1
|
Kreling SES, Reese EM, Cavalluzzi OM, Bozzi NB, Messinger R, Schell CJ, Long RA, Prugh LR. City divided: Unveiling family ties and genetic structuring of coyotes in Seattle. Mol Ecol 2024; 33:e17427. [PMID: 38837263 DOI: 10.1111/mec.17427] [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: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non-urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.
Collapse
Affiliation(s)
- Samantha E S Kreling
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Ellen M Reese
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Olivia M Cavalluzzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Natalee B Bozzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Riley Messinger
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, California, USA
| | | | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| |
Collapse
|
2
|
Soares LS, Freitas LB. The phylogeographic journey of a plant species from lowland to highlands during the Pleistocene. Sci Rep 2024; 14:3825. [PMID: 38360894 PMCID: PMC10869790 DOI: 10.1038/s41598-024-53414-4] [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: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Phylogeographic history refers to how species evolve and diversify in response to historical, ecological, and demographic factors. The climate fluctuation during the Pleistocene period marked a crucial time in shaping many species' distribution and genetic structure, particularly those from southern South American grasslands. This work investigated the phylogeographic history of a highland grassland, Petunia altiplana T. Ando & Hashim. (Solanaceae), its diversity, and geographic distribution using a population genomic approach based on RAD-seq data. Our results indicated that, during the Pleistocene, when the grasslands expanded to highlands, the lowland populations of P. altiplana reached the higher open fields, enlarging their geographic distribution. We found that the P. altiplana genetic diversity followed the geographic division into eastern (E) and western (WE) population groups, with a subtle division in the E group regarding the Pelotas River headwater. The results also showed that isolation by distance was the main divergence pattern, with elevation playing a pivotal role in shaping WE and E groups. Our findings indicated that lowland-adapted populations quickly colonized highlands during the late Pleistocene.
Collapse
Affiliation(s)
- Luana Sousa Soares
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil.
| |
Collapse
|
3
|
Ashley KA, Annis SL. Population Structure and Reproductive Biology of Monilinia vaccinii-corymbosi in Vaccinium angustifolium in Maine. PLANT DISEASE 2024; 108:182-189. [PMID: 37552166 DOI: 10.1094/pdis-07-22-1684-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: 08/09/2023]
Abstract
The fungus Monilinia vaccinii-corymbosi (Mvc) causes mummy berry disease in blueberries including lowbush blueberry, Vaccinium angustifolium, and is a significant pathogen of concern for Maine lowbush blueberry growers. This disease is typically managed with fungicides or by burning of plant debris containing overwintering pseudosclerotia. The population structure of Mvc in various fields in Maine was investigated using microsatellites and isolates collected from three stages in the Mvc lifecycle. The impacts of management strategies were also examined. A high level of genetic diversity was observed in Mvc from 12 lowbush blueberry fields with 199 unique multilocus haplotypes (MLHs) occurring in an original sample of 232 isolates. Twelve private alleles, including six private alleles with frequencies above 0.05, which indicated gene flow, were observed in six out of 12 fields. The population of Mvc in Maine as a whole is mostly a sexual, outcrossing population, as was seen in the diversity of MLHs and low amounts of linkage disequilibrium, although some apothecia appear to result from selfing. Three fields appear to have some clonal reproduction but were not strictly clonal, as multiple MLHs were noted in these fields. Management does not appear to affect population structure, and Mvc may be one large statewide population in Maine.
Collapse
Affiliation(s)
| | - Seanna L Annis
- School of Biology and Ecology, University of Maine, Orono, ME 04469
| |
Collapse
|
4
|
Sadeghpour N, Asadi-Gharneh HA, Nasr-Esfahani M, Khankahdani HH, Golabadi M. Assessing genetic diversity and population structure of Iranian melons ( Cucumis melo) collection using primer pair markers in association with resistance to Fusarium wilt. FUNCTIONAL PLANT BIOLOGY : FPB 2023; 50:347-362. [PMID: 36944375 DOI: 10.1071/fp22131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/12/2023] [Indexed: 05/03/2023]
Abstract
We evaluated genetic diversity and population structure of Iranian melons (Cucumis melo L.) using combinations of 35 primer pairs: 15 Simple-Sequence-Repeats (SSR); 10 Inter-Simple-Sequence-Repeats (ISSR); and 10 Sequence-related amplified polymorphism (SRAP) markers in association with resistance to melon Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis (FOM ). Genetic similarity was determined by simple matching coefficient (SSM) and dendrogram by clustering-analysis with unweighted pair groups using arithmetic averages (UPGMA). By combining ISSR-SSR-SRAP markers, a high degree of variation among the melons was detected. The mean polymorphism information content (PIC), marker index (MI), effective-number of alleles (I), expected heterozygosity (H), and Nei's gene diversity parameters were 0.392, 0.979, 1.350, 0.551 and 0.225, respectively. According to MI, PIC, I, H, and Nei indices evaluation, ISSR6, ISSR9, SRAP3, SRAP5, SSR3 and SSR6 had the best performance in genetic diversity of the related melons population. The 35 primers yielded a total of 264 bands, of which 142 showed polymorphism. Clustering of genotypes based on resistance to Fusarium wilt, and comparison with grouping on SSR, SRAP and ISSR marker revealed a significant compliance between disease severity and molecular marker dendrograms. Thus, increasing the number of molecular markers for genetic diversity provides a powerful tool for future agricultural and conservation tasks.
Collapse
Affiliation(s)
- Neda Sadeghpour
- Horticulture Department, College of Agriculture, Esfahan Branch (Khorasgan), Islamic Azad University, Isfahan, Iran
| | - Hossein Ali Asadi-Gharneh
- Horticulture Department, College of Agriculture, Esfahan Branch (Khorasgan), Islamic Azad University, Isfahan, Iran
| | - Mehdi Nasr-Esfahani
- Plant Protection Research Department, Esfahan Agriculture and Natural Resource Research and Education Center, AREEO, Esfahan, Iran
| | - Hamed Hassanzadeh Khankahdani
- Horticulture Crops Research Department, Hormozgan Agricultural and Natural Resources Research and Education Center, AREEO, Bandar Abbas, Iran
| | - Maryam Golabadi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| |
Collapse
|
5
|
Pereira AG, da Silva Ferreira MF, da Silveira TC, Soler-Guilhen JH, Canal GB, Alves LB, de Almeida FAN, Gaiotto FA, Ferreira A. Patterns of genetic diversity and structure of a threatened palm species (Euterpe edulis Arecaceae) from the Brazilian Atlantic Forest. Heredity (Edinb) 2022; 129:161-168. [PMID: 35697755 PMCID: PMC9411632 DOI: 10.1038/s41437-022-00549-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
The detection of distribution patterns of genetic diversity of plant and animal species has contributed to the understanding of biodiversity and evolutionary history of the Atlantic Forest. We used microsatellite markers to access the genetic diversity and structure of 26 populations and 527 adult individuals of Euterpe edulis, a native palm which is an important food resource for fauna and is intensively exploited due to economic reasons. We found high genetic diversity and inbreeding in all populations analyzed. We report highest rates of inbreeding for this species, which could reflect the anthropic impacts of selective cutting, fragmentation, and change in foraging behavior from pollinators and less availability and mobility of large dispersers. We detected by STRUCTURE, two genetic groups, Northern and Southern, which divide the Brazilian Atlantic Forest geographically. These groups have low genetic admixtures, but we found a region of lineage hybridization in the contact zone with low recent gene flow. Distribution pattern of this species corroborates results from previous studies reporting the Last Glacial Maximum (LGM) have shaped the structuring of the species through movements of forests' expansion and contraction. The STRUCTURE analysis of each group revealed the presence of genetic subgroups with low rates of recurrent gene flow. Southern subgroups have higher rates of admixtures than the Northern subgroups, revealing greater historical connectivity of forests in this region.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Fernanda Amato Gaiotto
- Department of Biological Sciences, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Adésio Ferreira
- Department of Agronomy, Universidade Federal do Espírito Santo, Alegre, Brazil
| |
Collapse
|
6
|
Vargas-Peralta CE, Araneda C, Galindo-Sánchez CE, Larraín MA, Del Río-Portilla MA, Lafarga-De la Cruz F. Species identification in Haliotis genus from the northeastern Pacific Ocean using genome-wide RAD-SNPs. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108979] [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]
|
7
|
Limongi Andrade R, Pico-Mendoza J, Morillo E, Buitrón J, Meneses S, Navarrete B, Pinoargote M, Carrasco B. Molecular characterization of mahogany tree ( Swietenia macrophylla King, Meliaceae) in the remnant natural forest of Ecuador. NEOTROPICAL BIODIVERSITY 2022. [DOI: 10.1080/23766808.2022.2080334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Ricardo Limongi Andrade
- Instituto Nacional de Investigaciones Agropecuarias-Estación experimental Portoviejo, Manabí, Ecuador
| | - José Pico-Mendoza
- Carrera de Agronomía, Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Lodana-Manabí- Ecuador
| | - Eduardo Morillo
- Instituto Nacional de Investigaciones Agropecuarias-Estación experimental Santa Catalina-Laboratorio de biotecnología, Quito, Ecuador
| | - Johanna Buitrón
- Instituto Nacional de Investigaciones Agropecuarias-Estación experimental Santa Catalina-Laboratorio de biotecnología, Quito, Ecuador
| | - Santiago Meneses
- Instituto Nacional de Investigaciones Agropecuarias-Estación experimental Santa Catalina-Laboratorio de biotecnología, Quito, Ecuador
| | - Bernardo Navarrete
- Instituto Nacional de Investigaciones Agropecuarias-Estación experimental Portoviejo, Manabí, Ecuador
| | - Miryan Pinoargote
- Carrera de Agronomía, Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Lodana-Manabí- Ecuador
| | | |
Collapse
|
8
|
Dooley KB, Thabang Madisha M, Strümpher S, Ehlers K. Forensic genetic value of 27 Y-STR loci (Y-Filer® Plus) in the South African population. Sci Justice 2022; 62:358-364. [PMID: 35598928 DOI: 10.1016/j.scijus.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 10/18/2022]
Abstract
South Africa has one of the highest rape statistics in the world, with an average of 117 rapes reported daily. Y-STR genotyping is becoming a popular tool in the analysis of DNA evidence collected after a crime of a sexual nature has been committed, but has yet to be implemented in South Africa's forensic laboratories. This study aimed to investigate the forensic value of the 27 Yfiler™ Plus loci in the South African population. A total of 271 samples from the African, Asian/Indian, Mixed Ancestry1, and Caucasian populations at the University of the Free State in Bloemfontein, South Africa were amplified and analysed using ThermoFisher Scientific's Yfiler™ Plus PCR Amplification kit. Of the 271 samples, 261 were identified to be unique, with an overall discrimination capacity of 98.15%. Discrimination capacities ranged from 91.67% for the Asian/Indian population to 100% for the Mixed Ancestry population. The haplotype diversity across the four populations is 0.9999, with an average gene diversity across all loci of 0.717. The forensic parameters estimated in this study provide evidence for the potential use of the commercial Yfiler™ Plus PCR amplification kit in a forensic application in South Africa.
Collapse
Affiliation(s)
- Kyla Bianca Dooley
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M Thabang Madisha
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Sonja Strümpher
- ThermoFisher Scientific, Fairland, Johannesburg 2195, South Africa
| | - Karen Ehlers
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa.
| |
Collapse
|
9
|
Genetic composition of queen conch (Lobatus gigas) population on Pedro Bank, Jamaica and its use in fisheries management. PLoS One 2021; 16:e0245703. [PMID: 33819265 PMCID: PMC8021194 DOI: 10.1371/journal.pone.0245703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/11/2021] [Indexed: 11/19/2022] Open
Abstract
The queen conch fishery in Jamaica is sustained by Pedro Bank, which is the main harvesting site located approximately 80 km south-west from Kingston. Due to its relative size, Pedro Bank has been subdivided into zones for management purposes by the Fisheries Division and the Veterinary Services Division. Understanding whether these sub-divisions reflect different sub-populations is critical for managing exploitation levels because fisheries management must demonstrate that harvesting does not endanger the future viability of the population as queen conch are on Appendix II of the Convention in Trade in Endangered Species of Wild Fauna and Flora (CITES). This determination is essential for the continued export to international markets such as the European Union. Two hundred and eight samples were collected across the entire Pedro Bank and were genetically characterized using nine polymorphic microsatellite loci. Population structure analysis for Lobatus gigas from Pedro Bank yielded low but significant values (FST = 0.009: p = 0.006) and suggested a high magnitude of gene flow indicative of a fit and viable population throughout the bank. Analysis of molecular variance (AMOVA) indicated a 100% variation within individual samples with little variation (0.9%) between populations. In contrast pairwise genetic comparisons identified significant differences between populations located to the south eastern and eastern region of the bank to those in the central and western locations. Bayesian clustering analysis also indicated the likelihood of two population sub-divisions (K = 2) on Pedro Bank. The results provided evidence of a weak but significant population structure which has crucial implications for the fishing industry as it suggests the use of ecosystem based management (EBM) in setting quotas to promote sustainable harvesting of L. gigas within each monitoring zone on Pedro Bank.
Collapse
|
10
|
Queiroz MCV, de Oliveira FA, de Souza AP, Sato ME. Development of microsatellite markers for the predatory mite Phytoseiulus macropilis and cross-amplification in three other species of phytoseiid mites. EXPERIMENTAL & APPLIED ACAROLOGY 2021; 83:1-12. [PMID: 33200337 DOI: 10.1007/s10493-020-00572-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Phytoseiid mites are efficient predators of mites and small pest insects. Understanding the dispersion and distribution pattern of phytoseiid mites is essential to promote the conservation of these natural enemies and support their use in biological control. Population genetic studies using molecular markers such as microsatellites have proved to be extremely informative to address questions about population structure and dispersion patterns of predatory mites. The objective of this work was to develop specific microsatellite markers for the predatory mite Phytoseiulus macropilis, aiming at improving field dispersion studies. For this purpose, the genomic DNA was extracted from the whole body of a pool of 260 adult females and used to build the genomic microsatellites-enriched library, using biotinylated probes (CT)8 and (GT)8. In total 26 pairs of primers were synthesized and screened across 30 adult females of P. macropilis for characterization. Seven loci were polymorphic, revealing from two to six alleles per locus. Cross amplifications were successfully obtained in the species Phytoseiulus persimilis, Amblyseius swirskii and Proprioseiopsis sp. The molecular markers obtained are the first developed for P. macropilis-they are effective for the detection and quantification of genetic variation, and show high transferability, thus can be used in genetic and molecular studies of this and other species of the same genus and also of close genera.
Collapse
Affiliation(s)
- Maria Cristina Vitelli Queiroz
- Laboratório de Acarologia, Instituto Biológico, APTA, Rodovia Heitor Penteado km 3.5, Caixa Postal 70, Campinas, SP, 13001-970, Brazil.
| | - Fernanda Ancelmo de Oliveira
- Plant Biology Department, Biology Institute, University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP, CEP 13083-970, Brazil
| | - Anete Pereira de Souza
- Plant Biology Department, Biology Institute, University of Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, Campinas, SP, CEP 13083-970, Brazil
| | - Mario Eidi Sato
- Laboratório de Acarologia, Instituto Biológico, APTA, Rodovia Heitor Penteado km 3.5, Caixa Postal 70, Campinas, SP, 13001-970, Brazil
| |
Collapse
|
11
|
The Genetic Diversity of Cranberry Crop Wild Relatives, Vaccinium macrocarpon Aiton and V. oxycoccos L., in the US, with Special Emphasis on National Forests. PLANTS 2020; 9:plants9111446. [PMID: 33114692 PMCID: PMC7716231 DOI: 10.3390/plants9111446] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/03/2022]
Abstract
Knowledge of the genetic diversity in populations of crop wild relatives (CWR) can inform effective strategies for their conservation and facilitate utilization to solve agricultural challenges. Two crop wild relatives of the cultivated cranberry are widely distributed in the US. We studied 21 populations of Vaccinium macrocarpon Aiton and 24 populations of Vaccinium oxycoccos L. across much of their native ranges in the US using 32 simple sequence repeat (SSR) markers. We observed high levels of heterozygosity for both species across populations with private alleles ranging from 0 to 26. For V. macrocarpon, we found a total of 613 alleles and high levels of heterozygosity (HO = 0.99, HT = 0.75). We also observed high numbers of alleles (881) and levels of heterozygosity (HO = 0.71, HT = 0.80) in V. oxycoccos (4x). Our genetic analyses confirmed the field identification of a native population of V. macrocarpon on the Okanogan-Wenatchee National Forest in the state of Washington, far outside the previously reported range for the species. Our results will help to inform efforts of the United States Department of Agriculture Agricultural Research Service (USDA-ARS) and the United States Forest Service (USFS) to conserve the most diverse and unique wild cranberry populations through ex situ preservation of germplasm and in situ conservation in designated sites on National Forests.
Collapse
|
12
|
Dar AH, Kumar S, Mukesh M, Ahmad SF, Singh DV, Sharma RK, Ghosh AK, Singh B, Rahman JU, Sodhi M. Genetic characterization and population structure of different coat colour variants of Badri cattle. Mol Biol Rep 2020; 47:8485-8497. [PMID: 33063149 DOI: 10.1007/s11033-020-05890-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/03/2020] [Indexed: 11/25/2022]
Abstract
The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon's indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon's indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, - 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed first-hand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities.
Collapse
Affiliation(s)
- Aashaq Hussain Dar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Sanjay Kumar
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Manishi Mukesh
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India
| | - Sheikh Firdous Ahmad
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Bareilly, Uttar Pradesh, 243122, India
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Dev Vrat Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Rabendra Kumar Sharma
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Ashis Kumar Ghosh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Balwinder Singh
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Javid Ur Rahman
- Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India
| | - Monika Sodhi
- ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, 132001, India.
| |
Collapse
|
13
|
Edwards TP, Trigiano RN, Ownley BH, Windham AS, Wyman CR, Wadl PA, Hadziabdic D. Genetic Diversity and Conservation Status of Helianthus verticillatus, an Endangered Sunflower of the Southern United States. Front Genet 2020; 11:410. [PMID: 32499812 PMCID: PMC7243268 DOI: 10.3389/fgene.2020.00410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in Helianthus verticillatus (whorled sunflower). This endangered, wild relative of the common sunflower, Helianthus annuus, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for H. verticillatus, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of H. verticillatus individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between H. verticillatus collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of H. verticillatus populations in Georgia. Our results can underpin an original recovery plan for H. verticillatus that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.
Collapse
Affiliation(s)
- Tyler P Edwards
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Bonnie H Ownley
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Alan S Windham
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Christopher R Wyman
- Department of Plant Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Phillip A Wadl
- United States Department of Agriculture, Agriculture Research Service, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| |
Collapse
|
14
|
Abstract
The year 2020 marks the 50th anniversary of Theoretical Population Biology. This special issue examines the past and continuing contributions of the journal. We identify some of the most important developments that have taken place in the pages of TPB, connecting them to current research and to the numerous forms of significance achieved by theory in population biology.
Collapse
|
15
|
|
16
|
Ahsan T, Urmi NJ, Sajib AA. Heterogeneity in the distribution of 159 drug-response related SNPs in world populations and their genetic relatedness. PLoS One 2020; 15:e0228000. [PMID: 31971968 PMCID: PMC6977754 DOI: 10.1371/journal.pone.0228000] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/03/2020] [Indexed: 12/25/2022] Open
Abstract
Interethnic variability in drug response arises from genetic differences associated with drug metabolism, action and transport. These genetic variations can affect drug efficacy as well as cause adverse drug reactions (ADRs). We retrieved drug-response related single nucleotide polymorphism (SNP) associated data from databases and analyzed to elucidate population specific distribution of 159 drug-response related SNPs in twenty six populations belonging to five super-populations (African, Admixed Americans, East Asian, European and South Asian). Significant interpopulation differences exist in the minor (variant) allele frequencies (MAFs), linkage disequilibrium (LD) and haplotype distributions among these populations. 65 of the drug-response related alleles, which are considered as minor (variant) in global population, are present as the major alleles (frequency ≥0.5) in at least one or more populations. Populations that belong to the same super-population have similar distribution pattern for majority of the variant alleles. These drug response related variant allele frequencies and their pairwise LD measure (r2) can clearly distinguish the populations in a way that correspond to the known evolutionary history of human and current geographic distributions, while D' cannot. The data presented here may aid in identifying drugs that are more appropriate and/or require pharmacogenetic testing in these populations. Our findings emphasize on the importance of distinct, ethnicity-specific clinical guidelines, especially for the African populations, to avoid ADRs and ensure effective drug treatment.
Collapse
Affiliation(s)
- Tamim Ahsan
- Department of Genetic Engineering & Biotechnology, Bangabandhu Sheikh Mujibur Rahman Maritime University, Dhaka, Bangladesh
| | | | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
17
|
da Silva PA, Fassini CG, Sampaio LS, Dequigiovanni G, Zucchi MI, Wulff NA. Genetic Diversity of ' Candidatus Liberibacter asiaticus' Revealed by Short Tandem Repeats and Prophage Typing Indicates Population Homogeneity in Brazil. PHYTOPATHOLOGY 2019; 109:960-971. [PMID: 30694114 DOI: 10.1094/phyto-08-18-0295-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
'Candidatus Liberibacter asiaticus' is the most common huanglongbing-associated bacteria, being present in Asia, South, Central, and North America. Genomic approaches enabled sequencing of 'Ca. L. asiaticus' genomes, allowing for a broader assessment of its genetic variability with the application of polymerase chain reaction (PCR)-based tools such as microsatellite or short tandem repeat (STR) analysis. Although these tools contributed to a detailed analysis of strains from Japan, China, and the United States, Brazilian strains were analyzed in either too few samples with several STRs or in several strains with only a single microsatellite and a single PCR marker. We used 573 'Ca. L. asiaticus' strains, mainly collected from São Paulo State (SPS), in our genetic analyses, employing three STRs and several prophage PCR markers. STR revealed a homogeneous population regardless of sampling year or geographic regions of SPS. Thirty-eight haplotypes were recognized with a predominance of VNTR_005 higher than 10 repeats, with VNTR_002 and VNTR_077 containing 11 and 8 repeats, respectively. This haplotype is indicated as class HE, which comprised 80.28% of strains. Classes HA and HB, predominant in Florida, were not found. A new genomic organization in the junction of prophages SC2 and SC1 is prevalent in Brazilian strains, indicating gene rearrangement and a widespread occurrence of a type 1 prophage as well as the presence of a type 2-like prophage. Our results indicate that 'Ca. L. asiaticus' populations are homogeneous and harbor a new genomic organization in prophages type 1 and 2.
Collapse
Affiliation(s)
| | - Camila Giacomo Fassini
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Laís Simões Sampaio
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
| | - Gabriel Dequigiovanni
- 2 Agência Paulista de Tecnologia dos Agronegócios, Polo Regional Centro-Sul, Rodovia SP 127, km 30, Piracicaba, SP, 13400-970 Brazil; and
| | - Maria Imaculada Zucchi
- 2 Agência Paulista de Tecnologia dos Agronegócios, Polo Regional Centro-Sul, Rodovia SP 127, km 30, Piracicaba, SP, 13400-970 Brazil; and
| | - Nelson Arno Wulff
- 1 Departamento de Pesquisa & Desenvolvimento-Fundecitrus, Araraquara, SP, 14807-040, Brazil
- 3 PPG Biotecnologia, IQ/UNESP Araraquara, SP, 14800-060, Brazil
| |
Collapse
|
18
|
Sajeela KA, Gopalakrishnan A, Basheer VS, Mandal A, Bineesh KK, Grinson G, Gopakumar SD. New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean. Mol Phylogenet Evol 2019; 136:53-64. [PMID: 30954588 DOI: 10.1016/j.ympev.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 03/09/2019] [Accepted: 04/03/2019] [Indexed: 01/03/2023]
Abstract
Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.
Collapse
Affiliation(s)
- K A Sajeela
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India.
| | - A Gopalakrishnan
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
| | - V S Basheer
- Peninsular and Marine Fish Genetic Resources (PMFGR) Centre-NBFGR, CMFRI, Kochi 682 018, Kerala, India
| | - A Mandal
- Rajiv Gandhi Centre for Aquaculture (RGCA), Sirkali 609 113, Nagapattinam, Tamil Nadu, India
| | - K K Bineesh
- Zoological Survey of India, Andaman and Nicobar Regional Centre, Haddo, Port Blair 744 102, India
| | - G Grinson
- Central Marine Fisheries Research Institute, Kochi 682 018, Kerala, India
| | | |
Collapse
|
19
|
Di Giambattista L, Fulvo A, Fabiani A, Bonanni J, Carrión JE, Gentile G. Molecular data exclude current hybridization between iguanas Conolophus marthae and C. subcristatus on Wolf Volcano (Galápagos Islands). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1114-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
20
|
Abstract
Signatures of recent historical admixture are ubiquitous in human populations. We present a mechanistic model of admixture with two source populations, encompassing recurrent admixture periods and study the distribution of admixture fractions for finite but arbitrary genome size. We provide simulation-based methods to estimate the introgression parameters and discuss the implications of reaching stationarity on estimability of parameters when there are recurrent admixture events with different rates.
Collapse
Affiliation(s)
- Erkan Ozge Buzbas
- Department of Statistical Science, University of Idaho, United States.
| | - Paul Verdu
- CNRS/MNHN/Université Paris Diderot/Sorbonne Paris Cité, France
| |
Collapse
|
21
|
Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation. PLoS One 2018; 13:e0196969. [PMID: 29738577 PMCID: PMC5940214 DOI: 10.1371/journal.pone.0196969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022] Open
Abstract
The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H. obsoletus. Host-plant use was confirmed for Convolvulus arvensis, Urtica dioica, Vitex agnus-castus and Crepis foetida. Mitochondrial genetic analysis showed sympatric occurrence of three phylogenetic lineages that were ecologically delineated by host-plant preference, but were morphologically inseparable. Nuclear data supported the existence of three genetic groups (Evanno’s ΔK(3) = 803.72) with average genetic membership probabilities > 90%. While populations associated with C. arvensis and U. dioica form a homogenous group, populations affiliated with V. agnus-castus and C. foetida constitute two independent plant-associated lineages. The geographical signal permeating the surveyed populations indicated complex diversification processes associated with host-plant selection and likely derived from post-glacial refugia in the eastern Mediterranean. This study provides evidence for cryptic species diversification within H. obsoletus sensu lato: i) consistent mitochondrial differentiation (1.1–1.5%) among host-associated populations in syntopy and in geographically distant areas, ii) nuclear genetic variance supporting mitochondrial data, and iii) average mitochondrial genetic distances among host-associated meta-populations are comparable to the most closely related, morphologically distinguishable species, i.e., Hyalesthes thracicus (2.1–3.3%).
Collapse
|
22
|
Llorens TM, Ayre DJ, Whelan RJ. Anthropogenic fragmentation may not alter pre-existing patterns of genetic diversity and differentiation in perennial shrubs. Mol Ecol 2018. [PMID: 29533477 DOI: 10.1111/mec.14552] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Many plant species have pollination and seed dispersal systems and evolutionary histories that have produced strong genetic structuring. These genetic patterns may be consistent with expectations following recent anthropogenic fragmentation, making it difficult to detect fragmentation effects if no prefragmentation genetic data are available. We used microsatellite markers to investigate whether severe habitat fragmentation may have affected the structure and diversity of populations of the endangered Australian bird-pollinated shrub Grevillea caleyi R.Br., by comparing current patterns of genetic structure and diversity with those of the closely related G. longifolia R.Br. that has a similar life history but has not experienced anthropogenic fragmentation. Grevillea caleyi and G. longifolia showed similar and substantial population subdivision at all spatial levels (global F'ST = 0.615 and 0.454; Sp = 0.039 and 0.066), marked isolation by distance and large heterozygous deficiencies. These characteristics suggest long-term effects of inbreeding in self-compatible species that have poor seed dispersal, limited connectivity via pollen flow and undergo population bottlenecks because of periodic fires. Highly structured allele size distributions, most notably in G. caleyi, imply historical processes of drift and mutation were important in isolated subpopulations. Genetic diversity did not vary with population size but was lower in more isolated populations for both species. Through this comparison, we reject the hypothesis that anthropogenic fragmentation has impacted substantially on the genetic composition or structure of G. caleyi populations. Our results suggest that highly self-compatible species with limited dispersal may be relatively resilient to the genetic changes predicted to follow habitat fragmentation.
Collapse
Affiliation(s)
- Tanya M Llorens
- Centre for Sustainable Ecosystem Solutions and School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - David J Ayre
- Centre for Sustainable Ecosystem Solutions and School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Robert J Whelan
- Centre for Sustainable Ecosystem Solutions and School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia
| |
Collapse
|
23
|
Zannella C, Carucci F, Aversano R, Prohaska T, Vingiani S, Carputo D, Adamo P. Genetic and geochemical signatures to prevent frauds and counterfeit of high-quality asparagus and pistachio. Food Chem 2017; 237:545-552. [DOI: 10.1016/j.foodchem.2017.05.158] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 11/27/2022]
|
24
|
Ywasaki Lima J, Machado FB, Farro APC, Barbosa LDA, da Silveira LS, Medina-Acosta E. Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil. PLoS One 2017; 12:e0183645. [PMID: 28837691 PMCID: PMC5570289 DOI: 10.1371/journal.pone.0183645] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/08/2017] [Indexed: 11/19/2022] Open
Abstract
Sotalia guianensis is a small dolphin that is vulnerable to anthropogenic impacts. Along the Brazilian Atlantic coast, this species is threatened with extinction. A prioritized action plan for conservation strategies relies on increased knowledge of the population. The scarcity of studies about genetic diversity and assessments of population structure for this animal have precluded effective action in the region. Here, we assessed, for the first time, the genetic differentiation at 14 microsatellite loci in 90 S. guianensis specimens stranded on the southeastern Atlantic coast of the State of Espírito Santo, Brazil. We estimated population parameters and structure, measured the significance of global gametic disequilibrium and the intensity of non-random multiallelic interallelic associations and constructed a provisional synteny map using Bos taurus, the closest terrestrial mammal with a reference genome available. All microsatellite loci were polymorphic, with at least three and a maximum of ten alleles each. Allele frequencies ranged from 0.01 to 0.97. Observed heterozygosity ranged from 0.061 to 0.701. The mean inbreeding coefficient was 0.103. Three loci were in Hardy-Weinberg disequilibrium even when missing genotypes were inferred. Although 77 of the 91 possible two-locus associations were in global gametic equilibrium, we unveiled 13 statistically significant, sign-based, non-random multiallelic interallelic associations in 10 two-locus combinations with either coupling (D' values ranging from 0.782 to 0.353) or repulsion (D' values -0.517 to -1.000) forces. Most of the interallelic associations did not involve the major alleles. Thus, for either physically or non-physically linked loci, measuring the intensity of non-random interallelic associations is important for defining the evolutionary forces at equilibrium. We uncovered a small degree of genetic differentiation (FST = 0.010; P-value = 0.463) with a hierarchical clustering into one segment containing members from the southern and northern coastal regions. The data thus support the scenario of little genetic structure in the population of S. guianensis in this geographic area.
Collapse
Affiliation(s)
- Juliana Ywasaki Lima
- Laboratory of Morphology and Animal Pathology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
- * E-mail: (JYL); (EMA)
| | - Filipe Brum Machado
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Ana Paula Cazerta Farro
- Laboratory of Genetics and Animal Conservation, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo, Brazil
| | | | - Leonardo Serafim da Silveira
- Laboratory of Morphology and Animal Pathology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
- * E-mail: (JYL); (EMA)
| |
Collapse
|
25
|
Gariboldi MC, Túnez JI, Failla M, Hevia M, Panebianco MV, Paso Viola MN, Vitullo AD, Cappozzo HL. Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin ( Pontoporia blainvillei). Ecol Evol 2016; 6:8764-8776. [PMID: 28035267 PMCID: PMC5192793 DOI: 10.1002/ece3.2596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/07/2016] [Accepted: 10/19/2016] [Indexed: 12/25/2022] Open
Abstract
The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F‐statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex‐biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long‐term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.
Collapse
Affiliation(s)
- María Constanza Gariboldi
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad MaimónidesCiudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
| | - Juan Ignacio Túnez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Grupo de Estudios en Ecología de Mamíferos Departamento de Ciencias Básicas Universidad Nacional de Luján Luján Argentina
| | | | | | - María Victoria Panebianco
- Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina
| | - María Natalia Paso Viola
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología y Conservación de Vida Silvestre Centro Austral de Investigaciones Científicas (CADIC) Ushuaia Argentina
| | - Alfredo Daniel Vitullo
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad MaimónidesCiudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina
| | - Humberto Luis Cappozzo
- Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico (CEBBAD) Universidad Maimónides Ciudad Autónoma de Buenos Aires Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires Argentina; Laboratorio de Ecología Comportamiento y Mamíferos Marinos Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" Ciudad Autónoma de Buenos Aires Argentina; Fundación de Historia Natural Félix de Azara Universidad Maimónides Ciudad Autónoma de Buenos Aires Argentina
| |
Collapse
|
26
|
Velando A, Morán P, Romero R, Fernández J, Piorno V. Invasion and eradication of the American mink in the Atlantic Islands National Park (NW Spain): a retrospective analysis. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1326-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
27
|
Adams CE, Bean CW, Dodd JA, Down A, Etheridge EC, Gowans ARD, Hooker O, Knudsen R, Lyle AA, Winfield IJ, Præbel K. Inter and intra-population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus, a rare freshwater fish in Scotland. JOURNAL OF FISH BIOLOGY 2016; 88:580-594. [PMID: 26748995 DOI: 10.1111/jfb.12855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
This study revealed between-lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (FST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common-garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (FST = 0·001-0·024) and evidence of private alleles related to the basin structure of the lake. Within-lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.
Collapse
Affiliation(s)
- C E Adams
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - C W Bean
- Scottish Natural Heritage, Caspian House, Clydebank Business Park, Clydebank, Glasgow G81 2NR, U.K
| | - J A Dodd
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A Down
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - E C Etheridge
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A R D Gowans
- Environment Agency, Ghyll Mount, Gillan Way, Penrith 40 Business Park, Penrith, Cumbria CA11 9BP, U.K
| | - O Hooker
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - R Knudsen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - A A Lyle
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - I J Winfield
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, U.K
| | - K Præbel
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| |
Collapse
|
28
|
Sanarana Y, Visser C, Bosman L, Nephawe K, Maiwashe A, van Marle-Köster E. Genetic diversity in South African Nguni cattle ecotypes based on microsatellite markers. Trop Anim Health Prod 2015; 48:379-85. [PMID: 26611262 DOI: 10.1007/s11250-015-0962-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
The Nguni cattle breed is a landrace breed adapted to different ecological regions of South Africa. A number of ecotypes are recognised based on phenotype within the breed, but it is not known if they are genetically distinct. In this study, molecular characterisation was performed on Makhathini (MAK), Pedi (PED), Shangaan (SHA) and Venda (VEN) Nguni cattle ecotypes. Two Nguni cattle populations, not kept as separate ecotypes, from the University of Fort Hare (UFH) and Agricultural Research Council Loskop South farm (LOS) were also included. Genotypic data was generated for 189 unrelated Nguni cattle selected based on pedigree records using 22 microsatellite markers. The expected heterozygosity values varied from 69 % (UFH) to 72 % (PED) with a mean number of alleles ranging from 6.0 to 6.9. The F ST estimate demonstrated that 4.8 % of the total genetic variation was due to the genetic differentiation between the populations and 92.2 % accounted for differences within the populations. The genetic distances and structure analysis revealed the closest relationship between MAK, PEDI and SHA ecotypes, followed by SHA and VEN. The UFH population clustered with the MAK ecotype, indicating that they are more genetically similar, while the LOS cattle grouped as a distinct cluster. Results suggest that the genetic differentiation between the PED and SHA ecotypes is low and can be regarded as one ecotype based on limited genetic differences. The results of this study can be applied as a point of reference for further genetic studies towards conservation of Nguni cattle ecotypes.
Collapse
Affiliation(s)
- Yandisiwe Sanarana
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.,Agricultural Research Council, Private Bag X2, Irene, 0062, South Africa
| | - Carina Visser
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Lydia Bosman
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Khathutshelo Nephawe
- Department of Animal Science, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | | | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| |
Collapse
|
29
|
Kwong M, Pemberton TJ. Sequence differences at orthologous microsatellites inflate estimates of human-chimpanzee differentiation. BMC Genomics 2014; 15:990. [PMID: 25407736 PMCID: PMC4253012 DOI: 10.1186/1471-2164-15-990] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/30/2014] [Indexed: 02/06/2023] Open
Abstract
Background Microsatellites---contiguous arrays of 2–6 base-pair motifs---have formed the cornerstone of population-genetic studies for over two decades. Their genotype data typically takes the form of PCR fragment lengths obtained using locus-specific primer pairs to amplify the genomic region encompassing the microsatellite. Recently, we reported a dataset of 5,795 human and 84 chimpanzee individuals with genotypes at 246 human-derived autosomal microsatellites as a resource to facilitate interspecies comparisons. A major assumption underlying this dataset is that PCR amplicons at orthologous microsatellites are commensurable between species. Results We find this assumption to be frequently incorrect owing to discordance in microsatellite organization and variability, as well as nontrivial length imbalances caused by small species-specific indels in microsatellite flanking sequences. Converting PCR fragment lengths into the repeat numbers they represent at 138 microsatellites whose organization and variability was found to be highly similar in both species, we show that interspecies incommensurability among PCR amplicons can inflate FST and DPS estimates by up to 10.6%. Separate investigations of determinants of microsatellite variability in humans and chimpanzees uncover similar patterns with mean and maximum numbers of repeats, as well as numbers and ranges of distinct alleles, all important factors in predicting heterozygosity. In contrast, across microsatellites, numbers of repeats were significantly smaller in chimpanzees than in humans, while numbers and ranges of distinct alleles were instead larger. Conclusions Our findings have fundamental implications for interspecies comparisons using microsatellites and offer new opportunities for more accurate comparisons of patterns of human and chimpanzee genetic variation in numerous areas of application. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-990) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
30
|
Torutaeva E, Asanaliev A, Prieto-Linde ML, Zborowska A, Ortiz R, Bryngelsson T, Garkava-Gustavsson L. Evaluation of microsatellite-based genetic diversity, protein and mineral content in chickpea accessions grown in Kyrgyzstan. Hereditas 2014; 151:81-90. [PMID: 25363275 DOI: 10.1111/hrd2.00042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 08/31/2014] [Indexed: 11/30/2022] Open
Abstract
The genetic diversity of 23 chickpea accessions representing Kyrgyz landraces and cultivars, ICARDA breeding lines, Spanish and Turkish cultivars was characterized using nine microsatellite (SSR) markers which generated a total of 122 alleles. The number of alleles (Na) per locus varied from 9 to 20. The observed heterozygosity (Ho) ranged between 0.05 and 0.43 (average 0.13) whereas both the expected heterozygosity (He) and polymorphic information content (PIC) ranged from 0.71 to 0.90 (average 0.83). Analysis of molecular variance (AMOVA) showed that 62% of the total genetic variation was found within accessions while the remaining 38% was found among accessions. Principal coordinate analysis (PCoA) indicated the presence of two groups. The two Kyrgyz cultivars were found apart from these groups. Cluster analysis generally confirmed the results of PCoA and also separated the Kyrgyz cultivars from the subcluster formed by Kyrgyz landraces and the subclusters formed by breeding lines from ICARDA along with landraces from Turkey and Spain. In addition, protein content and mineral concentration were determined. Protein content and mineral concentrations for Ca, S, Mg, P, K, Fe, Mn, Cu and Zn varied significantly among accessions. The results show that Kyrgyz germplasm provides a source of diversity for improvement of chickpea.
Collapse
Affiliation(s)
- Elnura Torutaeva
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Alnarp, Sweden; Kyrgyz National Agrarian University, Bishkek, Kyrgyzstan.
| | | | | | | | | | | | | |
Collapse
|
31
|
Omondi BA, van den Berg J, Masiga D, Schulthess F. Molecular markers reveal narrow genetic base and culturing-associated genetic drift in Teretrius nigrescens Lewis populations released for the biological control of the larger grain borer in Africa. BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:143-154. [PMID: 24308303 DOI: 10.1017/s0007485313000552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In biological control, successful establishment of a natural enemy species depends on its adaptability in the introduced range including its ability to re-establish desired ecological interactions with the pest. These are affected by genetic parameters hitherto largely unresolved in biological control. The larger grain borer (LGB), Prostephanus truncatus, an invasive species from meso-America, is the most important post-harvest pest of maize in Africa. We studied the genetic structure of Teretrius nigrescens, a predatory beetle previously released for the control of the pest in Africa, to test the hypothesis that establishment patterns were a result of ecotype-environment mismatch and to follow up on our earlier reports of distinct lineages of the predator. We studied 13 populations of T. nigrescens, using 16 polymorphic microsatellite markers. Five genetic populations with a hierarchical structure and significant isolation by distance were detected. The most diverse population was found in southern Mexico, consistent with earlier lineage coexistence observations. Populations introduced to Africa maintained genetic similarity to local geographic populations of their area of origin. The more successful Benin releases were also more genetically diverse. Loss of rare alleles and a higher frequency of existing private alleles in some populations indicated population expansions following bottleneck events. Sustainable biological control should accommodate pest and natural enemy species, and monitor genetic changes associated with introduction and release.
Collapse
Affiliation(s)
- B A Omondi
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - J van den Berg
- School of Environmental Sciences and Development, North West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - D Masiga
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| | - F Schulthess
- International Centre of Insect Physiology and Ecology, P. O. Box 30772-00100, Nairobi, Kenya
| |
Collapse
|
32
|
Population structure in a comprehensive genomic data set on human microsatellite variation. G3-GENES GENOMES GENETICS 2013; 3:891-907. [PMID: 23550135 PMCID: PMC3656735 DOI: 10.1534/g3.113.005728] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the past two decades, microsatellite genotypes have provided the data for landmark studies of human population-genetic variation. However, the various microsatellite data sets have been prepared with different procedures and sets of markers, so that it has been difficult to synthesize available data for a comprehensive analysis. Here, we combine eight human population-genetic data sets at the 645 microsatellite loci they share in common, accounting for procedural differences in the production of the different data sets, to assemble a single data set containing 5795 individuals from 267 worldwide populations. We perform a systematic analysis of genetic relatedness, detecting 240 intra-population and 92 inter-population pairs of previously unidentified close relatives and proposing standardized subsets of unrelated individuals for use in future studies. We then augment the human data with a data set of 84 chimpanzees at the 246 loci they share in common with the human samples. Multidimensional scaling and neighbor-joining analyses of these data sets offer new insights into the structure of human populations and enable a comparison of genetic variation patterns in chimpanzees with those in humans. Our combined data sets are the largest of their kind reported to date and provide a resource for use in human population-genetic studies.
Collapse
|