Genetic variation and phylogeography of Psammosilene tunicoides (Caryophyllaceae), a narrowly distributed and endemic species in south-western China

2011 ◽  
Vol 59 (5) ◽  
pp. 450 ◽  
Author(s):  
Qing-Ying Zhang ◽  
Yu-Juan Zhao ◽  
Xun Gong
Keyword(s):  
Genetic Differentiation ◽  
Endemic Species ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Population History ◽  
Western China ◽  
Phylogeographic Structure ◽  
Population Subdivision ◽  
Chloroplast Haplotypes

Psammosilene tunicoides is a narrowly distributed and endemic species in south-western China. An investigation of sequence variation at two chloroplast DNA (cpDNA) regions (rpL16, trnQ-5′rps16) and one nuclear DNA (nDNA) locus (GPA1) were carried out to survey the population structure and population history of the species. Among the 22 populations across its geographical range, nine chloroplast haplotypes and 17 nuclear alleles were identified. Both cpDNA and nDNA consistently revealed high levels of population differentiation (GST = 0.604 and 0.540, respectively), suggesting a distinct phylogeographic structure (NST > GST, P < 0.01). This high genetic differentiation might be a combined effect of breeding system, limited pollen and seed dispersal and geographic isolation of populations. The level of haplotype diversities (cpDNA, hT = 0.575; nDNA, hT = 0.724) were high, but the nucleotide diversities (cpDNA, π = 0.00099; nDNA, π = 0.00105) were low. These results together with the star-like phylogenetic pattern and neutrality tests indicate that P. tunicoides has experienced a population expansion event in its evolution. Limited genetic exchange after population expansion was supported by the pronounced genetic differentiation among populations as well as evidence for ‘isolation-by-distance’ revealed by cpDNA. Due to high population subdivision and complex landscape, as many populations as possible should be considered for genetic conservation.

scholarly journals Phylogeographic Patterns in Motacilla Flava and Motacilla Citreola: Species Limits and Population History

The Auk ◽  
2003 ◽  
Vol 120 (3) ◽  
pp. 744-758
Author(s):  
Alexandra Pavlova ◽  
Robert M. Zink ◽  
Sergei V. Drovetski ◽  
Yaroslav Red'kin ◽  
Sievert Rohwer
Keyword(s):  
Dna Sequences ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Population History ◽  
Phylogeographic Structure ◽  
Restricted Gene Flow ◽  
Western Group ◽  
History Of ◽  
Group A ◽  
Past Population

Abstract We conducted phylogeographic analyses of Motacilla flava (Yellow Wagtail) and M. citreola (Citrine Wagtail). We analyzed mitochondrial DNA sequences from 167 M. flava specimens obtained from 17 localities throughout Eurasia and Alaska, and 38 specimens of M. citreola obtained from 7 Eurasian localities. Phylogenetic analysis revealed three clades within traditionally recognized M. flava: Europe and southwestern Asia, northeastern Eurasia, and southeastern Asia. Those groups should be considered species, because together they are not monophyletic, and are interspersed with M. citreola, M. cinerea, and M. alba. Motacilla citreola also is paraphyletic, consisting of two species-level groups. Northeastern and southeastern groups of M. flava each appear to be sister taxa to eastern and western groups of M. citreola, respectively. Together those four groups form a clade, whereas the western M. flava group is considerably more distant. Within each of the three groups of M. flava, and the two groups of M. citreola, little phylogeographic structure was detected. Signatures of past population expansion are evident for some populations of M. flava; expansion is more recent in Moscow, Kursk (western group), Yamal, and Anabar (northeastern group), and older in Tyva and Vyatka (western group). A history of population stability is inferred for the Yamal population of M. citreola. Nested-clade analyses detected contiguous range expansion for southeastern M. flava and restricted gene flow with isolation by distance for northeastern M. flava and eastern M. citreola.

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.

Genetic homogeneity of weathervane scallops (Patinopecten caurinus) in the northeastern Pacific

2010 ◽  
Vol 67 (11) ◽  
pp. 1827-1839 ◽  
Author(s):  
Patrick M. Gaffney ◽  
Carita M. Pascal ◽  
Jeffery Barnhart ◽  
W. Stewart Grant ◽  
James E. Seeb
Keyword(s):  
Genetic Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Gulf Of Alaska ◽  
Nucleotide Sequencing ◽  
Mt Dna ◽  
Northeastern Pacific ◽  
Nuclear Loci ◽  
Allozyme Loci

We assessed genetic differentiation among populations of weathervane scallop ( Patinopecten caurinus ) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy–Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.

scholarly journals Pliocene Origin, Ice Ages and Postglacial Population Expansion Have Influenced a Panmictic Phylogeography of the European Bee-Eater Merops apiaster

Diversity ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 12 ◽  
Author(s):  
Carina Carneiro de Melo Moura ◽  
Hans-Valentin Bastian ◽  
Anita Bastian ◽  
Erjia Wang ◽  
Xiaojuan Wang ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Nuclear Dna ◽  
Bird Species ◽  
Population Expansion ◽  
Genetic Connectivity ◽  
Middle Pleistocene ◽  
Ice Ages ◽  
Breeding Sites ◽  
Late Tertiary ◽  
Merops Apiaster

Oscillations of periods with low and high temperatures during the Quaternary in the northern hemisphere have influenced the genetic composition of birds of the Palearctic. During the last glaciation, ending about 12,000 years ago, a wide area of the northern Palearctic was under lasting ice and, consequently, breeding sites for most bird species were not available. At the same time, a high diversity of habitats was accessible in the subtropical and tropical zones providing breeding grounds and refugia for birds. As a result of long-term climatic oscillations, the migration systems of birds developed. When populations of birds concentrated in refugia during ice ages, genetic differentiation and gene flow between populations from distinct areas was favored. In the present study, we explored the current genetic status of populations of the migratory European bee-eater. We included samples from the entire Palearctic-African distribution range and analyzed them via mitochondrial and nuclear DNA markers. DNA data indicated high genetic connectivity and panmixia between populations from Europe, Asia and Africa. Negative outcomes of Fu’s Fs and Tajima’s D tests point to recent expansion events of the European bee-eater. Speciation of Merops apiaster started during the Pliocene around three million years ago (Mya), with the establishment of haplotype lineages dated to the Middle Pleistocene period circa 0.7 Mya. M. apiaster, which breed in Southern Africa are not distinguished from their European counterparts, indicating a recent separation event. The diversification process of the European bee-eater was influenced by climatic variation during the late Tertiary and Quaternary. Bee-eaters must have repeatedly retracted to refugia in the Mediterranean and subtropical Africa and Asia during ice ages and expanded northwards during warm periods. These processes favored genetic differentiation and repeated lineage mixings, leading to a genetic panmixia, which we still observe today.

Significant population genetic structuring but a lack of phylogeographic structuring in the endemic Tasmanian tree frog (Litoria burrowsae)

2014 ◽  
Vol 62 (3) ◽  
pp. 238 ◽  
Author(s):  
Z. Y. Zhang ◽  
S. Cashins ◽  
A. Philips ◽  
C. P. Burridge
Keyword(s):  
Population Genetic ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Global Climate ◽  
Haplotype Diversity ◽  
Habitat Destruction ◽  
Phylogeographic Structure ◽  
Tree Frog ◽  
Genetic Structuring ◽  
Management Units

Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments.

scholarly journals Genetic differentiation in an endangered and strongly philopatric, migrant shorebird

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nelli Rönkä ◽  
Veli-Matti Pakanen ◽  
Angela Pauliny ◽  
Robert L. Thomson ◽  
Kimmo Nuotio ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Population Subdivision ◽  
Genetic Structuring ◽  
Long Distance ◽  
Mobile Species ◽  
High Dispersal ◽  
The Baltic

Abstract Background Populations living in fragmented habitats may suffer from loss of genetic variation and reduced between-patch dispersal, which are processes that can result in genetic differentiation. This occurs frequently in species with reduced mobility, whereas genetic differentiation is less common among mobile species such as migratory birds. The high dispersal capacity in the latter species usually allows for gene flow even in fragmented landscapes. However, strongly philopatric behaviour can reinforce relative isolation and the degree of genetic differentiation. The Southern Dunlin (Calidris alpina schinzii) is a philopatric, long-distance migratory shorebird and shows reduced dispersal between isolated breeding patches. The endangered population of the Southern Dunlin breeding at the Baltic Sea has suffered from habitat deterioration and fragmentation of coastal meadows. We sampled DNA across the entire population and used 12 polymorphic microsatellite loci to examine whether the environmental changes have resulted in genetic structuring and loss of variation. Results We found a pattern of isolation-by-distance across the whole Baltic population and genetic differentiation between local populations, even within the southern Baltic. Observed heterozygosity was lower than expected throughout the range and internal relatedness values were positive indicating inbreeding. Conclusions Our results provide long-term, empirical evidence for the theoretically expected links between habitat fragmentation, population subdivision, and gene flow. They also demonstrate a rare case of genetic differentiation between populations of a long-distance migratory species. The Baltic Southern Dunlin differs from many related shorebird species that show near panmixia, reflecting its philopatric life history and the reduced connectivity of its breeding patches. The results have important implications as they suggest that reduced connectivity of breeding habitats can threaten even long-distance migrants if they show strong philopatry during breeding. The Baltic Southern Dunlin warrants urgent conservation efforts that increase functional connectivity and gene flow between breeding areas.

scholarly journals Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

2021 ◽  
Author(s):  
◽  
Hayden Murray Smith
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Fish Species ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Genetic Population ◽  
Biological Trait

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 845-864
Author(s):  
Raquel C. Buranelli ◽  
Fernando L. Mantelatto
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Dna Barcode ◽  
Population Expansion ◽  
Haplotype Network ◽  
Sudden Expansion ◽  
Restricted Gene Flow ◽  
Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

scholarly journals Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

2021 ◽  
Author(s):  
◽  
Hayden Murray Smith
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Fish Species ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Genetic Population ◽  
Biological Trait

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

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

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