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Evolutionary Migration of the Disjunct Salt Cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America.

Wang XJ, Shi DC, Wang XY, Wang J, Sun YS, Liu JQ - PLoS ONE (2015)

Bottom Line: All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America.The fast demographic expansions should have occurred in northern China in a more recent past.Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.

View Article: PubMed Central - PubMed

Affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.

ABSTRACT
Eutrema salsugineum (= Thellungiella salsuginea Brassicaceae), a species growing in highly saline habitats, is a good model for use in salt-stress research. However, its evolutionary migrations and genetic variations within and between disjunct regions from central Asia to northern China and North America remain largely unknown. We examined genetic variations and phylogeographic patterns of this species by sequencing ITS, 9 chloroplast (cp) DNA fragments (4379 bp) and 10 unlinked nuclear loci (6510 bp) of 24 populations across its distributional range. All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America. Further modelling of nuclear population-genetic data based on approximate bayesian computation (ABC) analyses indicated that the long-distance dispersals after the recent origin of E. salsugineum may have occurred from central Asia to the other two regions respectively within 20000 years. The fast demographic expansions should have occurred in northern China in a more recent past. Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.

No MeSH data available.


STRUCTURE analyses of the sampled populations.24 sampled E. salsuginea populations and individuals based on nuclear loci. Bar plots showing the proportion of inferred co-ancestry from Bayesian population assignment tests. Results are shown for K = 1 to K = 7. Population numbers in the Group A, B and C referred to those in the Fig 1. These three groups were further used for ABC analyses.
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pone.0124010.g002: STRUCTURE analyses of the sampled populations.24 sampled E. salsuginea populations and individuals based on nuclear loci. Bar plots showing the proportion of inferred co-ancestry from Bayesian population assignment tests. Results are shown for K = 1 to K = 7. Population numbers in the Group A, B and C referred to those in the Fig 1. These three groups were further used for ABC analyses.

Mentions: ABC is as a powerful approach to select obtain the most suitable demographic history by statistically testing alternative hypotheses [10]. We used the software DIYABC v1.0.4.39 [43–44] to select the evolutionary scenario of E. salsugineum based on population genetic data from 10 loci. The assorted population genetic data were simulated under four hypothesized scenarios with population divergence, population size change and admixture [43]. Three groups (Group A, B and C) were defined based on the results from the STRUCTURE analyses (Fig 2). Moreover, initial LAMARC and mismatch distribution analyses indicated that populations from northern China experienced a common rapid population expansion. Therefore, we added population size change models to these four scenarios. For the ABC analyses, parameter values were set from the minimum to maximum range of priors. We used the number of haplotypes, number of segregating sites and mean pairwise difference as one-sample summary statistics. We chose pairwise differences (W) and (B) as two-sample summary statistics to compare between the observed and simulated datasets. We conducted one million simulations for each scenario, and selected the most likely scenario through the posterior probabilities with both direct approach and logistic regression methods. In addition, we also evaluated the most scenario by a principal component analysis (PCA) using the option “model checking” in DIYABC. We assumed a generation time of one year for E. salsugineum as observed for all populations.


Evolutionary Migration of the Disjunct Salt Cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America.

Wang XJ, Shi DC, Wang XY, Wang J, Sun YS, Liu JQ - PLoS ONE (2015)

STRUCTURE analyses of the sampled populations.24 sampled E. salsuginea populations and individuals based on nuclear loci. Bar plots showing the proportion of inferred co-ancestry from Bayesian population assignment tests. Results are shown for K = 1 to K = 7. Population numbers in the Group A, B and C referred to those in the Fig 1. These three groups were further used for ABC analyses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4430283&req=5

pone.0124010.g002: STRUCTURE analyses of the sampled populations.24 sampled E. salsuginea populations and individuals based on nuclear loci. Bar plots showing the proportion of inferred co-ancestry from Bayesian population assignment tests. Results are shown for K = 1 to K = 7. Population numbers in the Group A, B and C referred to those in the Fig 1. These three groups were further used for ABC analyses.
Mentions: ABC is as a powerful approach to select obtain the most suitable demographic history by statistically testing alternative hypotheses [10]. We used the software DIYABC v1.0.4.39 [43–44] to select the evolutionary scenario of E. salsugineum based on population genetic data from 10 loci. The assorted population genetic data were simulated under four hypothesized scenarios with population divergence, population size change and admixture [43]. Three groups (Group A, B and C) were defined based on the results from the STRUCTURE analyses (Fig 2). Moreover, initial LAMARC and mismatch distribution analyses indicated that populations from northern China experienced a common rapid population expansion. Therefore, we added population size change models to these four scenarios. For the ABC analyses, parameter values were set from the minimum to maximum range of priors. We used the number of haplotypes, number of segregating sites and mean pairwise difference as one-sample summary statistics. We chose pairwise differences (W) and (B) as two-sample summary statistics to compare between the observed and simulated datasets. We conducted one million simulations for each scenario, and selected the most likely scenario through the posterior probabilities with both direct approach and logistic regression methods. In addition, we also evaluated the most scenario by a principal component analysis (PCA) using the option “model checking” in DIYABC. We assumed a generation time of one year for E. salsugineum as observed for all populations.

Bottom Line: All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America.The fast demographic expansions should have occurred in northern China in a more recent past.Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.

View Article: PubMed Central - PubMed

Affiliation: MOE Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, China.

ABSTRACT
Eutrema salsugineum (= Thellungiella salsuginea Brassicaceae), a species growing in highly saline habitats, is a good model for use in salt-stress research. However, its evolutionary migrations and genetic variations within and between disjunct regions from central Asia to northern China and North America remain largely unknown. We examined genetic variations and phylogeographic patterns of this species by sequencing ITS, 9 chloroplast (cp) DNA fragments (4379 bp) and 10 unlinked nuclear loci (6510 bp) of 24 populations across its distributional range. All markers suggested the high genetic poverty of this species and the limited number of genetic variations recovered was congruently partitioned between central Asia, northern China and North America. Further modelling of nuclear population-genetic data based on approximate bayesian computation (ABC) analyses indicated that the long-distance dispersals after the recent origin of E. salsugineum may have occurred from central Asia to the other two regions respectively within 20000 years. The fast demographic expansions should have occurred in northern China in a more recent past. Our study highlights the importance of using ABC analyses and nuclear population genetic data to trace evolutionary migrations of the disjunct distributions of the plants in the recent past.

No MeSH data available.