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

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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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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Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation

Genes & Genetic Systems ◽

10.1266/ggs.82.465 ◽

2007 ◽

Vol 82 (6) ◽

pp. 465-477 ◽

Cited By ~ 65

Author(s):

Takatomi Okaura ◽

Nguyen Duc Quang ◽

Masatoshi Ubukata ◽

Ko Harada

Keyword(s):

Chloroplast Dna ◽

Related Species ◽

Late Quaternary ◽

Population History ◽

Phylogeographic Structure ◽

Dna Variation ◽

Quercus Mongolica ◽

History Of ◽

Chloroplast Dna Variation

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

The Auk ◽

10.1093/auk/120.3.744 ◽

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.

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First steps towards assessing the evolutionary history and phylogeography of a widely distributed Neotropical grassland bird (Motacillidae: Anthus correndera)

PeerJ ◽

10.7717/peerj.5886 ◽

2018 ◽

Vol 6 ◽

pp. e5886 ◽

Cited By ~ 4

Author(s):

Heraldo V. Norambuena ◽

Paul Van Els ◽

Carlos P. Muñoz-Ramírez ◽

Pedro F. Victoriano

Keyword(s):

South America ◽

Population History ◽

Middle Pleistocene ◽

Phylogeographic Structure ◽

General View ◽

South American ◽

Distribution Models ◽

Grassland Bird ◽

Southern South America ◽

History Of

Grasslands in southern South America are extensive ecosystems which harbor a unique biodiversity; however, studies on the evolution of their taxa are scarce. Here we studied the phylogeography and population history of the Correndera Pipit (Anthus correndera), a grassland specialist bird with a large breeding distribution in southern South America, with the goals of investigating its phylogeographic history and relate it to the historical development of South American grasslands. The mitochondrial NADH dehydrogenase subunit II gene (ND2) was sequenced in 66 individuals from 19 localities and the intron 9 of the sex-linked gene for aconitase (ACOI9) was sequenced from a subset of those individuals, including all five subspecies of A. correndera, as well as the closely related A. antarcticus. Phylogenetic analysis revealed two distinct lineages within the complex: the first (A) corresponding to Andean subspecies A. c. calcaratus and A. c. catamarcae and the second (B) including birds traditionally assigned to A. c. correndera, A. c. chilensis, A. c. grayi and some individuals of A. c. catamarcae. A. antarcticus is nested within this second lineage. These results were also supported by evidence of niche divergence for variables associated with precipitation. The oldest split between clade A and B was estimated at c. 0.37 Mya, during the middle Pleistocene. Species distribution models for the present and the Last Glacial Maximum (LGM) suggest that grassland areas in southern South America remained relatively stable, in contrast to the general view of a reduction in grassland cover in South America since the LGM. Recent divergences and low phylogeographic structure (for lowland vs. highland geographic groups, intra-population genetic variance was greater than inter-groups; e.g., for ACOI9: 95.47% and ND2: 51.51% respectively), suggest widespread gene flow between lowland populations.

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