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Gao C, Wang K, Hu X, Lei Y, Xu C, Tian Y, Sun G, Tian Y, Kang X, Li W. Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources. Poult Sci 2023; 102:103030. [PMID: 37716234 PMCID: PMC10511814 DOI: 10.1016/j.psj.2023.103030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/30/2023] [Accepted: 08/11/2023] [Indexed: 09/18/2023] Open
Abstract
The conservation of genetic resources is becoming increasingly important for the sustainable development of the poultry industry. In the present study, we systematically analyzed the population structure, conservation priority, runs of homozygosity (ROH) of chicken breeds globally, and proposed rational conservation strategies. We used a 600K Affymetrix Axiom HD genotyping SNP array dataset of 2,429 chickens from 134 populations. The chickens were divided into 5 groups based on their country of origin and sampling location: Asian chickens (AS-LOC), African chickens (AF), European local chickens (EU-LOC), Asian breeds sampled in Germany (AS-DE), and European breeds sampled in Germany (EU-DE). The results indicated that the population structure was consistent with the actual geographical distribution of the populations. AS-LOC had the highest positive contribution to the total gene (HT, 1.00%,) and allelic diversity (AT, 0.0014%), the lowest inbreeding degree and the fastest linkage disequilibrium (LD) decay rate; the lowest contribution are derived by European ex situ chicken breeds (EU-DE:HT = -0.072%, AT = -0.0014%), which showed the highest inbreeding and slowest LD decay. Breeds farmed in ex situ (AS-DE, EU-DE) conditions exhibited reduced genetic diversity and increased inbreeding due to small population size. Given limited funds, it is a better choice for government to conserve the breeds with the highest contribution to genetic diversity in each group. Therefore, we evaluated the contribution of each breed to genetic and allelic diversity in 5 groups. Among each group, KUR(AF), BANG(AS-LOC), ALxx(EU-LOC), BHwsch(AS-DE), and ARw(EU-DE) had the highest contribution to gene diversity in the order of the above grouping. Similarly, according to the allelic diversity standard (in the same order), ZIMxx, PIxx, ALxx, SHsch, and ARsch had the highest contribution. After analyzing ROH, we found a total of 144,708 fragments and 27 islands. The gene and genome regions identified by the ROH islands and QTLs indicate that chicken breeds have potential for adaptation to different production systems. Based on these findings, it is recommended to prioritize the conservation of breeds with the highest genetic diversity in each group, while paying more attention to the conservation of Asian and African breeds. Furthermore, providing a valuable reference for the conservation and utilization of chicken.
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Affiliation(s)
- Chaoqun Gao
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Kejun Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Xiaoyu Hu
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yanru Lei
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Chunhong Xu
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yixiang Tian
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, Henan, China
| | - Guirong Sun
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Yadong Tian
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Xiangtao Kang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China
| | - Wenting Li
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, Henan, China; The Shennong Laboratory, Zhengzhou 450046, Henan, China.
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Jan M, Stronen AV, Boljte B, Černe R, Huber Đ, Iosif R, Kljun F, Konec M, Kos I, Krofel M, Kusak J, Luštrik R, Majić Skrbinšek A, Promberger-Füerpass B, Potočnik H, Rigg R, Trontelj P, Skrbinšek T. Wolf genetic diversity compared across Europe using the yardstick method. Sci Rep 2023; 13:13727. [PMID: 37608038 PMCID: PMC10444868 DOI: 10.1038/s41598-023-40834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023] Open
Abstract
Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the "yardstick" method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4-17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.
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Affiliation(s)
- Maja Jan
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
| | - Astrid Vik Stronen
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Barbara Boljte
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Rok Černe
- Slovenia Forest Service, Večna pot 2, 1000, Ljubljana, Slovenia
| | - Đuro Huber
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Ruben Iosif
- Foundation Conservation Carpathia, 27 Calea Feldioarei, 500471, Brașov, Romania
| | - Franc Kljun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Marjeta Konec
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | - Ivan Kos
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Miha Krofel
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Josip Kusak
- Faculty of Veterinary Medicine, University of Zagreb, Vjekoslava Heinzelova 55, 10000, Zagreb, Croatia
| | - Roman Luštrik
- Genialis Inc, Vojkova cesta 63, 1000, Ljubljana, Slovenia
| | - Aleksandra Majić Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
| | | | - Hubert Potočnik
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Robin Rigg
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Slovak Wildlife Society, Belanská 574/6, P.O. Box 72, Liptovský Hrádok, 033 01, Slovakia
| | - Peter Trontelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Tomaž Skrbinšek
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- DivjaLabs d.o.o., Aljaževa ulica 35a, 1000, Ljubljana, Slovenia
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Aliaga-Samanez GG, Bulhões Javarotti N, Orecife G, Chávez-Congrains K, Pissinatti A, Monticelli C, Cristina Marques M, Galbusera P, Galetti PM, Domingues de Freitas P. Genetic diversity in ex situ populations of the endangered Leontopithecus chrysomelas and implications for its conservation. PLoS One 2023; 18:e0288097. [PMID: 37531319 PMCID: PMC10395972 DOI: 10.1371/journal.pone.0288097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans.
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Affiliation(s)
| | | | - Gisele Orecife
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Karla Chávez-Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Guapimirim, Rio de Janeiro, Brazil
| | - Cauê Monticelli
- Departamento de Conservação e Pesquisas Aplicadas, Coordenadoria de Fauna Silvestre, Secretaria de Meio Ambiente, Infraestrutura e Logística do Estado de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Peter Galbusera
- Antwerp Zoo Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Scaranto BMS, Ribolli J, Vieira GC, Ferreira JPR, de Miranda Gomes CHA, de Melo CMR. Genetic Structure and Diversity in Wild and Cultivated Populations of the Mangrove Oyster Crassostrea gasar from Southern Brazil. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:548-556. [PMID: 37335411 DOI: 10.1007/s10126-023-10224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
The mangrove oyster (Crassostrea gasar) is Brazil's second most cultured species and presents a high potential for aquaculture. However, artificial selection in a highly fecund species and significant variance in reproductive success can result in the loss of genetic diversity and increases the inbreeding rate, especially in cultivated populations. In this study, we investigated the genetic structure and diversity of C. gasar in wild and cultivated populations using 14 microsatellites. Spatial genetic comparisons revealed the existence of two main genetic groups of C. gasar, one comprising the population in cultivation and the other formed by wild populations along the southern and southeastern Brazilian coasts. Although no common genetic structure exists among wild populations, it is possible to observe a distribution gradient based on discriminant analysis of principal components consistent with their geographic distribution. However, it is insufficient to differentiate them genetically. Despite artificial reproduction, the genetic diversity values of the cultivated population remained relatively high and did not show a reduction. Therefore, monitoring the cultivated population and establishing reference values for genetic diversity will allow the adoption of strategies both for the viability of the cultivated population and the management of wild populations.
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Affiliation(s)
- Bianca Maria Soares Scaranto
- Laboratory of Marine Mollusks, Department of Aquaculture, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Department of Aquaculture, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Graziela Cleuza Vieira
- Laboratory of Marine Mollusks, Department of Aquaculture, Federal University of Santa Catarina, Florianópolis, Brazil
| | - João Paulo Ramos Ferreira
- Laboratory of Marine Mollusks, Department of Aquaculture, Federal University of Santa Catarina, Florianópolis, Brazil
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Nunes I, Passos K, Mourão Ximenes A, Hrbek T, Farias IP. Spatial and temporal population genetic analysis of Semaprochilodus insignis (Prochilodontidae), an overexploited fish from the Amazon basin. PeerJ 2023; 11:e15503. [PMID: 37361032 PMCID: PMC10289084 DOI: 10.7717/peerj.15503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/14/2023] [Indexed: 06/28/2023] Open
Abstract
Background Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.
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Affiliation(s)
- Ingrid Nunes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Kelmer Passos
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Aline Mourão Ximenes
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brasil
| | - Tomas Hrbek
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
- Department of Biology, Trinity University, San Antonio, TX, United States of America
| | - Izeni Pires Farias
- Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
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Zimmerman SJ, Aldridge CL, O'Donnell MS, Edmunds DR, Coates PS, Prochazka BG, Fike JA, Cross TB, Fedy BC, Oyler-McCance SJ. A genetic warning system for a hierarchically structured wildlife monitoring framework. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2787. [PMID: 36482030 DOI: 10.1002/eap.2787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Genetic variation is a well-known indicator of population fitness yet is not typically included in monitoring programs for sensitive species. Additionally, most programs monitor populations at one scale, which can lead to potential mismatches with ecological processes critical to species' conservation. Recently developed methods generating hierarchically nested population units (i.e., clusters of varying scales) for greater sage-grouse (Centrocercus urophasianus) have identified population trend declines across spatiotemporal scales to help managers target areas for conservation. The same clusters used as a proxy for spatial scale can alert managers to local units (i.e., neighborhood-scale) with low genetic diversity, further facilitating identification of management targets. We developed a genetic warning system utilizing previously developed hierarchical population units to identify management-relevant areas with low genetic diversity within the greater sage-grouse range. Within this warning system we characterized conservation concern thresholds based on values of genetic diversity and developed a statistical model for microsatellite data to robustly estimate these values for hierarchically nested populations. We found that 41 of 224 neighborhood-scale clusters had low genetic diversity, 23 of which were coupled with documented local population trend decline. We also found evidence of cross-scale low genetic diversity in the small and isolated Washington population, unlikely to be reversed through typical local management actions alone. The combination of low genetic diversity and a declining population suggests relatively high conservation concern. Our findings could further facilitate conservation action prioritization in combination with population trend assessments and (or) local information, and act as a base-line of genetic diversity for future comparison. Importantly, the approach we used is broadly applicable across taxa.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Michael S O'Donnell
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - David R Edmunds
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Peter S Coates
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Brian G Prochazka
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Todd B Cross
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Bradley C Fedy
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, Ontario, Canada
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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Gao C, Du W, Tian K, Wang K, Wang C, Sun G, Kang X, Li W. Analysis of Conservation Priorities and Runs of Homozygosity Patterns for Chinese Indigenous Chicken Breeds. Animals (Basel) 2023; 13:ani13040599. [PMID: 36830386 PMCID: PMC9951684 DOI: 10.3390/ani13040599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
To achieve sustainable development of the poultry industry, the effective conservation of genetic resources has become increasingly important. In the present study, we systematically elucidated the population structure, conservation priority, and runs of homozygosity (ROH) patterns of Chinese native chicken breeds. We used a high-density genotyping dataset of 157 native chickens from eight breeds. The population structure showed different degrees of population stratification among the breeds. Chahua chicken was the most differentiated breed from the other breeds (Nei = 0.0813), and the Wannan three-yellow chicken (WanTy) showed the lowest degree of differentiation (Nei = 0.0438). On the basis of contribution priority, Xiaoshan chicken had the highest contribution to the total gene diversity (1.41%) and the maximum gene diversity of the synthetic population (31.1%). WanTy chicken showed the highest contribution to the total allelic diversity (1.31%) and the maximum allelic diversity of the syntenic population (17.0%). A total of 5242 ROH fragments and 5 ROH island regions were detected. The longest ROH fragment was 41.51 Mb. A comparison of the overlapping genomic regions between the ROH islands and QTLs in the quantitative trait loci (QTL) database showed that the annotated candidate genes were involved in crucial economic traits such as immunity, carcass weight, drumstick and leg muscle development, egg quality and egg production, abdominal fat precipitation, body weight, and feed intake. In conclusion, our findings revealed that Chahua, Xiaoshan, and WanTy should be the priority conservation breeds, which will help optimize the conservation and breeding programs for Chinese indigenous chicken breeds.
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Affiliation(s)
- Chaoqun Gao
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Wenping Du
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Kaiyuan Tian
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Kejun Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Chunxiu Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Guirong Sun
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiangtao Kang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- Correspondence: (X.K.); (W.L.)
| | - Wenting Li
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- Correspondence: (X.K.); (W.L.)
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Madsen T, Ujvari B, Bauwens D, Gruber B, Georges A, Klaassen M. Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus). Heredity (Edinb) 2023; 130:64-72. [PMID: 36474024 PMCID: PMC9905584 DOI: 10.1038/s41437-022-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022] Open
Abstract
Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12-171), the population maintains high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest are underpinning the maintenance of the population's high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.
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Affiliation(s)
- Thomas Madsen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, 3217, Australia.
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, 3217, Australia
| | - Dirk Bauwens
- Department of Biology, Laboratory of Functional Morphology, University of Antwerp, Wilrijk, Belgium
| | - Bernd Gruber
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, 3217, Australia
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Madgwick PG, Kanitz R. Beyond redundant kill: A fundamental explanation of how insecticide mixtures work for resistance management. PEST MANAGEMENT SCIENCE 2023; 79:495-506. [PMID: 36098048 PMCID: PMC10092901 DOI: 10.1002/ps.7180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 05/17/2023]
Abstract
The use of insecticide mixtures for resistance management has been a controversial topic for many decades. Here, we provide a reassessment of the fundamental theory of insecticide mixtures. First, we examine how mixtures differ from other strategies. We suggest that the fundamental strategy concept of a mixture is defined by the simultaneous use of insecticides and their overlapping exposure. Second, we provide a simple, illustrative model to show how mixtures affect resistance evolution. Following the existing literature, we identify a role for 'redundant kill' acting against resistant individuals, which we link to the overlapping exposure of insecticides. We also identify the occurrence of 'additional kill' acting against susceptible individuals, which is the immediate consequence of the simultaneous use of insecticides. Third, we take a basic approach to the comparison of mixtures and other strategies using a simple model. We find that a common comparison of the time to resistance alone leaves the effects of additional kill unaccounted for. Moreover, we demonstrate that different approaches to comparison can lead to different results because of biases that are introduced in the comparison setup. Fourth, still using the same model, we showcase a more sophisticated approach to comparison using optimised strategies. We find that optimised mixtures always perform better than other strategies due to the combination of redundant and additional kill. We suggest that the comparison of optimised strategies is unbiased because each strategy is performing the best that it can. On this basis, in theory (but not necessarily practice), we believe that mixtures are better than other strategies and, through the steps of our argument, we can tie this success back to the fundamental properties (of simultaneous use and overlapping exposure) that distinguish mixtures from other strategy concepts. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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10
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Tarpy DR, Caren JR, Delaney DA. Meta-analysis of genetic diversity and intercolony relatedness among reproductives in commercial honey bee populations. FRONTIERS IN INSECT SCIENCE 2023; 3:1112898. [PMID: 38469471 PMCID: PMC10926410 DOI: 10.3389/finsc.2023.1112898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/16/2023] [Indexed: 03/13/2024]
Abstract
Honey bee colonies are large kin groups, each with a single mother queen and thousands of female workers. Queen bees are highly polyandrous, each mating with an average of approximately 12 drones from other colonies. We used a meta-analysis approach to compare the pedigree relationships of honey bee reproductives (queens and their mates) across five different studies and to quantify the overall genetic diversity of breeding populations. We compared the inferred genotypes of queens and their mates from microsatellite analyses of worker offspring from a feral Africanized honey bee population (which served as a negative control for inbreeding), an experimentally derived population of sister queens (which served as a positive control for inbreeding), and three separate commercially managed populations. We then compared the relatedness of all drones mated to each queen (mate-mate), all queens within each population (queen-queen), each queen with each of her mates (queen-mate), and all drones within each population (drone-drone). We found, as expected, the lowest levels of genetic similarity in the outcrossed population and highest levels of genetic similarity in the inbred population. Levels of genetic similarity among the managed honey bee populations were intermediate but closer to that of the inbred population. Genetic structuring of the entire breeding population resulted in two major subpopulations, likely deriving from breeders on the east and west coast. The effects that these findings have on the overall population genetic diversity of managed honey bees is discussed.
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Affiliation(s)
- David R. Tarpy
- Department of Applied Ecology, Graduate Program in Biology—Evolution & Ecology, North Carolina State University, Raleigh, NC, United States
| | - Joel R. Caren
- USDA-ARS, Pollinator Health Center, Stoneville, MS, United States
| | - Deborah A. Delaney
- Department of Entomology & Wildlife Biology, University of Delaware, Newark, DE, United States
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11
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Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti). DIVERSITY 2022. [DOI: 10.3390/d14121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.
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Kimble SJA, Unger SD, Williams RN. Genetically derived effective population size estimates of herpetofaunal species should be used with caution. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Shem D. Unger
- Department of Biology Wingate University Wingate NC 28174 USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources Purdue University West Lafayette IN 47907 USA
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13
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Sequeira F, Aguilar FF, Madeira FM, Teixeira J, Crespo E, Ferrand N, Rebelo R. What can genetics tell us about the history of a human-mediated introduction of the golden-striped salamander south of its native range? EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01628-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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14
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Systemic racism alters wildlife genetic diversity. Proc Natl Acad Sci U S A 2022; 119:e2102860119. [PMID: 36256811 PMCID: PMC9618126 DOI: 10.1073/pnas.2102860119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the United States, systemic racism has had lasting effects on the structure of cities, specifically due to government-mandated redlining policies that produced racially segregated neighborhoods that persist today. However, it is not known whether varying habitat structures and natural resource availability associated with racial segregation affect the demographics and evolution of urban wildlife populations. To address this question, we repurposed and reanalyzed publicly archived nuclear genetic data from 7,698 individuals spanning 39 terrestrial vertebrate species sampled in 268 urban locations throughout the United States. We found generally consistent patterns of reduced genetic diversity and decreased connectivity in neighborhoods with fewer White residents, likely because of environmental differences across these neighborhoods. The strength of relationships between the racial composition of neighborhoods, genetic diversity, and differentiation tended to be weak relative to other factors affecting genetic diversity, possibly in part due to the recency of environmental pressures on urban wildlife populations. However, the consistency of the direction of effects across disparate taxa suggest that systemic racism alters the demography of urban wildlife populations in ways that generally limit population sizes and negatively affect their chances of persistence. Our results thus support the idea that limited capacity to support large, well-connected wildlife populations reduces access to nature and builds on existing environmental inequities shouldered by predominantly non-White neighborhoods.
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Cossu P, Mura L, Dedola GL, Lai T, Sanna D, Scarpa F, Azzena I, Fois N, Casu M. Detection of Genetic Patterns in Endangered Marine Species Is Affected by Small Sample Sizes. Animals (Basel) 2022; 12:ani12202763. [PMID: 36290149 PMCID: PMC9597844 DOI: 10.3390/ani12202763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Knowledge of Genetic diversity and its spatial distribution is crucial to improve conservation plans for endangered species. Genetic tools help ensure species' long-term persistence by unraveling connectivity patterns and evolutionary trajectories of populations. Here, microsatellite genotypes of individuals from populations of Patella ferruginea are used to assess the effect of sample size on metrics of within-and between-population genetic diversity by combining empirical and simulated data. Within-population metrics are slightly to moderately affected by small sample size, albeit the magnitude of the bias is proportional to the effective population size and gene flow. The power of detecting genetic differentiation among populations increases with sample size, albeit the gain of increasing the number of sampled individuals tends to be negligible between 30 and 50. Our results line up with those of previous studies and highlight that small sample sizes are not always a hindrance to investigating genetic patterns in endangered marine species. Caution is needed in interpreting genetic patterns based on small sample sizes when the observed genetic differentiation is weak. This study also highlights the importance of carrying out genetic monitoring in seemingly well-preserved but potentially isolated populations.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-2280924
| | - Laura Mura
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Ilenia Azzena
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Nicola Fois
- Dipartimento per la Ricerca nelle Produzioni Animali, Agris Sardegna, 07040 Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, 07100 Sassari, Italy
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
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Li J, Shi L, Vasseur L, Zhao Q, Chen J, You M, You S. Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China. PEST MANAGEMENT SCIENCE 2022; 78:2838-2850. [PMID: 35393736 DOI: 10.1002/ps.6908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The tea green leafhopper, Empoasca onukii Matsuda, is the most destructive insect pest of tea plantations in East Asia. Despite its economic importance and previous studies on this species, it remains unclear as to how this small-sized pest can have such wide range. RESULTS By sequencing three mitochondrial genes and 17 microsatellite loci, we revealed the regional structure and demographic expansion of 59 E. onukii populations in China. Bayesian analysis of population genetic structure (BAPS) on microsatellites identified four genetic groups with spatial discontinuities, while analysis on mitochondrial genes inferred five nested and differentiated clusters. Both the Mantel test and the generalized linear model indicated a significant pattern of isolation by geographic distance in E. onukii populations. Based on the approximate Bayesian computation approach, E. onukii was found to have originated from southwestern China and expanded northward and eastward. While MIGRATE-N and Bayesian stochastic search variable selection (BSSVS) procedure in BEAST confirmed the possible eastward and northward dispersal from Yunnan, they also detected more gene flow from the derived populations in central and southeastern China. CONCLUSION Our results suggest that the current distribution and structure of E. onukii is complicatedly influenced by human activities of cultivation, wide dissemination of tea in ancient China as well as recent transportation of tea seedlings for establishing new tea plantations. Insights into genetic differentiation and demographic expansion patterns from this study provide an important basis for the development of area-wide management of the E. onukii populations. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jinyu Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Longqing Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
| | - Qian Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Jie Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Canada
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
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17
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Molecular Genetic Identification Explains Differences in Bud Burst Timing among Progenies of Selected Trees of the Swedish Douglas Fir Breeding Programme. FORESTS 2022. [DOI: 10.3390/f13060895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Douglas fir is expected to play an increasingly important role in Swedish forestry under a changing climate. Thus far, seed orchards with clones of phenotypically selected trees (plus trees) have been established to supply the market with highly qualitative reproductive material. Given the high genetic variation of the species, its growth properties are significantly affected by the provenance. Here, we applied microsatellite markers to identify the origin of clones selected within the Swedish breeding programme. Moreover, we analysed the timing of bud burst in open-pollinated families of these clones. In particular, we aimed to explain the provenance effect on phenology by using molecular identification as a proxy. A Bayesian clustering analysis with microsatellite data enabled the assignment of the clones to one of the two varieties and also resolved within-variety origins. The phenological observations indicated an earlier bud burst of the interior variety. Within the coastal variety, the northern provenances exhibited a later bud burst. We found a significant effect of the identified origin on bud burst timing. The results of this study will be used to support further breeding efforts.
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18
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Human Leukocyte Antigen (HLA) System: Genetics and Association with Bacterial and Viral Infections. J Immunol Res 2022; 2022:9710376. [PMID: 35664353 PMCID: PMC9162874 DOI: 10.1155/2022/9710376] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/08/2022] [Indexed: 12/19/2022] Open
Abstract
The human leukocyte antigen (HLA) system is one of the most crucial host factors influencing disease progression in bacterial and viral infections. This review provides the basic concepts of the structure and function of HLA molecules in humans. Here, we highlight the main findings on the associations between HLA class I and class II alleles and susceptibility to important infectious diseases such as tuberculosis, leprosy, melioidosis, Staphylococcus aureus infection, human immunodeficiency virus infection, coronavirus disease 2019, hepatitis B, and hepatitis C in populations worldwide. Finally, we discuss challenges in HLA typing to predict disease outcomes in clinical implementation. Evaluation of the impact of HLA variants on the outcome of bacterial and viral infections would improve the understanding of pathogenesis and identify those at risk from infectious diseases in distinct populations and may improve the individual treatment.
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19
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Bumble bees exhibit body size clines across an urban gradient despite low genetic differentiation. Sci Rep 2022; 12:4166. [PMID: 35264687 PMCID: PMC8907314 DOI: 10.1038/s41598-022-08093-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/28/2022] [Indexed: 11/23/2022] Open
Abstract
Environmental heterogeneity resulting from human-modified landscapes can increase intraspecific trait variation. However, less known is whether such phenotypic variation is driven by plastic or adaptive responses to local environments. Here, we study five bumble bee (Apidae: Bombus) species across an urban gradient in the greater Saint Louis, Missouri region in the North American Midwest and ask: (1) Can urban environments induce intraspecific spatial structuring of body size, an ecologically consequential functional trait? And, if so, (2) is this body size structure the result of plasticity or adaptation? We additionally estimate genetic diversity, inbreeding, and colony density of these species—three factors that affect extinction risk. Using ≥ 10 polymorphic microsatellite loci per species and measurements of body size, we find that two of these species (Bombus impatiens, Bombus pensylvanicus) exhibit body size clines across the urban gradient, despite a lack of population genetic structure. We also reaffirm reports of low genetic diversity in B. pensylvanicus and find evidence that Bombus griseocollis, a species thought to be thriving in North America, is inbred in the greater Saint Louis region. Collectively, our results have implications for conservation in urban environments and suggest that plasticity can cause phenotypic clines across human-modified landscapes.
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20
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Ordoñez D, Bohórquez MD, Avendaño C, Patarroyo MA. Comparing Class II MHC DRB3 Diversity in Colombian Simmental and Simbrah Cattle Across Worldwide Bovine Populations. Front Genet 2022; 13:772885. [PMID: 35186024 PMCID: PMC8854852 DOI: 10.3389/fgene.2022.772885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/17/2022] [Indexed: 11/22/2022] Open
Abstract
The major histocompatibility complex (MHC) exerts great influence on responses to infectious diseases and vaccination due to its fundamental role in the adaptive immune system. Knowledge about MHC polymorphism distribution among breeds can provide insights into cattle evolution and diversification as well as population-based immune response variability, thus guiding further studies. Colombian Simmental and Simbrah cattle’s BoLA-DRB3 genetic diversity was compared to that of taurine and zebuine breeds worldwide to estimate functional diversity. High allele richness was observed for Simmental and Simbrah cattle; nevertheless, high homozygosity was associated with individual low sequence variability in both the β1 domain and the peptide binding region (PBR), thereby implying reduced MHC-presented peptide repertoire size. There were strong signals of positive selection acting on BoLA-DRB3 in all populations, some of which were poorly structured and displayed common alleles accounting for their high genetic similarity. PBR sequence correlation analysis suggested that, except for a few populations exhibiting some divergence at PBR, global diversity regarding potential MHC-presented peptide repertoire could be similar for the cattle populations analyzed here, which points to the retention of functional diversity in spite of the selective pressures imposed by breeding.
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Affiliation(s)
- Diego Ordoñez
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
- PhD Program in Tropical Health and Development, Universidad de Salamanca, Salamanca, Spain
| | - Michel David Bohórquez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- MSc Program in Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Catalina Avendaño
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- *Correspondence: Manuel Alfonso Patarroyo,
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Aitnazarov RB, Mishakova TM, Yudin NS. Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers. Vavilovskii Zhurnal Genet Selektsii 2022; 25:831-838. [PMID: 35088018 PMCID: PMC8761576 DOI: 10.18699/vj21.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 12/02/2022] Open
Abstract
There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks
to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of
local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great
relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible
to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the
most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations
in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle
populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent
populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of
the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises
in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic
variability parameters were found between individual populations. Private alleles have been identified in five out of
six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity
excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis,
and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic
diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant
differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises,
which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we
recommend focusing on the two populations with significant genetic distinctions from the others.
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Affiliation(s)
- R. B. Aitnazarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. M. Mishakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - N. S. Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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22
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Stahlke AR, Bitume EV, Özsoy ZA, Bean DW, Veillet A, Clark MI, Clark EI, Moran P, Hufbauer RA, Hohenlohe PA. Hybridization and range expansion in tamarisk beetles ( Diorhabda spp.) introduced to North America for classical biological control. Evol Appl 2022; 15:60-77. [PMID: 35126648 PMCID: PMC8792477 DOI: 10.1111/eva.13325] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 01/31/2023] Open
Abstract
With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle (Diorhabda carinata, D. carinulata, D. elongata, and D. sublineata), introduced from six localities across Eurasia to control the invasive shrub tamarisk (Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D. carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D. carinata, D. elongata, and D. sublineata hybridize in the field to varying extents, with D. carinata × D. sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems.
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Affiliation(s)
- Amanda R. Stahlke
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS)Beltsville Agricultural Research Center, Bee Research LaboratoryBeltsvilleMarylandUSA
| | - Ellyn V. Bitume
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
- U.S. Department of Agriculture, Forest Service (USDA‐FS), Pacific Southwest, Institute of Pacific Islands ForestryHiloHawaiiUSA
| | - Zeynep A. Özsoy
- Department of Biological SciencesColorado Mesa UniversityGrand JunctionColoradoUSA
| | - Dan W. Bean
- Colorado Department of AgriculturePalisadeColoradoUSA
| | - Anne Veillet
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
| | - Meaghan I. Clark
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eliza I. Clark
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Patrick Moran
- U.S. Department of Agriculture, Agricultural Research Service (USDA‐ARS), Invasive Species and Pollinator Health Research UnitAlbanyCaliforniaUSA
| | - Ruth A. Hufbauer
- Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Paul A. Hohenlohe
- Initiative for Bioinformatics and Evolutionary StudiesDepartment of Biological SciencesUniversity of IdahoMoscowIdahoUSA
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Fischer NM, Altewischer A, Ranpal S, Dool S, Kerth G, Puechmaille SJ. Population genetics as a tool to elucidate pathogen reservoirs: Lessons from Pseudogymnoascus destructans, the causative agent of White-Nose disease in bats. Mol Ecol 2021; 31:675-690. [PMID: 34704285 DOI: 10.1111/mec.16249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022]
Abstract
Emerging infectious diseases pose a major threat to human, animal, and plant health. The risk of species-extinctions increases when pathogens can survive in the absence of the host. Environmental reservoirs can facilitate this. However, identifying such reservoirs and modes of infection is often highly challenging. In this study, we investigated the presence and nature of an environmental reservoir for the ascomycete fungus Pseudogymnoascus destructans, the causative agent of White-Nose disease. Using 18 microsatellite markers, we determined the genotypic differentiation between 1497 P. destructans isolates collected from nine closely situated underground sites where bats hibernate (i.e., hibernacula) in Northeastern Germany. This approach was unique in that it ensured that every isolate and resulting multilocus genotype was not only present, but also viable and therefore theoretically capable of infecting a bat. The distinct distribution of multilocus genotypes across hibernacula demonstrates that each hibernaculum has an essentially unique fungal population. This would be expected if bats become infected in their hibernaculum (i.e., the site they spend winter in to hibernate) rather than in other sites visited before they start hibernating. In one hibernaculum, both the walls and the hibernating bats were sampled at regular intervals over five consecutive winter seasons (1062 isolates), revealing higher genotypic richness on walls compared to bats and a stable frequency of multilocus genotypes over multiple winters. This clearly implicates hibernacula walls as the main environmental reservoir of the pathogen, from which bats become reinfected annually during the autumn.
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Affiliation(s)
- Nicola M Fischer
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,Institut des Sciences de l'Évolution Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Andrea Altewischer
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Surendra Ranpal
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Serena Dool
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,CBGP, INRAE, CIRAD, IRD, Institut Agro, University of Montpellier, Montpellier, France
| | - Gerald Kerth
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Sebastien J Puechmaille
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany.,Institut des Sciences de l'Évolution Montpellier (ISEM), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Institut Universitaire de France, Paris, France
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24
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Thintip J, Singchat W, Ahmad SF, Ariyaraphong N, Muangmai N, Chamchumroon W, Pitiwong K, Suksavate W, Duangjai S, Duengkae P, Srikulnath K. Reduced genetic variability in a captive-bred population of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) revealed by microsatellite genotyping and D-loop sequencing. PLoS One 2021; 16:e0256573. [PMID: 34449789 PMCID: PMC8396778 DOI: 10.1371/journal.pone.0256573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Captive breeding programs are crucial to ensure the survival of endangered species and ultimately to reintroduce individuals into the wild. However, captive-bred populations can also deteriorate due to inbreeding depression and reduction of genetic variability. We genotyped a captive population of 82 individuals of the endangered Hume's pheasant (Syrmaticus humiae, Hume 1881) at the Doi Tung Wildlife Breeding Center to assess the genetic consequences associated with captive breeding. Analysis of microsatellite loci and mitochondrial D-loop sequences reveal significantly reduced genetic differentiation and a shallow population structure. Despite the low genetic variability, no bottleneck was observed but 12 microsatellite loci were informative in reflecting probable inbreeding. These findings provide a valuable source of knowledge to maximize genetic variability and enhance the success of future conservation plans for captive and wild populations of Hume's pheasant.
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Affiliation(s)
- Jitmat Thintip
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
| | - Worapong Singchat
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Syed Farhan Ahmad
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Nattakan Ariyaraphong
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
- Faculty of Fisheries, Department of Fishery Biology, Kasetsart University, Bangkok, Thailand
| | - Wiyada Chamchumroon
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Klinsak Pitiwong
- Department of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, Thailand
| | - Warong Suksavate
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Sutee Duangjai
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Faculty of Forestry, Department of Forest Biology, Special Research Unit for Wildlife Genomics (SRUWG), Kasetsart University, Bangkok, Thailand
- Faculty of Science, Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Kasetsart University, Bangkok, Thailand
- Faculty of Science, Animal Genomics and Bioresource Research Center (AGB), Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
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25
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Barragán-Ruiz CE, Silva-Santos R, Saranholi BH, Desbiez ALJ, Galetti PM. Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla. Front Genet 2021; 12:669350. [PMID: 34276776 PMCID: PMC8280777 DOI: 10.3389/fgene.2021.669350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 11/15/2022] Open
Abstract
In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (Fis, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.
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Affiliation(s)
| | - Rosane Silva-Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres, Campo Grande, Brazil.,Royal Zoological Society of Scotland, Edinburgh, United Kingdom.,Instituto de Pesquisas Ecológicas, Nazaré Paulista, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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26
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Guo W, Banerjee AK, Wu H, Ng WL, Feng H, Qiao S, Liu Y, Huang Y. Contrasting Phylogeographic Patterns in Lumnitzera Mangroves Across the Indo-West Pacific. FRONTIERS IN PLANT SCIENCE 2021; 12:637009. [PMID: 34249031 PMCID: PMC8261646 DOI: 10.3389/fpls.2021.637009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/27/2021] [Indexed: 06/13/2023]
Abstract
Mangroves are ecologically important forest communities in tropical and subtropical coasts, the effective management of which requires understanding of their phylogeographic patterns. However, these patterns often vary among different species, even among ecologically similar taxa or congeneric species. Here, we investigated the levels and patterns of genetic variation within Lumnitzera consisting of two species (L. racemosa and L. littorea) with nearly sympatric ranges across the Indo-West Pacific (IWP) region by sequencing three chloroplast DNA regions (for both species) and genotyping 11 nuclear microsatellite loci (for L. littorea). Consistent with findings in studies on other mangrove species, we found that both L. racemosa and L. littorea showed relatively high genetic variation among populations but low genetic variation within populations. Haplotype network and genetic clustering analyses indicated two well-differentiated clades in both L. racemosa and L. littorea. The relationship between geographic and genetic distances and divergence time estimates of the haplotypes indicated that limited dispersal ability of the propagules, emergence of land barriers during ancient sea-level changes, and contemporary oceanic circulation pattern in the IWP influenced the current population structure of the two species. However, the position of genetic break was found to vary between the two species: in L. racemosa, strong divergence was observed between populations from the Indian Ocean and the Pacific Ocean possibly due to land barrier effect of the Malay Peninsula; in L. littorea, the phylogeographic pattern was created by a more eastward genetic break along the biogeographic barrier identified as the Huxley's line. Overall, our findings strongly supported previous hypothesis of mangrove species divergence and revealed that the two Lumnitzera species have different phylogeographic patterns despite their close genetic relationship and similar current geographic distribution. The findings also provided references for the management of Lumnitzera mangroves, especially for the threatened L. littorea.
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Affiliation(s)
- Wuxia Guo
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haidan Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Malaysia
| | - Hui Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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27
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Schmidt C, Garroway CJ. The population genetics of urban and rural amphibians in North America. Mol Ecol 2021; 30:3918-3929. [PMID: 34053153 DOI: 10.1111/mec.16005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Human land transformation is one of the leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing animal population sizes in disturbed habitats. With time, this can lead to declines in effective population size and genetic diversity which restrict the ability of wildlife to efficiently cope with environmental change through genetic adaptation. However, it is not well understood whether these effects generally hold across taxa. We address this question by repurposing and synthesizing raw microsatellite data from online repositories for 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density, the Human Footprint Index, and impervious surface cover, we tested for generalizable effects of human land use on amphibian genetic diversity. We found minimal evidence, either positive or negative, for relationships between genetic metrics and urbanization. Together with previous work on focal species that also found varying effects of urbanization on genetic composition, it seems likely that the consequences of urbanization are not easily generalizable within or across amphibian species. Questions about the genetic consequences of urbanization for amphibians should be addressed on a case-by-case basis. This contrasts with general negative effects of urbanization in mammals and consistent, but species-specific, positive and negative effects in birds.
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Affiliation(s)
- Chloé Schmidt
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Colin J Garroway
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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28
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Genetic Diversity of Campomanesia adamantium and Its Correlation with Land Use and Land Cover. DIVERSITY 2021. [DOI: 10.3390/d13040160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
(1) Background: Campomanesia adamantium is an endemic species of the Cerrado and this biome has been under threat by its constant degradation. The genetic diversity of C. adamantium was characterized using species-specific microsatellites in two different time periods and correlations of these parameters of genetic diversity with the land use and land cover data. (2) Methods: We used 10 microsatellite loci to analyze C. adamantium from five populations, collected in 2011 and 2017. Maps of land use and land cover of the collection sites in both years were generated and subsequently correlated with genetic diversity. (3) Results: No significant loss of genetic diversity was observed in the analyzed period and a positive inbreeding coefficient was observed in all populations. AMOVA and STRUCTURE showed that there is no population structure between years and populations. Significant Pearson correlations were observed in 2017 between parameters of genetic diversity and land use and land cover, with a positive correlation between expected heterozygosity and secondary vegetation, and a negative correlation between inbreeding coefficient and exposed soil. (4) Conclusions: There was no decline in genetic diversity from 2011 to 2017. The high rates of the inbreeding coefficient could lead, for the species, in the long run, to an inbreeding depression as the Cerrado fragmentation might cause a population bottleneck.
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29
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Fontaine MC, Labbé F, Dussert Y, Delière L, Richart-Cervera S, Giraud T, Delmotte F. Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola. Curr Biol 2021; 31:2155-2166.e4. [PMID: 33770491 DOI: 10.1016/j.cub.2021.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/04/2021] [Accepted: 03/02/2021] [Indexed: 12/18/2022]
Abstract
Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.
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Affiliation(s)
- Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France; Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche pour le Développement (IRD), 34394 Montpellier, France.
| | - Frédéric Labbé
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103 CC, Groningen, the Netherlands; Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - Yann Dussert
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Sylvie Richart-Cervera
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, UMR 8079, Université Paris-Saclay, CNRS, AgroParisTech, Orsay 91400, France
| | - François Delmotte
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, 33140 Villenave d'Ornon, France.
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30
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Korablev MP, Poyarkov AD, Karnaukhov AS, Zvychaynaya EY, Kuksin AN, Malykh SV, Istomov SV, Spitsyn SV, Aleksandrov DY, Hernandez-Blanco JA, Munkhtsog B, Munkhtogtokh O, Putintsev NI, Vereshchagin AS, Becmurody A, Afzunov S, Rozhnov VV. Large-scale and fine-grain population structure and genetic diversity of snow leopards (Panthera uncia Schreber, 1776) from the northern and western parts of the range with an emphasis on the Russian population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01347-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Ribolli J, Zaniboni-Filho E, Machado CB, Guerreiro TCDS, Freitas PDD, Galetti Jr PM. Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2020-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.
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Affiliation(s)
- Josiane Ribolli
- Universidade Federal de São Carlos, Brazil; Universidade Federal de Santa Catarina, Brazil; Universidade Federal de São Carlos, Brazil
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32
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Dilipan E, Ramachandran M, Arulbalachandran D. Population genetics and gene flow of the seagrass, Syringodium isoetifolium based on Start codon targeted (SCoT) marker from Palk Bay and Chilika Lake, India. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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33
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Creech TG, Epps CW, Wehausen JD, Crowhurst RS, Jaeger JR, Longshore K, Holton B, Sloan WB, Monello RJ. Genetic and Environmental Indicators of Climate Change Vulnerability for Desert Bighorn Sheep. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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de Jager D, Harper CK, Bloomer P. Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa. PLoS One 2020; 15:e0236717. [PMID: 32797056 PMCID: PMC7428177 DOI: 10.1371/journal.pone.0236717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/13/2020] [Indexed: 12/03/2022] Open
Abstract
Wildlife ranching, although not considered a conventional conservation system, provides a sustainable model for wildlife utilization and could be a source of valuable genetic material. However, increased fragmentation and intensive management may threaten the evolutionary potential and conservation value of species. Disease-free Cape buffalo (Syncerus caffer caffer) in southern Africa exist in populations with a variety of histories and management practices. We compared the genetic diversity of buffalo in national parks to private ranches and found that, except for Addo Elephant National Park, genetic diversity was high and statistically equivalent. We found that relatedness and inbreeding levels were not substantially different between ranched populations and those in national parks, indicating that breeding practices likely did not yet influence genetic diversity of buffalo on private ranches in this study. High genetic differentiation between South African protected areas highlighted their fragmented nature. Structure analysis revealed private ranches comprised three gene pools, with origins from Addo Elephant National Park, Kruger National Park and a third, unsampled gene pool. Based on these results, we recommend the Addo population be supplemented with disease-free Graspan and Mokala buffalo (of Kruger origin). We highlight the need for more research to characterize the genetic diversity and composition of ranched wildlife species, in conjunction with wildlife ranchers and conservation authorities, in order to evaluate the implications for management and conservation of these species across different systems.
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Affiliation(s)
- Deon de Jager
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Cindy Kim Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Paulette Bloomer
- Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
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35
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Shang P, Li W, Tan Z, Zhang J, Dong S, Wang K, Chamba Y. Population Genetic Analysis of Ten Geographically Isolated Tibetan Pig Populations. Animals (Basel) 2020; 10:ani10081297. [PMID: 32751240 PMCID: PMC7460208 DOI: 10.3390/ani10081297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed in this study. Population genetic analyses, including Principal Component Analysis (PCA), phylogenic tree, genetic differentiation, deleterious variant, contribution to meta-population genetic diversity and selective sweep were performed. Limited genetic differentiation was identified among these Tibetan pig populations. Most deleterious variants were low-frequency mutations and population specific. Contribution to the meta-population was largest in the TT population, based on gene and allelic diversity. Genes under selection were involved in hypoxia adaptation, hard palate development, facial appearance, and perception of smell. Abstract Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation.
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Affiliation(s)
- Peng Shang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Wenting Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450001, China;
| | - Zhankun Tan
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Jian Zhang
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Shixiong Dong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450001, China;
- Correspondence: or (K.W.); (Y.C.)
| | - Yangzom Chamba
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Linzhi 860000, China; (P.S.); (Z.T.); (J.Z.); (S.D.)
- Correspondence: or (K.W.); (Y.C.)
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Local dispersal pathways during the invasion of the cactus moth, Cactoblastis cactorum, within North America and the Caribbean. Sci Rep 2020; 10:11012. [PMID: 32620784 PMCID: PMC7335065 DOI: 10.1038/s41598-020-66864-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/26/2020] [Indexed: 11/22/2022] Open
Abstract
Cactoblastis cactorum, a species of moth native to Argentina, feeds on several prickly pear cactus species (Opuntia) and has been successfully used as a biological control of invading Opuntia species in Australia, South Africa and native ruderal Opuntia species in some Caribbean islands. Since its introduction to the Caribbean its spread was uncontrolled, invading successfully Florida, Texas and Louisiana. Despite this long history of invasion, we are still far from understanding the factors determining the patterns of invasion of Cactoblastis in North America. Here, we explored three non-mutually exclusive explanations: a) a stepping stone model of colonization, b) long distance colonization due to hurricanes, and/or c) hitchhiking through previously reported commercial routes. Genetic diversity, genetic structure and the patterns of migration among populations were obtained by analyzing 10 nuclear microsatellite loci. Results revealed the presence of genetic structure among populations of C. cactorum in the invaded region and suggest that both marine commercial trade between the Caribbean islands and continental USA, as well as recurrent transport by hurricanes, explain the observed patterns of colonization. Provided that sanitary regulations avoiding human-mediated dispersal are enforced, hurricanes probably represent the most important agent of dispersal and future invasion to continental areas.
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Banerjee AK, Guo W, Qiao S, Li W, Xing F, Lin Y, Hou Z, Li S, Liu Y, Huang Y. Land masses and oceanic currents drive population structure of Heritiera littoralis, a widespread mangrove in the Indo-West Pacific. Ecol Evol 2020; 10:7349-7363. [PMID: 32760533 PMCID: PMC7391321 DOI: 10.1002/ece3.6460] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/24/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Phylogeographic forces driving evolution of sea-dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo-West Pacific region and identify the phylogeographic factors influencing its present-day distribution. Analysis of five chloroplast DNA fragments' sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo-Malesia and Australasia was not so prominent. Long-distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- South China Botanical GardenChinese Academy of SciencesGuangzhouGuangdongChina
| | - Sitan Qiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Weixi Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
- Division of Ecology & BiodiversitySchool of Biological SciencesThe University of Hong KongHong KongChina
| | - Fen Xing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhuangwei Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouGuangdongChina
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Konopiński MK. Shannon diversity index: a call to replace the original Shannon's formula with unbiased estimator in the population genetics studies. PeerJ 2020; 8:e9391. [PMID: 32655992 PMCID: PMC7331625 DOI: 10.7717/peerj.9391] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/29/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Shannon diversity index has been widely used in population genetics studies. Recently, it was proposed as a unifying measure of diversity at different levels-from genes and populations to whole species and ecosystems. The index, however, was proven to be negatively biased at small sample sizes. Modifications to the original Shannon's formula have been proposed to obtain an unbiased estimator. METHODS In this study, the performance of four different estimators of Shannon index-the original Shannon's formula and those of Zahl, Chao and Shen and Chao et al.-was tested on simulated microsatellite data. Both the simulation and analysis of the results were performed in the R language environment. A new R function was created for the calculation of all four indices from the genind data format. RESULTS Sample size dependence was detected in all the estimators analysed; however, the deviation from parametric values was substantially smaller in the derived measures than in the original Shannon's formula. Error rate was negatively associated with population heterozygosity. Comparisons among loci showed that fast-mutating loci were less affected by the error, except for the original Shannon's estimator which, in the smallest sample, was more strongly affected by loci with a higher number of alleles. The Zahl and Chao et al. estimators performed notably better than the original Shannon's formula. CONCLUSION The results of this study show that the original Shannon index should no longer be used as a measure of genetic diversity and should be replaced by Zahl's unbiased estimator.
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Jażdżewska AM, Rewicz T, Mamos T, Wattier R, Bącela-Spychalska K, Grabowski M. Cryptic diversity and mtDNA phylogeography of the invasive demon shrimp, Dikerogammarus haemobaphes (Eichwald, 1841), in Europe. NEOBIOTA 2020. [DOI: 10.3897/neobiota.57.46699] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The regions of the Black, Caspian, and Azov seas are known for being both (i) the place of extensive crustacean radiation dated to the times of Paratethys and Sarmatian basins, and (ii) present donors of alien and invasive taxa to many areas worldwide. One amphipod morphospecies,Dikerogammarus haemobaphes, is known both as native to rivers draining to the Black and Caspian seas as well as a successful invader (nicknamed demon shrimp) in Central and Western European rivers. Based on mitochondrial (COI and 16S) and nuclear (28S) datasets and 41 sampling sites, representing both the native (19) and the invaded (22) range, we assessed cryptic diversity, phylogeography and population genetics of this taxon. First, we revealed the presence of two divergent lineages supported by all markers and all species delimitation methods. The divergence between the lineages was high (18.3% Kimura 2-parameter distance for COI) and old (ca. 5.1 Ma), suggesting the presence of two cryptic species withinD. haemobaphes. Lineage A was found only in a few localities in the native range, while lineage B was widespread both in the native and in the invaded range. Although genetic divergence within lineage B was shallow, geographic distribution of 16S and COI haplotypes was highly heterogeneous, leading us to the definition of four Geo-Demographic Units (GDUs). Two GDUs were restricted to the native range: GDU-B1 was endemic for the Durugöl (aka Duruşu) Liman in Turkey, whereas GDU-B2 occurred only in the Dniester River. GDU-B3 was both present in several localities in the native range in the Black Sea drainage area and widespread in Central and Western Europe. The GDU-B4 was found exclusively in the Moskva River in Russia. Extended Bayesian Skyline Plot indicated steady growth of GDU-B3 population size since 30 ka, pointing to the rather old history of its expansion, first in the late Pleistocene in the native range and nowadays in Central and Western Europe. The analysis of haplotype distribution across the present distribution range clearly showed two invasion routes to Central and Western Europe. The first one, originating from the lower Dnieper, allowed the demon shrimp to colonize Polish rivers and the Mittellandkanal in Germany. The second one, originating from the Danube delta, allowed to colonize the water bodies in the upper Danube basin. The UK population has originated from the Central Corridor, as only a haplotype found exclusively along this route was recorded in the UK. Population genetics analysis showed that the invasion of the demon shrimp along the Central Corridor was not associated with the loss of genetic diversity, which might contribute to the success of this invader in the newly colonized areas.
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Borzée A, Fong JJ, Nguyen HQ, Jang Y. Large-Scale Hybridisation as an Extinction Threat to the Suweon Treefrog (Hylidae: Dryophytes suweonensis). Animals (Basel) 2020; 10:ani10050764. [PMID: 32349428 PMCID: PMC7278489 DOI: 10.3390/ani10050764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/05/2020] [Accepted: 04/13/2020] [Indexed: 01/09/2023] Open
Abstract
Simple Summary A large number of amphibian species are now endangered, mostly because of human activities. An example is land modification, which may bring species that were previously isolated in contact, and allows them to hybridise. Here, we assessed the presence of hybrid individuals between the endangered Suweon treefrog (Dryophytes suweonensis) and the widespread Japanese treefrog (Dryophytes japonicus). We found hybrids to be relatively widespread and present at all populations where the Suweon treefrog occurred. This is important, as it results in an additional threat to the Suweon treefrog. Abstract Amphibians are in the midst of a sixth mass extinction, and human activities play a major role in pushing species towards extinction. Landscape anthropisation has impacts that indirectly threaten species, in addition to the obvious destruction of natural habitats. For instance, land modification may bring human-commensal species in contact with sister-clades from which they were previously isolated. The species in these new contact zones are then able to hybridise to the point of reaching lineage fusion, through which the gene pool of the two species merges and one of the parental lineages becomes extirpated. Here, we documented the patterns of hybridisation between the spatially restricted D. suweonensis and the widespread D. japonicus. On the basis of the analysis of Cytochrome c oxidase subunit I mitochondrial DNA sequences (404 individuals from 35 sites) and six polymorphic microsatellites (381 individuals from 34 sites), we revealed a generalised, bi-directional, and geographically widespread hybridisation between the two species. Evidence of fertile back-crosses is provided by relatively high numbers of individuals in cyto-nuclear disequilibrium, as well as the presence of hybrid individuals further south than the species distribution limit, determined on the basis of call properties. Hybridisation is an additional threat to the endangered D. suweonensis.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
| | | | - Hoa Quynh Nguyen
- Department of Life Sciences and Division of EcoScience, Ewha Woman’s University, Seoul 03760, Korea
- Centre for Research and Development of Membrane Technology, Institute of Environmental Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Woman’s University, Seoul 03760, Korea
- Correspondence:
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41
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CapellÀ-Marzo B, SÁnchez-Montes G, MartÍnez-Solano I. Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population. Integr Zool 2020; 15:482-497. [PMID: 32329558 DOI: 10.1111/1749-4877.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (Nb ) to the total number of adults (Na ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate Na in each breeding season, and multilocus genotypes to estimate the effective population size (Ne ), Nb , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The Nb /Na ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.
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Affiliation(s)
- Berta CapellÀ-Marzo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Iñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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Venta PJ, Nguyen AK, Senut MC, Poulos WG, Prukudom S, Cibelli JB. A 13-plex of tetra- and penta-STRs to identify zebrafish. Sci Rep 2020; 10:3851. [PMID: 32123258 PMCID: PMC7052278 DOI: 10.1038/s41598-020-60842-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/09/2020] [Indexed: 11/09/2022] Open
Abstract
The zebrafish species Danio rerio has become one of the major vertebrate model organisms used in biomedical research. However, there are aspects of the model that need to be improved. One of these is the ability to identify individual fish and fish lines by DNA profiling. Although many dinucleotide short tandem repeat (diSTR) markers are available for this and similar purposes, they have certain disadvantages such as an excessive polymerase slippage ("stutter") that causes difficulties in automated genotyping and cross-laboratory comparisons. Here we report on the development of a 13-plex of tetranucleotide and pentanucleotide STRs (tetraSTRs and pentaSTRs, respectively) that have low stutter. The system uses an inexpensive universal primer labelling system, which can easily be converted to a direct labeling system if desired. This 13-plex was examined in three zebrafish lines (NHGRI-1, kca33Tg, and kca66Tg, originally obtained from ZIRC). The average observed heterozygosity (Ho) and expected heterozygosity (He) in these highly inbred lines were 0.291 and 0.359, respectively, which is very similar to what has been found with diSTRs. The probability of identity (PI) for all fish tested was 2.1 × 10-5 and the PI for siblings (PIsib) was 6.4 × 10-3, as calculated by the Genalex package. Ninety percent of the fish tested were correctly identified with their respective strains. It is also demonstrated that this panel can be used to confirm doubled-haploid cell lines. This multiplex should find multiple uses for improving the accuracy and reproducibility of studies using the zebrafish model.
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Affiliation(s)
- Patrick J Venta
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA. .,Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
| | - Anthony K Nguyen
- Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48823, USA
| | - Marie-Claude Senut
- Biomilab LLC, Lansing, MI, 48910, USA.,Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - William G Poulos
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA
| | - Sukumal Prukudom
- Center for Advanced Studies for Agriculture and Food, Kasetsart University Institute for Advanced Studies, Kasetsart University (CASAF, NRU-KU), Bangkok, 10900, Thailand
| | - Jose B Cibelli
- Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, 48823, USA. .,Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI, 48823, USA.
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Genetic diversity and population structure of the Chinese lake gudgeon (Sarcocheilichthys sinensis) using microsatellite markers. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2019.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Schmidt C, Domaratzki M, Kinnunen RP, Bowman J, Garroway CJ. Continent-wide effects of urbanization on bird and mammal genetic diversity. Proc Biol Sci 2020; 287:20192497. [PMID: 32019443 PMCID: PMC7031673 DOI: 10.1098/rspb.2019.2497] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 01/13/2020] [Indexed: 11/12/2022] Open
Abstract
Urbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is a cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalysed publicly archived genetic datasets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41 023 individuals, sampled from 1008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.
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Affiliation(s)
- C. Schmidt
- Department Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - M. Domaratzki
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - R. P. Kinnunen
- Department Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - J. Bowman
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada K9 L 0G2
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada K9 J 8M5
| | - C. J. Garroway
- Department Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
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Jangtarwan K, Koomgun T, Prasongmaneerut T, Thongchum R, Singchat W, Tawichasri P, Fukayama T, Sillapaprayoon S, Kraichak E, Muangmai N, Baicharoen S, Punkong C, Peyachoknagul S, Duengkae P, Srikulnath K. Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus). PLoS One 2019; 14:e0223726. [PMID: 31600336 PMCID: PMC6786576 DOI: 10.1371/journal.pone.0223726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/26/2019] [Indexed: 11/18/2022] Open
Abstract
The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woolly-necked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand.
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Affiliation(s)
- Kornsuang Jangtarwan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Tassika Koomgun
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Tulyawat Prasongmaneerut
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Ratchaphol Thongchum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Panupong Tawichasri
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Toshiharu Fukayama
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Siwapech Sillapaprayoon
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Ekaphan Kraichak
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Narongrit Muangmai
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Sudarath Baicharoen
- Bureau of Research and Conservation, The Zoological Park Organization (ZPO), Bangkok, Thailand
| | | | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, Thailand.,Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok, Thailand.,Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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López-Cortegano E, Pouso R, Labrador A, Pérez-Figueroa A, Fernández J, Caballero A. Optimal Management of Genetic Diversity in Subdivided Populations. Front Genet 2019; 10:843. [PMID: 31572448 PMCID: PMC6753960 DOI: 10.3389/fgene.2019.00843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 08/13/2019] [Indexed: 11/29/2022] Open
Abstract
One of the main objectives of conservation programs is the maintenance of genetic diversity because this provides the adaptive potential of populations to face new environmental challenges. Genetic diversity is generally assessed by means of neutral molecular markers, and it is usually quantified by the expected heterozygosity under Hardy-Weinberg equilibrium and the number of alleles per locus or allelic diversity. These two measures of genetic diversity are complementary because whereas the former is directly related to genetic variance for quantitative traits and, therefore, to the short-term response to selection and adaptation, the latter is more sensitive to population bottlenecks and relates more strongly to the long-term capacity of adaptation of populations. In the context of structured populations undergoing conservation programs, it is important to decide the optimum management strategy to preserve as much genetic diversity as possible while avoiding inbreeding. Here we examine, through computer simulations, the consequences of choosing a conservation strategy based on maximizing either heterozygosity or allelic diversity of single-nucleotide polymorphism haplotypes in a subdivided population. Our results suggest that maximization of allelic diversity can be more efficient in maintaining the genetic diversity of subdivided populations than maximization of expected heterozygosity because the former maintains a larger number of alleles while making a better control of inbreeding. Thus, maximization of allelic diversity should be a recommended strategy in conservation programs for structured populations.
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Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Ramón Pouso
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Adriana Labrador
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain
| | - Jesús Fernández
- Departamento de Mejora Genética, Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
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48
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Farias IP, Willis S, Leão A, Verba JT, Crossa M, Foresti F, Porto-Foresti F, Sampaio I, Hrbek T. The largest fish in the world's biggest river: Genetic connectivity and conservation of Arapaima gigas in the Amazon and Araguaia-Tocantins drainages. PLoS One 2019; 14:e0220882. [PMID: 31419237 PMCID: PMC6697350 DOI: 10.1371/journal.pone.0220882] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/25/2019] [Indexed: 12/02/2022] Open
Abstract
Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.
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Affiliation(s)
- Izeni Pires Farias
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- * E-mail: (IPF); (TH)
| | - Stuart Willis
- Department of Ichthyology, California Academy of Sciences, San Francisco, CA, United States of America
| | - Adam Leão
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Júlia Tovar Verba
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
| | | | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Fabio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Campus de Bauru, Bauru, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Pará, Brazil
| | - Tomas Hrbek
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- * E-mail: (IPF); (TH)
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49
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Hanna ZR, Cicero C, Bowie RCK. Molecular evidence that the Channel Islands populations of the orange-crowned warbler ( Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage. PeerJ 2019; 7:e7388. [PMID: 31404458 PMCID: PMC6688592 DOI: 10.7717/peerj.7388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/01/2019] [Indexed: 11/23/2022] Open
Abstract
We used molecular data to assess the degree of genetic divergence across the breeding range of the orange-crowned warbler (Oreothlypis celata) in western North America with particular focus on characterizing the divergence between O. celata populations on the mainland of southern California and on the Channel Islands. We obtained sequences of the mitochondrial gene ND2 and genotypes at ten microsatellite data for 192 O. celata from populations spanning all four recognized subspecies. We recovered shallow, but significant, levels of divergence among O. celata populations across the species range. Our results suggest that island isolation, subspecies (delineation by morphology, ecological, and life-history characteristics), and isolation-by-distance, in that order, are the variables that best explain the geographic structure detected across the range of O. celata. Populations on the Channel Islands were genetically divergent from those on the mainland. We found evidence for greater gene flow from the Channel Islands population to mainland southern California than from the mainland to the islands. We discuss these data in the context of differentiation in phenotypic and ecological characters.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
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50
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Vuković R, Liber Z, Ježić M, Sotirovski K, Ćurković-Perica M. Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica. Environ Microbiol 2019; 21:4521-4536. [PMID: 31314941 DOI: 10.1111/1462-2920.14742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.
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Affiliation(s)
- Rosemary Vuković
- Department of Biology, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Zlatko Liber
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kiril Sotirovski
- Faculty of Forestry, Ss. Cyril and Methodius University of Skopje, Skopje, North Macedonia
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