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Kouakou JL, Gonedelé-Bi S. Population genetic structure and historical demography of the population of forest elephants in Côte d'Ivoire. PLoS One 2024; 19:e0300468. [PMID: 39186735 PMCID: PMC11346955 DOI: 10.1371/journal.pone.0300468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/27/2024] [Indexed: 08/28/2024] Open
Abstract
The population of forest elephant (Loxodonta cyclotis) has continuously declined in Côte d'Ivoire and, the remaining population largely consists of subpopulations that are fragmented and isolated. No data actually exist on the level of genetic diversity and population genetic structure of current forest elephant populations in Côte d'Ivoire. In this sense, determining genetic diversity and the underlying mechanisms of population differentiation is crucial for the initiation of effective conservation management. A total of 158 dung samples of forest elephants were collected at stage 1 of decompositions (dung pile intact, very fresh) in three Classified Forests (CF) (Bossématié, Dassioko and Port-Gauthier) in Côte d'Ivoire. A total of 101 sequences of the mitochondrial DNA control region measuring 600 base pair and 26 haplotypes were obtained. A haplotypic diversity ranging from 0.655 ± 0.050 at Bossématié and 0.859 ± 0.088 at Port Gauthier was obtained. Fifteen (15) out of 26 haplotypes observed were singletons and only the Dassioko and Port Gauthier CFs shared the same haplotypes. The strong genetic connectivity between forest elephant populations of the Dassioko and Port Gauthier CFs is supported by the grouping of these populations into a single cluster by Bayesian analysis. Although populations of L. cyclotis exhibit relatively high genetic diversity, habitat fragmentation could affect the genetic variability of current populations. Urgent measures including the reinforcement/establishment of genetic corridors and the strengthening of protection measures need to be undertaken to save the remaining populations of forest elephants in Côte d'Ivoire.
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Affiliation(s)
- Jean-Louis Kouakou
- Laboratoire de Génomique Fonctionnelle et Amélioration Génétique, Université Nangui Abrogoua, Abidjan, Côte d’Ivoire
| | - Sery Gonedelé-Bi
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources Biologiques, Université Félix Houphouët Boigny, Abidjan-Cocody, Côte d’Ivoire
- Centre Suisse de Recherches Scientifiques en Côte d’Ivoire, Adiopodoumé, Côte d’Ivoire
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Zhao R, He Q, Chu X, He A, Zhang Y, Zhu Z. Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China. FRONTIERS IN PLANT SCIENCE 2024; 15:1277173. [PMID: 38405582 PMCID: PMC10885731 DOI: 10.3389/fpls.2024.1277173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/10/2024] [Indexed: 02/27/2024]
Abstract
Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.
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Affiliation(s)
- Runan Zhao
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Qianqian He
- Research Center for Urban and Rural Living Environment, Zhijiang College of Zhejiang University of Technology, Shaoxing, China
| | - Xiaojie Chu
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Anguo He
- Administration of Zhejiang Dapanshan National Nature Reserve, Pan’an, China
| | - Yuanlan Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Life Sciences, Nanjing Forestry University, Nanjing, China
| | - Zunling Zhu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Jinpu Research Institute, Nanjing Forestry University, Nanjing, China
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Sommaro LV, Martínez JJ, Chiappero MB, Steinmann AR, Gardenal CN, Priotto JW. Relatedness dynamics and sex-biased dispersal in a seasonal cycle of corn mice from intensively managed agroecosystems. Curr Zool 2024; 70:1-12. [PMID: 38476139 PMCID: PMC10926262 DOI: 10.1093/cz/zoac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/17/2022] [Indexed: 03/14/2024] Open
Abstract
The sex-biased dispersal and kinship dynamics are important factors shaping the spatial distribution of individuals and are key parameters affecting a variety of ecological and evolutionary processes. Here, we studied the spatial distribution of related individuals within a population of corn mice Calomys musculinus in a seasonal cycle to infer dispersal patterns. The sampling was carried out from spring 2005 to winter 2006 in field borders of intensively managed agroecosystems. Genotyping data from 346 individuals with 9 microsatellites showed spatial genetic structure was weak for males, but not for females. The results indicate a complex spatial kinship dynamic of related females across all seasons. Which, contrary to our expectations, dispersal distances decrease with the increase of the population abundance. Meanwhile, male dispersal distances were greater when population abundance increased and thus the availability of active females. Males disperse greater distances to mate and sire offspring with distant females as a possible inbreeding avoidance mechanism. This study shows that C. musculinus is capable of much greater scattering distances than previously reported and that dispersal occurs fluidly and without barriers across the agroecosystem. The indirect benefit of dispersal on individual fitness could be related to relaxing the competition in the natal area and increasing the mating rate. Our study highlights the value of combining genetic relatedness, fieldwork observations, and behavioral data to estimate dispersal at a fine geographical scale.
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Affiliation(s)
- Lucia V Sommaro
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), Universidad Nacional de Jujuy - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Salvador de Jujuy, Jujuy, Argentina
| | - Juan J Martínez
- Laboratorio de Ecología Evolutiva y Biogeografía, Instituto de Ecorregiones Andinas (INECOA), Universidad Nacional de Jujuy - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Salvador de Jujuy, Jujuy, Argentina
| | - Marina B Chiappero
- Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Universidad Nacional de Córdoba, Córdoba, Argentina
- Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea R Steinmann
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - Cristina N Gardenal
- Instituto de Diversidad y Ecología Animal (IDEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Universidad Nacional de Córdoba, Córdoba, Argentina
- Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - José W Priotto
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
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Verbylaitė R, Aravanopoulos FA, Baliuckas V, Juškauskaitė A, Ballian D. Can a Forest Tree Species Progeny Trial Serve as an Ex Situ Collection? A Case Study on Alnus glutinosa. PLANTS (BASEL, SWITZERLAND) 2023; 12:3986. [PMID: 38068622 PMCID: PMC10708541 DOI: 10.3390/plants12233986] [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: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 02/12/2024]
Abstract
Scientifically informed decisions for the long-term conservation of extant genetic diversity should combine in situ and ex situ conservation methods. The aim of the present study was to assess if a progeny plantation consisting of several open pollinated (OP) families and established for breeding purposes can also serve as an ex situ conservation plantation, using the case study of a Lithuanian progeny trial of Alnus glutinosa, a keystone species of riparian ecosystems that warrants priority conservation actions. We employed 17 nuclear microsatellite (Simple Sequence Repeat) markers and compared the genetic diversity and copy number of the captured alleles of 22 OP progeny families from this plantation, with 10 wild A. glutinosa populations, originating from the two provenance regions of the species in Lithuania. We conclude that the progeny plantation could be used as an ex situ plantation for the A. glutinosa populations from the first provenance region (represented by eight genetic conservation units (GCU)). Based on the present study's results, we can expect that the A. glutinosa progeny plantation harbors enough genetic diversity of wild A. glutinosa populations from the first provenance region. This progeny plantation can serve as a robust ex situ collection containing local alleles present in at least one wild population with at least 0.05 frequency with 25 replications.
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Affiliation(s)
- Rita Verbylaitė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Kėdainiai District, Lithuania; (F.A.A.); (V.B.); (A.J.)
| | - Filippos A. Aravanopoulos
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Kėdainiai District, Lithuania; (F.A.A.); (V.B.); (A.J.)
- Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, P.O. Box 238, GR 541 24 Thessaloniki, Greece
| | - Virgilijus Baliuckas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Kėdainiai District, Lithuania; (F.A.A.); (V.B.); (A.J.)
| | - Aušra Juškauskaitė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, LT-58344 Kėdainiai District, Lithuania; (F.A.A.); (V.B.); (A.J.)
| | - Dalibor Ballian
- Faculty of Forestry, University of Sarajevo, Zagrebacka 20, 71000 Sarajevo, Bosnia and Herzegovina;
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
- Academy of Sciences and Arts of Bosnia and Hercegovina, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina
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Wang Z, Song M, Lyu Q, Ying J, Wu Q, Song F, Jiang L, Wei X, Wang S, Wang F, Zhou Y, Song X, Luo H. A forensic population database of autosomal STR and X-STR markers in the Qiang ethnic minority of China. Heliyon 2023; 9:e21823. [PMID: 38034634 PMCID: PMC10685182 DOI: 10.1016/j.heliyon.2023.e21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
The Qiang ethnic group is one of the oldest ethnic groups in China and is the most active ethnic group among all the populations along the Tibetan-Yi corridor. They have had a profound impact nationally and internationally. The paternal and maternal genetic feature of the Qiang ethnic group has been revealed, leaving the question of the genetic characteristics from autosomes and X chromosome not answered. The aim of this study was to explore the potential of 36 A-STR (Microreader™ 36A ID System) and 19 X-STR (Microreader™ 19X System) for application in the Qiang population and to elucidate their genetic diversity in southwest China. The cumulative probability of exclusion (CPE) for autosomal STRs is 1-1.3814 × 10-15 and the mean paternity exclusion chance (MEC) for X-STRs is 1-1.7323 × 10-6. Forensic parameters suggest that the STRs analyzed here are well-suited for forensic applications. The results of phylogenetic, interpopulation differentiation, and principal coordinates analysis (PCoA) indicate that the Qiang people have extensive connections with ethnic minorities in China, supporting the view that the Qiang people are the oldest group in the entire Sino-Tibetan language family. The Qiang appeared genetically more associated with most ethnic groups in China, especially the Han. The calculation of random matching probability (RMP) was improved by Fst correction of allele frequencies to make RMP more accurate and reasonable. This study can fill in the gaps in the Qiang STR reference database, providing valuable frequency data for forensic applications and evidence for the Qiang's genetic pattern as an important ancestral position in the Sino-Tibetan populations.
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Affiliation(s)
- Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Lyu
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan, 622750, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai, 621100, China
| | - Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Fei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
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Kovács Z, Mlinarec J, Höhn M. Living on the edge: morphological, karyological and genetic diversity studies of the Hungarian Plantago maxima populations and established ex situ collection. BOTANICAL STUDIES 2023; 64:2. [PMID: 36692644 PMCID: PMC9873897 DOI: 10.1186/s40529-022-00365-6] [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: 08/23/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The analysis of genetic diversity of protected plant species can greatly support conservation efforts. Plantago maxima Juss. ex Jacq. is a perennial species distributed along the Eurasian steppe. The westernmost range edge of the species' distribution is located in the Pannonian basin, in Hungary where it is represented by a few, fragmented and highly endangered populations. We studied population diversity of all Hungarian range edge, natural populations, and one established ex situ population. One population from the centre of distribution (Kazakhstan) was implemented in the cpDNA haplotype study to compare the peripheral vs. central populations. We performed morphometric trait-based analysis, chromosome studies (morphometric analyses and FISH) and genetic diversity evaluations using inter simple sequence repeats (ISSR) and cpDNA trnL-trnF to evaluate differences between the in situ and ex situ populations as well as central vs. peripheral populations. RESULTS Our results showed no obvious morphological differences among the in situ and ex situ populations in the period between 2018 and 2020. One ex situ subpopulation develops flowers three years in a row from 2019, which is a favourable indicator of the introduction success. Hungarian populations are exclusively diploids (2n = 2x = 12). The karyogram consists of 5 metacentric and 1 acrocentric chromosome pair. Plantago maxima has one 35S and two 5S rDNA loci, located on the acrocentric chromosome pair. Eight variable ISSR primers yielded 100 fragments, of which 74.6% were polymorphic (mean He = 0.220). A high level of genetic variation within population was observed (92%) while the genetic differentiation among the populations was only 8%. STRUCTURE analysis revealed that the largest Kunpeszér population separated from the rest of the Hungarian populations, indicating a high rate of admixture among the other ones. Based on the trnL-trnF sequence analysis the Hungarian populations represent a single haplotype, which can indicate a reduced diversity due to isolation and recent population decline. By contrast, Kazakh population represents a distinct haplotype compared to the Hungarian samples. CONCLUSIONS The present study draws the attention to the high conservation value of the Plantago maxima populations from the westernmost range edge of the species' distribution.
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Affiliation(s)
- Zsófia Kovács
- Institute of Agronomy, Department of Botany, Hungarian University of Agriculture and Life Sciences, Villányi Út 29-43, Budapest, 1118, Hungary.
- Department of Zoology, Plant Protection Institute, Centre for Agricultural Research, ELKH, Budapest, Hungary.
| | - Jelena Mlinarec
- Department of Nature Protection and Landscape Architecture, Oikon Ltd.-Institute of Applied Ecology, Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Mária Höhn
- Institute of Agronomy, Department of Botany, Hungarian University of Agriculture and Life Sciences, Villányi Út 29-43, Budapest, 1118, Hungary
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Genetic Diversity and Population Structure of the Native Pulawska and Three Commercial Pig Breeds Based on Microsatellite Markers. Genes (Basel) 2023; 14:genes14020276. [PMID: 36833204 PMCID: PMC9956297 DOI: 10.3390/genes14020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Swine DNA profiling is highly important for animal identification and parentage verification and also increasingly important for meat traceability. This work aimed to analyze the genetic structure and genetic diversity in selected Polish pig breeds. The study used a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in the native Puławska pig (PUL, n = 85) and three commercial pig breeds: Polish Large White (PLW, n = 74), Polish Landrace (PL, n = 85) and foreign breed Duroc (DUR, n = 84). Genetic differentiation among breeds accounted for 18% of the total genetic variability (AMOVA). Bayesian structure analysis (STRUCTURE) indicated that the four distinct genetic clusters obtained corresponded to the four breeds studied. The genetic Reynolds distances (Ɵw) showed a close relationship between PL and PLW breeds and the most distant for DUR and PUL pigs. The genetic differentiation values (FST) were lower between PL and PLW and higher between PUL and DUR. The principal coordinate analysis (PCoA) supported the classification of the populations into four clusters.
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Shi M, Wang Y, Olvera-Vazquez SG, Iñiguez JC, Thein MS, Watanabe KN. Comparison of Chayote ( Sechium edule (Jacq.) Sw.) Accessions from Mexico, Japan, and Myanmar Using Reproductive Characters and Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:476. [PMID: 36771559 PMCID: PMC9919900 DOI: 10.3390/plants12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Promoting neglected and underutilized crop species is a possible solution to deal with the complex challenges of global food security. Chayote is a Neglected and Underutilized Cucurbit Species (NUCuS), which is recognized as a fruit vegetable in Latin America and is widely grown in Asia and Africa. However, basic biological knowledge about the crop is insufficient in scientific sources, especially outside of its center of origin. In this study, limited observations on reproductive characters were conducted, differentiating accessions from Mexico, Japan, and Myanmar. Cytological evaluation among Mexican and Japanese accessions showed that the relative nuclear DNA content is 1.55 ± 0.05 pg, the estimated genome size is 1511 at 2C/Mbp, and the observed mitotic chromosomal number is 2n = 28. The genetic diversity of 21 chayote accessions was also examined using six microsatellite markers. A global low genetic heterozygosity (Ho = 0.286 and He = 0.408) and three genetic groups were detected. The results established the basis to provide insights into chayote arrival history in Asia by looking at the crop's reproductive morphology, cytology, and genetic diversity status outside its origin center. This could help in developing sustainable utilization and conservation programs for chayote.
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Affiliation(s)
- Miao Shi
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Yihang Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Sergio Gabriel Olvera-Vazquez
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
- GQE-Le Moulon, INRAe et University Paris-Saclay, Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette, France
| | - Jorge Cadena Iñiguez
- Colegio de Postgraduados, Campus San Luis Potosí, Salias de Hidalgo, San Luis Potosí 78622, Mexico
| | - Min San Thein
- Department of Agricultural Research, Ministry of Agriculture, Livestock and Irrigation, Yezin, Myanmar
| | - Kazuo N. Watanabe
- Tsukuba Plant Innovation Research Center, Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
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Buono V, Burgio S, Macrì N, Catania G, Hauffe HC, Mucci N, Davoli F. Microsatellite Characterization and Panel Selection for Brown Bear ( Ursus arctos) Population Assessment. Genes (Basel) 2022; 13:2164. [PMID: 36421838 PMCID: PMC9690282 DOI: 10.3390/genes13112164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 10/28/2023] Open
Abstract
An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.
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Affiliation(s)
- Vincenzo Buono
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Salvatore Burgio
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, 40100 Bologna, Italy
| | - Nicole Macrì
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Giovanni Catania
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, 40100 Bologna, Italy
| | - Heidi C. Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione E. Mach, San Michele all’Adige, 38098 Trento, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Francesca Davoli
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
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Morishima K, Fukui E, Aizawa M. Concordant genetic structures of sika deer and Japanese land leeches suggest that the current range expansion of
Haemadipsa japonica
is dependent on sika deer migration: A case study from Tochigi Prefecture, Japan. Ecol Res 2022. [DOI: 10.1111/1440-1703.12366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kaori Morishima
- Forestry and Forest Products Research Institute Ibaraki Japan
| | - Emiko Fukui
- Department of Agrobiology and Bioresources, School of Agriculture Utsunomiya University Tochigi Japan
| | - Mineaki Aizawa
- Department of Forest Science, School of Agriculture Utsunomiya University Tochigi Japan
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Mattupalli C, Cuenca FP, Shiller JB, Watkins T, Hansen K, Garzon CD, Marek SM, Young CA. Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System. PLANT DISEASE 2022; 106:2105-2116. [PMID: 35156845 DOI: 10.1094/pdis-01-22-0013-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.
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Affiliation(s)
- Chakradhar Mattupalli
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant Pathology, Washington State University, Mount Vernon NWREC, Mount Vernon, WA 98273, U.S.A
| | - Fernanda Proaño Cuenca
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK 74078, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Jason B Shiller
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Scion, Rotorua 3046, New Zealand
| | - Tara Watkins
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Karen Hansen
- Department of Botany, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Carla D Garzon
- Department of Plant Science and Landscape Architecture, Delaware Valley University, Doylestown, PA 18901, U.S.A
| | - Stephen M Marek
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
| | - Carolyn A Young
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, U.S.A
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Ahammad AKS, Asaduzzaman M, Ferdusy T, Islam MM, Wong LL, Rahman MM, Haque MM, Hassan J. Morphogenetic diversity of the selected hatchery populations of an Indian major carp (Labeo rohita, Hamilton, 1822) in the Mymensingh region of Bangladesh. ANIMAL GENE 2022; 25:200131. [DOI: 10.1016/j.angen.2022.200131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
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13
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Shiragaki K, Seko S, Yokoi S, Tezuka T. Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia. PLoS One 2022; 17:e0271091. [PMID: 35802562 PMCID: PMC9269386 DOI: 10.1371/journal.pone.0271091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/24/2022] [Indexed: 11/21/2022] Open
Abstract
Reproductive isolation, including hybrid weakness, plays an important role in the formation of species. Hybrid weakness in Capsicum, the cessation of plant growth, is caused by two complementary dominant genes, A from C. chinense or C. frutescens and B from C. annuum. In the present study, we surveyed whether 94 C. annuum accessions had B or b alleles by crossing with C. chinense having the A allele. Of the 94 C. annuum accessions, five had the B allele, three of which were native to Latin America and two were native to Asia. When combined with previous studies, the percentage of B carriers was 41% in Japan, 13% in Asia excluding Japan, 6% in Latin America, and 0% in Europe and Africa. In addition, 48 accessions of C. annuum from various countries were subjected to SSR analysis. Clades with high percentages of B-carriers were formed in the phylogenetic trees. In the principal coordinate analysis, most B-carriers were localized in a single group, although the group also included b-carriers. Based on these results, we presumed that the B allele was acquired in some C. annuum lines in Latin America, and B-carriers were introduced to the world during the Age of Discovery, as along with the b-carriers.
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Affiliation(s)
- Kumpei Shiragaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Shonosuke Seko
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
| | - Shuji Yokoi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
- Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
- Bioeconomy Research Institute, Research Center for the 21st Century, Osaka Metropolitan University, Osaka, Japan
| | - Takahiro Tezuka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
- Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
- Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai, Osaka, Japan
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14
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Singh P, Mehl HL, Orbach MJ, Callicott KA, Cotty PJ. Genetic Diversity of Aspergillus flavus Associated with Chili in Nigeria and Identification of Haplotypes with Potential in Aflatoxin Mitigation. PLANT DISEASE 2022; 106:1818-1825. [PMID: 35084943 DOI: 10.1094/pdis-07-21-1464-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Dried red chili (Capsicum spp.), a widely produced and consumed spice in Nigeria, is often contaminated by aflatoxins. Aflatoxins are potent mycotoxins of severe health and economic concern worldwide. Aspergillus flavus often contaminates crops with aflatoxins in warm regions; however, not all isolates are aflatoxin producers. Nonaflatoxigenic isolates have potential as biocontrol agents for aflatoxin mitigation. The current study examined the genetic diversity of A. flavus (n = 325) associated with chilies in Nigeria and identified 123 nonaflatoxigenic isolates. The Nigerian A. flavus isolates from chili were diverse at 17 microsatellite loci, with 5 to 36 alleles per locus, and included 152 haplotypes. The isolates that are active ingredients in Aflasafe, registered for aflatoxin biocontrol on maize and groundnuts in Nigeria, did not share haplotypes with the chili isolates. Of the 152 haplotypes, 65% produced aflatoxins in autoclaved maize, some of which (17%) produced >100,000 µg/kg of aflatoxins. Aflatoxins were not detected in 35% of the haplotypes. Cluster amplification pattern assay detected large deletions in the aflatoxin biosynthetic clusters of some (32%) of the nonaflatoxigenic haplotypes. Coinfection of chili with nonaflatoxigenic isolates from chilies (n = 7) and A. aflatoxiformans resulted in a significantly greater average reduction in total aflatoxins compared with that achieved by Aflasafe active ingredient isolates (P < 0.01). These nonaflatoxigenic isolates are a genetic resource for the development of biological control products for aflatoxin mitigation in chilies in Nigeria and should be evaluated under field conditions.
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Affiliation(s)
- Pummi Singh
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, U.S.A
| | | | - Marc J Orbach
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, U.S.A
| | | | - Peter J Cotty
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, U.S.A
- USDA-ARS, Tucson, AZ 85701, U.S.A
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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15
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Assessing the Speciation of Lutjanus campechanus and Lutjanus purpureus through Otolith Shape and Genetic Analyses. FISHES 2022. [DOI: 10.3390/fishes7020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Based on their morphological and genetic similarity, several studies have proposed that Lutjanus campechanus and Lutjanus purpureus are the same species, but there is no confirmed consensus yet. A population-based study concerning otolith shape and genetic analyses was used to evaluate if L. campechanus and L. purpureus are the same species. Samples were collected from populations in the southwestern Gulf of Mexico and the Venezuelan Caribbean. Otolith shape was evaluated by traditional and outline-based geometric morphometrics. Genetic characterization was performed by sequencing the mtDNA control region and intron 8 of the nuclear gene FASD2. The otolith shape analysis did not indicate differences between species. A nested PERMANOVA identified differences in otolith shape for the nested population factor (fishing area) in morphometrics and shape indexes (p = 0.001) and otolith contour (WLT4 anterior zone, p = 0.005 and WLT4 posterodorsal zone, p = 0.002). An AMOVA found the genetic variation between geographic regions to be 10%, while intrapopulation variation was 90%. Network analysis identified an important connection between haplotypes from different regions. A phylogenetic analysis identified a monophyletic group formed by L. campechanus and L. purpureus, suggesting insufficient evolutionary distances between them. Both otolith shape and molecular analyses identified differences, not between the L. campechanus and L. purpureus species, but among their populations, suggesting that western Atlantic red snappers are experiencing a speciation process.
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Antonova EV, Röder MS. Evaluation of the genetic structure of Bromus inermis populations from chemically and radioactively polluted areas using microsatellite markers from closely related species. Int J Radiat Biol 2021; 98:1289-1300. [PMID: 34855571 DOI: 10.1080/09553002.2022.2013569] [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: 10/19/2022]
Abstract
Hypothesis The ecotoxicological and radiobiological effects can be manifested in a decrease in genetic diversity with an increase in toxic and radiation load, in an increase in the frequencies of rare and/or unique (private) alleles in impact samples, and in a decrease in the differentiation of B. inermis populations within each pollution area.Materials and methods We have selected a collection of primers for Bromus inermis, consisting of 21 microsatellite (SSR) loci from B. sterilis, B. tectorum and Triticum aestivum. The level of toxic load (chemically polluted area) was 4-19 conventional units, and the absorbed dose rate (the Kyshtym accident area) varied from 0.153 to 21.5 μGy h-1, which is up to two orders higher than the natural background radiation level (≈ 0.1 μGy h-1).Results Only eight of 21 (38%) of SSR primers showed good transferability and were used for B. inermis population studies from areas of technogenic pollution (heavy metals and radionuclides). We revealed 42 alleles at eight loci, and the number of alleles per locus varied from one to 13 in B. inermis populations. The percentage of polymorphic loci in B. inermis populations was 48.44%, the polymorphism information content (PIC) value was 0.556, and Shannon information index was 0.69 ± 0.3. A total of 22 rare, 14 private and 9 both rare and private alleles were reported for all B. inermis populations. There were no correlations between geographic and genetic distances. Only 6.8% of the genetic variability was distributed among B. inermis populations.Conclusion There was no decrease in genetic diversity ("genetic erosion") found in B. inermis populations growing for a long time under anthropogenic stress. No significant differences in the number of rare and private alleles in the background and impact populations of B. inermis were found. The smooth brome is characterized by low differentiation of the populations. Possible reasons for this phenomenon are discussed.
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Affiliation(s)
- Elena V Antonova
- Laboratory of Population Radiobiology, Institute of Plant & Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta str. 202, Ekaterinburg 620144, Russia
| | - Marion S Röder
- Group of Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Stadt Seeland OT Gatersleben 06466, Germany
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17
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Genetic Diversity and Differentiation of Pedunculate Oak (Quercus robur L.) Populations at the Southern Margin of Its Distribution Range—Implications for Conservation. DIVERSITY 2021. [DOI: 10.3390/d13080371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding intraspecific genetic variation is one of the principal requirements for the evaluation of tree species capacity to cope with intensive climatic changes, as well as designing long-term conservation programs. Herein, we evaluated the genetic diversity and genetic structure of seven pedunculate oak (Quercus robur L.) populations, located at the southern margin of its distribution range on the Balkan Peninsula (Serbia). The objective of the study was to propose future in situ conservation measures aimed at protection of pedunculate oak adaptive and neutral genetic diversity at the species rear-edge. Genetic diversity and structure were estimated using twelve highly polymorphic simple sequence repeat (SSR) markers. The mean expected heterozygosity (He) was 0.769, allelic richness (AR) 9.63, and private allelic richness (pAR) 0.79, indicating high genetic diversity in the studied populations. Genetic differentiation among the populations was low (Fst = 0.032). Structure analysis, the unweighted pair group method with arithmetic mean (UPGMA) showed the existence of two gene pools unrelated to the populations’ area of occurrence. Taking into consideration the results of the current study and previous conservation activities on the pedunculate oak in Serbia, as well as the importance of rear-edge populations in the long-term conservation of the species genetic diversity, we suggested establishing three additional gene conservation units for securing long-term sustainability of the species.
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Poommouang A, Kriangwanich W, Buddhachat K, Brown JL, Piboon P, Chomdej S, Kampuansai J, Mekchay S, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Genetic diversity in a unique population of dugong (Dugong dugon) along the sea coasts of Thailand. Sci Rep 2021; 11:11624. [PMID: 34078973 PMCID: PMC8172547 DOI: 10.1038/s41598-021-90947-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/12/2021] [Indexed: 11/09/2022] Open
Abstract
Dugong (Dugong dugon) populations have been shrinking globally, due in large part to habitat fragmentation, degradation and ocean pollution, and today are listed as Vulnerable by the IUCN. Thus, determining genetic diversity in the remaining populations is essential for conservation planning and protection. In this study, measures of inter-simple sequence repeat (ISSR) markers and mtDNA D-loop typing were used to evaluate the genetic diversity of 118 dugongs from skin samples of deceased dugongs collected in Thai waters over a 29-year period. Thirteen ISSR primers revealed that dugongs from the Andaman Sea and Gulf of Thailand exhibited more genetic variation in the first 12 years of the study (1990-2002) compared to the last decade (2009-2019). Dugongs from the Andaman Sea, Trang, Satun and some areas of Krabi province exhibited greater diversity compared to other coastal regions of Thailand. Eleven haplotypes were identified, and when compared to other parts of the world (235 sequences obtained from NCBI), five clades were apparent from a total 353 sequences. Moreover, dugongs from the Andaman Sea were genetically distinct, with a separate haplotype belonging to two clades found only in Thai waters that separated from other groups around 1.2 million years ago. Genetic diversity of dugongs in present times was less than that of past decades, likely due to increased population fragmentation. Because dugongs are difficult to keep and breed in captivity, improved in situ conservation actions are needed to sustain genetically healthy wild populations, and in particular, the specific genetic group found only in the Andaman Sea.
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Affiliation(s)
- Anocha Poommouang
- Animal Bone and Joint Research Laboratory, Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Wannapimol Kriangwanich
- Animal Bone and Joint Research Laboratory, Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai, 50100, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Janine L Brown
- Smithsonian Conservation Biology Institute, Center for Species Survival, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Promporn Piboon
- Animal Bone and Joint Research Laboratory, Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | | | | | - Korakot Nganvongpanit
- Animal Bone and Joint Research Laboratory, Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.
- Excellence Center in Veterinary Bioscience, Chiang Mai, 50100, Thailand.
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Genetic diversity and population structure of wild and domesticated black tiger shrimp (Penaeus monodon) broodstocks in the Indo-Pacific regions using consolidated mtDNA and microsatellite markers. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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von Takach B, Penton CE, Murphy BP, Radford IJ, Davies HF, Hill BM, Banks SC. Population genomics and conservation management of a declining tropical rodent. Heredity (Edinb) 2021; 126:763-775. [PMID: 33664461 PMCID: PMC8102610 DOI: 10.1038/s41437-021-00418-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (FST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.
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Affiliation(s)
- Brenton von Takach
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Cara E. Penton
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Brett P. Murphy
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia ,grid.1043.60000 0001 2157 559XNESP Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Ian J. Radford
- grid.452589.70000 0004 1799 3491Department of Biodiversity, Conservation and Attractions, Kununurra, WA Australia
| | - Hugh F. Davies
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia ,grid.1043.60000 0001 2157 559XNESP Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
| | - Brydie M. Hill
- grid.483876.60000 0004 0394 3004Flora and Fauna Division, Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, Northern Territory Australia
| | - Sam C. Banks
- grid.1043.60000 0001 2157 559XResearch Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory Australia
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21
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Stelmach K, Macko-Podgórni A, Allender C, Grzebelus D. Genetic diversity structure of western-type carrots. BMC PLANT BIOLOGY 2021; 21:200. [PMID: 33902460 PMCID: PMC8077844 DOI: 10.1186/s12870-021-02980-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/15/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Carrot is a crop with a wide range of phenotypic and molecular diversity. Within cultivated carrots, the western gene pool comprises types characterized by different storage root morphology. First western carrot cultivars originated from broad-based populations. It was followed by intercrosses among plants representing early open-pollinated cultivars, combined with mass phenotypic selection for traits of interest. Selective breeding improved root uniformity and led to the development of a range of cultivars differing in root shape and size. Based on the root shape and the market use of cultivars, a dozen of market types have been distinguished. Despite their apparent phenotypic variability, several studies have suggested that western cultivated carrot germplasm was genetically non-structured. RESULTS Ninety-three DcS-ILP markers and 2354 SNP markers were used to evaluate the structure of genetic diversity in the collection of 78 western type open-pollinated carrot cultivars, each represented by five plants. The mean percentage of polymorphic loci segregating within a cultivar varied from 31.18 to 89.25% for DcS-ILP markers and from 45.11 to 91.29% for SNP markers, revealing high levels of intra-cultivar heterogeneity, in contrast to its apparent phenotypic stability. Average inbreeding coefficient for all cultivars was negative for both DcS-ILP and SNP, whereas the overall genetic differentiation across all market classes, as measured by FST, was comparable for both marker systems. For DcS-ILPs 90-92% of total genetic variation could be attributed to the differences within the inferred clusters, whereas for SNPs the values ranged between 91 to 93%. Discriminant Analysis of Principal Components enabled the separation of eight groups cultivars depending mostly on their market type affiliation. Three groups of cultivars, i.e. Amsterdam, Chantenay and Imperator, were characterized by high homogeneity regardless of the marker system used for genotyping. CONCLUSIONS Both marker systems used in the study enabled detection of substantial variation among carrot plants of different market types, therefore can be used in germplasm characterization and analysis of genome relationships. The presented results likely reveal the actual genetic diversity structure within the western carrot gene pool and point at possible discrepancies within the cultivars' passport data.
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Affiliation(s)
- Katarzyna Stelmach
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425, Kraków, Poland
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425, Kraków, Poland
| | | | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425, Kraków, Poland.
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22
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Genetic Diversity and Association Analysis among Germplasms of Diospyros kaki in Zhejiang Province Based on SSR Markers. FORESTS 2021. [DOI: 10.3390/f12040422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In subtropical to temperate regions, persimmon (Diospyros kaki Thunb.) is an economically important fruit crop cultivated for its edible fruits. Persimmons are distributed abundantly and widely in Zhejiang Province, representing a valuable resource for the breeding of new cultivars and studying the origin and evolution of persimmon. In this study, we elucidated the genetic structures and diversity patterns of 179 persimmon germplasms from 16 different ecologic populations in Zhejiang Province based on the analysis of 17 SSR markers. The results show that there was a medium degree of genetic diversity for persimmon found in Zhejiang Province. With the exception of the Tiantai Mountain and Xin’an River populations, we found extensive gene exchange had occurred among the other populations. The 179 D. kaki germplasms from the 16 populations could be separated into three distinct clusters (I, II, and III) with a higher mean pairwise genetic differentiation index (FST) (0.2714). Nearly all samples of Cluster-I were distributed inland. Cluster-II and Cluster-III contained samples that were widely distributed throughout Zhejiang Province including all samples from the coastal populations and the Northeast Plain populations. In addition, we performed association mapping with nine traits (fruit crude fiber content, fruit calcium content, fruit water content, fruit longitudinal diameter, fruit aspect ratio, seed width, seed length, leaf aspect ratio, and number of lateral veins) using these markers. This led to the identification of 13 significant marker–trait associations (MTAs; p < 0.00044, 0.1/228) using a general linear model, of which, six MTAs with a correlation coefficient (R2) >10% were consistently represented in the general linear model with p < 0.00044 in the two models. The genetic structures and diversity patterns of the persimmon germplasms revealed in this study will provide a reference for the efficient conservation and further utilization of persimmon germplasms. The MTAs identified in this study will be useful for future marker-assisted breeding of persimmon.
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Tesson SVM, Sha Y. Population connectivity, dispersal, and swimming behavior in Daphnia. Ecol Evol 2021; 11:2873-2885. [PMID: 33767843 PMCID: PMC7981204 DOI: 10.1002/ece3.7246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/23/2022] Open
Abstract
The water flea Daphnia has the capacity to respond rapidly to environmental stressors, to disperse over large geographical scales, and to preserve its genetic material by forming egg banks in the sediment. Spatial and temporal distributions of D. magna have been extensively studied over the last decades using behavioral or genetic tools, although the correlation between the two has rarely been the focus. In the present study, we therefore investigated the population genetic structure and behavioral response to a lethal threat, ultraviolet radiation (UVR), among individuals from two different water bodies. Our results show two genetic populations with moderate gene flow, highly correlated with geographical location and with inheritable traits through generations. However, despite the strong genetic differences between populations, we show homogeneous refuge demand between populations when exposed to the lethal threat solar UVR.
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Affiliation(s)
- Sylvie V. M. Tesson
- Department of BiologyAarhus UniversityAarhusDenmark
- Department of BiologyLund UniversityLundSweden
| | - Yongcui Sha
- Department of BiologyLund UniversityLundSweden
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Ye JW, Wu HY, Fu MJ, Zhang P, Tian B. Insights Into the Significance of the Chinense Loess Plateau for Preserving Biodiversity From the Phylogeography of Speranskia tuberculata (Euphorbiaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:604251. [PMID: 33613598 PMCID: PMC7889603 DOI: 10.3389/fpls.2021.604251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
The significance of the Chinese Loess Plateau (CLP) in maintaining biodiversity for northern China has rarely been shown, as previous phylogeographic studies are mostly woody species and they have revealed that Quaternary refugia are mainly located in mountain regions. We selected a drought-enduring endemic herb, Speranskia tuberculata (Euphorbiaceae), to determine its glacial refugia and postglacial demographic history. To this end, we sampled 423 individuals from 38 populations covering its entire geographic distribution. Three chloroplast DNA (cpDNA) fragments, two low-copy nuclear genes, and six nuclear microsatellites (nSSRs) were used and supplemented with ecological niche modeling (ENM) to infer the phylogeographic history of this species. Populations with private haplotypes and high haplotype diversity of cpDNA are mainly located in the CLP or scattered around northeastern China and the coastal region. Spatial expansion, detected using a neutrality test and mismatch distribution, may have resulted in a widely distributed ancestral cpDNA haplotype, especially outside of the CLP. For nuclear DNA, private haplotypes are also distributed mainly in the CLP. In nSSRs, STRUCTURE clustering identified two genetic clusters, which are distributed in the west (western cluster) and east (eastern cluster), respectively. Many populations belonged, with little to no admixture, to the western cluster while (hardly) pure populations of the eastern cluster were barely found. Genetic differentiation is significantly correlated with geographic distance, although genetic diversity is uniformly distributed. ENM suggests that the distribution of S. tuberculata has recently expanded northwards from the southern CLP, whereas it has experienced habitat loss in the south. Thus, S. tuberculata populations probably survived the last glacial maximum (LGM) in the southern CLP and experienced post-glacial expansion. Wind-dispersed pollen could bring the majority of genotypes to the front during spatial expansion, resulting in uniformly distributed genetic diversity. Based on evidence from molecular data and vegetation and climate changes since the LGM, we conclude that drought-enduring species, especially herbaceous species, are likely to have persisted in the CLP during the LGM and to have experienced expansion to other regions in northern China.
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Affiliation(s)
- Jun-Wei Ye
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Meng-Jiao Fu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Pei Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Page RB, Conarroe C, Quintanilla D, Palomo A, Solis J, Aguilar A, Bezold K, Sackman AM, Marsh DM. Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone. Ecol Evol 2020; 10:9948-9967. [PMID: 33005356 PMCID: PMC7520177 DOI: 10.1002/ece3.6653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 11/21/2022] Open
Abstract
Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk-particularly in range-restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red-backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.
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Affiliation(s)
- Robert B. Page
- Department of Life SciencesTexas A&M University‐San AntonioSan AntonioTXUSA
| | - Claire Conarroe
- Department of BiologyWashington and Lee UniversityLexingtonVAUSA
| | - Diana Quintanilla
- Department of Life SciencesTexas A&M University‐San AntonioSan AntonioTXUSA
| | - Andriea Palomo
- Department of Life SciencesTexas A&M University‐San AntonioSan AntonioTXUSA
| | - Joshua Solis
- Department of Life SciencesTexas A&M University‐San AntonioSan AntonioTXUSA
| | - Ashley Aguilar
- Department of Life SciencesTexas A&M University‐San AntonioSan AntonioTXUSA
| | - Kelly Bezold
- Department of BiologyWashington and Lee UniversityLexingtonVAUSA
| | | | - David M. Marsh
- Department of BiologyWashington and Lee UniversityLexingtonVAUSA
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Singh P, Callicott KA, Orbach MJ, Cotty PJ. Molecular Analysis of S-morphology Aflatoxin Producers From the United States Reveals Previously Unknown Diversity and Two New Taxa. Front Microbiol 2020; 11:1236. [PMID: 32625180 PMCID: PMC7315800 DOI: 10.3389/fmicb.2020.01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/14/2020] [Indexed: 01/12/2023] Open
Abstract
Aflatoxins are highly toxic carcinogens that detrimentally influence profitability of agriculture and the health of humans and domestic animals. Several phylogenetically distinct fungi within Aspergillus section Flavi have S-morphology (average sclerotial size < 400 μm), and consistently produce high concentrations of aflatoxins in crops. S-morphology fungi have been implicated as important etiologic agents of aflatoxin contamination in the United States (US), but little is known about the diversity of these fungi. The current study characterized S-morphology fungi (n = 494) collected between 2002 and 2017, from soil and maize samples, in US regions where aflatoxin contamination is a perennial problem. Phylogenetic analyses based on sequences of the calmodulin (1.9 kb) and nitrate reductase (2.1 kb) genes resolved S-morphology isolates from the US into four distinct clades: (1) Aspergillus flavus S-morphotype (89.7%); (2) Aspergillus agricola sp. nov. (2.4%); (3) Aspergillus texensis (2.2%); and (4) Aspergillus toxicus sp. nov. (5.7%). All four S-morphology species produced high concentrations of aflatoxins in maize at 25, 30, and 35°C, but only the A. flavus S-morphotype produced unacceptable aflatoxin concentrations at 40°C. Genetic typing of A. flavus S isolates using 17 simple sequence repeat markers revealed high genetic diversity, with 202 haplotypes from 443 isolates. Knowledge of the occurrence of distinct species and haplotypes of S-morphology fungi that are highly aflatoxigenic under a range of environmental conditions may provide insights into the etiology, epidemiology, and management of aflatoxin contamination in North America.
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Affiliation(s)
- Pummi Singh
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Kenneth A. Callicott
- United States Department of Agriculture, Agricultural Research Service, Tucson, AZ, United States
| | - Marc J. Orbach
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Peter J. Cotty
- School of Food Science and Engineering, Ocean University of China, Qingdao, China
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Developing novel microsatellite markers by NGS technology for Rhopilema nomadica, an invasive jellyfish. Mol Biol Rep 2020; 47:4821-4825. [PMID: 32424518 DOI: 10.1007/s11033-020-05533-0] [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: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
Twelve microsatellite loci, obtained by whole genome sequencing approach, were developed and validated for the rhizostomatid jellyfish Rhopilema nomadica, the most pernicious invasive species in the Mediterranean Sea. A sample of 40 specimens collected at six locations along the Mediterranean coast of Israel were genotyped and all loci presented suitable outcomes to population genetic studies, revealing 5-19 alleles/locus with clean and reproducible amplifications. Observed and expected heterozygosity ranged 0.0.353 to 0.971 and 0.335 to 0.870, respectively, and the fixation index (inbreeding coefficient) and the polymorphic information content (PIC) ranged between - 0.190 and 0.240 and 0.32 to 0.858, respectively. The new set of microsatellite loci will be used to study long-term changes in the population genetic parameters of this invasive species.
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von Takach Dukai B, Peakall R, Lindenmayer DB, Banks SC. The influence of fire and silvicultural practices on the landscape-scale genetic structure of an Australian foundation tree species. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01245-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Crates R, Olah G, Adamski M, Aitken N, Banks S, Ingwersen D, Ranjard L, Rayner L, Stojanovic D, Suchan T, von Takach Dukai B, Heinsohn R. Genomic impact of severe population decline in a nomadic songbird. PLoS One 2019; 14:e0223953. [PMID: 31647830 PMCID: PMC6812763 DOI: 10.1371/journal.pone.0223953] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/02/2019] [Indexed: 01/27/2023] Open
Abstract
Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.
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Affiliation(s)
- Ross Crates
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - George Olah
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Marcin Adamski
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Nicola Aitken
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Sam Banks
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | | | - Louis Ranjard
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Laura Rayner
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Tomasz Suchan
- W. Szafer institute of Botany, Polish Academy of Sciences, Krakow, Poland
| | - Brenton von Takach Dukai
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
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