scholarly journals Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping‐by‐sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Harriet V. Hunt ◽  
Natalia A. S. Przelomska ◽  
Michael G. Campana ◽  
James Cockram ◽  
H. Frances J. Bligh ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Foxtail Millet ◽  
Genotyping By Sequencing ◽  
Population Genomic ◽  
Landrace Accessions

Distinct lineages and population genomic structure of the coral Pachyseris speciosa in the small equatorial reef system of Singapore

Coral Reefs ◽  
2021 ◽  
Author(s):  
Bar Feldman ◽  
Lutfi Afiq-Rosli ◽  
Noa Simon-Blecher ◽  
Elena Bollati ◽  
Benjamin John Wainwright ◽  
...  
Keyword(s):  
Genomic Structure ◽  
Reef System ◽  
Population Genomic

scholarly journals Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7484 ◽  
Author(s):  
Amanda E. Haponski ◽  
Diarmaid Ó Foighil
Keyword(s):  
New World ◽  
Genomic Structure ◽  
Initial Study ◽  
Illinois River ◽  
Phylogenomic Analysis ◽  
Tropical Regions ◽  
Population Genomic ◽  
Sequencing Method ◽  
Freshwater Clams ◽  
Phylogenomic Analyses

The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.

scholarly journals Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea

2019 ◽  
Vol 10 (1) ◽  
pp. 11-25
Author(s):  
Christophe Verwimp ◽  
Lies Vansteenbrugge ◽  
Sofie Derycke ◽  
Thomas Kerkhove ◽  
Hilde Muylle ◽  
...  
Keyword(s):  
North Sea ◽  
Genomic Structure ◽  
Gelatinous Zooplankton ◽  
Mnemiopsis Leidyi ◽  
Zooplankton Species ◽  
The North ◽  
Population Genomic ◽  
The North Sea

scholarly journals Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Giovanny Covarrubias-Pazaran ◽  
Luis Diaz-Garcia ◽  
Brandon Schlautman ◽  
Joseph Deutsch ◽  
Walter Salazar ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Genomic Structure ◽  
Genotyping By Sequencing ◽  
High Density ◽  
American Cranberry

scholarly journals Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping

2016 ◽  
Author(s):  
Brandon Schlautman ◽  
Giovanny Covarrubias-Pazaran ◽  
Luis Diaz-Garcia ◽  
Massmo Iorizzo ◽  
James Polashock ◽  
...  
Keyword(s):  
Association Studies ◽  
Genomic Structure ◽  
Genetic Research ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Vaccinium Macrocarpon ◽  
Nucleotide Polymorphisms ◽  
Common Mean ◽  
American Cranberry ◽  
Ssr Loci

ABSTRACTThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three inter-related cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman Rank Correlations > 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.

scholarly journals Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 

2020 ◽  
Author(s):  
Eeva Jansson ◽  
Francois Besnier ◽  
Ketil Malde ◽  
Carl André ◽  
Geir Dahle ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
De Novo ◽  
Genomic Structure ◽  
Snp Markers ◽  
Genomic Diversity ◽  
Full Genome Sequencing ◽  
Population Genomic ◽  
Genome Wide ◽  
Ctenolabrus Rupestris ◽  
Goldsinny Wrasse

Abstract Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse ( Ctenolabrus rupestris ) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33 235 genome wide SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F ST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~1% within Scandinavia. SNPs showing large divergence ( F ST >0.15) were picked as candidate diagnostic markers for population assignment. 173 of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. 69 of these SNPs were significantly ( p <0.05) differentiated (mean F ST_173_loci = 0.065, F ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

scholarly journals Fine scale population structure and extensive gene flow within an Eastern Nearctic snake complex (Pituophis melanoleucus)

2021 ◽  
Author(s):  
Zachary L Nikolakis ◽  
Richard Orton ◽  
Brian I Crother
Keyword(s):  
Gene Flow ◽  
Isolation By Distance ◽  
Genomic Structure ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Population Genomic ◽  
Isolation By Environment ◽  
Pituophis Melanoleucus ◽  
Lineage Divergence

Understanding the processes and mechanisms that promote lineage divergence is a central goal in evolutionary biology. For instance, studies investigating the spatial distribution of genomic variation often highlight biogeographic barriers underpinning geographic isolation, as well as patterns of isolation by environment and isolation by distance that can also lead to lineage divergence. However, the patterns and processes that shape genomic variation and drive lineage divergence may be taxa-specific, even across closely related taxa co-occurring within the same biogeographic region. Here, we use molecular data in the form of ultra-conserved elements (UCEs) to infer the evolutionary relationships and population genomic structure of the Eastern Pinesnake complex (Pituophis melanoleucus) – a polytypic wide-ranging species that occupies much of the Eastern Nearctic. In addition to inferring evolutionary relationships, population genomic structure, and gene flow, we also test relationships between genomic diversity and putative barriers to dispersal, environmental variation, and geographic distance. We present results that reveal shallow population genomic structure and ongoing gene flow, despite an extensive geographic range that transcends geographic features found to reduce gene flow among many taxa, including other squamate reptiles within the Eastern Nearctic. Further, our results indicate that the observed genomic diversity is spatially distributed as a pattern of isolation by distance and suggest that the current subspecific taxonomy do not adhere to independent lineages, but rather, show a significant amount of admixture across the entire P. melanoleucus range.

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