scholarly journals Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrea Chiocchio ◽  
Jan. W. Arntzen ◽  
Iñigo Martínez-Solano ◽  
Wouter de Vries ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Environmental Changes ◽  
Glacial Refugia ◽  
Bufo Bufo ◽  
Genetic Admixture ◽  
Secondary Contact ◽  
Last Interglacial ◽  
Contact Zones ◽  
Genetic Lineages

AbstractGenetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad Bufo bufo along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.

scholarly journals Publisher Correction: Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrea Chiocchio ◽  
Jan. W. Arntzen ◽  
Iñigo Martínez‑Solano ◽  
Wouter de Vries ◽  
Roberta Bisconti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Glacial Refugia ◽  
Bufo Bufo

scholarly journals The genetic structure of the European black pine (Pinus nigra Arnold) is shaped by its recent Holocene demographic history

2019 ◽  
Author(s):  
Guia Giovannelli ◽  
Caroline Scotti-Saintagne ◽  
Ivan Scotti ◽  
Anne Roig ◽  
Ilaria Spanu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
Pinus Nigra ◽  
Forest Tree ◽  
Black Pine ◽  
Genetic Lineages ◽  
European Black Pine

AbstractFragmentation acting over geological times confers wide, biogeographical scale, genetic diversity patterns to species, through demographic and natural selection processes. To test the effects of historical fragmentation on the genetic diversity and differentiation of a major European forest tree and to resolve its demographic history, we describe and model its spatial genetic structure and gene genealogy. We then test which Pleistocene event, whether recent or ancient, could explain its widespread but patchy geographic distribution using population genetic data, environmental data and realistic demographic timed scenarios.The taxon of interest is a conifer forest tree, Pinus nigra (Arnold), the European black pine, whose populations are located in the mountains of southern Europe and North Africa, most frequently at mid-elevation. We used a set of different genetic markers, both neutral and potentially adaptive, and either bi-parentally or paternally inherited, and we sampled natural populations across the entire range of the species. We analysed the data using frequentist population genetic methods as well as Bayesian inference methods to calibrate realistic, demographic timed scenarios.Species with geographically fragmented distribution areas are expected to display strong among-population genetic differentiation and low within-population genetic diversity. Contrary to these expectations, we show that the current diversity of Pinus nigra and its weak genetic spatial structure are best explained as resulting from late Pleistocene or early Holocene fragmentation of one ancestral population into seven genetic lineages, which we found to be the main biogeographical contributors of the natural black pine forests of today. Gene flow among the different lineages is strong across forests and many current populations are admixed between lineages. We propose to modify the currently accepted international nomenclature made of five subspecies and name these seven lineages using regionally accepted subspecies-level names.HighlightsThe European black pine, Pinus nigra (Arnold), has a weak spatial genetic structure.Gene flow among populations is frequent and populations are often of admixed origin.Current genealogies result from recent, late Pleistocene or Holocene events.Seven modern genetic lineages emerged from divergence and demographic contractions.These seven lineages warrant a revision of subspecies taxonomic nomenclature.

scholarly journals Genetic diversity of a widespread annual killifish from coastal Tanzania

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Veronika Bartáková ◽  
Béla Nagy ◽  
Matej Polačik ◽  
Radim Blažek ◽  
Hieromin Lamtane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Elevation Gradient ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Secondary Contact ◽  
River Channels ◽  
Contact Zones ◽  
Annual Killifish ◽  
Main River

Abstract Background African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. Results In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. Conclusions We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.

scholarly journals Congruent population genetic structures and divergence histories in anther-smut fungi and their host plants Silene italica and the S. nutans species complex

2020 ◽  
Author(s):  
Fanny E. Hartmann ◽  
Alodie Snirc ◽  
Amandine Cornille ◽  
Cécile Godé ◽  
Pascal Touzet ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Host Plant ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Species Complex ◽  
Host Plants ◽  
Glacial Refugia ◽  
Smut Fungi ◽  
Genetic Lineages ◽  
Anther Smut

AbstractThe study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryum genus) and of their host plants, the Silene nutans species complex, and the morphologically and genetically close S. italica, which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.

scholarly journals The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation

Heredity ◽  
2021 ◽  
Vol 126 (4) ◽  
pp. 656-667
Author(s):  
Filip Thörn ◽  
Patrik Rödin-Mörch ◽  
Maria Cortazar-Chinarro ◽  
Alex Richter-Boix ◽  
Anssi Laurila ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Glacial Refugia ◽  
Bufo Bufo ◽  
Clinal Variation ◽  
Sequencing Data ◽  
Common Toad ◽  
Local Adaptations ◽  
The North ◽  
Genetic Landscape

AbstractClinal variation is paramount for understanding the factors shaping genetic diversity in space and time. During the last glacial maximum, northern Europe was covered by glacial ice that rendered the region uninhabitable for most taxa. Different evolutionary processes during and after the recolonisation of this area from different glacial refugia have affected the genetic landscape of the present day European flora and fauna. In this study, we focus on the common toad (Bufo bufo) in Sweden and present evidence suggesting that these processes have resulted in two separate lineages of common toad, which colonised Sweden from two directions. Using ddRAD sequencing data for demographic modelling, structure analyses, and analysis of molecular variance (AMOVA), we provide evidence of a contact zone located between Uppland and Västerbotten in central Sweden. Genetic diversity was significantly higher in southern Sweden compared to the north, in accordance with a pattern of decreased genetic diversity with increasing distance from glacial refugia. Candidate genes under putative selection are identified through outlier detection and gene–environment association methods. We provide evidence of divergent selection related to stress response and developmental processes in these candidate genes. The colonisation of Sweden by two separate lineages may have implications for how future conservation efforts should be directed by identifying management units and putative local adaptations.

Ecological genetics of the wind-pollinated, tetraploid, Allocasuarina emuina L. Johnson (Casuarinaceae) from southeast Queensland reveals montane refugia for coastal heath during the last interglacial

2012 ◽  
Vol 60 (8) ◽  
pp. 718 ◽  
Author(s):  
R. W. Lamont ◽  
R. L. Stokoe ◽  
A. Shapcott
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Population Genetic ◽  
Genetic Material ◽  
Natural Populations ◽  
Seed Viability ◽  
Ecological Genetics ◽  
Last Interglacial ◽  
Study Results ◽  
Southeast Queensland

The subtropical coastal heathlands of southeast Queensland contain many rare and threatened species and have undergone considerable habitat loss in recent years due to high levels of urbanisation. We used morphological and microsatellite markers to investigate the reproductive ecology, in relation to fire, and population genetic structure of the endangered shrub Allocasuarina emuina. Highly significant differences (P < 0.001) were detected among populations for all cone- and seed-related morphological traits, which revealed distinct northern and southern groups of populations, a pattern repeated in the genetic component of the study. Results also indicated that the reproductive viability of A. emuina is more related to fire interval than population size and confirmed that seed viability declines with time since fire. The highest level of genetic diversity for the species was observed in the population on Mt Emu (AE4A; HE = 0.688). Contrary to the expectations of population genetic theory, no relationship was found between the level of genetic variation and population size, density or degree of isolation, hinting that genetic diversity is being conserved as a result of polyploidy and apomixis. However, genetic signatures in the northern populations indicated that unidirectional dispersal of genetic material from the putatively refugial population on Mt Emu to the surrounding coastal plain has been occurring with recession of sea levels following the last interglacial. The findings of the study will aid in both the conservation of natural populations and translocations of A. emuina and have significant implications relating to the biogeographical history of a considerable number of co-occurring heathland taxa.

scholarly journals So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe

2020 ◽  
Vol 11 ◽  
Author(s):  
Andrea Melichárková ◽  
Marek Šlenker ◽  
Judita Zozomová-Lihová ◽  
Katarína Skokanová ◽  
Barbora Šingliarová ◽  
...  
Keyword(s):  
Genome Size ◽  
Central Europe ◽  
Size Variation ◽  
Glacial Refugia ◽  
Genetic Admixture ◽  
Environmental Niche ◽  
Genome Size Variation ◽  
Genetic Lineages ◽  
Polyploid Formation ◽  
Cardamine Pratensis

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid Cardamine majovskyi evolved at least twice in different regions by autopolyploidy from diploid Cardamine matthioli. The extensive genome size and genetic variation of Cardamine rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

scholarly journals Intraspecific population admixture of a top piscivore correlates with anthropogenic alteration of freshwater ecosystems

2019 ◽  
Author(s):  
Erik Eschbach ◽  
Arne Wolfram Nolte ◽  
Klaus Kohlmann ◽  
Josep Alos ◽  
Sandro Schöning ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Environmental Changes ◽  
Ecological Status ◽  
Freshwater Ecosystems ◽  
Genetic Admixture ◽  
Freshwater Biodiversity ◽  
Policy Objective ◽  
Complete Replacement ◽  
Intraspecific Genetic Diversity

AbstractConservation of local genetic diversity is an important policy objective, but intraspecific genetic diversity can be transformed by natural ecological processes associated with anthropogenic changes in ecosystems. Environmental changes and a strong interconnection of drainage systems impact freshwater biodiversity from gene to population level. Populations can either become extinct or expand their range and accompanying secondary contacts can lead to genetic admixture. We investigated how the genetic population structure and the patterns of genetic admixture of Esox lucius L. (the northern pike) vary with the type of ecosystem and the integrity of the ecosystem assessed by measures under the European Water Framework Directive. The pike inhabits river, lake and brackish water ecosystems, where it is confronted with different ecological disturbances. We analysed 1,384 pike samples from the North, Baltic and Black Sea drainages and differentiated between metapopulations from each hydrogeographic region using genotypes from 15 microsatellites and mitochondrial cyt b sequences. Individual populations showed signs of genetic admixture ranging from almost zero to complete replacement by foreign genotypes. Hierarchical general linear modeling revealed a highly significant positive association of the degree of genetic admixture with decreasing ecological status. This may mean that populations in disturbed environments are more prone to influences by foreign genotypes or, alternatively, increased genetic admixture may indicate adaptation to rapid environmental changes. Regardless of the underlying mechanisms, our results suggest that anthropogenic alterations of natural freshwater ecosystems can influence genetic structures, which may lead to a large-scale reduction of intraspecific genetic diversity.

Genetic diversity hotspots and refugia identified by mapping multi-plant species haplotype diversity in China

2019 ◽  
Vol 66 (3-4) ◽  
pp. 136-151 ◽  
Author(s):  
Tao Deng ◽  
Richard J. Abbott ◽  
Wenqing Li ◽  
Hang Sun ◽  
Sergei Volis
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Haplotype Diversity ◽  
Glacial Refugia ◽  
Genetic Lineages ◽  
Historical Processes ◽  
Haplotype Data ◽  
Multiple Species ◽  
Diversity Metrics

Historical processes during the Quaternary are likely to have left a signature on the geographical distribution of intraspecific genetic variation. In particular, high genetic uniqueness could be expected within glacial refugia for multiple species. We aimed to test this for plants in China and whether multi-species hotspots of genetic diversity are good indicators of glacial refugia in this region. From chloroplast DNA haplotype data for 116 species we calculated two local genetic diversity metrics for each species: haplotype genetic richness and genetic uniqueness. From these two, only uniqueness could reliably identify refugia, whereas richness may indicate either glacial refugia or areas recolonized by genetic lineages from different refugia in the postglacial period. Our results suggest the occurrence of numerous cryptic refugia and their likely importance in the maintenance and evolution of the Chinese flora, and indicate that an approach that locates geographic hotspots of genetic diversity data can reliably identify refugia.

KERAGAMAN GENETIK INDUK UDANG WINDU DI PERAIRAN SELATAN PANGANDARAN DAN BINUANGEUN, JAWABARAT

2018 ◽  
Vol 5 (3) ◽  
Author(s):  
Ratu Siti Aliah
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Gene Locus ◽  
Penaeus Monodon ◽  
12S Rrna ◽  
Brood Stock ◽  
Population Genetic Diversity ◽  
Result Show ◽  
Mtdna Diversity

An evaluation of the Black Tiger Brood Stock (Penaeus monodon) genetic diversity of Pangandaran and Binuangeun was conducted by using the mtDNA diversity of two gene locus of CO I and 12S rRNA to understand their population genetic diversity. The result show that the brood stock of Pangandaran has 17 haplotipe, while from Binuangeun has 13 haplotipe. The result indicated that the genetic diversity of the Balck Tiger brood stock of Pangandaran was higher than thatBinuangeun.Key words : Genetic diversity, Black Tiger brood stock, Pangandaran, Binuangeun

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