Genetic structure, phylogeography, and migration routes of Bouteloua gracilis (Kunth) Lag. ex Griffiths (Poaceae:Chloridoideae)

Avendaño-González, Marcela; Morales-Domínguez, José Francisco; Siqueiros-Delgado, María Elena

doi:10.1016/j.ympev.2019.01.005

Cited by 11 publications

(11 citation statements)

References 58 publications

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“…The species with the most prior population‐level analyses is Bouteloua gracilis : Aguado‐Santacruz et al (2004) and Phan (2000) found high variability in B. gracilis populations at opposite ends of its range, but these studies used RAPD markers, and so heterozygosity estimates could not be made. More recently, Avendaño‐González et al (2019) used RAD‐seq to characterize genetic structure across this species’ range and found a maximum heterozygosity of 0.32% and a Tajima’s D of −1.75. These results are in stark contrast to the values estimated here (Fig.…”

Section: Discussionmentioning

confidence: 99%

On the potential of Angiosperms353 for population genomic studies

et al. 2021

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The estimation of demographic parameters in natural populations is a critical tool for species delimitation (Duminil and Di Michele, 2009), biogeography studies (Overcast et al., 2019), and monitoring of populations and species in a dynamically changing environment (Allendorf et al., 2010). The feasibility of estimating demographic parameters (including heterozygosity, effective population size, and levels of introgression) in non-model taxa relies on retrieving homologous markers that allow detection of sufficient variation across the genome, while remaining cost-effective for the analysis of hundreds of individuals. In plants, population genomic studies could benefit from markers that enable the further unlocking of herbarium specimens for botanical research, paralleling the impact of herbarium specimens in phylogenomics (e.g., Shee et al., 2020), microbiome research (e.g., Heberling and Burke, 2019), and studies of the effects of climate change on plant populations (e.g., Miller-Rushing et al., 2009). Traditional Sanger sequencing of PCR amplicons often employs universal primer sequences, but the genes targeted (e.g., the plastid markers matK and rbcL, or the nuclear ribosomal ITS) do not

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Section: Discussionmentioning

confidence: 99%

On the potential of Angiosperms353 for population genomic studies

et al. 2021

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“…Our analysis of wild sunflower adds to the growing body of work demonstrating the general trend of south-north postglacial migration inferred in wide-ranging North American plant species. Interestingly, there is a dearth of phylogeographic studies that have examined a wide-ranging plant species that spans the entirety of the Great Plains (but see [78]). As such, our study provides interesting insights into central North American plant phylogeography.…”

Section: Phylogeography Of Wild Sunflowermentioning

confidence: 99%

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

Park

Burke

2020

Genes

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Patterns of genetic variation in crops are the result of selection and demographic changes that occurred during their domestication and improvement. In many cases, we have an incomplete picture of the origin of crops in the context of their wild progenitors, particularly with regard to the processes producing observed levels of standing genetic variation. Here, we analyzed sequence diversity in cultivated sunflower (Helianthus annuus L.) and its wild progenitor (common sunflower, also H. annuus) to reconstruct phylogeographic relationships and population genetic/demographic patterns across sunflower. In common sunflower, south-north patterns in the distribution of nucleotide diversity and lineage splitting indicate a history of rapid postglacial range expansion from southern refugia. Cultivated sunflower accessions formed a clade, nested among wild populations from the Great Plains, confirming a single domestication event in central North America. Furthermore, cultivated accessions sorted by market type (i.e., oilseed vs. confectionery) rather than breeding pool, recapitulating the secondary development of oil-rich cultivars during its breeding history. Across sunflower, estimates of nucleotide diversity and effective population sizes suggest that cultivated sunflower underwent significant population bottlenecks following its establishment ~5000 years ago. The patterns inferred here corroborate those from previous studies of sunflower domestication, and provide a comprehensive overview of its evolutionary history.

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“…Further, positive values of Tajima’s D for each population indicated past population contraction (Table 1; Tajima, 1989). Temperate grass species of Europe (Hensen et al, 2010; Blanco-Pastor et al, 2019; Blanco-Pastor et al, 2021), Africa (Mairal et al, 2021), and North America (Avendaño-González et al, 2019; Palacio-Mejía et al, 2021) demonstrate comparable regional patterns of differentiation and gene flow also influenced by Pleistocene glacial cycles.…”

Section: Discussionmentioning

confidence: 99%

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

Osuna‐Mascaró

Agneray

Galland

et al. 2022

Preprint

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Analyses of the factors shaping spatial genetic structure in widespread plant species are important for understanding evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5,677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and inbreeding, were consistent with self-fertilization as a contributor to population differentiation. Moreover, variance partitioning and partial RDA indicated local adaptation to the environment as an additional factor influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation in order to delineate seed zones. However, our analyses also reveal a complex evolutionary history of A. thurberanium in the Great Basin, where previously delineated seed zones contain distantly related populations. Overall, our results indicate that numerous factors shape genetic variation in A. thurberianum and that evolutionary history, along with differentiation across distinct geographic and environmental scales, should be considered for conservation and restoration plans.

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Genetic structure, phylogeography, and migration routes of Bouteloua gracilis (Kunth) Lag. ex Griffiths (Poaceae:Chloridoideae)

Cited by 11 publications

References 58 publications

On the potential of Angiosperms353 for population genomic studies

On the potential of Angiosperms353 for population genomic studies

Phylogeography and the Evolutionary History of Sunflower (Helianthus annuus L.): Wild Diversity and the Dynamics of Domestication

Fine-scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

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