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Wang Q, Wang R, Wang S, Zhang A, Duan Q, Sun S, Jin L, Wang X, Zhang Y, Wang C, Kang H, Zhang Z, Liao K, Guo Y, Jin L, Liu Z, Yang C, Wang H. Expansion and transmission dynamics of high risk carbapenem-resistant Klebsiella pneumoniae subclones in China: An epidemiological, spatial, genomic analysis. Drug Resist Updat 2024; 74:101083. [PMID: 38593500 DOI: 10.1016/j.drup.2024.101083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
AIMS Carbapenem-resistant Klebsiella pneumonia (CRKP) is a global threat that varies by region. The global distribution, evolution, and clinical implications of the ST11 CRKP clone remain obscure. METHODS We conducted a multicenter molecular epidemiological survey using isolates obtained from 28 provinces and municipalities across China between 2011 and 2021. We integrated sequences from public databases and performed genetic epidemiology analysis of ST11 CRKP. RESULTS Among ST11 CRKP, KL64 serotypes exhibited considerable expansion, increasing from 1.54% to 46.08% between 2011 and 2021. Combining our data with public databases, the phylogenetic and phylogeography analyses indicated that ST11 CRKP appeared in the Americas in 1996 and spread worldwide, with key clones progressing from China's southeastern coast to the inland by 2010. Global phylogenetic analysis showed that ST11 KL64 CRKP has evolved to a virulent, resistant clade with notable regional spread. Single-nucleotide polymorphism (SNP) analysis identified BMPPS (bmr3, mltC, pyrB, ppsC, and sdaC) as a key marker for this clade. The BMPPS SNP clade is associated with high mortality and has strong anti-phagocytic and competitive traits in vitro. CONCLUSIONS The high-risk ST11 KL64 CRKP subclone showed strong expansion potential and survival advantages, probably owing to genetic factors.
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Affiliation(s)
- Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Anru Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qiaoyan Duan
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Longyang Jin
- Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan, Friendship Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chunlei Wang
- Laboratory of Clinical Microbiology and Infectious Diseases, China-Japan, Friendship Hospital, Beijing, China
| | - Haiquan Kang
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zhijie Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Liaoning Clinical Research Center for Laboratory Medicine, Shenyang, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yinghui Guo
- Hebei Children's Hospital, Shijiazhuang, China
| | - Liang Jin
- Department of Clinical Laboratory, First Hospital of Qinhuangdao, Hebei, China
| | - Zhiwu Liu
- Department of Medical Laboratory Center, the First Hospital of Lanzhou University, Lanzhou, China
| | - Chunxia Yang
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital Affiliated to the Capital University of Medical Sciences, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Wymazał A, Nowak S, Mysłajek RW, Bajer A, Welc-Falęciak R, Szewczyk M, Kwiatkowska I, Stępniak KM, Figura M, Kloch A. Tick-borne infections in wolves from an expanding population in Eastern Europe. Ticks Tick Borne Dis 2024; 15:102272. [PMID: 37890206 DOI: 10.1016/j.ttbdis.2023.102272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
In Central and Eastern Europe, wolf populations have been increasing over the last two decades, recolonizing areas from which the species had been previously exterminated. As wolves are still recovering after years of persecution by humans, recognizing pathogens infecting this species, including tick-borne infections, is crucial for its conservation. On the other hand the high mobility of wolves and their frequent contacts with humans, dogs, and other domestic species make them a potentially important zoonotic reservoir. In this paper, we used molecular methods to determine the prevalence of tick-borne pathogens in the following genera: Anaplasma, Babesia, Bartonella, Borrelia, and Rickettsia in 50 free-ranging wolves from Poland. We detected Babesia canis in the blood of nine individuals (prevalence 9/50=18 %). The obtained sequence showed the highest similarity to B. canis isolated from dogs and ticks, and all infected individuals originated from regions endemic to the ornate tick, Dermacentor reticulatus. Anaplasma phagocytophilum was found in tissue from one individual (1/50=2 %), and the sequence was assigned to the zoonotic ecotype I.
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Affiliation(s)
- Aleksander Wymazał
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sabina Nowak
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Robert W Mysłajek
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Anna Bajer
- Faculty of Biology, Department of Eco-Epidemiology of Parasitic Diseases, University of Warsaw, Miecznikowa 1, Warszawa 02-096, Poland
| | - Renata Welc-Falęciak
- Faculty of Biology, Department of Parasitology, University of Warsaw, Miecznikowa 1, Warszawa 02-096, Poland
| | - Maciej Szewczyk
- Faculty of Biology, Department of Vertebrate Ecology and Zoology, University of Gdańsk, Wita Stwosza 59, Gdańsk 80-308, Poland
| | - Iga Kwiatkowska
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Kinga M Stępniak
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Michał Figura
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland; Association for Nature "Wolf", Cynkowa 4, Twardorzeczka 34-324, Poland
| | - Agnieszka Kloch
- Faculty of Biology, Department of Ecology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland.
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Ochoa-Zavala M, Diaz-Jaimes P, Ortega-García S, Galván-Magaña F. Genetic divergence at species boundaries of the dolphinfish ( Coryphaena hippurus) in the Tropical Eastern Pacific. PeerJ 2022; 10:e14389. [PMID: 36415864 PMCID: PMC9676019 DOI: 10.7717/peerj.14389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Marine species constitute commercially important resources, and knowledge about mechanisms that shape phylogeographic patterns and genetic structure provides valuable information for conservation. The dolphinfish, Coryphaena hippurus, is one of the most important species caught in the Tropical Eastern Pacific (TEP). However, the lack of consensus about the existence of genetically differentiated populations in the area has hindered the adoption of management strategies to ensure its viability. Methods We assessed genetic variation and phylogeographic structure using two mitochondrial genes and 14 nuclear DNA microsatellite loci. Population genetic tools were used to characterize the spatial distribution of genetic variation of C. hippurus in the TEP, evaluate the extent of connectivity between dolphinfish populations, infer potential barriers to gene flow, and test for signals of contemporary and historical demographic expansions. Results Mitochondrial DNA sequences showed genetic homogeneity across locations in the TEP, as well as a strong signal of population expansion dated to the late Pleistocene. In contrast, nuclear microsatellite markers resolved four genetically distinct groups with a remarked genetic differentiation between the most distant locations, at the northern and southern boundaries of the species' range. High mean genetic diversity was found at all localities (Hs = 0.66-0.81). Notwithstanding, positive F IS and low effective population size (Ne = 77.9-496.4) were also recorded. Conclusions The distribution of genetic variation could be related to expansion-contraction cycles following seasonal temperature changes at transitional areas, promoting population subdivisions. However, we cannot rule out the effect of oceanographic dynamics to the observed patterns. Although this marine species remains highly abundant despite commercial exploitation, the low Ne values are of conservation concern and must be considered in fishery management plans.
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Affiliation(s)
- Maried Ochoa-Zavala
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnnología, Universidad Nacional Autónoma de México, CDMX, Mexico,Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Pindaro Diaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnnología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Sofía Ortega-García
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, México
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Buhari Lawan Muhammad, Yoseph Seo, Jinho Chae, Jang-Seu Ki. Population Genetic Structures and Demographic Expansion of the Exotic
Jellyfish Carybdea brevipedalia in Korean Coasts Inferred from
Mitochondrial COI Analysis. Zool Stud 2022; 61:e48. [PMID: 36568814 PMCID: PMC9745567 DOI: 10.6620/zs.2022.61-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/30/2022] [Indexed: 12/27/2022]
Abstract
Carybdea brevipedalia Kishinouye, 1891 is a poisonous jellyfish that usually occurs only in Japanese coastal regions. However, it was recently found on the Korean coast, thus expanding its known geographical range. In this study, we analyzed the population genetics and demographic histories of 113 C. brevipedalia specimens from the southern and eastern coastal regions of Korea by sequencing mitochondrial DNA cytochrome c oxidase subunit I (COI). We identified 42 C. brevipedalia COI haplotypes with high genetic diversity and a significant genetic structure. Populations were highly differentiated based on geographic location and distinctly divided into A and B clades. The results of Mantel tests indicated that geographic distance influenced the genetic distance between the two clades. Moreover, demographic analyses (neutrality tests) and the star-like profile of the Templeton, Crandall, and Sing (TCS) haplotype network indicated that C. brevipedalia had recently expanded into the southern and eastern coastal regions of Korea. These findings suggest that C. brevipedalia populations along the Korean coast have significant genetic differentiation that could be influenced by geographic isolation and subsequent adaptation to regional ecological conditions.
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Pramual P, Jomkumsing P, Wathasith P, Wongpakam K. Population structure and population history of the black fly Simulium chumpornense (Diptera: Simuliidae) from Thailand. Acta Trop 2022; 227:106301. [PMID: 34986384 DOI: 10.1016/j.actatropica.2021.106301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
Abstract
Understanding genetic structure and diversity of insect vectors is crucial for disease epidemiology. In this study, mitochondrial cytochrome c oxidase I sequences were used to infer genetic diversity, genetic structure and population history of the black fly, Simulium chumpornense Takaoka and Kuvangkadilok, a suspected vector of blood protozoa of the genus Leucocytozoon and Trypanosoma. High intraspecific genetic divergence (max. 3.76%) was found among 142 specimens obtained from 19 locations across Thailand. A median joining network revealed two genetic lineages (A and B) that were geographically associated. Lineage A is representative of central and northeastern regions. Lineage B represents specimens from diverse locations in northern, western, and southern Thailand, including the type locality. Mismatch distribution and the neutrality tests provided signals of past population expansions in both lineages. The expansion time dating back to the end of last glaciations at 12,000 - 15,000 years ago is possibly related to increasing of precipitation at the end of last glacial period. Despite recent population history, population pairwise FST analysis revealed that almost all population comparisons were genetically significantly different. The high level of genetic structuring is possibly a result of historical isolation of the population that survived in different refugia sites during the dry conditions during glaciations.
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Affiliation(s)
- Pairot Pramual
- Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham, 44150, Thailand.
| | - Panya Jomkumsing
- Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham, 44150, Thailand
| | - Pornthida Wathasith
- Department of Biology, Faculty of Science, Mahasarakham University, Kantharawichai District, Maha Sarakham, 44150, Thailand
| | - Komgrit Wongpakam
- Walai Rukhavej Botanical Research Institute, Mahasarakham University, Kantharawichai District, Maha Sarakham 44150 Thailand
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Lin HC, Tsai CJ, Wang HY. Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes. PeerJ 2022; 9:e12639. [PMID: 35003932 PMCID: PMC8684317 DOI: 10.7717/peerj.12639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/24/2021] [Indexed: 01/04/2023] Open
Abstract
Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22-39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these differences, a single well-mixing fish stock, thus one management unit, was identified in each of the four species, presumably due to expansion of their population sizes predated the Last Glacial Maximum and a lack of distribution barrier. The most dominant T. japonicus, which have at least one magnitude higher effective population size than the others, show a unique abrupt size expansion event at 75 to 50-kilo years ago when the low sea level occurred during the ice age. Main conclusions The demographic history revealed by our genetic analyses advances understanding of the current distribution and population structure for these congeneric species. Moreover, the uncovered population structure provides insight into the assessment and management of these species. Such information complements contemporary knowledge about these species and enables us to forecast their ability to resist future environmental and anthropogenic disturbances.
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Affiliation(s)
- Hsiu-Chin Lin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chia-Jung Tsai
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Hui-Yu Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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Syahida Kasim N, Mat Jaafar TNA, Mat Piah R, Mohd Arshaad W, Mohd Nor SA, Habib A, Abd. Ghaffar M, Sung YY, Danish-Daniel M, Tan MP. Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers. PeerJ 2020; 8:e9679. [PMID: 32844067 PMCID: PMC7415224 DOI: 10.7717/peerj.9679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 07/17/2020] [Indexed: 01/12/2023] Open
Abstract
The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989-1.000; ND5 = 0.848-0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019-0.025; ND5 = 0.0017-0.003), "star-like" haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.
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Affiliation(s)
- Noorhani Syahida Kasim
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | | | - Rumeaida Mat Piah
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Wahidah Mohd Arshaad
- Marine Fishery Resources Development and Management Department (MFRDMD), Taman Perikanan, Chendering, Kuala Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute Marine Biotechnology (IMB), Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Ahasan Habib
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mazlan Abd. Ghaffar
- Institute Marine Biotechnology (IMB), Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Yeong Yik Sung
- Institute Marine Biotechnology (IMB), Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Muhd Danish-Daniel
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
- Institute Marine Biotechnology (IMB), Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Min Pau Tan
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Terengganu, Malaysia
- Institute Marine Biotechnology (IMB), Universiti Malaysia Terengganu, Terengganu, Malaysia
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Fačkovcová Z, Slovák M, Vďačný P, Melichárková A, Zozomová-Lihová J, Guttová A. Spatio-temporal formation of the genetic diversity in the Mediterranean dwelling lichen during the Neogene and Quaternary epochs. Mol Phylogenet Evol 2019; 144:106704. [PMID: 31821879 DOI: 10.1016/j.ympev.2019.106704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 10/14/2019] [Accepted: 12/06/2019] [Indexed: 01/06/2023]
Abstract
Genetic patterns of lichenized fungi often display a mosaic-like and difficult to interpret structure blurring their evolutionary history. The genetic diversity and phylogeographic pattern of a mycobiont of the predominantly Mediterranean dwelling lichen Solenopsora candicans were investigated on the base of extensive sampling (361 individuals, 77 populations) across its entire distribution range. We tested whether the genetic pattern of S. candicans mirrors paleoclimatic and paleogeological events in the Mediterranean and adjacent regions. The divergence time estimates indicated a Tertiary origin for S. candicans, with formation of intraspecific diversity initiated in the Late Miocene. The distribution of the most divergent haplotypes, mostly of a pre-Pleistocene origin, was restricted to the eastern or western extremities of the Mediterranean exhibiting Kiermack disjunction. The population genetic diversity analyses indicated multiple diversity centres and refugia for S. candicans across the entire Mediterranean Basin. While the south Mediterranean regions harboured both the Tertiary and Quaternary born diversity, conforming to the 'cumulative refugia' paradigm, the Apennine and Balkan Peninsulas in the north hosted mostly younger Pleistocene haplotypes and lineages. The recent population expansion of S. candicans might have occurred in the middle Pleistocene with a population burst in the Apennine and Balkan peninsulas. The presence of unique haplotypes in Central Europe indicates the existence of extra-Mediterranean microrefugia. This study presents the first comprehensive lichen phylogeography from the Mediterranean region and simultaneously reports for the first time the glacial survival of a warm-adapted lichen in the temperate zone.
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Affiliation(s)
- Zuzana Fačkovcová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia.
| | - Marek Slovák
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia; Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Andrea Melichárková
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
| | - Judita Zozomová-Lihová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
| | - Anna Guttová
- Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84523 Bratislava, Slovakia
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Li J, Song G, Liu N, Chang Y, Bao X. Deep south-north genetic divergence in Godlewski's bunting (Emberiza godlewskii) related to uplift of the Qinghai-Tibet Plateau and habitat preferences. BMC Evol Biol 2019; 19:161. [PMID: 31370783 PMCID: PMC6676563 DOI: 10.1186/s12862-019-1487-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. RESULTS A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. CONCLUSIONS Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.
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Affiliation(s)
- Jiande Li
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Naifa Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xinkang Bao
- School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
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Godfrey LR, Scroxton N, Crowley BE, Burns SJ, Sutherland MR, Pérez VR, Faina P, McGee D, Ranivoharimanana L. A new interpretation of Madagascar's megafaunal decline: The "Subsistence Shift Hypothesis". J Hum Evol 2019; 130:126-140. [PMID: 31010539 DOI: 10.1016/j.jhevol.2019.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 12/24/2022]
Abstract
Fundamental disagreements remain regarding the relative importance of climate change and human activities as triggers for Madagascar's Holocene megafaunal extinction. We use stable isotope data from stalagmites from northwest Madagascar coupled with radiocarbon and butchery records from subfossil bones across the island to investigate relationships between megafaunal decline, climate change, and habitat modification. Archaeological and genetic evidence support human presence by 2000 years Before Common Era (BCE). Megafaunal decline was at first slow; it hastened at ∼700 Common Era (CE) and peaked between 750 and 850 CE, just before a dramatic vegetation transformation in the northwest that resulted in the replacement of C3 woodland habitat with C4 grasslands, during a period of heightened monsoonal activity. Cut and chop marks on subfossil lemur bones reveal a shift in primary hunting targets from larger, now-extinct species prior to ∼900 CE, to smaller, still-extant species afterwards. By 1050 CE, megafaunal populations had essentially collapsed. Neither the rapid megafaunal decline beginning ∼700 CE, nor the dramatic vegetation transformation in the northwest beginning ∼890 CE, was influenced by aridification. However, both roughly coincide with a major transition in human subsistence on the island from hunting/foraging to herding/farming. We offer a new hypothesis, which we call the "Subsistence Shift Hypothesis," to explain megafaunal decline and extinction in Madagascar. This hypothesis acknowledges the importance of wild-animal hunting by early hunter/foragers, but more critically highlights negative impacts of the shift from hunting/foraging to herding/farming, settlement by new immigrant groups, and the concomitant expansion of the island's human population. The interval between 700 and 900 CE, when the pace of megafaunal decline quickened and peaked, coincided with this economic transition. While early megafaunal decline through hunting may have helped to trigger the transition, there is strong evidence that the economic shift itself hastened the crash of megafaunal populations.
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Affiliation(s)
- Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003, USA.
| | - Nick Scroxton
- Department of Geosciences, University of Massachusetts, Amherst, MA 01003, USA; Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brooke E Crowley
- Departments of Geology and Anthropology, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Stephen J Burns
- Department of Geosciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael R Sutherland
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA 01003, USA
| | - Ventura R Pérez
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003, USA
| | - Peterson Faina
- Département Bassins Sédimentaires Evolution Conservation (BEC), Université D'Antananarivo, Antananarivo 101, Madagascar
| | - David McGee
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lovasoa Ranivoharimanana
- Département Bassins Sédimentaires Evolution Conservation (BEC), Université D'Antananarivo, Antananarivo 101, Madagascar
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11
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Ogura T, Watanabe HK, Chen C, Sasaki T, Kojima S, Ishibashi JI, Fujikura K. Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific. PeerJ 2018; 6:e5673. [PMID: 30280041 PMCID: PMC6163031 DOI: 10.7717/peerj.5673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/28/2018] [Indexed: 11/29/2022] Open
Abstract
Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.
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Affiliation(s)
- Tomomi Ogura
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Hiromi Kayama Watanabe
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Shigeaki Kojima
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Jun-Ichiro Ishibashi
- Department of Earth and Planetary Sciences, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Katsunori Fujikura
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan.,Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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12
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Jenkins TL, Castilho R, Stevens JR. Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions. PeerJ 2018; 6:e5684. [PMID: 30280047 PMCID: PMC6166638 DOI: 10.7717/peerj.5684] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). Methods A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. Results Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. Conclusion This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.
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Affiliation(s)
- Tom L Jenkins
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rita Castilho
- Center for Marine Sciences, Campus de Gambelas, University of Algarve, Faro, Portugal
| | - Jamie R Stevens
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
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Zhu C, Chen P, Han Y, Ruan L. Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China. Biochem Genet 2018; 56:586-617. [PMID: 29754387 DOI: 10.1007/s10528-018-9862-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
Abstract
The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.
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Affiliation(s)
- Chaoying Zhu
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Peng Chen
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Yuqing Han
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China
| | - Luzhang Ruan
- School of Life Sciences, State Ministry of Education Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, 330031, People's Republic of China.
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Nada Raja T, Hu TH, Zainudin R, Lee KS, Perkins SL, Singh B. Malaria parasites of long-tailed macaques in Sarawak, Malaysian Borneo: a novel species and demographic and evolutionary histories. BMC Evol Biol 2018; 18:49. [PMID: 29636003 PMCID: PMC5894161 DOI: 10.1186/s12862-018-1170-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 12/28/2022] Open
Abstract
Background Non-human primates have long been identified to harbour different species of Plasmodium. Long-tailed macaques (Macaca fascicularis), in particular, are reservoirs for P. knowlesi, P. inui, P. cynomolgi, P. coatneyi and P. fieldi. A previous study conducted in Sarawak, Malaysian Borneo, however revealed that long-tailed macaques could potentially harbour novel species of Plasmodium based on sequences of small subunit ribosomal RNA and circumsporozoite genes. To further validate this finding, the mitochondrial genome and the apicoplast caseinolytic protease M genes of Plasmodium spp. were sequenced from 43 long-tailed macaque blood samples. Results Apart from several named species of malaria parasites, long-tailed macaques were found to be potentially infected with novel species of Plasmodium, namely one we refer to as “P. inui-like.” This group of parasites bifurcated into two monophyletic clades indicating the presence of two distinct sub-populations. Further analyses, which relied on the assumption of strict co-phylogeny between hosts and parasites, estimated a population expansion event of between 150,000 to 250,000 years before present of one of these sub-populations that preceded that of the expansion of P. knowlesi. Furthermore, both sub-populations were found to have diverged from a common ancestor of P. inui approximately 1.5 million years ago. In addition, the phylogenetic analyses also demonstrated that long-tailed macaques are new hosts for P. simiovale. Conclusions Malaria infections of long-tailed macaques of Sarawak, Malaysian Borneo are complex and include a novel species of Plasmodium that is phylogenetically distinct from P. inui. These macaques are new natural hosts of P. simiovale, a species previously described only in toque monkeys (Macaca sinica) in Sri Lanka. The results suggest that ecological factors could affect the evolution of malaria parasites. Electronic supplementary material The online version of this article (10.1186/s12862-018-1170-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thamayanthi Nada Raja
- Malaria Research Centre, Faculty of Medicine & Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Ting Huey Hu
- Malaria Research Centre, Faculty of Medicine & Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Ramlah Zainudin
- Malaria Research Centre, Faculty of Medicine & Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.,Faculty of Resource Science & Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Kim Sung Lee
- Malaria Research Centre, Faculty of Medicine & Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.,School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, 599489, Singapore
| | - Susan L Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA
| | - Balbir Singh
- Malaria Research Centre, Faculty of Medicine & Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
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Wang X, Liu D, Luo Y, Zhao L, Liu Z, Chou M, Wang E, Wei G. Comparative analysis of rhizobial chromosomes and plasmids to estimate their evolutionary relationships. Plasmid 2018; 96-97:13-24. [PMID: 29608935 DOI: 10.1016/j.plasmid.2018.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 11/26/2022]
Abstract
In the present study, complete genomic sequences retrieved from 57 rhizobial strains that covered four genera including 11 species were analyzed comprehensively. The four types of replicons: chromosomes, chromids, nonsymbiotic plasmids, and symbiotic plasmids were investigated and compared among these strains. Results showed that co-evolution occurred among these four replicons based on the similarities in average nucleotide identity. High correlation coefficient r values were observed between chromosomes and chromids, as well as between chromosomes and nonsymbiotic plasmids. Chromosomes and symbiotic plasmids showed different phylogenetic topology based on their core genes. Population structure analyses were performed to extrapolate the evolutionary histories of the test strains based on their chromosomal and symbiotic plasmid background. This resulted in seven ancestral types for chromosomal genes and three ancestral types for symbiotic plasmid genes. Rhizobial strains containing chromosome genes with ancestral type E tend to contain symbiotic plasmid genes with ancestral type II, while rhizobial strains containing chromosome genes with ancestral type G tend to contain symbiotic plasmid genes with ancestral type III. Seventeen strains associated with different host plant species which harbored the symbiotic genes with ancestral type I, exhibited high genetic diversity. In addition, Fu's test of the symbiotic plasmid genes with ancestral type III had undergone an expansion event, implying the influence of negative selection on these symbiotic plasmid genes.
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Affiliation(s)
- Xinye Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Dongying Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Yantao Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Zhenshan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, 712100 Yangling, People's Republic of China.
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Leone A, Urso I, Damalas D, Martinsohn J, Zanzi A, Mariani S, Sperone E, Micarelli P, Garibaldi F, Megalofonou P, Bargelloni L, Franch R, Macias D, Prodöhl P, Fitzpatrick S, Stagioni M, Tinti F, Cariani A. Genetic differentiation and phylogeography of Mediterranean-North Eastern Atlantic blue shark ( Prionace glauca, L. 1758) using mitochondrial DNA: panmixia or complex stock structure? PeerJ 2017; 5:e4112. [PMID: 29230359 PMCID: PMC5723133 DOI: 10.7717/peerj.4112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/09/2017] [Indexed: 11/25/2022] Open
Abstract
Background The blue shark (Prionace glauca, Linnaeus 1758) is one of the most abundant epipelagic shark inhabiting all the oceans except the poles, including the Mediterranean Sea, but its genetic structure has not been confirmed at basin and interoceanic distances. Past tagging programs in the Atlantic Ocean failed to find evidence of migration of blue sharks between the Mediterranean and the adjacent Atlantic, despite the extreme vagility of the species. Although the high rate of by-catch in the Mediterranean basin, to date no genetic study on Mediterranean blue shark was carried out, which constitutes a significant knowledge gap, considering that this population is classified as “Critically Endangered”, unlike its open-ocean counterpart. Methods Blue shark phylogeography and demography in the Mediterranean Sea and North-Eastern Atlantic Ocean were inferred using two mitochondrial genes (Cytb and control region) amplified from 207 and 170 individuals respectively, collected from six localities across the Mediterranean and two from the North-Eastern Atlantic. Results Although no obvious pattern of geographical differentiation was apparent from the haplotype network, Φst analyses indicated significant genetic structure among four geographical groups. Demographic analyses suggest that these populations have experienced a constant population expansion in the last 0.4–0.1 million of years. Discussion The weak, but significant, differences in Mediterranean and adjacent North-eastern Atlantic blue sharks revealed a complex phylogeographic structure, which appears to reject the assumption of panmixia across the study area, but also supports a certain degree of population connectivity across the Strait of Gibraltar, despite the lack of evidence of migratory movements observed by tagging data. Analyses of spatial genetic structure in relation to sex-ratio and size could indicate some level of sex/stage biased migratory behaviour.
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Affiliation(s)
- Agostino Leone
- Department of Biological, Geological and Environmental Sciences (BiGeA), Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Ilenia Urso
- Department of Biological, Geological and Environmental Sciences (BiGeA), Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Dimitrios Damalas
- Joint Research Centre (JRC), Directorate D-Sustainable Resources, Unit D2-Water and Marine Resources, European Commission, Ispra, Italy.,Current affiliation: Hellenic Centre for Marine Research, Athinon, Anavyssos, Greece
| | - Jann Martinsohn
- Joint Research Centre (JRC), Directorate D-Sustainable Resources, Unit D2-Water and Marine Resources, European Commission, Ispra, Italy
| | - Antonella Zanzi
- Joint Research Centre (JRC), Directorate D-Sustainable Resources, Unit D2-Water and Marine Resources, European Commission, Ispra, Italy
| | - Stefano Mariani
- School of Environment & Life Sciences, University of Salford, Salford, Greater Manchester, United Kingdom
| | - Emilio Sperone
- Department of Biology, Ecology and Earth Science (DiBEST), University of Calabria, Arcavacata di Rende, Italy
| | - Primo Micarelli
- Sharks Research Center, Aquarium Mondo Marino, Massa Marittima, Italy
| | - Fulvio Garibaldi
- Department of Earth, Environment and Life Sciences, University of Genova, Genova, Italy
| | - Persefoni Megalofonou
- Department of Biology, National and Kapodistrian University of Athens, Ilissia, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - David Macias
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Málaga, Spain
| | - Paulo Prodöhl
- School of Biological Sciences, Queen's University, Institute for Global Food Security, Belfast, United Kingdom
| | - Séan Fitzpatrick
- School of Biological Sciences, Queen's University, Institute for Global Food Security, Belfast, United Kingdom
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, Marine Biology and Fisheries Laboratory, University of Bologna, Fano, Italy
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences (BiGeA), Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences (BiGeA), Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), University of Bologna, Ravenna, Italy
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Suárez-Montes P, Chávez-Pesqueira M, Núñez-Farfán J. Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest. PeerJ 2016; 4:e2764. [PMID: 28028460 PMCID: PMC5183091 DOI: 10.7717/peerj.2764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 11/06/2016] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. METHODS Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28-30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. RESULTS Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne ) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep ) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. DISCUSSION Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape.
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Affiliation(s)
- Pilar Suárez-Montes
- Laboratory of Ecological Genetics and Evolution, Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Mariana Chávez-Pesqueira
- Laboratory of Ecological Genetics and Evolution, Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico
| | - Juan Núñez-Farfán
- Laboratory of Ecological Genetics and Evolution, Department of Evolutionary Ecology, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Mexico
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Tsao YF, Lin WW, Chang CH, Ueda T, Jang-Liaw NH, Zhao YH, Kao HW. Phylogeography, Historical Demography, and Genetic Structure of the Rose Bitterling, Rhodeus ocellatus (Kner, 1866) (Cypriniformes: Acheilognathidae), in East Asia. Zool Stud 2016; 55:e49. [PMID: 31966194 DOI: 10.6620/ZS.2016.55-49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/11/2016] [Indexed: 11/18/2022]
Abstract
Yao-Feng Tsao, Wen-Wen Lin, Chia-Hao Chang, Takayoshi Ueda, Nian-Hong Jang-Liaw, Ya-Hui Zhao, and Hsiao-Wei Kao (2016) Rose bitterling, Rhodeus ocellatus, is a small cyprinid fish distributed in East Asia. To infer its phylogeography and genetic structure, specimens from Taiwan, China, and Japan were collected, and complete mitochondrial cytochrome b (cyt b) DNA sequences were amplified and sequenced. Phylogenetic analyses identified seven mitochondrial lineages (A-G). Among them, three lineages (A, B, and C) distributed in mainland China. Lineages D, E, and F distributed in Japan, Korea, and Taiwan, respectively. Lineage G distributed in both China and Japan. The results of the Bayesian Binary MCMC analysis (BBM) suggested that the most recent common ancestor of R. ocellatus was from Lower Yangtze region. Divergence times among lineages inferred by molecular clock ranged from 7.55 to 1.44 million years ago. We propose that topography and climate changes by uplift of the Tibetan Plateau in the Late Miocene-Pliocene and the glacial-interglacial cycles in the Pleistocene might account for population expansion and genetic differentiation. Divergence times among lineages A, B, and C in Yangtze River basin ranged from 7.55 to 2.27 million years ago that might result from changes of flow directions of rivers from westward to eastward driven by the uplift of the Tibetan Plateau. The glacial-interglacial cycles in the Pleistocene might further cause population expansion to the northward of lineage G at about 0.19 million years ago. Lineage D in Japan was dispersed from the mainland China before the opening of the Sea of Japan, and lineage F in Taiwan was dispersed from the mainland China through the land bridge in the Pleistocene. Because of the genetic differentiation is statistically significant among populations, protection of genetic diversity and distinctness of R. ocellatus should be considered in the future conservation management.
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Jaskuła R, Rewicz T, Płóciennik M, Grabowski M. Pleistocene phylogeography and cryptic diversity of a tiger beetle, Calomera littoralis, in North-Eastern Mediterranean and Pontic regions inferred from mitochondrial COI gene sequences. PeerJ 2016; 4:e2128. [PMID: 27547517 PMCID: PMC4958013 DOI: 10.7717/peerj.2128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 05/23/2016] [Indexed: 11/23/2022] Open
Abstract
Background. Calomera littoralis is a Palearctic species, widely distributed in Europe; inhabiting predominantly its Atlantic, Mediterranean and Black Sea coastlines. Methods. Its phylogeography on the Balkan Peninsula and on the north-western Black Sea coast was inferred using a 697 bp long portion of the mitochondrial COI gene, amplified from 169 individuals collected on 43 localities. Results. The results revealed two genetically divergent groups/lineages, the southern one inhabiting both the Balkan Peninsula and the Pontic Region and the northern one found exclusively in the Pontic Region. Species delimitation based on DNA barcoding gap suggested an interspecific level of divergence between these groups. Multivariate analysis of eight male and female morphometric traits detected no difference between the groups, implying they may represent cryptic species. The Bayesian time-calibrated reconstruction of phylogeny suggested that the lineages diverged ca. 2.3 Ma, in early Pleistocene. Discussion. The presence of the two genetically divergent groups results most likely from contemporary isolation of the Pontic basin from the Mediterranean that broke the continuous strip of coastal habitats inhabited by C. littoralis. Demographic analyses indicated that both lineages have been in demographic and spatial expansion since ca. 0.15 Ma. It coincides with the terminal stage of MIS-6, i.e., Wartanian/Saalian glaciation, and beginning of MIS-5e, i.e., Eemian interglacial, during which, due to eustatic sea level rise, a wide connection between Mediterranean and the Pontic basin was re-established. This, along with re-appearance of coastal habitats could initiate north-east expansion of the southern lineage and its secondary contact with the northern one. The isolation of the Pontic basin from the Mediterranean during the Weichselian glaciation most likely did not have any effect on their phylogeography.
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Affiliation(s)
- Radomir Jaskuła
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Tomasz Rewicz
- Laboratory of Microscopic Imaging and Specialized Biological Techniques, University of Lodz, Łódź, Poland
| | - Mateusz Płóciennik
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
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Fong JJ, Li PP, Yang BT, Zhou ZY, Leaché AD, Min MS, Waldman B. Influence of geology and human activity on the genetic structure and demography of the Oriental fire-bellied toad (Bombina orientalis). Mol Phylogenet Evol 2015; 97:69-75. [PMID: 26748269 DOI: 10.1016/j.ympev.2015.12.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/18/2015] [Accepted: 12/24/2015] [Indexed: 11/18/2022]
Abstract
The Oriental fire-bellied toad (Bombina orientalis) is a commonly used study organism, but knowledge of its evolutionary history is incomplete. We analyze sequence data from four genetic markers (mtDNA genes encoding cytochrome c oxidase subunit I, cytochrome b, and 12S-16S rRNA; nuDNA gene encoding recombination activating gene 2) from 188 individuals across its range in Northeast Asia to elucidate phylogeographic patterns and to identify the historic events that shaped its evolutionary history. Although morphologically similar across its range, B. orientalis exhibits phylogeographic structure, which we infer was shaped by geologic, climatic, and anthropogenic events. Phylogenetic and divergence-dating analyses recover four genetically distinct groups of B. orientalis: Lineage 1-Shandong Province and Beijing (China); Lineage 2-Bukhan Mountain (Korea); Lineage 3-Russia, Northeast China, and northern South Korea; and Lineage 4-South Korea. Lineage 2 was previously unknown. Additionally, we discover an area of secondary contact on the Korean Peninsula, and infer a single dispersal event as the origin of the insular Jeju population. Skyline plots estimate different population histories for the four lineages: Lineages 1 and 2 experienced population decreases, Lineage 3 remained stable, while Lineage 4 experienced a sharp increase during the Holocene. The timing of the population expansion of Lineage 4 coincides with the advent of rice cultivation, which may have facilitated the increase in population size by providing additional breeding habitat.
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Affiliation(s)
- Jonathan J Fong
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea; Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Pi-Peng Li
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China.
| | - Bao-Tian Yang
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Zheng-Yan Zhou
- Center for Chinese Endemic Herp-breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Adam D Leaché
- Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA
| | - Mi-Sook Min
- College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea.
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea.
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Kim HR, Park YC. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea. Gene 2015; 572:292-7. [PMID: 26263836 DOI: 10.1016/j.gene.2015.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 11/25/2022]
Abstract
The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (π=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae.
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Affiliation(s)
- Hye Ri Kim
- College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Yung Chul Park
- College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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Joshi J, Salar RK, Banerjee P, Sharma U, Tantia MS, Vijh RK. Assessment of genetic variability and structuring of riverine buffalo population (Bubalus bubalis) of Indo-Gangetic basin. Anim Biotechnol 2015; 26:148-55. [PMID: 25380468 DOI: 10.1080/10495398.2014.955613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The buffalo population of Uttar Pradesh (UP) constitutes 26.1% of the total buffalo population of India, yet this population has not been classified into distinct breeds or subpopulations due to lack of systematic study. Genetic variation at 30 microsatellite loci was examined and statistical analysis was carried out to reveal genetic diversity, demographic parameters of these buffaloes and to investigate the existence of population substructures underlying geographical distribution. The mean number of alleles per locus was 13.26 and mean effective number of alleles was 3.74, whereas mean observed and expected heterozygosities were found to be 0.57 and 0.67 in UP buffaloes. Principal component analysis (PCA) based on allele frequency data revealed subclustering of UP buffalo population. Bayesian analysis result also revealed clear membership of individuals into five clusters indicating a genetic subdivision within the UP buffalo population. The buffaloes of Western and Central regions of UP were subtly separated while buffaloes of Tarai area and Bhadawari buffaloes revealed distinctive population structure. The buffaloes of Mau, Ballia and Ghazipur districts of Eastern region also had a distinctive genetic structure. The analysis of data on buffaloes of Indo-Gangetic plains revealed that population was in mutation drift equilibrium. The observed mean M ratio in the population was above the critical significance value (Mc) suggesting that it has not suffered any severe reduction in effective population size. The statistical tests revealed a historical constancy of size of buffalo in this geographical area. The high level of genetic variability indicates UP buffalo population is a vast reservoir of genetic diversity and this shall help in taking informed conservation decisions and sustainable utilization.
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Affiliation(s)
- Jyoti Joshi
- a National Bureau of Animal Genetic Resources , Karnal , Haryana , India
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Padhi A. Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris. Gene 2014; 538:63-8. [PMID: 24440244 DOI: 10.1016/j.gene.2014.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 01/04/2014] [Accepted: 01/08/2014] [Indexed: 10/25/2022]
Abstract
The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity.
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Affiliation(s)
- Abinash Padhi
- Department of Biological Sciences, University of Tulsa, 800 S. Tucker Dr., OK 74104, USA.
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Legg JP, Sseruwagi P, Boniface S, Okao-Okuja G, Shirima R, Bigirimana S, Gashaka G, Herrmann HW, Jeremiah S, Obiero H, Ndyetabula I, Tata-Hangy W, Masembe C, Brown JK. Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa. Virus Res 2013; 186:61-75. [PMID: 24291251 DOI: 10.1016/j.virusres.2013.11.018] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 11/26/2022]
Abstract
The greatest current threat to cassava in sub-Saharan Africa, is the continued expansion of plant virus pandemics being driven by super-abundant populations of the whitefly vector, Bemisia tabaci. To track the association of putatively genetically distinct populations of B. tabaci with pandemics of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), a comprehensive region-wide analysis examined the phylogenetic relationships and population genetics of 642 B. tabaci adults sampled from cassava in six countries of East and Central Africa, between 1997 and 2010, using a mitochondrial DNA cytochrome oxidase I marker (780 bases). Eight phylogenetically distinct groups were identified, including one, designated herein as 'East Africa 1' (EA1), not previously described. The three most frequently occurring groups comprised >95% of all samples. Among these, the Sub-Saharan Africa 2 (SSA2) group diverged by c. 8% from two SSA1 sub-groups (SSA1-SG1 and SSA1-SG2), which themselves were 1.9% divergent. During the 14-year study period, the group associated with the CMD pandemic expansion shifted from SSA2 to SSA1-SG1. Population genetics analyses of SSA1, using Tajima's D, Fu's Fs and Rojas' R2 statistics confirmed a temporal transition in SSA1 populations from neutrally evolving at the outset, to rapidly expanding from 2000 to 2003, then back to populations more at equilibrium after 2004. Based on available evidence, hybrid introgression appears to be the most parsimonious explanation for the switch from SSA2 to SSA1-SG1 in whitefly populations driving cassava virus pandemics in East and Central Africa.
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Affiliation(s)
- James P Legg
- International Institute of Tropical Agriculture (IITA), PO Box 34441, Dar es Salaam, Tanzania.
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, PO Box 6226, Dar es Salaam, Tanzania
| | - Simon Boniface
- International Institute of Tropical Agriculture (IITA), PO Box 34441, Dar es Salaam, Tanzania
| | - Geoffrey Okao-Okuja
- National Agricultural Crops Resources Research Institute, PO Box 7084, Kampala, Uganda
| | - Rudolph Shirima
- International Institute of Tropical Agriculture (IITA), PO Box 34441, Dar es Salaam, Tanzania
| | - Simon Bigirimana
- Institut des Sciences Agronomiques du Burundi, BP 173, Gitega, Burundi
| | | | | | - Simon Jeremiah
- Lake Zone Agricultural Research and Development Institute, PO Box 1433, Mwanza, Tanzania
| | | | | | - Willy Tata-Hangy
- Institut National Pour l'Etude et la Recherche Agronomique (INERA-DR Congo), BP 327, Cyangugu, Rwanda
| | | | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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Kowalczyk R, Krasińska M, Kamiński T, Górny M, Struś P, Hofman-Kamińska E, Krasiński ZA. Movements of European bison ( Bison bonasus) beyond the Białowieża Forest (NE Poland): range expansion or partial migrations? ACTA ACUST UNITED AC 2013; 58:391-401. [PMID: 24244043 DOI: 10.1007/s13364-013-0136-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 02/14/2013] [Indexed: 11/12/2022]
Abstract
The European bison is the largest terrestrial mammal in Europe. After extinction in the wild at the beginning of the twentieth century, it was re-introduced to Białowieża Forest and other woodlands in Eastern Europe. In this paper, we analysed the movements of European bison beyond the continuous woodlands of the Białowieża Forest (NE Poland) between 1964 and 2010. In total, 1,117 direct observations of bison were collected. The number of males moving out of the forest fluctuated during the study period, whilst the number of females steadily increased. The number of male observations outside of the forest per annum was dependent on the population size and snow depth, whilst the number of cows in mixed groups moving outside of the forest was correlated with the population size only. Males were observed mainly alone (50 % of observations) or in small groups of two to three individuals (25 %); however, distribution of group size differed from those observed in the population. There was a significant difference between the direction of movement of males and females out of the forest—males moved mainly west and southwest, whilst females moved to the north. This was also significantly different from the expected movement direction. The mean distance of bison observations from the forest border was 1.8 ± 0.13 km and did not differ significantly between sexes. After 1990, males were observed significantly farther away from the forest (2.2 km) than in the previous years (0.9 km). Most observations (94 % of bulls and 93 % of cows) were up to 5 km from the forest edge. The range of bison in the vicinity of the Białowieża Forest was strictly seasonal. Most observations (78 % in males and 88 % in females) were recorded from November to April. Increasing utilisation of areas beyond the forest habitats may be driven by different factors but most probably it is related to range expansion and the bison's preference for open habitats. The strong seasonal pattern of bison movements indicate that the partial seasonal migrations were initiated in the Białowieża population.
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