scholarly journals Historical demography of freshwater mussels (Bivalvia: Unionidae): genetic evidence for population expansion and contraction during the late Pleistocene and Holocene

2015 ◽  
Vol 114 (2) ◽  
pp. 376-397 ◽  
Author(s):  
Jess W. Jones ◽  
Richard J. Neves ◽  
Eric M. Hallerman
Keyword(s):  
Late Pleistocene ◽  
Freshwater Mussels ◽  
Population Expansion ◽  
Historical Demography ◽  
Genetic Evidence

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.

Genetic evidence for population expansion in Hydrotaea irritans (Fallen) (Diptera: Muscidae)

2004 ◽  
Vol 42 (3) ◽  
pp. 257-261
Author(s):  
V. Loeschcke ◽  
B. O. Nielsen ◽  
A. Aa. Pedersen ◽  
J. G. Sorensen ◽  
H. R. Siegismund
Keyword(s):  
Population Expansion ◽  
Genetic Evidence

scholarly journals Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

2021 ◽  
Author(s):  
Zheng Li ◽  
Jie Zhou ◽  
Minzhi Gao ◽  
Wei Liang ◽  
Lu Dong
Keyword(s):  
Sexual Selection ◽  
Gene Flow ◽  
Late Pleistocene ◽  
Approximate Bayesian Computation ◽  
De Novo ◽  
Demographic History ◽  
Population Expansion ◽  
Secondary Contact ◽  
Bayesian Computation ◽  
Approximate Bayesian

Background: Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrid recordings in field. Methods: In this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) method based on the multiple genes data. With a new assembled de novo genome of Lady Amherst's pheasant and resequencing of widely distributed individuals, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC). Results: The results provide clear evidence that the gene flow between the two pheasants were consistent with the prediction of isolation with migration model for allopatric populations, indicating that there was long-term gene flow after the initially divergence (ca. 2.2 million years ago), and further support the secondary contact when included the parapatric populations since around 30 ka ongoing gene flow to now, which might be induced by the population expansion of the Golden pheasant in late Pleistocene. Conclusions: The results of the study support the scenario of speciation between Golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae) with cycles of mixing-isolation-mixing due to the dynamics of natural selection and sexual selection in late Pleistocene that provide a good research system as evolutionary model to test reinforcement selection in speciation. Keywords: Golden pheasant (Chrysolophus pictus), Lady Amherst's pheasant (Chrysolophus amherstiae), speciation, gene flow, Approximate Bayesian Computation (ABC), Pairwise Sequentially Markovian coalescent (PSMC).

scholarly journals Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

2016 ◽  
Vol 3 (10) ◽  
pp. 160350 ◽  
Author(s):  
Riddhi P. Patel ◽  
Daniel W. Förster ◽  
Andrew C. Kitchener ◽  
Mark D. Rayan ◽  
Shariff W. Mohamed ◽  
...  
Keyword(s):  
Late Pleistocene ◽  
Species Distribution ◽  
Nucleotide Diversity ◽  
Demographic History ◽  
Population Expansion ◽  
Molecular Data ◽  
Peninsular Malaysia ◽  
Sister Species ◽  
Morphological Data ◽  
Island Endemic

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based on morphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis .

scholarly journals Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas

2020 ◽  
Vol 6 (9) ◽  
pp. eaax5751 ◽  
Author(s):  
Yibo Hu ◽  
Arjun Thapa ◽  
Huizhong Fan ◽  
Tianxiao Ma ◽  
Qi Wu ◽  
...  
Keyword(s):  
Large Population ◽  
Genetic Load ◽  
Population Expansion ◽  
High Linkage Disequilibrium ◽  
Genetic Evidence ◽  
Morphological Evidence ◽  
Population Bottlenecks ◽  
Phylogenetic Species ◽  
Low Genetic Diversity ◽  
Red Panda

The red panda (Ailurus fulgens), an endangered Himalaya-endemic mammal, has been classified as two subspecies or even two species – the Himalayan red panda (A. fulgens) and the Chinese red panda (Ailurus styani) – based on differences in morphology and biogeography. However, this classification has remained controversial largely due to lack of genetic evidence, directly impairing scientific conservation management. Data from 65 whole genomes, 49 Y-chromosomes, and 49 mitochondrial genomes provide the first comprehensive genetic evidence for species divergence in red pandas, demonstrating substantial inter-species genetic divergence for all three markers and correcting species-distribution boundaries. Combined with morphological evidence, these data thus clearly define two phylogenetic species in red pandas. We also demonstrate different demographic trajectories in the two species: A. styani has experienced two population bottlenecks and one large population expansion over time, whereas A. fulgens has experienced three bottlenecks and one very small expansion, resulting in very low genetic diversity, high linkage disequilibrium, and high genetic load.

Evidence for late Pleistocene population expansion of the malarial mosquitoes, Anopheles arabiensis and Anopheles gambiae in Nigeria

2007 ◽  
Vol 21 (4) ◽  
pp. 358-369 ◽  
Author(s):  
S. D. MATTHEWS ◽  
L. J. MEEHAN ◽  
D. Y. ONYABE ◽  
J. VINEIS ◽  
I. NOCK ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Late Pleistocene ◽  
Anopheles Arabiensis ◽  
Population Expansion

scholarly journals Historical Demography and the Crisis of the Seventeenth Century

2009 ◽  
Vol 40 (2) ◽  
pp. 195-214 ◽  
Author(s):  
Anne E. C. McCants
Keyword(s):  
Seventeenth Century ◽  
Population Growth ◽  
Turning Point ◽  
Population Expansion ◽  
European Population ◽  
Historical Demography ◽  
Population Movements ◽  
History Of ◽  
Fundamental Shift

The seventeenth century, broadly conceived, marks an important turning point in the history of European population movements. Long cycles characterized, first, by population expansion and subsequently by mortality contractions due to famine or disease held long-term population growth largely in check. The subsistence and mortality crises of the middle decades of the seventeenth century and the fundamental shift in the capacity of the European population to grow after 1750 together suggest that the case for a “general crisis of the seventeenth century” has strong demographic support.

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