scholarly journals Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 346
Author(s):  
Chaochao Hu ◽  
Sijia Yuan ◽  
Wan Sun ◽  
Wan Chen ◽  
Wei Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Wild Boar ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Phylogeographic Structure ◽  
Qinling Mountains ◽  
Wild Boars ◽  
The Impact

Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.

Conservation genetics of red pandas in the wild

2018 ◽  
Author(s):  
Yibo Hu ◽  
Dunwu Qi ◽  
Fuwen Wei
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Conservation Genetics ◽  
Human Activities ◽  
Population Genetic ◽  
Large Scale ◽  
Demographic History ◽  
Genetic Research ◽  
Phylogeographic Structure ◽  
Red Panda

The red panda is listed on the 2016 IUCN red list as Endangered. It is now distributed only in China, Myanmar, India, Bhutan and Nepal. Human activities such as poaching and large-scale deforestation have caused serious declines in this forest-dwelling species. Although its ecological research has made much progress in the past decades, only recently witnessed the population genetic research advances of this species. This chapter reviews the advances in wild red panda conservation genetics from non-invasive genetics, genetic diversity, phylogeographic structure, population genetic structure, demographic history, subspecies differentiation, to its conservation and management. It presents detailed estimates of genetic diversity, assesses the role of paleo-climate changes, human activities and landscape features in shaping the genetic structure and demographic history of red pandas, and discusses the implications of conservation genetics findings for effective genetic monitoring and conservation management.

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 Structure and Geographical Differentiation of Larix sibirica Ledeb. in the Urals

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1401
Author(s):  
Nikita Chertov ◽  
Yulia Vasilyeva ◽  
Andrei Zhulanov ◽  
Yulia Nechaeva ◽  
Svetlana Boronnikova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Forest Fragmentation ◽  
Spatial Genetic Structure ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Forest Steppe ◽  
Middle Urals ◽  
The Urals ◽  
The Impact

The Ural Mountains and the West Eurasian Taiga forests are one of the most important centers of genetic diversity for Larix sibirica Ledeb. Forest fragmentation negatively impacts forest ecosystems, especially due to the impact of their intensive use on the effects of climate change. For the preservation and rational use of forest genetic resources, it is necessary to carefully investigate the genetic diversity of the main forest-forming plant species. The Larix genus species are among the most widespread woody plants in the world. The Siberian larch (Larix sibirica, Pinaceae) is found in the forest, forest-tundra, tundra (Southern part), and forest-steppe zones of the North, Northeast, and partly East of the European part of Russia and in Western and Eastern Siberia; in the Urals, the Siberian larch is distributed fragmentarily. In this study, eight pairs of simple sequence repeat (SSR) primers were used to analyse the genetic diversity and population structure of 15 Siberian larch populations in the Urals. Natural populations in the Urals exhibit indicators of genetic diversity comparable to those of Siberia populations (expected heterozygosity, He = 0.623; expected number of alleles, Ne = 4017; observed heterozygosity, Ho = 0.461). Genetic structure analysis revealed that the examined populations are relatively highly differentiated (Fst = 0.089). Using various algorithms for determining the spatial genetic structure, the examined populations formed three groups according to geographical location. The data obtained are required for the development of species conservation and restoration programs, which are especially important in the Middle Urals, which is the region with strong forest fragmentation.

The impact of postglacial marine invasions on the genetic diversity of an obligate freshwater fish, the longnose dace (Rhinichthys cataractae), on the Quebec peninsula

2006 ◽  
Vol 63 (6) ◽  
pp. 1429-1438 ◽  
Author(s):  
Philippe Girard ◽  
Bernard Angers
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Freshwater Species ◽  
Postglacial Colonization ◽  
Genetic Structure Of Populations ◽  
Marine Invasions ◽  
Rhinichthys Cataractae ◽  
Mitochondrial Dna Variability ◽  
The Impact

Postglacial seas are expected to have had significant effects on the genetic structure of populations of obligate freshwater fishes. To assess this influence, mitochondrial DNA variability was evaluated in 32 populations of longnose dace (Rhinichthys cataractae) of the Quebec peninsula located within and outside of the maximum extent of marine invasions of the Champlain and Laflamme seas. Three clades of haplotypes diverging from one to two mutations were defined. Despite this low divergence, a clear and significant spatial genetic structure was observed outside of the extent of marine invasions. However, a higher genetic diversity was observed in populations located within the extent of marine invasions because of the admixture of these clades with an additional lineage restricted almost exclusively to those areas. The low genetic divergence between the main haplotypes suggests a single origin, despite the known presence of this species in various refuges. Marine invasions preventing entry to the peninsula, especially from Atlantic refuge, are proposed as a possible explanation to this particular result. This study is a relevant argument for integrating postglacial marine invasions into postglacial colonization models of freshwater species in the northeastern part of North America.

scholarly journals Global gene flow releases invasive plants from environmental constraints on genetic diversity

2020 ◽  
Vol 117 (8) ◽  
pp. 4218-4227 ◽  
Author(s):  
Annabel L. Smith ◽  
Trevor R. Hodkinson ◽  
Jesus Villellas ◽  
Jane A. Catford ◽  
Anna Mária Csergő ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Invasive Plants ◽  
Spatial Genetic Structure ◽  
Plantago Lanceolata ◽  
Research Network ◽  
Environmental Constraints ◽  
Long Distance ◽  
Precipitation Seasonality ◽  
The Impact

When plants establish outside their native range, their ability to adapt to the new environment is influenced by both demography and dispersal. However, the relative importance of these two factors is poorly understood. To quantify the influence of demography and dispersal on patterns of genetic diversity underlying adaptation, we used data from a globally distributed demographic research network comprising 35 native and 18 nonnative populations of Plantago lanceolata. Species-specific simulation experiments showed that dispersal would dilute demographic influences on genetic diversity at local scales. Populations in the native European range had strong spatial genetic structure associated with geographic distance and precipitation seasonality. In contrast, nonnative populations had weaker spatial genetic structure that was not associated with environmental gradients but with higher within-population genetic diversity. Our findings show that dispersal caused by repeated, long-distance, human-mediated introductions has allowed invasive plant populations to overcome environmental constraints on genetic diversity, even without strong demographic changes. The impact of invasive plants may, therefore, increase with repeated introductions, highlighting the need to constrain future introductions of species even if they already exist in an area.

Spatial genetic structure of a keystone long-lived semiarid shrub: historical effects prevail but do not cancel the impact of recent severe habitat loss on genetic diversity

2020 ◽  
Vol 21 (5) ◽  
pp. 853-867 ◽  
Author(s):  
Ana González-Robles ◽  
Antonio J. Manzaneda ◽  
Teresa Salido ◽  
Francisco Valera ◽  
Cristina García ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Loss ◽  
Spatial Genetic Structure ◽  
The Impact

scholarly journals Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 654
Author(s):  
Jian-Feng Huang ◽  
Clive T. Darwell ◽  
Yan-Qiong Peng
Keyword(s):  
Genetic Diversity ◽  
Human Activity ◽  
Spatial Genetic Structure ◽  
Haplotype Diversity ◽  
Habitat Destruction ◽  
Phylogeographic Structure ◽  
Data Set ◽  
Chloroplast Haplotype ◽  
Nuclear Microsatellite ◽  
Extinction Events

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.

scholarly journals Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽  
2019 ◽  
Vol 830 ◽  
pp. 127-144 ◽  
Author(s):  
Lu Liu ◽  
Xiumei Zhang ◽  
Chunhou Li ◽  
Hui Zhang ◽  
Takashi Yanagimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Fishery Management ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Northwestern Pacific ◽  
Distribution Analysis ◽  
Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

scholarly journals Impact of cyclones on hard coral and metapopulation structure, connectivity and genetic diversity of coral reef fish

Coral Reefs ◽  
2021 ◽  
Author(s):  
Gabriele Gerlach ◽  
Philipp Kraemer ◽  
Peggy Weist ◽  
Laura Eickelmann ◽  
Michael J. Kingsford
Keyword(s):  
Genetic Diversity ◽  
Coral Reef ◽  
Genetic Structure ◽  
Reef Fish ◽  
Coral Reef Fish ◽  
Population Genetic Study ◽  
Hard Coral ◽  
Great Loss ◽  
Metapopulation Structure ◽  
The Impact

AbstractCyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km2); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

scholarly journals Low effective population size and high spatial genetic structure of black poplar populations from the Oder valley in Poland

2021 ◽  
Vol 78 (2) ◽  
Author(s):  
Błażej Wójkiewicz ◽  
Andrzewj Lewandowski ◽  
Weronika B. Żukowska ◽  
Monika Litkowiec ◽  
Witold Wachowiak
Keyword(s):  
Genetic Structure ◽  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Spatial Genetic Structure ◽  
Demographic History ◽  
River Valley ◽  
Ex Situ ◽  
Effective Population ◽  
Black Poplar

Abstract Context Black poplar (Populus nigra L.) is a keystone species of European riparian ecosystems that has been negatively impacted by riverside urbanization for centuries. Consequently, it has become an endangered tree species in many European countries. The establishment of a suitable rescue plan of the remaining black poplar forest stands requires a preliminary knowledge about the distribution of genetic variation among species populations. However, for some parts of the P. nigra distribution in Europe, the genetic resources and demographic history remain poorly recognized. Aims Here, we present the first study on identifying and characterizing the genetic resources of black poplar from the Oder valley in Poland. This study (1) assessed the genetic variability and effective population size of populations and (2) examined whether gene flow is limited by distance or there is a single migrant pool along the studied river system. Methods A total of 582 poplar trees derived from nine black poplar populations were investigated with nuclear microsatellite markers. Results (1) The allelic richness and heterozygosity level were high and comparable between populations. (2) The genetic structure of the studied poplar stands was not homogenous. (3) The signatures of past bottlenecks were detected. Conclusion Our study (1) provides evidence for genetic substructuring of natural black poplar populations from the studied river catchment, which is not a frequent phenomenon reported for this species in Europe, and (2) indicates which poplar stands may serve as new genetic conservation units (GCUs) of this species in Europe. Key message The genetic resources of black poplar in the Oder River valley are still substantial compared to those reported for rivers in Western Europe. On the other hand, clear signals of isolation by distance and genetic erosion reflected in small effective population sizes and high spatial genetic structure of the analyzed populations were detected. Based on these findings, we recommend the in situ and ex situ conservation strategies for conserving and restoring the genetic resources of black poplar populations in this strongly transformed by human river valley ecosystem.

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