Neutral Genetic Variation

Neale, David B.; Wheeler, Nicholas C.

doi:10.1007/978-3-319-46807-5_9

Cited by 4 publications

(3 citation statements)

References 155 publications

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“…The results of the presented genome-wide analysis of the structure and genetic variation of natural populations of Siberian larch are generally consistent with previous conclusions about the relatively weak selectively neutral structure of closely located populations of conifers, including larch [25,26], explained mostly by intensive gene flow [27]. PCAdapt demonstrated that none of the PCs had eigenvalues greater than random.…”

Section: Discussionsupporting

confidence: 87%

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Novikova

Sharov

Орешкова

et al. 2023

IJMS

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Forest trees growing in high altitude conditions offer a convenient model for studying adaptation processes. They are subject to a whole range of adverse factors that are likely to cause local adaptation and related genetic changes. Siberian larch (Larix sibirica Ledeb.), whose distribution covers different altitudes, makes it possible to directly compare lowland with highland populations. This paper presents for the first time the results of studying the genetic differentiation of Siberian larch populations, presumably associated with adaptation to the altitudinal gradient of climatic conditions, based on a joint analysis of altitude and six other bioclimatic variables, together with a large number of genetic markers, single nucleotide polymorphisms (SNPs), obtained from double digest restriction-site-associated DNA sequencing (ddRADseq). In total, 25,143 SNPs were genotyped in 231 trees. In addition, a dataset of 761 supposedly selectively neutral SNPs was assembled by selecting SNPs located outside coding regions in the Siberian larch genome and mapped to different contigs. The analysis using four different methods (PCAdapt, LFMM, BayeScEnv and RDA) revealed 550 outlier SNPs, including 207 SNPs whose variation was significantly correlated with the variation of some of environmental factors and presumably associated with local adaptation, including 67 SNPs that correlated with altitude based on either LFMM or BayeScEnv and 23 SNPs based on both of them. Twenty SNPs were found in the coding regions of genes, and 16 of them represented non-synonymous nucleotide substitutions. They are located in genes involved in the processes of macromolecular cell metabolism and organic biosynthesis associated with reproduction and development, as well as organismal response to stress. Among these 20 SNPs, nine were possibly associated with altitude, but only one of them was identified as associated with altitude by all four methods used in the study, a nonsynonymous SNP in scaffold_31130 in position 28092, a gene encoding a cell membrane protein with uncertain function. Among the studied populations, at least two main groups (clusters), the Altai populations and all others, were significantly genetically different according to the admixture analysis based on any of the three SNP datasets as follows: 761 supposedly selectively neutral SNPs, all 25,143 SNPs and 550 adaptive SNPs. In general, according to the AMOVA results, genetic differentiation between transects or regions or between population samples was relatively low, although statistically significant, based on 761 neutral SNPs (FST = 0.036) and all 25,143 SNPs (FST = 0.017). Meanwhile, the differentiation based on 550 adaptive SNPs was much higher (FST = 0.218). The data showed a relatively weak but highly significant linear correlation between genetic and geographic distances (r = 0.206, p = 0.001).

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Section: Discussionsupporting

confidence: 87%

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Novikova

Sharov

Орешкова

et al. 2023

IJMS

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“…Genetic distance is defined as the genomic diversity between species or populations [36]. Low genetic distance indicates that the genotypes or species are closely related [37].…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR Markers, ITS1 and trnL-F Intergenic spacer sequences

Uras

Özyiğit

Filiz

et al. 2023

Preprint

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Background Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aimed to evaluate the genetic diversity of of R. pseudoacacia plants planted in urban ecosystems using R. pseudoacacia genotypes collected from Istanbul (Prince Island, Bağdat Avenue, Barbaros Boulevard and TEM highway) and Kocaeli (Dilovası District) cities. Methods and Results 15 ISSR primers were tested, nine of which gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Genetic diversity values based on Nei’s (1978) were calculated between 0.165 and 0.251. The lowest and highest PPL were found in Barbaros Boulevard and Dilovası District populations, respectively. Population structure analysis showed seven different structures for the five populations. The most genetically similar populations were found as Prince Island and Barbaros Boulevard populations, while the most diverged population was the Dilovası population. Phylogeny analysis was conducted based on ITS1 and trnL-F IGS sequences. The length of the ITS1 sequence was found as 239 bp, and the GC content ranged from 52.72% to 56.56% while the length of the trnL-F IGS sequence was found as 453 bp with GC content between 29.14-29.80%. Conclusion It is considered that the main reasons for the genetic similarities and differences is originating from either the parents of these trees or the pollution they are exposed to. In phylogenetic analysis, both region sequences showed a high discriminant value and effective discriminatory power at the family level.

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“…Genetic distance is defined as the genomic diversity between species or populations (Neale & Wheeler 2019). Here, a dendrogram based on Nei's (1987) genetic distance was constructed using the UPGMA method to reveal genetic distances between 73 populations.…”

mentioning

confidence: 99%

Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences

Emin Uras,

Filiz,

Sen

et al. 2024

J. For. Sci.

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Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovası District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.

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Neutral Genetic Variation

Cited by 4 publications

References 155 publications

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Genetic Adaptation of Siberian Larch (Larix sibirica Ledeb.) to High Altitudes

Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR Markers, ITS1 and trnL-F Intergenic spacer sequences

Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences

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