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 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 PHYLOGEOGRAPHIC STRUCTURE OF THE COMMERCIALLY IMPOR- TANT TROPICAL TREE SPECIES, DRYOBALANOPS AROMATICA GAERTN. F. (DIPTEROCARPACEAE) REVEALED BY MICROSATELLITE MARKERS

REINWARDTIA ◽  
2014 ◽  
Vol 14 (1) ◽  
pp. 43 ◽  
Author(s):  
Fifi Gus Dwiyanti ◽  
Koichi Kamiya ◽  
Ko Harada
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Tree Species ◽  
National Park ◽  
Tropical Tree ◽  
Phylogeographic Structure ◽  
Timber Species ◽  
Malay Peninsula ◽  
Tropical Tree Species ◽  
The Impact

DWIYANTI, F.G., KAMIYA, K. & HARADA, K. 2014. Phylogeographic structure of the commercially important tropical tree species Dryobalanops aromatica Gaertn. F. (Dipterocarpaceae) revealed by microsatellite markers. Reinwardtia 14(1): 43 – 51. ? Dryobalanops aromatica Gaertn. F. (Kapur) is an economically important timber species in Southeast Asia that can serve as a good model for studying the impact of the Pleistocene glaciations on the genetic diversity and distribution of species in tropical regions. Seven polymorphic microsatellite markers were analyzed in five natural populations of D. aromatica (N = 120 individuals): Gunung Panti in Malay Peninsula, Lingga Island in Lingga Archipelago, Lambir Hills National Park, Limbang and Similajau National Park in Borneo. The level of gene diversity (HE) for the five populations was relatively high with a range from 0.571 (Similajau) to 0.729 (Gunung Panti). The high genetic diversity in the present study could be attributed to the larger refugia population sizes of D. aromatica than that of other species. The population genetic structure revealed two distinct groups: the Malay Peninsula-Lingga Archipelago and Borneo. This pattern suggests that populations in each geographical area might be the consequence of post-glacial expansion from one or two refugia, but that gene flow between different glacial refugia was fairly restricted.

scholarly journals Impact of Late Pleistocene-Holocene climatic fluctuations on the phylogeographic structure and historical demographics of Zamia prasina (Cycadales: Zamiaceae)

2019 ◽  
Vol 97 (4) ◽  
pp. 588-608 ◽  
Author(s):  
Grecia Montalvo-Fernández ◽  
Lorenzo Felipe Sánchez-Teyer ◽  
Germán Carnevali ◽  
Andrew P. Vovides ◽  
Ricardo Gaytán-Legaria ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Late Pleistocene ◽  
Population Expansion ◽  
Historical Demography ◽  
Phylogeographic Structure ◽  
Glacial Refugium ◽  
Tropical Species ◽  
High Genetic Diversity ◽  
Climatic Fluctuations ◽  
Glacial Periods

Background: Glacial periods during the Pleistocene have been hypothesized to have greatly influenced geographical patterns of genetic structure and demography of many tropical species. The Glacial Refugium Hypothesis proposes that, during cold, dry glacial periods, populations of moisture-affinities tropical species were restricted to sheltered, humid areas and that, during warmer and more humid interglacial periods, these populations expanded. Some mountain regions in the tropics acted as refugia during the cold, dry periods of the Pleistocene for several temperate forest taxa, which recolonized the humid areas farther north during the interglacial periods.Questions: (1) Did Late Pleistocene-Holocene climate changes affect the historical demophraphy of Zamia prasina? (2) Does the historical distribution of Zamia prasina agree with the Glacial Refugium Hypothesis?Study species: Zamia prasina W.Bull. (Zamiaceae), the only cycad native to the Yucatan Peninsula Biotic Province (YPBP). Methods: Five individuals were collected in 23 populations and characterized using two DNA regions: plastid atpF-atpH, and nuclear ITS2. Genetic diversity, phylogeographic structure, historical demography, and potential distributions were assessed. Results: Our results showed moderately high genetic diversity and low, but significant, phylogeographic structure. Two genetic groups were identified, one in the eastern part of the Peninsula, the other in the western. The changes in historical demography suggest that Z. prasina experienced a population expansion following the warm conditions of the Holocene.Conclusions: The population dynamics of Zamia prasina are in accordance with the Glacial Refugium Hypothesis.

scholarly journals Genetic Diversity and Population Structure of Rhododendron rex Subsp. rex Inferred from Microsatellite Markers and Chloroplast DNA Sequences

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 338 ◽  
Author(s):  
Xue Zhang ◽  
Yuan-Huan Liu ◽  
Yue-Hua Wang ◽  
Shi-Kang Shen
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Chloroplast Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Population Decline ◽  
Population Expansion ◽  
Distribution Models ◽  
Recent Population Expansion

Genetic diversity is vital to the sustainable utilization and conservation of plant species. Rhododendron rex subsp. rex Lévl. is an endangered species endemic to the southwest of China. Although the natural populations of this species are facing continuous decline due to the high frequency of anthropogenic disturbance, the genetic information of R. rex subsp. rex is not yet elucidated. In the present study, 10 pairs of microsatellite markers (nSSRs) and three pairs of chloroplast DNA (cpDNAs) were used in the elucidation of the genetic diversity, population structure, and demographic history of 11 R. rex subsp. rex populations. A total of 236 alleles and 12 haplotypes were found. A moderate genetic diversity within populations (HE = 0.540 for nSSRs, Hd = 0.788 for cpDNA markers), high historical and low contemporary gene flows, and moderate genetic differentiation (nSSR: FST = 0.165***; cpDNA: FST = 0.841***) were detected among the R. rex subsp. rex populations. Genetic and geographic distances showed significant correlation (p < 0.05) determined by the Mantel test. The species exhibited a conspicuous phylogeographical structure among the populations. Using the Bayesian skyline plot and species distribution models, we found that R. rex subsp. rex underwent a population demography contraction approximately 50,000–100,000 years ago. However, the species did not experience a recent population expansion event. Thus, habitat loss and destruction, which result in a population decline and species inbreeding depression, should be considered in the management and conservation of R. rex subsp. rex.

scholarly journals Population genetics and phylogeography of Tabanus bromius (Diptera: Tabanidae)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sumeyra Nur Sanal Demirci ◽  
Volkan Kilic ◽  
Serap Mutun ◽  
A. Yavuz Kilic
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Its Region ◽  
Early Pleistocene ◽  
Phylogeographic Structure ◽  
The Past ◽  
Haplotype Allele

Abstract Background Tabanus bromius (Diptera: Tabanidae) is one of the most notable Tabanidae species of veterinary and medical importance distributed throughout the Palearctic region. In this study, we investigate the genetic diversity and the phylogeographic structure of T. bromius sampled from Turkey, Croatia, and Iran. Methods For this purpose, a 686-base-pair (bp) fragment of mitochondrial DNA cytochrome oxidase I gene (COI) and 1339 bp of the nuclear DNA internal transcribed spacer (ITS) were sequenced from 247 individuals representing 15 populations. Results The sequences generated 169 COI haplotypes and 90 ITS alleles. A higher haplotype/allele diversity (h = 0.9909 for the COI gene and Ad = 0.8193 for the ITS region) compared to a low nucleotide diversity (π = 0.020605 for COI gene and π = 0.013667 for the ITS region), present for a high number of singleton and private haplotypes/alleles imply population expansion in the past. The results of phylogenetic analysis led to the uncovering of geographically significant groupings of lineages with regard to the entrance of the species into Anatolia and the location of major geographic barriers. According to current data, the species appears to have entered Turkey from Caucasia and Iran. A molecular clock applied to the COI data suggests that T. bromius diverged from the outgroup species nearly 8.83 million years ago, around the end of the Miocene era. Conclusions The results of this study indicate remarkable genetic diversity across the studied range of the species. High haplotype/allele versus low nucleotide diversity and demographic analyses implied that the T. bromius populations have undergone a series of expansions and retreats in the past. Our current findings suggest that T. bromius split from outgroups around the Late Miocene. Subsequent diversification events during the climatic and environmental fluctuation times of the Late Pliocene and Early Pleistocene periods also significantly influenced the species, resulting in the formation of some major genetic lineages. The phylogenetic analyses indicate that T. bromius most likely entered Turkey from the Caucasus region and Iran. Graphical Abstract

Genetic diversity based on microsatellite markers in five Nile tilapia strains

2009 ◽  
Vol 17 (1) ◽  
pp. 82 ◽  
Author(s):  
Liang Hongwei ◽  
Li Zhong ◽  
Luo Xiangzhong ◽  
Wang Changzhong ◽  
Hu Guangfu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Nile Tilapia

scholarly journals Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers

Heredity ◽  
2001 ◽  
Vol 86 (4) ◽  
pp. 469-479 ◽  
Author(s):  
Stéphanie Mariette ◽  
David Chagné ◽  
Céline Lézier ◽  
Patrick Pastuszka ◽  
Annie Raffin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Pinus Pinaster

scholarly journals Phylogeography of Prunus armeniaca L. revealed by chloroplast DNA and nuclear ribosomal sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wen-Wen Li ◽  
Li-Qiang Liu ◽  
Qiu-Ping Zhang ◽  
Wei-Quan Zhou ◽  
Guo-Quan Fan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Chloroplast Dna ◽  
Population Expansion ◽  
Prunus Armeniaca ◽  
River Valley ◽  
Nuclear Ribosomal Dna ◽  
Glacial Refugium ◽  
Ili River Valley ◽  
Wild Apricot

AbstractTo clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: HT = 0.499; ITS: HT = 0.876) and a low level of genetic differentiation (cpDNA: FST = 0.1628; ITS: FST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (NST) was significantly higher than the number of substitution types (GST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

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