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A statistical procedure to assess the significance level of barriers to gene flow

Journal of genetics and Genomics 2009年第11期36卷 685-693页

作者： Sébastien Rioux Paquette Franois-Joseph Lapointe Allan Wilson Centre for Molecular Ecology & School of Biological Sciences Victoria University of Wellington Département de Sciences Biologiques Université de Montréal

Although several methods are available to study the extent of isolation by distance （IBD） among natural populations, comparatively few exist to detect the presence of sharp genetic breaks in genetic distance datasets. In recent years, Monmonier＇s maximum-difference algorithm has been increasingly used by population geneticists. However, this method does not provide means to measure the statistical significance of such barriers, nor to determine their relative contribution to population differentiation with respect to IBD. Here, we propose an approach to assess the significance of genetic boundaries. The method is based on the calculation of a multiple regression from distance matrices, where binary matrices represent putative genetic barriers to test, in addition to geographic and genetic distances. Simulation results suggest that this method reliably detects the presence of genetic barriers, even in situations where IBD is also significant. We also illustrate the methodology by analyzing previously published datasets. Conclusions about the importance of genetic barriers can be misleading if one does not take into consideration their relative contribution to the overall genetic structure of species.

关键词： genetic barriers genetic distances isolation by distance multiple regression on distance matrices partial regression coefficients

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Integrative taxonomy of the Plain-backed Thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species

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Chinese Birds 2016年第1期7卷 2-39,1页

作者： Per Alstrom Pamela C.Rasmussen Chao Zhao Jingzi Xu Shashank Dalvi Tianlong Cai Yuyan Guan Ruiying Zhang Mikhail V.Kalyakin Fumin Lei Urban Olsson Department of Animal Ecology Evolutionary Biology CentreUppsala University Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences Swedish Species Information Centre Swedish University of Agricultural Sciences Department of Integrative Biology and MSU Museum Michigan State University Bird Group The Natural History Museum at Tring Cloud Mountain Conservation Department of Evolutionary Biology Evolutionary Biology CentreUppsala University Researchers for Wildlife Conservation F-21National Centre for Biological Sciences College of Life Sciences University of Chinese Academy of Sciences Zoological Museum of Lomonosov Moscow State University Systematics and Biodiversity Department of Biology and Environmental SciencesUniversity of Gothenburg

Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly sympatric.Methods: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic(two mitochondrial and two nuclear markers), ecological and distributional datasets.Results: In earlier field observations, we noted two very different song types of "Plain-backed" Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China("Alpine Thrush"); a forest breeder in the eastern Himalayas and northwest Yunnan(at least), China("Himalayan Forest Thrush"); and a forest breeder in central Sichuan("Sichuan Forest Thrush"). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists("Yunnan Thrush"). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative "Yunnan Thrush" as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato(s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto(s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest Thrush.Conclusions: The Plain-backed Thrush Z. mollissima s.l. comprises

关键词： Systematics Morphology Bioacoustics Altitudinal distributions genetic distances Undescribed taxa Zoothera dixoni Lectotypification Holotype

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Molecular Diversity of Fusarium oxysporum and Geotrichum candidum Isolated from Two Tomato Varieties Commonly Consumed in Some Southwestern Town in Nigeria

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American Journal of Plant Sciences 2022年第5期13卷 668-685页

作者： Ayodele Adegboyega Sobowale Olalekan Ajibolade Ogunoye Department of Botany University of Ibadan Ibadan Nigeria Department of Crop Soil and Pest Management Technology Rufus Giwa Polytechnic Owo Owo Nigeria

Fusarium oxysporum and Geotrichum candidum, which are among important pathogens of Solanum lycopersicum L. (Tomato), are sometimes misidentified during morphological misidentification. The study was carried out to evaluate molecular diversity of F. oxysporum and G. candidum isolated from two tomato varieties obtained from Akure, Ilorin and Ibadan, Nigeria. The tomato samples were collected and brought back to the laboratory for fungal isolation. Isolation of the pathogens were done following standard procedures. DNA extraction from pure cultures of the pathogens was done at the Centre Laboratory of University of Ibadan. genetic relationships among the organisms were also estimated by constructing a Dendrogram through UPGMA using the Mega6 Software and genetic distance was computed also using the Mega6 Software. Five strains of F. oxysporum and seven strains of G. candidum were identified. Percentage similarity of the pathogens with those in GenBank was 99.17% - 100.00% for F. oxysporum and 98.48% - 100.00% for G. candidum. The T-01 marker showed the lowest major allele frequency of 0.0833, while T-10 marker has the highest value for major allele frequency of 0.6667 and an average value of 0.3958. Evolutionary relationship showed that the two strains of G. candidum (MN650247 and MN650250) were similar. The three strains of F. oxysporum (MN650246 and MN650248, MN650245 and MN650253) were also similar. genetic distances among pairs of the fungal strains ranged from 0.12 to 6.30 in pairwise fashion, with an average of 1.32. Evolutionary relationship or closeness among strains of a fungal species can thus be said not to depend on location.

关键词： Fusarium oxysporum Geotricum candidum genetic distances Evolutionary Relationship and Genes

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genetic Diversity and Population Structure of Three Strains of Indigenous Tswana Chickens and Commercial Broiler Using Single Nucleotide Polymormophic (SNP) Markers

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Open Journal of Animal Sciences 2021年第4期11卷 515-531页

作者： James Buttie Machete Patrick Monametsi Kgwatalala Shalaulani James Nsoso Nompilo Lucia Hlongwane John Cassius Moreki Department of Animal Science and Production Botswana University of Agriculture and Natural Resources Gaborone Botswana Biotechnology Platform Agricultural Research Council Pretoria South Africa

The Tswana chicken is native to Botswana and comprises strains such as the naked neck, normal, dwarf, frizzled, and rumples. The origins of the different strains of Tswana chicken remain unknown and it is not yet clear if the different strains represent distinct breeds within the large Tswana chicken population. Genetic characterization of different strains of Tswana chickens using SNP arrays can elucidate their genetic relationships and ascertain if the strains represent distinct breeds of Tswana chicken population. The aim of this study was therefore to investigate population structure and diversity and to estimate genetic distances/identity between the naked neck, normal and dwarf strains of Tswana chickens. A total of 96 chickens (normal strain (n = 39), naked neck strain (n = 32), dwarf strain (n = 13) and commercial broiler (n = 12)) were used in the study. SNP genotyping was carried out using the Illumina chicken iSelect SNP 60 Bead chip using the Infinium assay compatible with the Illumina HiScan SQ genotyping platform. The observed heterozygosity (Ho) values were 0.610 ± 0.012, 0.611 ± 0.014, 0.613 ± 0.0006 for normal, naked neck and dwarf strains of Tswana chickens respectively and averaged 0.611 ± 0.016 across the three strains

关键词： genetic distances genetic Diversity Indigenous Tswana Chickens Population Structure SNPs

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