Insights from putatively neutral EST-SSR markers on the population genetic structure and genetic diversity of the Qinghai-Tibetan Plateau endemic Medicago archiducis-nicolai Sirjaev

Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of the USA. A few studies have been conducted on the population genetic structure and genetic diversity of the soybean aphid and the source of its invasion in North America. Molecular markers, such as simple sequence repeats (SSRs) are very useful in the evaluation of population structure and genetic diversity. We used 18 SSR markers to assess the genetic diversity of soybean aphid collections from the USA, South Korea, and Japan. The aphids were collected from two sites in the USA (Indiana and South Dakota), two sites in South Korea (Yeonggwang district and Cheonan city), and one site in Japan (Utsunomiya). The SSR markers were highly effective in differentiating among aphid collections from different countries. The level of differentiation within each population and among populations from the same country was limited, even in the case of the USA where the two collection sites were more than 1200 km apart.

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Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers

PLoS ONE ◽

10.1371/journal.pone.0243556 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243556

Author(s):

Natalie Breidenbach ◽

Oliver Gailing ◽

Konstantin V. Krutovsky

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Ssr Markers ◽

Population Genetic Structure ◽

Population Genetic ◽

Sequoia Sempervirens ◽

Data Sets ◽

Data Set ◽

Coast Redwood ◽

Natural Range

Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial timber species, especially in perspective to climate warming that makes more regions in Germany suitable for its growing. The well performing trees in colder Germany could be potential frost resistant genotypes, but their genetic properties and origin are mostly unknown. Within the natural range in southern Oregon and northern California, only two relatively weak clusters were identified, one northern and one southern, separated by the San Francisco Bay. High genetic diversity, but low differentiation was found based on the 12 nuclear SSR markers for all three data sets F, C and G. We found that investigated 147 German trees represented only 37 different genotypes. They showed genetic diversity at the level less than diversity observed within the natural range in the northern or southern cluster, but more similar to the diversity observed in the southern cluster. It was difficult to assign German trees to the original single native populations using the six cpSSR markers, but rather to either the northern or southern cluster. The high number of haplotypes found in the data sets based on six cpSSR markers and low genetic differentiation based on 12 nuclear SSRs found in this study helps us study and better understand population genetic structure of this complex polyploid tree and supports the selection of potential genotypes for German forestry.

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Genomic epidemiology ofMycobacterium bovisinfection in sympatric badger and cattle populations in Northern Ireland

10.1101/2021.03.12.435101 ◽

2021 ◽

Cited By ~ 1

Author(s):

Assel Akhmetova ◽

Jimena Guerrero ◽

Paul McAdam ◽

Liliana C.M. Salvador ◽

Joseph Crispell ◽

...

Keyword(s):

Genetic Diversity ◽

Spatial Distribution ◽

Genetic Structure ◽

Northern Ireland ◽

Population Genetic Structure ◽

Population Genetic ◽

Transmission Dynamics ◽

Data Set ◽

Hair Samples ◽

Disease Persistence

AbstractBackgroundBovine tuberculosis (bTB) is a costly epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra- species host transmission for disease persistence. We sequenced an exceptional data set of 619Mycobacterium bovisisolates from badgers and cattle in a 100km2bTB ‘hotspot’ in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area.ResultsGraph transmission tree methods and structured coalescent analyses indicated the majority of bacterial diversity was found in the local cattle population. Results pointed to transmission from cattle to badger being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution ofM. bovisgenetic diversity, suggesting that badger-to-badger transmission may not be a key determinant of disease persistence.SignificanceOur data were consistent with badgers playing a smaller role in the maintenance ofM. bovisinfection in this study site, compared to cattle. Comparison to other areas suggests thatM. bovistransmission dynamics are likely to be context dependent, and the role of wildlife difficult to generalise.

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Genetic Diversity and Population Genetic Structure of Teak

10.1007/978-3-030-79311-1_12 ◽

2021 ◽

pp. 181-190

Author(s):

Thwe Thwe Win

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic

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Diverging Genetic Structure of Coexisting Populations of the Black Storm-Petrel and the Least Storm-Petrel in the Gulf of California

Tropical Conservation Science ◽

10.1177/1940082920949177 ◽

2020 ◽

Vol 13 ◽

pp. 194008292094917

Author(s):

Misael D. Mancilla-Morales ◽

Santiago Romero-Fernández ◽

Araceli Contreras-Rodríguez ◽

José J. Flores-Martínez ◽

Víctor Sánchez-Cordero ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic Structure ◽

Mate Selection ◽

Gulf Of California ◽

Population Genetic ◽

Life Histories ◽

Gene Diversity ◽

Isolation By Distance ◽

Storm Petrel

Estimations on the influence of evolutionary and ecological forces as drivers of population gene diversity and genetic structure have been performed on a growing number of colonial seabirds, but many remain poorly studied. In particular, the population genetic structure of storm-petrels (Hydrobatidae) has been evaluated in only a few of the 24 recognized species. We assessed the genetic diversity and population structure of the Black Storm-Petrel ( Hydrobates melania) and the Least Storm-Petrel ( Hydrobates microsoma) in the Gulf of California. The two species were selected because they are pelagic seabirds with comparable ecological traits and breeding grounds. Recent threats such as introduced species of predators and human disturbance have resulted in a decline of many insular vertebrate populations in this region and affected many different aspects of their life histories (ranging from reproductive success to mate selection), with a concomitant loss of genetic diversity. To elucidate to what extent the population genetic structure occurs in H. melania and H. microsoma, we used 719 base pairs from the mitochondrial cytochrome oxidase c subunit I gene. The evaluation of their molecular diversity, genetic structure, and gene flow were performed through diversity indices, analyses of molecular and spatial variance, and isolation by distance (IBD) across sampling sites, respectively. The population genetic structure (via AMOVA and SAMOVA) and isolation by distance (pairwise p-distances and FST/1– FST (using ΦST) were inferred for H. microsoma. However, for H. melania evidence was inconclusive. We discuss explanations leading to divergent population genetic structure signatures in these species, and the consequences for their conservation.

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Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

Heredity ◽

10.1038/s41437-020-0344-6 ◽

2020 ◽

Vol 126 (1) ◽

pp. 63-76

Author(s):

Sarah M. Griffiths ◽

Mark J. Butler ◽

Donald C. Behringer ◽

Thierry Pérez ◽

Richard F. Preziosi

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic Structure ◽

Larval Dispersal ◽

Population Genetic ◽

Spatial Genetic Structure ◽

Florida Keys ◽

The United States ◽

Limited Dispersal ◽

Mass Mortalities

AbstractUnderstanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.

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