Trans-oceanic host dispersal explains high seabird tick diversity on Cape Verde islands

Parasites represent ideal models for unravelling biogeographic patterns and mechanisms of diversification on islands. Both host-mediated dispersal and within-island adaptation can shape parasite island assemblages. In this study, we examined patterns of genetic diversity and structure of Ornithodoros seabird ticks within the Cape Verde Archipelago in relation to their global phylogeography. Contrary to expectations, ticks from multiple, geographically distant clades mixed within the archipelago. Trans-oceanic colonization via host movements probably explains high local tick diversity, contrasting with previous research that suggests little large-scale dispersal in these birds. Although host specificity was not obvious at a global scale, host-associated genetic structure was found within Cape Verde colonies, indicating that post-colonization adaptation to specific hosts probably occurs. These results highlight the role of host metapopulation dynamics in the evolutionary ecology and epidemiology of avian parasites and pathogens.

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Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽

10.1371/journal.pone.0247586 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247586

Author(s):

Christine E. Edwards ◽

Brooke C. Tessier ◽

Joel F. Swift ◽

Burgund Bassüner ◽

Alexander G. Linan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Plant Species ◽

Genetic Drift ◽

Rare Species ◽

Ex Situ ◽

Ouachita Mountains ◽

Genetic Diversity And Structure ◽

Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

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Short Note: Development and characterization of 16 new polymorphic microsatellite loci for Schima superba (Theaceae)

Silvae Genetica ◽

10.1515/sg-2013-0016 ◽

2013 ◽

Vol 62 (1-6) ◽

pp. 124-126 ◽

Cited By ~ 1

Author(s):

Hong-Yu Niu ◽

Wan-Hui Ye ◽

Zheng-Feng Wang ◽

Ying Chen ◽

Hong-Lin Cao ◽

...

Keyword(s):

Genetic Diversity ◽

Large Scale ◽

Short Note ◽

Schima Superba ◽

Broad Leaved Forest ◽

Genetic Diversity And Structure ◽

Scale Structures ◽

Polymorphic Microsatellite ◽

Leaved Forest

Abstract Schima superba is a common dominant tree species in evergreen broad-leaved forest in subtropical China. Despite its multiple usages in wood industry, reforestation and traditional Chinese medicine, its genetic diversity is poorly studied. To help studying its genetic diversity and structure in the future, after microsatellite enrichment and screening, we identified 16 microsatellites in S. superba. These markers showed polymorphism in three populations. The number of alleles per locus ranged from 3 to 32 with a mean of 14. Within populations, the observed and unbiased expected heterozygosities ranged from 0.048 to 0.926 and from 0.048 to 0.949, respectively. The newly developed 16 microsatellites will be useful for investigating the genetic diversity and structure from large scale patterns to fine-scale structures in this species.

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Genetic structure and diversity in Sorghum bicolor (L.) Moench landraces from marginal sorghum production lands in Senegal, based on SSR markers

Journal of Plant Breeding and Genetics ◽

10.33687/pbg.007.03.3204 ◽

2020 ◽

Vol 7 (3) ◽

pp. 134-144

Author(s):

Amy Bodian ◽

Bassiaka Ouattara ◽

Awa Sarr ◽

Boubacar Gano ◽

Mbaye-Ndoye Sall ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Production Systems ◽

Classification Model ◽

Germplasm Management ◽

Genetic Diversity And Structure ◽

Food And Feed ◽

Sorghum Production ◽

In Situ Management

Data on sorghum genetic diversity in Senegal are missing despite its importance in the food and feed in the country. In order to contribute to the sustainable in situ management of sorghum germplasm, we investigated its genetic diversity and structure in its marginal production areas. Investigations were focused on Thiès, Diourbel and Kédougou regions where sorghum landraces have been less investigated and genetic information on landraces is unknown. A total of 148 sorghum accessions representative of landraces used in production systems have been sampled and analyzed with 30 microsatellite markers. A total of 138 alleles have been recorded. The number of alleles per locus varied from 3 (7 loci) to 8 (3 loci). The observed heterozygosity varied from 0 to 0.62. The low genetic distance (0.12) was recorded between Thiès and Diourbel populations and the highest distance (0.22) between Thiès and Kédougou populations. Dendrogram obtained according to Neighbour joining classification model allowed the classification of sorghum accessions into three main groups. The Genetic structure is not function to the regions indicating that landraces are not specific to a region. The results are a first step toward the sustainable in situ management of genetic resources. Data on the whole range of existing diversity of sorghum in Senegal is an important key for its germplasm management; so, the genotyping must be extended to accessions from the whole country.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

10.1101/2020.05.29.124685 ◽

2020 ◽

Author(s):

Godfrey Kinyori Wagutu ◽

Xiangrong Fan ◽

Wenlong Fu ◽

Wei Li ◽

Yuanyuan Chen

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Local Adaptation ◽

Landscape Heterogeneity ◽

Maximum Temperature ◽

Zizania Latifolia ◽

Precipitation Seasonality ◽

Isolation By Environment

AbstractGlobal aquatic habitats are undergoing rapid degradation and fragmentation as a result of land-use change and climate change. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the role of environment, landscape heterogeneity and geographical distance in shaping the genetic structure of 28 natural populations of Zizania latifolia (Griseb.) Turcz. Ex Stapf in China based on 25 microsatellite markers. Genetic structure was investigated by analysis of molecular variance (AMOVA), estimation of FST, Bayesian clustering and Thermodynamic Integration (TI) methods. Isolation by environment (IBE), isolation by resistance (IBR) and isolation by distance (IBD) hypotheses were compared using a reciprocal causal model (RCM). Further, generalized linear models and spatially explicit mixed models, by using geographic, landscape and genetic variables, were developed to elucidate the role of environment in driving Z. latifolia genetic diversity. The genetic differentiation across all populations was high: FST = 0.579; Øpt = 0.578. RCM exclusively supported IBE in shaping genetic structuring, only partial support for IBR, but not for IBD. Maximum temperature of the warmest month and precipitation seasonality were the plausible parameters responsible for genetic diversity. After controlling for spatial effect and landscape complexity, precipitation seasonality was significantly associated with genetic diversity. Based on these findings, genetic structure of Z. latifolia across China seem to be as a result of local adaptation. Environmental gradient and topographical barriers, rather than geographical isolation, influence genetic differentiation of aquatic species across China resulting in instances of local adaptation.

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Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica

10.7287/peerj.preprints.1095 ◽

2015 ◽

Author(s):

Eric J Fuchs ◽

Allan Meneses Martínez ◽

Amanda Calvo ◽

Melania Muñoz ◽

Griselda Arrieta-Espinoza

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Costa Rica ◽

Genetic Structure ◽

Wild Species ◽

Wild Rice ◽

Wild Rice Species ◽

Genetic Diversity And Structure ◽

Diversity Estimates ◽

Oryza Glumaepatula

Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.

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De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

10.21203/rs.2.18797/v3 ◽

2020 ◽

Author(s):

Duy Dinh Vu ◽

Syed Noor Muhammad Shah ◽

Mai Phuong Pham ◽

Van Thang Bui ◽

Minh Tam Nguyen ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Expressed Sequence Tag ◽

De Novo ◽

Average Length ◽

Species Conservation ◽

Group Method ◽

Arithmetic Means ◽

Illumina Hiseq ◽

Genetic Diversity And Structure

Abstract Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population is unknown due to lack of efficient molecular markers.Results: In this study, we employed Illumina HiSeq TM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). A total of 23,741,783 raw reads were obtained and assembled, from which, 89,271 unigenes with an average length of 598.3191 nt were generated. During functional annotation, 31,686 unigenes were annotated in Gene Ontology categories, Kyoto Encyclopedia of Genes and Genomes pathways, Swiss-Prot database, and Nucleotide Collection (NR/NT) database. In addition, 11,343 expressed sequence tag-simple sequence repeat (EST-SSRs) were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which, 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used to analyze genetic diversity and structure of the natural populations. The obtained results revealed that the shows high levels of genetic diversity in populations, the average observed and expected heterozygosity were H O = 0.422 and H E = 0.479. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of bottleneck in all populations. Genetic differentiation among populations was moderate (F ST = 0.133) and indicating limited gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. These results showed a moderate genetic structure of P. vietnamensis. STRUCTURE analysis and the unweighted pair-group method with arithmetic means (UPGMA) tree revealed strong genetic structure and two genetic clusters related to geographical distances, as well. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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Conservation genetics of red pandas in the wild

10.1093/oso/9780198759805.003.0029 ◽

2018 ◽

Author(s):

Yibo Hu ◽

Dunwu Qi ◽

Fuwen Wei

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Conservation Genetics ◽

Human Activities ◽

Population Genetic ◽

Large Scale ◽

Demographic History ◽

Genetic Research ◽

Phylogeographic Structure ◽

Red Panda

The red panda is listed on the 2016 IUCN red list as Endangered. It is now distributed only in China, Myanmar, India, Bhutan and Nepal. Human activities such as poaching and large-scale deforestation have caused serious declines in this forest-dwelling species. Although its ecological research has made much progress in the past decades, only recently witnessed the population genetic research advances of this species. This chapter reviews the advances in wild red panda conservation genetics from non-invasive genetics, genetic diversity, phylogeographic structure, population genetic structure, demographic history, subspecies differentiation, to its conservation and management. It presents detailed estimates of genetic diversity, assesses the role of paleo-climate changes, human activities and landscape features in shaping the genetic structure and demographic history of red pandas, and discusses the implications of conservation genetics findings for effective genetic monitoring and conservation management.

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Clinging to survival: Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum persists in shrinking forest patches

Oryx ◽

10.1017/s0030605320000952 ◽

2021 ◽

pp. 1-6

Author(s):

Krystal A. Tolley ◽

Colin R. Tilbury ◽

Jessica M. da Silva ◽

Gary Brown ◽

Yankho Chapeta ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Satellite Imagery ◽

Critically Endangered ◽

Forest Loss ◽

Mitochondrial Marker ◽

Forest Patches ◽

Genetic Diversity And Structure ◽

The Impact

Abstract The Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining forest patches and assess deforestation. We then surveyed forest patches for the presence of this chameleon, and assessed its genetic diversity and structure. We estimated that 80% of the forest has been destroyed since 1984, although we found extant populations of the chameleon in each of the patches surveyed. Differentiation of genetic structure was strong between populations, suggesting that gene flow has been impaired. Genetic diversity was not low, but this could be the result of a temporal lag as well as lack of sensitivity in the mitochondrial marker used. Overall, the impact of forest loss is assumed to have led to a large demographic decline, with forest fragmentation preventing gene flow.

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Absence of genetic structure reflects post-glacial history and present-day host use in Mapleleaf (Quadrula quadrula) mussel from Manitoba, Canada

Canadian Journal of Zoology ◽

10.1139/cjz-2019-0227 ◽

2020 ◽

Vol 98 (8) ◽

pp. 551-556

Author(s):

N.M. VanTassel ◽

C.E. Beaver ◽

D.A. Watkinson ◽

T.J. Morris ◽

D.T. Zanatta

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Great Lakes ◽

Host Use ◽

Ohio River ◽

Glacial History ◽

Genetic Population ◽

Genetic Diversity And Structure ◽

Declining Populations ◽

River Drainages

Our study documents and analyzes the absence of genetic diversity and structure of the Mapleleaf (Quadrula quadrula (Rafinesque, 1820)) (Bivalvia: Unionidae) mussel in the Lake Winnipeg, Assiniboine River, and Red River drainages (Manitoba, Canada). Previous studies have revealed patterns of genetic diversity and structure in the Mississippi and Ohio river drainages, as well as in the Laurentian Great Lakes drainage. Genotypes from six variable microsatellite loci showed that the Q. quadrula population in Manitoba was significantly differentiated from the population in the Great Lakes drainage (Ontario, Canada), supporting the existence of two Designatable Units in Canada. Conversely, there was no evidence of genetic structure within the sampled range of Q. quadrula in Manitoba. The lack of genetic structure in Q. quadrula across its distribution in Manitoba reflected its post-glacial history and use of a vagile host and necessitates that efforts should be made to ensure connectivity and maintain gene flow across the region. Given that the evidence suggests that Manitoba Q. quadrula belong to a single genetic population, movement of hatchery-propagated juvenile Q. quadrula, adult Q. quadrula, or glochidia-carrying host catfish sourced from any location in Manitoba could be used to augment declining populations or at-risk locations in Manitoba.

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