountain ranges during the LGM, early diversification events dated between the Upper Pleistocene and Lower Holocene for the main phylogeographic groups, and recent (post-LGM) patterns of demographic expansions. The results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.

scholarly journals Phylogeographical structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe

2020 ◽  
Vol 129 (4) ◽  
pp. 901-917 ◽  
Author(s):  
Rodrigo Vega ◽  
Allan D McDevitt ◽  
Joanna Stojak ◽  
Alina Mishta ◽  
Jan M Wójcik ◽  
...  
Keyword(s):  
Demographic History ◽  
Glacial Refugia ◽  
Intraspecific Diversity ◽  
Evolutionary Potential ◽  
Mountain Ranges ◽  
Early Diversification ◽  
Patterns And Processes ◽  
Sorex Minutus ◽  
Pygmy Shrew ◽  
The Last Glacial

Abstract Southern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Northern glacial refugia for the pygmy shrew Sorex minutus in Europe revealed by phylogeographic analyses and species distribution modelling

Ecography ◽  
2010 ◽  
pp. no-no ◽  
Author(s):  
Rodrigo Vega ◽  
Camilla Fløjgaard ◽  
Andrés Lira-Noriega ◽  
Yoshinori Nakazawa ◽  
Jens-Christian Svenning ◽  
...  
Keyword(s):  
Species Distribution ◽  
Glacial Refugia ◽  
Species Distribution Modelling ◽  
Distribution Modelling ◽  
Sorex Minutus ◽  
Pygmy Shrew

scholarly journals Small-mammal assemblages inhabiting Sphagnum peat bogs in various regions of Poland

2012 ◽  
Vol 49 (2) ◽  
pp. 115-133
Author(s):  
Mateusz Ciechanowski ◽  
Jan Cichocki ◽  
Agnieszka Ważna ◽  
Barbara Piłacińska
Keyword(s):  
Small Mammal ◽  
Western Europe ◽  
Habitat Degradation ◽  
Myodes Glareolus ◽  
Peat Bogs ◽  
Trophic Conditions ◽  
Characteristic Features ◽  
Mammal Assemblages ◽  
Sorex Minutus ◽  
Pygmy Shrew

Abstract We studied species composition of assemblages of small mammals (rodents and shrews) inhabiting Polish 25 ombrotrophic mires and quaking bogs in several regions in order to reveal characteristic features of their quantitative structure and compare them between regions, internal zones of the bog habitats, and different levels of anthropogenic degradation. We reviewed also all published results of small-mammal trapping in such habitats. Mammals were captured in pitfalls, snap traps and live traps on 12 bogs of the Pomerania region, 4 bogs of the Orawa-Nowy Targ Basin (Kotlina Orawsko-Nowotarska), 3 bogs in the Świętokrzyskie Mts, and 6 bogs in Wielkopolska and the Lubusz Land. Additionally, we included materials collected from Barber traps (pitfalls) used during studies of epigeic invertebrates on 4 bogs. In total, 598 individuals of 12 species were collected. The number of pitfall captures per 100 trapnights was very low (7.0-7.8), suggesting low population density. Shrews predominated among mammals captured in pitfalls, and the assemblage structure appeared to be similar to impoverished forest fauna, slightly enriched with ubiquitous species from meadows and agroecosystems, with a very small percentage of typical wetland species (Neomys fodiens, Neomys anomalus, Microtus oeconomus). Rodents (mostly Myodes glareolus) predominated only in samples obtained by live and snap traps. Pygmy shrew Sorex minutus was the most numerous species at most sites, sometimes being the only small mammal in that habitat, especially in well-preserved, treeless parts of bogs, dominated by Sphagnum peatmoss. The dominance and high constancy of S. minutus appear to be a characteristic feature of small-mammal assemblages inhabiting ombrotrophic mires, at least in some regions of Central and Western Europe. Enrichment of the fauna with other species might be related to either improved trophic conditions (by contact with mineralized ground waters) or habitat degradation (by peat mining, drainage, and subsequent secondary succession).

scholarly journals Expansion of Genetic Diversity in Randomly Mating Founder Populations of Alternaria brassicicola Infecting Cakile maritima in Australia

2010 ◽  
Vol 76 (6) ◽  
pp. 1946-1954 ◽  
Author(s):  
C. C. Linde ◽  
J. A. Liles ◽  
P. H. Thrall
Keyword(s):  
Genetic Diversity ◽  
Plant Pathogens ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Alternaria Brassicicola ◽  
Evolutionary Potential ◽  
Recent Population Expansion ◽  
Fungal Plant Pathogens ◽  
Cakile Maritima ◽  
Founder Populations

ABSTRACT Founder populations of fungal plant pathogens are expected to have low levels of genetic diversity coupled with further genetic drift due to, e.g., limited host availability, which should result in additional population bottlenecks. This study used microsatellite markers in the interaction between Cakile maritima and the fungal pathogen Alternaria brassicicola to explore genetic expectations associated with such situations. The host, C. maritima, was introduced into Australia approximately 100 years ago, but it is unknown whether the pathogen was already present in Australia, as it has a wide occurrence, or whether it was introduced to Australia on brassicaceous hosts. Eleven A. brassicicola populations were studied, and all showed moderate levels of gene and genotypic diversity. Chi-square tests of the frequencies of mating type alleles, a large number of genotypes, and linkage equilibrium among microsatellite loci all suggest A. brassicicola reproduces sexually. Significant genetic differentiation was found among populations, but there was no evidence for isolation by distance effects. Bayesian analyses identified eight clusters where the inferred clusters did not represent geographical populations but instead consisted of individuals admixed from all populations. Further analysis indicated that fungal populations were more likely to have experienced a recent population expansion than a population bottleneck. It is suggested that A. brassicicola has been introduced into Australia multiple times, potentially increasing the diversity and size of any A. brassicola populations already present there. Combined with its ability to reproduce sexually, such processes appear to have increased the evolutionary potential of the pathogen through recent population expansions.

scholarly journals Reef development and Sea level changes drive Acanthaster Population Expansion in the Indo-Pacific region

2020 ◽  
Author(s):  
P.C. Pretorius ◽  
T.B. Hoareau
Keyword(s):  
Population Size ◽  
Sea Level ◽  
Environmental Changes ◽  
Sequence Data ◽  
Demographic History ◽  
Population Expansion ◽  
Population Level ◽  
Sea Level Changes ◽  
Reef Development ◽  
Curve Fitting Method

AbstractMolecular clock calibration is central in population genetics as it provides an accurate inference of demographic history, whereby helping with the identification of driving factors of population changes in an ecosystem. This is particularly important for coral reef species that are seriously threatened globally and in need of conservation. Biogeographic events and fossils are the main source of calibration, but these are known to overestimate timing and parameters at population level, which leads to a disconnection between environmental changes and inferred reconstructions. Here, we propose the Last Glacial Maximum (LGM) calibration that is based on the assumptions that reef species went through a bottleneck during the LGM, which was followed by an early yet marginal increase in population size. We validated the LGM calibration using simulations and genetic inferences based on Extended Bayesian Skyline Plots. Applying it to mitochondrial sequence data of crown-of-thorns starfish Acanthaster spp., we obtained mutation rates that were higher than phylogenetically based calibrations and varied among populations. The timing of the greatest increase in population size differed slightly among populations, but all started between 10 and 20 kya. Using a curve-fitting method, we showed that Acanthaster populations were more influenced by sea-level changes in the Indian Ocean and by reef development in the Pacific Ocean. Our results illustrate that the LGM calibration is robust and can probably provide accurate demographic inferences in many reef species. Application of this calibration has the potential to help identify population drivers that are central for the conservation and management of these threatened ecosystems.

scholarly journals Genome-wide evolutionary signatures of climate adaptation in spotted sea bass inhabiting different latitudinal regions

2021 ◽  
Author(s):  
Baohua Chen ◽  
Zhixiong Zhou ◽  
Yue Shi ◽  
Jie Gong ◽  
Chengyu Li ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Climate Adaptation ◽  
Demographic History ◽  
Thermal Adaptation ◽  
Sea Bass ◽  
Latitudinal Gradients ◽  
Phylogeographic Structure ◽  
Northwest Pacific ◽  
Marginal Seas ◽  
Lateolabrax Maculatus

Temperature is an important climatic factor that shapes the distribution of eurythermal species. Thermal adaptation of species is important to both evolutionary biology and climate-change biology because it frequently leads to latitudinal gradients of various phenotypes among populations. Spotted sea bass (Lateolabrax maculatus) has a broad latitudinal distribution range along the marginal seas of the Northwest Pacific, providing an excellent teleost model for climate adaptation studies. We generated over 8.57 million SNP loci using whole genome re-sequencing from 100 samples collected at 14 geographic loci. We built the phylogeographic structure and demographic history of L. maculatus and determined sea surface temperature as the key environmental factor and major driving force for genetic divergence and local adaptation. We also identified distinct selective signatures and functional genes underlying adaptive mechanisms and ecological tradeoffs in the southernmost and northernmost populations inhabiting distinct climatic and latitudinal zones. The results offer an opportunity to better understand the genetic basis of the phenotypic variation in eurythermal fishes inhabiting different climatic regions.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Genome-wide Assessment Elucidates Connectivity and the Evolutionary History of the Highly Dispersive Marine Invertebrate Littoraria Flava (Littorinidae:Gastropoda)

2020 ◽  
Author(s):  
Thainá Cortez ◽  
Rafael Viana Amaral ◽  
Thadeu Sobral-Souza ◽  
Sonia Andrade
Keyword(s):  
Population Dynamics ◽  
Species Distribution ◽  
Marine Invertebrate ◽  
Demographic History ◽  
Population Expansion ◽  
Marine Ecosystems ◽  
Assignment Test ◽  
Niche Modelling ◽  
Marine Gastropod ◽  
Haplotype Networks

Abstract Background: An important goal of population genetics studies in marine ecosystems is understanding how connectivity patterns, both spatial and temporal, are influenced by historical and evolutionary factors. When it comes to dispersion and connectivity in marine ecosystems, the role of historical and evolutionary factors over population dynamics andstructure still remains enigmatic. We evaluated the demographic history and population structure of Littoraria flava, a highly dispersive and widely distributed marine gastropod on the Brazilian intertidal zone, to predict the effects of such factors on intrapopulation divergence. To test the hypotheses that (1) the species has historically high levels of geneflow on a macrogeographic spatial scale and (2) the species distribution in rocky shores consists of subpopulations due to high degrees of environmental heterogeneity, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, nuclear internal transcribed spacer 2, and single nucleotide polymorphisms) with niche-based modeling to predict species paleodistribution.Results: Low genetic structure was observed along the coastline, and all clustering and migration analyses supported the high gene flow over long distances hypothesis (> 3,000 km). Three genetic clusters were identified by the assignment test, each mostly composed of individuals from the three sampled regions. No fine-scale variation was observed for any location. The neutrality tests and the haplotype networks suggest that L. flava had experienced population bottleneck followed by population expansion. Both paleodistribution and coalescent simulations highlight that expansion events occurred in the Southeastern coastline during the Pleistocene interglacial cycles (21 kya).Conclusions: This is the first study on the South American coast that highlights the demographic history on a marine gastropod based on genomic markers associated with niche modelling. We found that climatic changes since the interglacial periods are potentially relevant drivers for the species distribution in the past. Our findings could enhance the understanding of the population dynamics under an evolutionary view for widely distributed non-model marine organisms.

scholarly journals Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Sara Lado ◽  
Jean Pierre Elbers ◽  
Angela Doskocil ◽  
Davide Scaglione ◽  
Emiliano Trucchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
Phylogeographic Structure ◽  
Arid Environments ◽  
Migration Patterns ◽  
Migration Rates ◽  
Global Migration ◽  
Genome Wide ◽  
A Genome ◽  
Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

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