Global Population Structure of a Worldwide Pest and Virus Vector: Genetic Diversity and Population History of the Bemisia tabaci Sibling Species Group

AbstractConventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic. However, most populations are structured. This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates. To develop a coalescent method unhampered by population structure, we perform two analyses. First, we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation (one generation back) is independent of population structure. Second, motivated by this finding, we propose a new coalescent method: i-coalescent analysis. i-coalescent analysis computes the instantaneous coalescent rate (iCR) by using a phylogenetic tree of sampled alleles. Using simulated data, we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations, although we find this method often requires larger sample sizes for structured populations than for panmictic populations. Overall, our results indicate i-coalescent analysis to be a useful tool, especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms.

Download Full-text

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).

Download Full-text

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common MoorhenGallinula chloropusin China

Ibis ◽

10.1111/ibi.12579 ◽

2018 ◽

Vol 160 (4) ◽

pp. 855-869 ◽

Cited By ~ 4

Author(s):

Luzhang Ruan ◽

Wei Xu ◽

Yuqing Han ◽

Chaoying Zhu ◽

Bicai Guan ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population History ◽

Stable Population ◽

Multiple Sources ◽

High Genetic Diversity ◽

History Of

Download Full-text

Phylogenetic Biology of the Bemisia tabaci Sibling Species Group

Bemisia: Bionomics and Management of a Global Pest ◽

10.1007/978-90-481-2460-2_2 ◽

2009 ◽

pp. 31-67 ◽

Cited By ~ 8

Author(s):

Judith K. Brown

Keyword(s):

Bemisia Tabaci ◽

Sibling Species ◽

Species Group

Download Full-text

Population structure, genetic diversity, and colonization history of the eastern pondmussel, Sagittunio nasutus , in the Great Lakes drainage

Aquatic Conservation Marine and Freshwater Ecosystems ◽

10.1002/aqc.3250 ◽

2020 ◽

Vol 30 (4) ◽

pp. 631-646 ◽

Cited By ~ 2

Author(s):

Mariah W. Scott ◽

Todd J. Morris ◽

David T. Zanatta

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Great Lakes ◽

Colonization History ◽

History Of

Download Full-text

Global Population Structure and Natural History of the Green Turtle (Chelonia mydas) in Terms of Matriarchal Phylogeny

Evolution ◽

10.2307/2409742 ◽

1992 ◽

Vol 46 (4) ◽

pp. 865 ◽

Cited By ~ 107

Author(s):

Brian W. Bowen ◽

Anne B. Meylan ◽

J. Perran Ross ◽

Colin J. Limpus ◽

George H. Balazs ◽

...

Keyword(s):

Population Structure ◽

Natural History ◽

Green Turtle ◽

Chelonia Mydas ◽

History Of ◽

Global Population

Download Full-text

TANAMAN INDIKATOR DAN TEKNIK RAPD-PCR UNTUK PENENTUAN BIOTIPE BEMISIA TABACI GENNADIUS (HEMIPTERA: ALEYRODIDAE)

JURNAL HAMA DAN PENYAKIT TUMBUHAN TROPIKA ◽

10.23960/j.hptt.181-7 ◽

2011 ◽

Vol 8 (1) ◽

pp. 1-7

Author(s):

Purnama Hidayat ◽

Noor Aidawati ◽

Sri Hendrastuti Hidayat ◽

Dewi Sartiami

Keyword(s):

Genetic Diversity ◽

Bemisia Tabaci ◽

Virus Vector ◽

Indicator Plant ◽

Chilli Pepper ◽

Genetic Types ◽

Rapd Pcr ◽

Major Pest ◽

Biotype B

Indicator Plant and PCR-RAPD for Biotype Determination of Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae).B. tabaci has been known world wide as a major pest and virus vector of horticulture. In Indonesia the presence of B.tabaci was reported since 1980 and its role as virus vector in tomato and chilli pepper has becoming more importantrecently. Genetic diversity of B. tabaci has been well recognized, but very little information available for diversity of B.tabaci in Indonesia. This research was conducted in Bogor, West Java from May 2004 to June 2005. The aim of thisresearch was to initiate basic information regarding genetic diversity of B. tabaci in Indonesia, particularly in Java Island.Whiteflies population collected from different crops, i.e. tomato, broccoli, chill pepper, eggplant, cucumber, soybean, andedamame, was evaluated using silverleaf-induction test, and RAPD-PCR. It was evidenced that only B. tabaci populationfrom broccoli was able to induce silverleaf. Two genetic types of B. tabaci, i.e. biotype B and non B, were identified basedon polymorphism character of DNA. Population from broccoli was belong to biotype B, whereas other populations fromtomato, chill pepper, eggplant, cucumber, soybean, and edamame were belong to biotype non B.

Download Full-text

The story of the lost twins: decoding the genetic identities of the Kumhar and Kurcha populations from the Indian subcontinent

BMC Genetics ◽

10.1186/s12863-020-00919-2 ◽

2020 ◽

Vol 21 (S1) ◽

Author(s):

Ranajit Das ◽

Vladimir A. Ivanisenko ◽

Anastasia A. Anashkina ◽

Priyanka Upadhyai

Keyword(s):

Population Structure ◽

South India ◽

Indian Subcontinent ◽

Uttar Pradesh ◽

Principal Component ◽

Population History ◽

North India ◽

Geographic Population ◽

Indian Populations ◽

History Of

Abstract Background The population structure of the Indian subcontinent is a tapestry of extraordinary diversity characterized by the amalgamation of autochthonous and immigrant ancestries and rigid enforcement of sociocultural stratification. Here we investigated the genetic origin and population history of the Kumhars, a group of people who inhabit large parts of northern India. We compared 27 previously published Kumhar SNP genotype data sampled from Uttar Pradesh in north India to various modern day and ancient populations. Results Various approaches such as Principal Component Analysis (PCA), Admixture, TreeMix concurred that Kumhars have high ASI ancestry, minimal Steppe component and high genomic proximity to the Kurchas, a small and relatively little-known population found ~ 2500 km away in Kerala, south India. Given the same, biogeographical mapping using Geographic Population Structure (GPS) assigned most Kumhar samples in areas neighboring to those where Kurchas are found in south India. Conclusions We hypothesize that the significant genomic similarity between two apparently distinct modern-day Indian populations that inhabit well separated geographical areas with no known overlapping history or links, likely alludes to their common origin during or post the decline of the Indus Valley Civilization (estimated by ALDER). Thereafter, while they dispersed towards opposite ends of the Indian subcontinent, their genomic integrity and likeness remained preserved due to endogamous social practices. Our findings illuminate the genomic history of two Indian populations, allowing a glimpse into one or few of numerous of human migrations that likely occurred across the Indian subcontinent and contributed to shape its varied and vibrant evolutionary past.

Download Full-text

Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa167 ◽

2020 ◽

Vol 132 (1) ◽

pp. 161-173

Author(s):

Camila D Ritter ◽

Laís A Coelho ◽

João Mg Capurucho ◽

Sergio H Borges ◽

Cíntia Cornelius ◽

...

Keyword(s):

Population Structure ◽

Bird Species ◽

Population History ◽

Sister Species ◽

White Sand ◽

Migration Rates ◽

History Of ◽

The Last Glacial Maximum ◽

Vegetation Patches ◽

The Last Glacial

Abstract Although the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.

Download Full-text