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.

The Origin of Isolated Populations of the Mountain Weevil, Liparus glabrirostris—The Flagship Species for Riparian Habitats

2020 ◽  
Author(s):  
Dorota Lachowska-Cierlik ◽  
Krzysztof Zając ◽  
Miłosz A Mazur ◽  
Arkadiusz Sikora ◽  
Daniel Kubisz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Glacial Refugia ◽  
Species Range ◽  
Flagship Species ◽  
Isolated Populations ◽  
The Carpathians ◽  
The North ◽  
Baltic Coast ◽  
Riparian Habitats ◽  
The Baltic

Abstract Liparus glabrirostris is one of the largest European weevils, and it has been recently proposed as the flagship species for threatened riparian habitats in the mountains. For effective conservation of its populations (and associated habitats), it is crucial to understand its history, contemporary distribution, genetic diversity and predict changes in the range, including its highly isolated populations on the Baltic coast. Here, we examined numerous populations of L. glabrirostris across almost the entire species range using phylogeography and species niche modeling (SNM) approaches. Analyses of mtDNA and nucDNA markers revealed the existence of 2 major mitochondrial lineages generally separated between 1) the Alpine region and 2) the Bohemian Massif, the Carpathians, and the Baltic coast areas. Genetic diversity in nuclear genes was more complicated with no clear division between populations. The origin of Baltic populations was derived from the Carpathians, but there were probably multiple expansion events to the north. SNM suggested the existence of glacial refugia for L. glabrirostris, mainly in the Alps and the Southern Carpathians. Current predictions of species range were found to be generally congruent with zoogeographic data; however, the Baltic coast was not really supported as a suitable area for L. glabrirostris. An important prediction of future distribution (2050–2070 CE) suggests a shrinkage of the L. glabrirostris range and extinction of some of its populations (particularly those isolated on lower altitudes). Based on the aforementioned data, proposals for the protection of this species are proposed, including the designation of several evolutionary units of conservation importance.

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

Molecular genetic diversity and population structure in Eucalyptus pauciflora subsp. pauciflora (Myrtaceae) on the island of Tasmania

2014 ◽  
Vol 62 (3) ◽  
pp. 175 ◽  
Author(s):  
Archana Gauli ◽  
Dorothy A. Steane ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Genetic ◽  
Glacial Refugia ◽  
Altitudinal Distribution ◽  
The North ◽  
Chloroplast Haplotype ◽  
Molecular Genetic Diversity ◽  
Nuclear Microsatellite ◽  
Chloroplast Dna Markers

Genetic diversity and population structure of Tasmanian populations of Eucalyptus pauciflora were assessed using chloroplast and nuclear microsatellite markers. Maternal trees and open-pollinated progeny from 37 populations were sampled across the species’ geographic and altitudinal distribution in Tasmania. The distribution of chloroplast haplotype richness showed a clear geographic structure with suggestion of three major refugia (Storm Bay, Tamar Valley and St Pauls River Valley), two of which are consistent with previously reported glacial refugia. Chloroplast haplotype affinities provided evidence of migration of populations from the north and east towards the south and west of Tasmania. High nuclear microsatellite diversity was observed across the species’ range. Most of this variation was distributed within populations with low but significant FST, suggesting high gene flow among populations that is more pronounced in mature stands. Higher nuclear genetic diversity in newly colonised areas compared with lowland putative refugial regions, and the converse in chloroplast DNA markers, suggest limited seed dispersal into newly colonised regions combined with high pollen flow between different source populations in newly colonised areas. Our results do not support the suggestion that highland populations of E. pauciflora originate from in situ high-altitude refugia, but instead argue they originate from lowland refugia.

scholarly journals Phylogeography in an “oyster” shell provides first insights into the genetic structure of an extinct Ostrea edulis population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah Hayer ◽  
Dirk Brandis ◽  
Alexander Immel ◽  
Julian Susat ◽  
Montserrat Torres-Oliva ◽  
...  
Keyword(s):  
Large Scale ◽  
Wadden Sea ◽  
Atlantic Coast ◽  
Phylogenetic Reconstruction ◽  
Oyster Shell ◽  
Glacial Refugia ◽  
Late Nineteenth Century ◽  
Ostrea Edulis ◽  
Geographic Ranges ◽  
The North

AbstractThe historical phylogeography of Ostrea edulis was successfully depicted in its native range for the first time using ancient DNA methods on dry shells from museum collections. This research reconstructed the historical population structure of the European flat oyster across Europe in the 1870s—including the now extinct population in the Wadden Sea. In total, four haplogroups were identified with one haplogroup having a patchy distribution from the North Sea to the Atlantic coast of France. This irregular distribution could be the result of translocations. The other three haplogroups are restricted to narrow geographic ranges, which may indicate adaptation to local environmental conditions or geographical barriers to gene flow. The phylogenetic reconstruction of the four haplogroups suggests the signatures of glacial refugia and postglacial expansion. The comparison with present-day O. edulis populations revealed a temporally stable population genetic pattern over the past 150 years despite large-scale translocations. This historical phylogeographic reconstruction was able to discover an autochthonous population in the German and Danish Wadden Sea in the late nineteenth century, where O. edulis is extinct today. The genetic distinctiveness of a now-extinct population hints at a connection between the genetic background of O. edulis in the Wadden Sea and for its absence until today.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

Landscape genetics in mammals

Mammalia ◽  
2014 ◽  
Vol 78 (2) ◽  
Author(s):  
Claudine Montgelard ◽  
Saliha Zenboudji ◽  
Anne-Laure Ferchaud ◽  
Véronique Arnal ◽  
Bettine Jansen van Vuuren
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Landscape Genetics ◽  
Metapopulation Dynamics ◽  
Local Adaptations ◽  
Future Developments ◽  
Ecological Features ◽  
Genetic Patterns ◽  
The Individual

AbstractThe focus of this review is on landscape genetics (LG), a relatively new discipline that arose approximately 10 years ago. LG spans the interface between population genetics and landscape ecology and thus incorporates the concepts, methods, and tools from both disciplines. On the basis of an understanding of the spatial distribution of genetic diversity, LG aims to explain how landscape and environmental characteristics influence microevolutionary processes and metapopulation dynamics, including gene flow (i.e., connectivity) and selection (i.e., local adaptations). LG is concerned with events that occurred during the recent time scale, and the individual is the operational unit. As a discipline that combines spatial genetic diversity with ecological features, LG is able to address questions relating to different evolutionary processes. We illustrate some of these here using examples taken from mammals: population structure; gene flow and the identification of barriers; fragmentation, connectivity, and corridors; local adaptation and selection; there are two different questions: applications in conservation genetics; and future developments in LG. We will then present the methods and tools commonly used in the different steps of LG analyses: the genetic and landscape sampling, the quantification of genetic variation, the characterization of spatial landscape structures, and finally, the correlation between genetic patterns and landscape features.

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