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Hong YK, Kim KR, Kim KS, Bang IC. The Impact of Weir Construction in Korea's Nakdong River on the Population Genetic Variability of the Endangered Fish Species, Rapid Small Gudgeon ( Microphysogobio rapidus). Genes (Basel) 2023; 14:1611. [PMID: 37628662 PMCID: PMC10454870 DOI: 10.3390/genes14081611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness (A = 18.3-18.4, AR = 13.8) compared to those from DC (A = 11.8, AR = 11.5). The observed heterozygosity among the fish examined ranged from HO = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy-Weinberg equilibrium (HWE) (p < 0.05). Despite having the largest effective population size (Ne = 175 and 157, respectively), the fish sampled from UN and LN showed the highest inbreeding coefficients (FIS = 0.056-0.053, respectively), which were highly significant (p < 0.01). In contrast, the fish sampled from DC exhibited the smallest effective population size (Ne = 61) and showed an inbreeding coefficient close to zero (p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341-0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation (FST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of FST between fish sampled from the Nam and Deokcheon Rivers revealed significant values (p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area.
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Affiliation(s)
- Yang-Ki Hong
- Natural History Division, National Science Museum, Daejeon 34143, Republic of Korea;
| | - Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea;
| | - Keun-Sik Kim
- Restoration Research Team (Fishes/Amphibians & Reptiles), Research Center for Endangered Species, National Institute of Ecology, Yeongyang-gun 36531, Republic of Korea;
| | - In-Chul Bang
- Department of Biosystem, Soonchunhyang University, Asan 31538, Republic of Korea
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Castillo-Morales CA, Sáenz-Arroyo A, Castellanos-Morales G, Ruíz-Montoya L. Mitochondrial DNA and local ecological knowledge reveal two lineages of leatherback turtle on the beaches of Oaxaca, Mexico. Sci Rep 2023; 13:8836. [PMID: 37258549 DOI: 10.1038/s41598-023-33931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
Despite multiple conservation efforts of the Mexican government, the leatherback turtle is at serious risk of extinction. In this study, we investigated the possible presence of a genetic bottleneck that could prevent the recovery of this species and compared these findings with those of the olive ridley turtle, which is in true recovery. Our results confirmed that a demographic change occurred in the past and the presence of two different leatherback turtle lineages that diverged approximately 13.5 million years ago. Local ecological knowledge (LEK) also described the presence of these two lineages and warned that one is at higher risk of extinction than the other. Genetic analysis confirmed 124 mutations between the two lineages, and much lower genetic diversity in one lineage than the other. Our study highlights and substantiates the power of mixing LEK, environmental history, and genetics to better understand conservation challenges of highly threatened species such as the leatherback turtle. Moreover, we report a new lineage of the leatherback turtle which may represent a distinct species. Future studies should focus on morphological, ecological, biogeographical, evolutionary and conservation perspectives for the analysis of the new lineage.
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Affiliation(s)
- Carlos Abraham Castillo-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur (ECOSUR), Carretera Panamericana y Periférico Sur S/N, Barrio de María Auxiliadora, San Cristóbal de las Casas, Chiapas, Mexico
| | - Andrea Sáenz-Arroyo
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur (ECOSUR), Carretera Panamericana y Periférico Sur S/N, Barrio de María Auxiliadora, San Cristóbal de las Casas, Chiapas, Mexico.
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (C3-UNAM), Mexico City, Mexico.
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa (ECOSUR-Villahermosa), Carretera Villahermosa-Reforma km 15.5, Ranchería Guineo 2a sección, Villahermosa, Tabasco, Mexico
| | - Lorena Ruíz-Montoya
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur (ECOSUR), Carretera Panamericana y Periférico Sur S/N, Barrio de María Auxiliadora, San Cristóbal de las Casas, Chiapas, Mexico
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Pérez-Alquicira J, Wehncke EV, García-Loza GA, Carstens BC, Domínguez CA, Pérez-Ishiwara R, Molina-Freaner FE, Zamora-Tavares MDP, Rico Y, Cabrera-Toledo D, Vargas-Ponce O, Rodríguez A, Ezcurra E. Geographic isolation and long-distance gene flow influence the genetic structure of the blue fan palm Brahea armata (Arecaceae). JOURNAL OF PLANT RESEARCH 2023; 136:277-290. [PMID: 36905462 DOI: 10.1007/s10265-023-01445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The formation of the Baja California Peninsula (BCP) has impacted the microevolutionary dynamics of different species in ways that depend on biological traits such as dispersal capacity. Plants with relatively low levels of vagility have exhibited high genetic divergence between the BCP and Continental mainland. Brahea armata (Arecaceae) is a palm species inhabiting the northern part of the BCP and Sonora; its distribution occurs in isolated oases of vegetation. We aimed to evaluate the influence of the formation of the BCP on the genetic structure of B. armata using nuclear microsatellites and chloroplast markers (cpDNA) to compare patterns of genetic diversity and structure with previous published studies. Because gene flow through seeds is usually more limited compared to pollen flow, we expect to find stronger genetic structure at (cpDNA) than at nuclear markers. Moreover, larger genetic structure might also be explained by the smaller effective population size of cpDNA. We analyzed six microsatellite markers and two cpDNA regions. The main results indicated high levels of genetic differentiation among isolated populations located in the BCP, while low genetic differentiation was found between southern populations of the BCP and Sonora, suggesting long distance gene flow. In contrast, chloroplast markers indicated high levels of genetic structure between BCP and Sonora populations, suggesting asymmetrical gene flow between pollen (measured by nuclear microsatellites) and seed (cpDNA markers). This study provides valuable information on genetic diversity of B. armata that can be relevant for conservation and management; and develops microsatellites markers that can be transferred to other Brahea species.
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Affiliation(s)
- Jessica Pérez-Alquicira
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico.
- CONACYT, Ciudad de Mexico, Mexico.
| | - Elisabet V Wehncke
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, 62209, Cuernavaca, Morelos, Mexico
| | - Gustavo A García-Loza
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology and Museum of Biological Diversity, The Ohio State University, 1315 Kinnear Rd., Columbus, OH, 43212, USA
| | - César A Domínguez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Rubén Pérez-Ishiwara
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, Mexico
| | - Francisco E Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, 83250, Hermosillo, Sonora, Mexico
| | - María Del Pilar Zamora-Tavares
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Sánchez Padilla 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Yessica Rico
- CONACYT, Ciudad de Mexico, Mexico
- Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Pátzcuaro, Michoacán, Mexico
| | - Dánae Cabrera-Toledo
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Ofelia Vargas-Ponce
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Aarón Rodríguez
- Departamento de Botánica Y Zoología, Instituto de Botánica, Centro Universitario de Ciencias Biológicas Y Agropecuarias, Universidad de Guadalajara, Ramón Padilla Sanchez 2100, Las Agujas, 45200, Zapopan, Jalisco, Mexico
| | - Exequiel Ezcurra
- Department of Botany and Plant Sciences, University of California, 2142 Batchelor Hall, Riverside, CA, 92521, USA
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Nouri-Aiin M, Connolly S, Keough C, Smigelsky AJ, Wen Y, Howland J, Schall JJ, Görres JH. Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis. PeerJ 2022; 10:e13622. [PMID: 35855901 PMCID: PMC9288164 DOI: 10.7717/peerj.13622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/02/2022] [Indexed: 01/17/2023] Open
Abstract
The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction, but with a great number of genotypes for each species, and the mix of triploid and diploid individuals could be explained if the worms have been sexually reproductive, with the switch to the uniparental system only recently (or even if sexual reproduction is episodic). Last, a large number of microsatellite loci were recovered for each species and there sequence and suggested PCR primers are provided for free use by other researchers.
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Affiliation(s)
- Maryam Nouri-Aiin
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Samantha Connolly
- Plant Biology Department, University of Vermont, Burlington, VT, United States of America
| | - Cheryl Keough
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Annie Jean Smigelsky
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Yiyi Wen
- Environmental Science, Rubinstein School of the Environment, University of Vermont, Burlington, VT, United States of America
| | - Jeremy Howland
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
| | - Jos. J. Schall
- Department of Biology, University of Vermont, Burlington, VT, United States of America
| | - Josef H. Görres
- Plant and Soil Science Department, University of Vermont, Burlington, VT, United States of America
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Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing. Mol Biol Rep 2021; 48:4273-4283. [PMID: 34057686 DOI: 10.1007/s11033-021-06442-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.
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Cruz-Salazar B, Ruiz-Montoya L. Population genetics of the common opossum, Didelphis marsupialis (Marsupialia: Didelphimorphia: Didelphidae), in southeastern Mexico. STUDIES ON NEOTROPICAL FAUNA AND ENVIRONMENT 2020. [DOI: 10.1080/01650521.2020.1844971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Bárbara Cruz-Salazar
- Consejo Nacional de Ciencia y Tecnología-Universidad Autónoma de Tlaxcala, Centro Tlaxcala de Biología de la Conducta, La Loma de Xicohténcatl, Mexico
| | - Lorena Ruiz-Montoya
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Mexico
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Cruz-Salazar B, García-Bautista M, Ruiz-Montoya L. Genetic Structure Associated with the Ecological Traits of Four Species of Phyllostomid Bats Inhabiting Selva El Ocote Biosphere Reserve, Chiapas, México. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Bárbara Cruz-Salazar
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Maricela García-Bautista
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Lorena Ruiz-Montoya
- Consejo Nacional de Ciencia y Tecnología, Universidad Autónoma de Tlaxcala, Carretera Federal Puebla-Tlaxcala Km 1.5, La Loma Xicohténcatl, CP 90062, Tlaxcala de Xicohténcatl, Tlaxcala, México
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Keller EL, Connolly ST, Görres JH, Schall JJ. Genetic diversity of an invasive earthworm, Lumbricus terrestris, at a long-term trading crossroad, the Champlain Valley of Vermont, USA. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02215-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Restrepo-Escobar N, Márquez EJ. Microsatellite loci development for three catfish species from northwestern South America. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The Neotropical catfish species Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus are important fishery resources in Colombia that show historical declines in their capture. This study used next-generation sequencing with 454 FLX technology (Roche Applied Science) and bioinformatics analysis to develop between 18 and 24 microsatellite loci for these species. The novel microsatellite loci showed high values of polymorphic information content -PIC (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876), and the average number of alleles/locus ranged from 7-15 for A. pardalis, 9-30 for P. grosskopfii and 5-14 for S. cuspicaudus. The average observed and expected heterozygosities were respectively, 0.757 ± 0.035 and 0.834 ± 0.015 for A. pardalis; 0.596 ± 0.040 and 0.881 ± 0.009 for P. grosskopfii; and 0.747 ± 0.031 and 0.757 ± 0.025 for S. cuspicaudus. For future studies, these loci can be useful to estimate the genetic diversity and population structure in these three Neotropical catfishes.
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Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula. Genes Genomics 2019; 42:165-178. [PMID: 31797315 DOI: 10.1007/s13258-019-00886-8] [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: 07/22/2019] [Accepted: 11/03/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions. OBJECTIVES To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius. METHODS Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus. RESULTS A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used. CONCLUSION Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.
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Mandel JR, Major CK, Bayer RJ, Moore JE. Clonal diversity and spatial genetic structure in the long-lived herb, Prairie trillium. PLoS One 2019; 14:e0224123. [PMID: 31634380 PMCID: PMC6802849 DOI: 10.1371/journal.pone.0224123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/07/2019] [Indexed: 02/03/2023] Open
Abstract
Combining population genetic studies with demographic surveys in long-lived clonal herbs can yield insight into the population dynamics of clonal plant populations. In this study, we assayed clonal diversity and spatial genetic structure in a population of a long-lived understory herb, Trillium recurvatum, that has been the focus of a demographic study spanning 26 years at the Meeman Biological Station in Memphis, Tennessee, USA. Using a set of five newly developed simple sequence repeat markers first reported here, we assessed 1) the extent of clonal diversity within the Meeman site, 2) the degree to which genetic diversity varies with stage class (juvenile, non-flowering, and flowering adults) at this site, 3) whether there is spatial genetic structure at the Meeman site, and 4) how measures of genetic diversity and inbreeding at the Meeman site compare to two additional nearby populations. Along with these analyses, we calculated and compared traditional population genetic metrics with information theory-based diversity indices. Although clonal propagation was present, the focal population displayed moderate levels of clonal diversity comprising 81 genets from the 174 individuals sampled. In the focal site, we also found that genetic diversity was highest in the flowering stage class when compared to the non-flowering and juvenile classes. We report that genets exhibited spatial genetic structure in the focal site exhibiting values for the Sp statistic of 0.00199 for linear distance and 0.0271 for log distance. Measures of unbiased gene diversity and the inbreeding coefficient were comparable across the sampled populations. Our results provide complementary genetic data to previous demographic studies in T. recurvatum, and these findings provide data for future studies aimed at integrating the degree of clonality, genetic variation, and population dynamics in this species. Our findings suggest that T. recurvatum at the focal Meeman site displays higher levels of sexual reproduction than were previously suggested, and spatial genetic structure estimates were comparable to other plant species with mixed and outcrossing mating strategies.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States of America
- Center for Biodiversity, The University of Memphis, Memphis, TN, United States of America
- Edward J. Meeman Biological Station, Millington, TN, United States of America
- * E-mail:
| | - C. Kendall Major
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States of America
| | - Randall J. Bayer
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States of America
- Edward J. Meeman Biological Station, Millington, TN, United States of America
| | - James E. Moore
- Edward J. Meeman Biological Station, Millington, TN, United States of America
- Department of Biology, Christian Brothers University, Memphis, TN, United States of America
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Sikdar P, Mazzola M, Xiao CL. Genetic and Pathogenic Characterization of Phacidiopycnis washingtonensis from Apple and Pacific Madrone from the Western United States. PHYTOPATHOLOGY 2019; 109:469-479. [PMID: 30156500 DOI: 10.1094/phyto-10-17-0358-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phacidiopycnis washingtonensis is the cause of speck rot of apple and leaf blight of Pacific madrone in Washington State. In total, 314 isolates were collected from apple production areas in eastern Washington and Pacific madrone in western Washington. Using eight microsatellite markers designed in this study, 58 unique multilocus haplotypes were identified. Only one of the haplotypes was shared between the apple and Pacific madrone populations. Analysis of molecular variance showed no genetic differentiation between the apple and Pacific madrone populations. Genetic variation was present within each subpopulation of apple from different geographic locations. The apple population possessed higher genotypic diversity than the Pacific madrone population, suggesting that isolates from apple may represent an older population and could have been introduced into the native habitat of Pacific madrone. P. washingtonensis likely reproduces asexually because populations examined in this study were not in linkage equilibrium. In pathogenicity tests, representative isolates from apple and Pacific madrone all incited leaf blight on Pacific madrone and speck rot on apple fruit regardless of their host of origin. Overall, our findings indicate that the P. washingtonensis population in Washington State is largely asexual, with high genotypic flow and that apple, crabapple, and Pacific madrone could serve as sources of P. washingtonensis inoculum for these hosts.
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Affiliation(s)
- P Sikdar
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
| | - M Mazzola
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
| | - C L Xiao
- First author: Department of Plant Pathology, Washington State University, Pullman 99164; second author: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tree Fruit Research Laboratory, 1104 N. Western Ave., Wenatchee, WA 98801; and third author: USDA-ARS, San Joaquin Valley Agricultural Sciences Center, 9611 S. Riverbend Ave, Parlier, CA 93648
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Tritsch C, Stuckas H, Martens J, Pentzold S, Kvist L, Lo Valvo M, Giacalone G, Tietze DT, Nazarenko AA, PÄckert M. Gene flow in the European coal tit, Periparus ater (Aves: Passeriformes): low among Mediterranean populations but high in a continental contact zone. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Christian Tritsch
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
| | - Heiko Stuckas
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Stefan Pentzold
- Institute of Biology, Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie biologiche, chimiche e farmaceutiche, Via Archirafi, Palermo, Italy
| | | | | | - Alexander A Nazarenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Martin PÄckert
- Senckenberg Natural History Collections, Königsbrücker Landstraße, Dresden, Germany
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15
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Assessment of genetic diversity and population genetic structure of Carthamus species and Iranian cultivar collection using developed SSR markers. J Genet 2018. [DOI: 10.1007/s12041-018-0956-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Pan T, Yan P, Yang M, Wang H, Ali I, Ayub M, Zhang JH, Wang JJ, Li E, Xue H, Zhang BW, Wu XB. Genetic differentiation of regional populations of the widespread Asiatic toad (Bufo gargarizans), as revealed by development of novel microsatellite markers. AUST J ZOOL 2018. [DOI: 10.1071/zo18059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Dispersal is a key component of a species’ life history, by influencing population persistence, genetic structure, adaptation and maintenance of genetic diversity. The Asiatic toad (Bufo gargarizans) is a widespread species in east Asia. However, we still have no knowledge of what kind of geographical scale equates to genetic differentiation within B. gargarizans. In this study, the population genetics of B. gargarizans was studied at five localities, with the Yangtze River running through the sampling area, in order to detect the level of genetic differentiation and the natural barriers to the species’ dispersal on a small geographic scale, by means of the development and use of novel microsatellite loci. These markers revealed a relatively high level of genetic diversity. Distinct genetic structure among populations in B. gargarizans was observed, as described by genetic distance, AMOVA, PCA and Geneland results. A weak but significant positive correlation between genetic distance and geographical distance. The combination of these findings suggests that the Yangtze River and geographic distance may act as effective barriers for B. gargarizans. These results serve as benchmark data for understanding the impacts of dispersal barriers and continued landscape research on B. gargarizans.
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17
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Richmond JQ, Backlin AR, Galst-Cavalcante C, O'Brien JW, Fisher RN. Loss of dendritic connectivity in southern California's urban riverscape facilitates decline of an endemic freshwater fish. Mol Ecol 2017; 27:369-386. [PMID: 29193550 DOI: 10.1111/mec.14445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/28/2017] [Accepted: 10/16/2017] [Indexed: 11/30/2022]
Abstract
Life history adaptations and spatial configuration of metapopulation networks allow certain species to persist in extreme fluctuating environments, yet long-term stability within these systems relies on the maintenance of linkage habitat. Degradation of such linkages in urban riverscapes can disrupt this dynamic in aquatic species, leading to increased extinction debt in local populations experiencing environment-related demographic flux. We used microsatellites and mtDNA to examine the effects of collapsed network structure in the endemic Santa Ana sucker Catostomus santaanae of southern California, a threatened species affected by natural flood-drought cycles, "boom-and-bust" demography, hybridization and presumed artificial transplantation. Our results show a predominance of drift-mediated processes in shaping population structure and that reverse mechanisms for counterbalancing the genetic effects of these phenomena have dissipated with the collapse of dendritic connectivity. We use approximate Bayesian models to support two cases of artificial transplantation and provide evidence that one of the invaded systems better represents the historic processes that maintained genetic variation within watersheds than any remaining drainages where C. santaanae is considered native. We further show that a stable dry gap in the northern range is preventing genetic dilution of pure C. santaanae persisting upstream of a hybrid assemblage involving a non-native sucker and that local accumulation of genetic variation in the same drainage is influenced by position within the network. This work has important implications for declining species that have historically relied on dendritic metapopulation networks to maintain source-sink dynamics in phasic environments, but no longer possess this capacity in urban-converted landscapes.
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Affiliation(s)
- Jonathan Q Richmond
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
| | | | - John W O'Brien
- California Department of Fish and Wildlife, Los Alamitos, CA, USA
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, USA
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18
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Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses. J Virol 2017; 91:JVI.00925-17. [PMID: 28768871 DOI: 10.1128/jvi.00925-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/25/2017] [Indexed: 11/20/2022] Open
Abstract
Our understanding of archaeal virus diversity and structure is just beginning to emerge. Here we describe a new archaeal virus, tentatively named Metallosphaera turreted icosahedral virus (MTIV), that was isolated from an acidic hot spring in Yellowstone National Park, USA. Two strains of the virus were identified and were found to replicate in an archaeal host species closely related to Metallosphaera yellowstonensis Each strain encodes a 9.8- to 9.9-kb linear double-stranded DNA (dsDNA) genome with large inverted terminal repeats. Each genome encodes 21 open reading frames (ORFs). The ORFs display high homology between the strains, but they are quite distinct from other known viral genes. The 70-nm-diameter virion is built on a T=28 icosahedral lattice. Both single particle cryo-electron microscopy and cryotomography reconstructions reveal an unusual structure that has 42 turret-like projections: 12 pentameric turrets positioned on the icosahedral 5-fold axes and 30 turrets with apparent hexameric symmetry positioned on the icosahedral 2-fold axes. Both the virion structural properties and the genome content support MTIV as the founding member of a new family of archaeal viruses.IMPORTANCE Many archaeal viruses are quite different from viruses infecting bacteria and eukaryotes. Initial characterization of MTIV reveals a virus distinct from other known bacterial, eukaryotic, and archaeal viruses; this finding suggests that viruses infecting Archaea are still an understudied group. As the first known virus infecting a Metallosphaera sp., MTIV provides a new system for exploring archaeal virology by examining host-virus interactions and the unique features of MTIV structure-function relationships. These studies will likely expand our understanding of virus ecology and evolution.
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19
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Gaynor KM, Solomon JW, Siller S, Jessell L, Duffy JE, Rubenstein DR. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes. Mol Ecol Resour 2017; 17:e160-e173. [PMID: 28776934 DOI: 10.1111/1755-0998.12705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 11/28/2022]
Abstract
Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes.
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Affiliation(s)
- Kaitlyn M Gaynor
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Joseph W Solomon
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Stefanie Siller
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Linnet Jessell
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - J Emmett Duffy
- Tennenbaum Marine Observatories Network, Smithsonian Institution, Washington, DC, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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20
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Guo Q, Wang JX, Su LZ, Lv W, Sun YH, Li Y. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). Genes (Basel) 2017; 8:genes8070177. [PMID: 28686183 PMCID: PMC5541310 DOI: 10.3390/genes8070177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/03/2017] [Accepted: 07/04/2017] [Indexed: 12/20/2022] Open
Abstract
Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033–0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000–0.931 and 0.035–0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.
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Affiliation(s)
- Qi Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Jin-Xing Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Li-Zhuo Su
- State-owned Linghai Hongqi Forest, Jinzhou 121228, China.
| | - Wei Lv
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yu-Han Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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21
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Kiesow AM, Warcken A. Characterization and Isolation of Ten Microsatellite Loci in False Map Turtles, Graptemys pseudogeographica (Emydidae, Testudines). AMERICAN MIDLAND NATURALIST 2017. [DOI: 10.1674/0003-0031-177.2.327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Alyssa M. Kiesow
- Northern State University, 1200 S Jay St, Aberdeen, South Dakota 57401
| | - Ambra Warcken
- Northern State University, 1200 S Jay St, Aberdeen, South Dakota 57401
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22
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Neal AT, Ross MS, Schall JJ, Vardo-Zalik AM. Genetic differentiation over a small spatial scale of the sand fly Lutzomyia vexator (Diptera: Psychodidae). Parasit Vectors 2016; 9:550. [PMID: 27756347 PMCID: PMC5070220 DOI: 10.1186/s13071-016-1826-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/02/2016] [Indexed: 02/08/2023] Open
Abstract
Background The geographic scale and degree of genetic differentiation for arthropod vectors that transmit parasites play an important role in the distribution, prevalence and coevolution of pathogens of human and wildlife significance. We determined the genetic diversity and population structure of the sand fly Lutzomyia vexator over spatial scales from 0.56 to 3.79 km at a study region in northern California. The study was provoked by observations of differentiation at fine spatial scales of a lizard malaria parasite vectored by Lu. vexator. Methods A microsatellite enrichment/next-generation sequencing protocol was used to identify variable microsatellite loci within the genome of Lu. vexator. Alleles present at these loci were examined in four populations of Lu. vexator in Hopland, CA. Population differentiation was assessed using Fst and D (of Cavalli-Sforza and Edwards), and the program Structure was used to determine the degree of subdivision present. The effective population size for the sand fly populations was also calculated. Results Eight microsatellite markers were characterized and revealed high genetic diversity (uHe = 0.79–0.92, Na = 12–24) and slight but significant differentiation across the fine spatial scale examined (average pairwise D = 0.327; FST = 0.0185 (95 % bootstrapped CI: 0.0102–0.0264). Even though the insects are difficult to capture using standard methods, the estimated population size was thousands per local site. Conclusions The results argue that Lu. vexator at the study sites are abundant and not highly mobile, which may influence the overall transmission dynamics of the lizard malaria parasite, Plasmodium mexicanum, and other parasites transmitted by this species. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1826-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allison T Neal
- Department of Biology, Norwich University, Northfield, VT, 05663, USA
| | - Max S Ross
- Department of Biology, University of Vermont, Burlington, VT, 05401, USA
| | - Jos J Schall
- Department of Biology, University of Vermont, Burlington, VT, 05401, USA
| | - Anne M Vardo-Zalik
- Department of Biology, Pennsylvania State University, York, PA, 17403, USA.
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23
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Glenn TC, Faircloth BC. Capturing Darwin's dream. Mol Ecol Resour 2016; 16:1051-8. [PMID: 27454358 PMCID: PMC5318190 DOI: 10.1111/1755-0998.12574] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 01/28/2023]
Abstract
Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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Kim KS, Noh CH, Moon SJ, Han SH, Bang IC. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing. Mol Biol Rep 2016; 43:541-8. [PMID: 27059503 DOI: 10.1007/s11033-016-3980-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
Abstract
Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.
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Affiliation(s)
- Keun-Sik Kim
- East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea
| | - Choong Hwan Noh
- East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea
| | - Shin-Joo Moon
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Seung-Hee Han
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - In-Chul Bang
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea.
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Genetic diversity of Didelphis virginiana related to different levels of disturbance in the Highlands and the Central Depression regions of Chiapas, Mexico. JOURNAL OF TROPICAL ECOLOGY 2016. [DOI: 10.1017/s0266467416000080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:The Virginia opossum (Didelphis virginiana) is considered highly adaptable to anthropogenic disturbances; however, the genetic effects of disturbance on this marsupial have not been studied in wild populations in Mexico. Here we evaluated the genetic diversity of D. virginiana at sites with different levels of disturbance within the Highlands and Central Depression regions of Chiapas in southern Mexico. Twelve microsatellite loci were used and the results demonstrated moderate mean heterozygosity (He = 0.60; Ho = 0.50). No significant differences in heterozygosity were found among sites with different levels of disturbance in both regions (range Ho = 0.42–0.57). We observed low but significant levels of genetic differentiation according to disturbance level. The inbreeding coefficient did not differ significantly from zero, suggesting that low genetic differentiation in these environments may be associated with sufficient random mating and gene flow, a result associated with the high dispersal and tolerance characteristics of this marsupial. Our results for D. virginiana in this particular area of Mexico provide a foundation for exploring the impact of human disturbance on the genetic diversity of a common and generalist species.
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Zhao J, Tong Y, Ge T, Ge J. Genetic diversity estimation and core collection construction of Sinojackia huangmeiensis based on novel microsatellite markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2015.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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Liu F, Guo QS, Shi HZ, Cheng BX, Lu YX, Gou L, Wang J, Shen WB, Yan SM, Wu MJ. Genetic variation in Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis, three endemic and endangered species in China using SSR and TRAP markers. Gene 2015; 579:172-82. [PMID: 26743128 DOI: 10.1016/j.gene.2015.12.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/30/2015] [Accepted: 12/27/2015] [Indexed: 01/12/2023]
Abstract
Leeches are not only important medicinal animals worldwide but also are endangered. We aimed to (i) explore the level of genetic diversity within/among populations of three leeches, (ii) assess genetic differentiation among these three leeches, and (iii) discuss an appropriate strategy for conserving leech germplasm. A total of 315 individuals of Whitmania pigra, Hirudo nipponica and Poecilobdella manillensis from 21 populations were collected in China and Vietnam. The genetic structure and genetic diversity among and within the 21 populations were evaluated using target region amplified polymorphism (TRAP) and simple sequence repeat (SSR) markers. Sixteen pairs of TRAP primers generated a total of 398 fragments, of which 396 (99.50%) were polymorphic; fourteen pairs of SSR primers generated a total of 60 fragments, of which 59 (98.33%) were polymorphic. Shannon's index (I) and Nei's gene diversity index (H) for the three leeches were high at the species level (I=0.4980 and H=0.3323 for TRAPs, I=0.4487 and H=0.2969 for SSRs in W. pigra; I=0.4147/0.3769, H=0.2788/0.2566 for H. nipponica; and I=0.4616/0.4717, H=0.3099/0.3203 for P. manillensis). However, low genetic diversity was determined at the population level; the average genetic diversity measures within populations were H=0.1767/0.1376, I=0.2589/0.2043 for W. pigra, H=0.2149/0.2021, I=0.3184/0.3000 for H. nipponica and H=0.2850/0.2724, I=0.4152/0.3967 for P. manillensis. We conclude that there was limited gene exchange within/among populations and species, as the gene flow number (Nm) was 0.5493/0.5807. However, for all three species, the genetic diversity was different at the population level. Gene differentiation (Gst) and Nm were 0.4682 /0.5364 and 0.5678/0.4321 for W. pigra, 0.2294/0.2127 and 1.6797/1.8512 for H. nipponica and 0.1214/0.1496 and 3.6202/2.8412 for P. manillensis. STRUCTURE analysis, Unweighted Pair-Group Method with Arithmetic means (UPGMA) cluster analysis and Principal Coordinates Analysis (PCOA) all yielded similar results. The isolation-by-distance pattern was not significant for any of the three species by the Mantel test. These data emphasize the need for management, conservation, and rehabilitation of this animal species. Finally, an appropriate strategy for conserving leech is proposed.
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Affiliation(s)
- Fei Liu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China; Biology Post-doctoral Mobile Stations, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China; Key Laboratory for Aquaculture and Ecology of Coastal Pool of Jiangsu Province, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Qiao-Sheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hong-Zhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China.
| | - Bo-Xing Cheng
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yu-Xi Lu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ling Gou
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jia Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wen-Biao Shen
- Biology Post-doctoral Mobile Stations, College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shi-Meng Yan
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Man-Jun Wu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing 210095, PR China
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Vandergast AG, Wood DA, Thompson AR, Fisher M, Barrows CW, Grant TJ. Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Dustin A. Wood
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Andrew R. Thompson
- Fisheries Resources Division; Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; La Jolla CA 92037 USA
| | - Mark Fisher
- Natural Reserve System; P.L. Boyd Deep Canyon Desert Research Center; University of California; 54900 Desert Research Tr. Indian Wells CA 92210 USA
| | - Cameron W. Barrows
- Center for Conservation Biology; University of California Riverside; Riverside CA 92251 USA
| | - Tyler J. Grant
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
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Kollars NM, Krueger-Hadfield SA, Byers JE, Greig TW, Strand AE, Weinberger F, Sotka EE. Development and characterization of microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla. PeerJ 2015; 3:e1159. [PMID: 26339541 PMCID: PMC4558075 DOI: 10.7717/peerj.1159] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/16/2015] [Indexed: 11/20/2022] Open
Abstract
Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere. Forty-two loci were screened for amplification and polymorphism. Nine of these loci were polymorphic across four populations of the extant range with two to eleven alleles observed. Mean observed and expected heterozygosities ranged from 0.265 to 0.527 and 0.317 to 0.387, respectively. Overall, these markers will aid in the study of the invasive history of this seaweed and further studies on the population dynamics of this important haploid-diploid primary producer.
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Affiliation(s)
- Nicole M Kollars
- Grice Marine Laboratory and the Department of Biology, College of Charleston, Charleston, SC, USA.,Current affiliation: Center for Population Biology, University of California, Davis, CA, USA
| | - Stacy A Krueger-Hadfield
- Grice Marine Laboratory and the Department of Biology, College of Charleston, Charleston, SC, USA
| | - James E Byers
- Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Thomas W Greig
- Center for Coastal Environmental Health and Biomolecular Research, National Oceanic and Atmospheric Administration, Charleston, SC, USA
| | - Allan E Strand
- Grice Marine Laboratory and the Department of Biology, College of Charleston, Charleston, SC, USA
| | | | - Erik E Sotka
- Grice Marine Laboratory and the Department of Biology, College of Charleston, Charleston, SC, USA
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31
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Jones BR, Jordan S. Genetic Consequences of Pleistocene Sea-Level Change on HawaiianMegalagrionDamselflies. J Hered 2015; 106:618-27. [DOI: 10.1093/jhered/esv036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 05/20/2015] [Indexed: 11/14/2022] Open
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Nair A, van Nouhuys S. Microsatellite markers for a hyperparasitoid wasp from a fragmented landscape. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0425-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Parine NR, Lakshmi P, Kumar D, Shaik JP, Alanazi M, Pathan AAK. Development and characterisation of nine polymorphic microsatellite markers for Tephrosia calophylla Bedd. (Fabaceae). Saudi J Biol Sci 2015; 22:164-7. [PMID: 25737647 PMCID: PMC4336440 DOI: 10.1016/j.sjbs.2014.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 11/05/2022] Open
Abstract
Tephrosia calophylla Bedd. (Fabaceae) is an endangered tropical plant endemic to southwestern Ghats, India. The objective of this study was to contribute to the characterisation of the diversity of this rare species, which is necessary for its future conservation. Accordingly, microsatellite markers were designed, and their ability to detect polymorphisms was determined. Nine microsatellite markers were developed using genomic libraries, and all of the markers were successfully amplified in 42 individuals. Three to nine alleles per locus were observed, and the heterozygosity of the loci ranged from 0.381 to 0.905. The nine newly developed polymorphic markers recognise a sufficient number of varying loci to perform further studies on the conservation and breeding of this medicinal cultivar.
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Affiliation(s)
- Narasimha Reddy Parine
- Dept of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia ; College of Science, Andhra University, Waltair, Visakhapatnam, India
| | - P Lakshmi
- College of Science, Andhra University, Waltair, Visakhapatnam, India
| | - Devinder Kumar
- Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad, India
| | - Jilani P Shaik
- Dept of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammed Alanazi
- Dept of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Akbar Ali Khan Pathan
- Dept of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia ; College of Science, Andhra University, Waltair, Visakhapatnam, India
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Habel JC, Brückmann SV, Krauss J, Schwarzer J, Weig A, Husemann M, Steffan-Dewenter I. Fragmentation genetics of the grassland butterfly Polyommatus coridon: Stable genetic diversity or extinction debt? CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0679-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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36
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Isolation and characterization of polymorphic microsatellite markers from the Korean common squid Todarodes pacificus (Ommastrephidae). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0206-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Isolation and characterization of 16 highly polymorphic tetranucleotide microsatellite DNA markers in Paa spinosa. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Island survivors: population genetic structure and demography of the critically endangered giant lizard of La Gomera, Gallotia bravoana. BMC Genet 2014; 15:121. [PMID: 25421732 PMCID: PMC4254221 DOI: 10.1186/s12863-014-0121-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/27/2014] [Indexed: 12/02/2022] Open
Abstract
Background The giant lizard of La Gomera (Gallotia bravoana), is an endemic lacertid of this Canary Island that lives confined to a very restricted area of occupancy in a steep cliff, and is catalogued as Critically Endangered by IUCN. We present the first population genetic analysis of the wild population as well as of captive-born individuals (for which paternity data are available) from a recovery center. Current genetic variability, and inferred past demographic changes were determined in order to discern the relative contribution of natural versus human-mediated effects on the observed decline in population size. Results Genetic analyses indicate that the only known natural population of the species shows low genetic diversity and acts as a single evolutionary unit. Demographic analyses inferred a prolonged decline of the species for at least 230 generations. Depending on the assumed generation time, the onset of the decline was dated between 1200–13000 years ago. Pedigree analyses of captive individuals suggest that reproductive behavior of the giant lizard of La Gomera may include polyandry, multiple paternity and female long-term sperm retention. Conclusions The current low genetic diversity of G. bravoana is the result of a long-term gradual decline. Because generation time is unknown in this lizard and estimates had large credibility intervals, it is not possible to determine the relative contribution of humans in the collapse of the population. Shorter generation times would favor a stronger influence of human pressure whereas longer generation times would favor a climate-induced origin of the decline. In any case, our analyses show that the wild population has survived for a long period of time with low levels of genetic diversity and a small effective population size. Reproductive behavior may have acted as an important inbreeding avoidance mechanism allowing the species to elude extinction. Overall, our results suggest that the species retains its adaptive potential and could restore its ancient genetic diversity under favorable conditions. Therefore, management of the giant lizard of La Gomera should concentrate efforts on enhancing population growth rates through captive breeding of the species as well as on restoring the carrying capacity of its natural habitat. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0121-8) contains supplementary material, which is available to authorized users.
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López-Villalobos A, Samis KE, Eckert CG. Microsatellite primers for Camissoniopsis cheiranthifolia (Onagraceae) and cross-amplification in related species. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400057. [PMID: 25309839 PMCID: PMC4189498 DOI: 10.3732/apps.1400057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/10/2014] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY We developed 24 nuclear microsatellite primers from an enriched genomic library for the Pacific coastal dune endemic Camissoniopsis cheiranthifolia to study the consequences of mating system differentiation, the genetics of species' range limits, and hybridization with its closest sister taxon, C. bistorta. • METHODS AND RESULTS Twenty-four primer pairs were developed and characterized in four populations of C. cheiranthifolia and one population of C. bistorta. We also tested eight additional taxa for cross-amplification. The average number of alleles per locus per species was 4.3 and 6.0, respectively. The number of loci that amplified and were variable within the eight related taxa ranged from six to 17. • CONCLUSIONS These markers will be useful in studying mating system evolution, the genetic structure of species' ranges, hybridization, and the provenance of material used for habitat restoration in C. cheiranthifolia, C. bistorta, and related species.
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Affiliation(s)
| | - Karen E. Samis
- Department of Biology, University of Prince Edward Island, Charlottetown, C1A 4P3 Prince Edward Island, Canada
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Weinman LR, Solomon JW, Rubenstein DR. A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird. Mol Ecol Resour 2014; 15:502-11. [DOI: 10.1111/1755-0998.12330] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Lucia R. Weinman
- Department of Ecology, Evolution and Environmental Biology; Columbia University; 1200 Amsterdam Avenue New York NY 10027 USA
| | - Joseph W. Solomon
- Department of Ecology, Evolution and Environmental Biology; Columbia University; 1200 Amsterdam Avenue New York NY 10027 USA
| | - Dustin R. Rubenstein
- Department of Ecology, Evolution and Environmental Biology; Columbia University; 1200 Amsterdam Avenue New York NY 10027 USA
- Department of Ornithology and Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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41
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Dávila JA, Morinha F, Blanco G. Eleven new polymorphic microsatellite markers for the Red-billed chough (Pyrrhocorax pyrrhocorax). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0293-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Cabello JE, Dávila JA. Isolation and characterization of microsatellite loci in Darwin’s fox (Lycalopex fulvipes) and cross-amplification in other canid species. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Development of microsatellite markers and a restriction endonuclease digest assay for non-invasive sampling of endangered White-rumped, Slender-billed and Red-headed vultures. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0186-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Schedina IM, Pfautsch S, Hartmann S, Dolgener N, Polgar A, Bianco PG, Tiedemann R, Ketmaier V. Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data. JOURNAL OF FISH BIOLOGY 2014; 85:960-964. [PMID: 25059996 DOI: 10.1111/jfb.12470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/12/2014] [Indexed: 06/03/2023]
Abstract
Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0·388 and 0·424 and a mean observed heterozygosity of 0·418 and 0·411, respectively.
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Affiliation(s)
- I M Schedina
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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45
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Wood DA, Fisher RN, Vandergast AG. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication. PLoS One 2014; 9:e97494. [PMID: 24848638 PMCID: PMC4029750 DOI: 10.1371/journal.pone.0097494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022] Open
Abstract
Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Hughes PW, Jaworski AF, Davis CS, Aitken SM, Simons AM. Development of polymorphic microsatellite markers for Indian tobacco, Lobelia inflata (Campanulaceae)(1.). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300096. [PMID: 25202618 PMCID: PMC4103137 DOI: 10.3732/apps.1300096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/03/2014] [Indexed: 05/26/2023]
Abstract
PREMISE OF THE STUDY Nuclear microsatellite markers were developed for Lobelia inflata (Campanulaceae), an obligately self-fertilizing plant species, for use in the study of temporal fluctuation in allele frequency and of the genetic structure within and among populations. • METHODS AND RESULTS We developed 28 primer pairs for L. inflata, all of which amplify CT dinucleotide repeats. We evaluated amplification of these loci in 53 L. inflata individuals at three sites in eastern North America and found that 24 loci showed microsatellite polymorphism. We also found that 16 loci amplified successfully in L. cardinalis, and 11 amplified successfully in L. siphilitica. • CONCLUSIONS These primers will be useful for assessing allelic diversity within and among populations of L. inflata, and show potential for use in congeneric species.
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Affiliation(s)
- P. William Hughes
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Allison F. Jaworski
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9 Alberta, Canada
| | - Susan M. Aitken
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
| | - Andrew M. Simons
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6 Ontario, Canada
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Talve T, McGlaughlin ME, Helenurm K, Wallace LE, Oja T. Population genetic diversity and species relationships in the genus Rhinanthus L. based on microsatellite markers. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:495-502. [PMID: 23889942 DOI: 10.1111/plb.12057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/01/2013] [Indexed: 06/02/2023]
Abstract
The genus Rhinanthus L. is complex, containing many taxonomically unresolved taxa. In this paper we studied genetic variation and species relationships in 15 populations of six Rhinanthus species from three sections. For this purpose, we developed new microsatellite primers for R. osiliensis and used them to investigate genetic variation in two narrow endemics (R. osiliensis, R. javorkae) and in four widespread species (R. rumelicus R. wagneri, R. angustifolius and R. minor). Species-specific private alleles were found in all species except R. osiliensis and R. angustifolius. The Bulgarian endemic R. javorkae showed the lowest genetic variation, followed by widespread R. minor and Estonian endemic R. osiliensis. Rhinanthus javorkae and R. minor were genetically most differentiated. Section Cleistolemus is weakly structured genetically, indicating close affinity between R. osiliensis, R. rumelicus, R. wagneri and R. angustifolius.
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Affiliation(s)
- T Talve
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Cheng F, Yang J, Zhang D, Hu D, Chu H, Cao J, Jiang F, Bu L, Li K. Isolation and characterization of microsatellite loci from Gasterophilus pecorum (Diptera: Gasterophilidae). CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-013-0136-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Guo SS, Zhang GR, Guo XZ, Wei KJ, Ji W, Wei QW. Isolation and characterization of eighteen polymorphic microsatellite loci in Schizopygopsis younghusbandi Regan and cross-amplification in three other schizothoracinae species. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Petersen JJ, Parker IM, Potter D. Ten polymorphic microsatellite primers in the tropical tree caimito, Chrysophyllum cainito (Sapotaceae). APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1300079. [PMID: 25202603 PMCID: PMC4103607 DOI: 10.3732/apps.1300079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/17/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We developed microsatellite primers for the tropical tree Chrysophyllum cainito (Sapotaceae) to determine the native range of the species, investigate the origin of cultivated populations, and examine the partitioning of genetic diversity in wild and cultivated populations. • METHODS AND RESULTS We developed 10 polymorphic primers from C. cainito genomic DNA libraries enriched for di-, tri-, and tetranucleotide repeat motifs. The loci amplified were polymorphic in samples collected from Jamaica and Panama. The number of alleles per locus ranged from two to 10 and three to 12, while observed heterozygosities ranged from 0.074 to 0.704 and 0.407 to 0.852 in Jamaica and Panama, respectively. • CONCLUSIONS The microsatellite primers will be useful in future population genetic studies as well as those aimed at understanding the geographic origin(s) of wild and cultivated populations.
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Affiliation(s)
- Jennifer J. Petersen
- Department of Plant Sciences, Mail Stop 3, University of California, Davis, One Shields Ave., Davis, California 95616 USA
| | - Ingrid M. Parker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95064 USA
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Daniel Potter
- Department of Plant Sciences, Mail Stop 3, University of California, Davis, One Shields Ave., Davis, California 95616 USA
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