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

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.

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Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

Animal Biology ◽

10.1163/157075610x523314 ◽

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.

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

Australian Journal of Botany ◽

10.1071/bt11024 ◽

2011 ◽

Vol 59 (5) ◽

pp. 450 ◽

Cited By ~ 5

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.

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A Large-scale Analysis of Human Mitochondrial DNA Sequences with Special Reference to the Population History of East Eurasian.

Anthropological Science ◽

10.1537/ase.110.293 ◽

2002 ◽

Vol 110 (3) ◽

pp. 293-312 ◽

Cited By ~ 4

Author(s):

H. Oota ◽

N. Saitou ◽

S. Ueda

Keyword(s):

Mitochondrial Dna ◽

Special Reference ◽

Dna Sequences ◽

Large Scale ◽

Population History ◽

Scale Analysis ◽

Human Mitochondrial Dna ◽

Large Scale Analysis ◽

History Of

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Population structure and demographic history of the chukar partridge Alectoris chukar in China

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

Author(s):

Sen Song ◽

Shijie Bao ◽

Ying Wang ◽

Xinkang Bao ◽

Bei An ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North America ◽

Demographic History ◽

Population Expansion ◽

Northwest China ◽

Population History ◽

Extant Species ◽

History Of ◽

Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2010.10.003 ◽

2010 ◽

Vol 57 (3) ◽

pp. 1091-1104 ◽

Cited By ~ 11

Author(s):

Qian Zhang ◽

Lin Xia ◽

Jingbo He ◽

Yonghua Wu ◽

Jinzhong Fu ◽

...

Keyword(s):

Tarim Basin ◽

Population History ◽

Phylogeographic Structure ◽

History Of

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Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽

10.3390/genes12081236 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1236

Author(s):

Elisabeth Hempel ◽

Michael V. Westbury ◽

José H. Grau ◽

Alexandra Trinks ◽

Johanna L. A. Paijmans ◽

...

Keyword(s):

Population Size ◽

Population History ◽

Phylogeographic Structure ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Effective Population ◽

Mammal Species ◽

Human Disturbances ◽

Most Recent Common Ancestor ◽

History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

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Population networks from DNA sequences: methodological developments

10.1101/188268 ◽

2017 ◽

Author(s):

B. Schaeffer ◽

V. Nicolas ◽

F. Austerlitz ◽

C. Larédo

Keyword(s):

Graphical Models ◽

Dna Sequences ◽

Genetic Material ◽

Simulated Data ◽

Original Method ◽

Population History ◽

Data Sets ◽

Key Factor ◽

History Of ◽

Simulated Data Sets

AbstractSeveral classes of methods have been proposed for inferring the history of populations from genetic polymorphism data. As connectivity is a key factor to explain the structure of populations, several graph-based methods have been developed to this aim, using population genetics data. Here we propose an original method based on graphical models that uses DNA sequences to provide relationships between populations. We tested our method on various simulated data sets, describing typical demographic scenarios, for different parameters values. We found that our method behaved noticeably well for realistic demographic evolutionary processes and recovered suitably the migration processes. Our method provides thus a complementary tool for investigating population history based on genetic material.

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Introgression makes waves in inferred histories of effective population size

10.1101/121483 ◽

2017 ◽

Author(s):

John Hawks

Keyword(s):

Gene Flow ◽

Population Size ◽

Effective Population Size ◽

Population History ◽

Human Populations ◽

Effective Population ◽

History Of ◽

Or Gene ◽

Time Of Origin ◽

Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

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