scholarly journals Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia

2021 ◽  
Author(s):  
Gautam Shirsekar ◽  
Jane Devos ◽  
Sergio M. Latorre ◽  
Andreas Blaha ◽  
Maique Queiroz Dias ◽  
...  

AbstractLarge-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can contribute to observed patterns of genetic diversity and our understanding of the adaptive spread of alleles. While human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of non-native species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present here the most comprehensive view of population structure of North American Arabidopsis thaliana by studying a set of 500 (whole-genome sequenced) and over 2800 (RAD-seq genotyped) individuals in the context of global diversity represented by Afro-Eurasian genomes. We use haplotype-sharing, phylogenetic modeling and rare-allele sharing based methods to identify putative sources of introductions of extant N. American A. thaliana from the native range of Afro-Eurasia. We find evidence of admixture among the introduced lineages that has resulted in the increased haplotype diversity and reduced mutational load. Further, we also present signals of selection in the immune-system related genes that impart qualitative disease resistance to pathogens of bacterial and oomycete origins. Thus, multiple introductions to a non-native range can quickly increase adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. The results presented here lay the foundation for further investigations into the functional significance of admixture.

Author(s):  
Gautam Shirsekar ◽  
Jane Devos ◽  
Sergio M Latorre ◽  
Andreas Blaha ◽  
Maique Queiroz Dias ◽  
...  

Abstract Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.


2006 ◽  
Vol 15 (6) ◽  
pp. 1507-1517 ◽  
Author(s):  
MARIE-FRANCE OSTROWSKI ◽  
JACQUES DAVID ◽  
SYLVAIN SANTONI ◽  
HEATHER MCKHANN ◽  
XAVIER REBOUD ◽  
...  

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.


Author(s):  
Tianxu Kuang ◽  
Fangmin Shuai ◽  
Xinhui Li ◽  
Weitao Chen ◽  
Sovan Lek

Understanding the genetic diversity and population structure of fish species is crucial for the sustainable use and protection of fish germplasm resources. Hemibagrus guttatus (Bagridae, Siluriformes) is widely distributed in the large subtropical Pearl River (China) and is commercially important. It's population have been declining. The genetic diversity of wild H. guttatus is not clear, despite its important ecological significance. In this paper, genes mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cyt b) were used to analyze the genetic structure of H. guttatus population collected from six geographical populations in the main streams of the Pearl River. The results showed that the nucleotide diversity (π) and haplotype diversity (Hd) of wild H. guttatus was low (π < 0.005; Hd < 0.5). In addition, H. guttatus haplotypes did not cluster into clades according to geographical distribution, as revealed by neighbor-joining tree analysis. Analysis of molecular variance analysis (AMOVA) and F-statistics (Fst) values showed high homogeneity among wild H. guttatus populations. Our results suggest that there is degradation in germplasm resources of H. guttatus that could destabilize the sustainable use of this species and there was an urgent need for conservation of this species in South China.


2019 ◽  
Vol 13 (1) ◽  
pp. 70-77 ◽  
Author(s):  
Jialiang Zhang ◽  
Evan Siemann ◽  
Baoliang Tian ◽  
Wei Huang ◽  
Jianqing Ding

Abstract Aims Seeds of many invasive plants germinate more quickly than those of native species, likely facilitating invasion success. Assessing the germination traits and seed properties simultaneously for introduced and native populations of an invasive plant is essential to understanding biological invasions. Here, we used Triadica sebifera as a study organism to examine intraspecific differences in seed germination together with seed characteristics. Methods We measured physical (volume, mass, coat hardness and coat thickness of seeds) and chemical (crude fat, soluble protein, sugar, gibberellins [GA] and abscisic acid [ABA] of kernels) properties of T. sebifera seeds collected in 2017 from 12 introduced (United States) populations and 12 native (China) populations and tested their germination rates and timing in a greenhouse experiment in China. Furthermore, we conducted an extra experiment in the United States using seeds collected in 2016 and 2017 to compare the effects of study sites (China vs. United States) and seed collection time (2016 vs. 2017) on seed germination. Important Findings Seeds from the introduced range germinated faster than those from the native range. Physical and chemical measurements showed that seeds from the introduced range were larger, had higher GA concentrations and GA:ABA ratio, but lower crude fat concentrations compared to those from the native range. There were no significant differences in seed mass, coat hardness and coat thickness or kernel ABA, soluble protein or sugar concentrations between seeds from introduced vs. native ranges. Germination rates were correlated between United States and China greenhouses but germination rates for populations varied between collection years. Our results suggest that larger seeds and higher GA likely contribute to faster germination, potentially facilitating T. sebifera invasion in the introduced range.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.


2010 ◽  
Vol 59 (1-6) ◽  
pp. 273-285 ◽  
Author(s):  
P. O. Aikpokpodion ◽  
M. Kolesnikova-Allen ◽  
V. O. Adetimirin ◽  
M. J. Guiltinan ◽  
A. B. Eskes ◽  
...  

Abstract Inadequate knowledge of the population structure and diversity present often hamper the efficient use of germplasm collections. Using a high through-put system, twelve microsatellite loci were used to analyze genetic diversity and population structure in a national field genebank repository of 243 cacao accessions grouped into 11 populations based on their known sources. Based on multi-locus profiles, the Bayesian method was used for individual assignment to verify membership in each population, determine mislabeling and ancestry of some important accessions used in breeding program. A total of 218 alleles was revealed with a mean number of 18.2 alleles per locus. Gene diversity (He = 0.70) and allelic richness (4.34 alleles per locus) were highest in the F1 hybrid population. Differential mating system was suggested as responsible for the observed deficit and excess of heterozygotes observed among the populations. Analysis of molecular variance showed that within-population variance accounted for 63.0% of the total variance while the rest 37% was accounted for by the among-population variance. Cluster dendrogram based on UPGMA revealed two main subsets. The first group was made up of the Amelonado/Trinitario ancestry and the other of Nanay/Parinari ancestry. We found that Nanay and Parinari populations were the major source of Upper Amazon genes utilized while a large proportion of genetic diversity in the field genebank remained under-utilized in development of improved cultivars released to farmers in Nigeria. This study showed that the presence of alleles of the Upper Amazon Forasteros (Nanay, Parinari and Iquitos Mixed Calabacillo) genetic materials in the locally available accessions predated the formal large scale introduction of Upper Amazon materials in 1944. This is the first report of population structure of field genebank collections of cacao in Nigeria since more than seven decades of formal cacao breeding research.


2009 ◽  
Vol 156 (8) ◽  
pp. 1573-1583 ◽  
Author(s):  
Liying Sui ◽  
Fumin Zhang ◽  
Xiaomei Wang ◽  
Peter Bossier ◽  
Patrick Sorgeloos ◽  
...  

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6572 ◽  
Author(s):  
Victoria Sosa ◽  
Israel Loera ◽  
Diego F. Angulo ◽  
Marilyn Vásquez-Cruz ◽  
Etelvina Gándara

Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.


Author(s):  
T.H. Oliver

Human activities in the Anthropocene are influencing the twin processes of biodiversity generation and loss in complex ways that threaten the maintenance of biodiversity levels that underpin human well-being. Yet many scientists and practitioners still present a simplistic view of biodiversity as a static stock rather than one determined by a dynamic interplay of feedback processes that are affected by anthropogenic drivers. Biodiversity describes the variety of life on Earth, from the genes within an organism to the ecosystem level. However, this article focuses on variation among living organisms, both within and between species. Within species, biodiversity is reflected in genetic, and consequent phenotypic, variations among individuals. Genetic diversity is generated by germ line mutations, genetic recombination during sexual reproduction, and immigration of new genotypes into populations. Across species, biodiversity is reflected in the number of different species present and also, by some metrics, in the evenness of their relative abundance. At this level, biodiversity is generated by processes of speciation and immigration of new species into an area. Anthropogenic drivers affect all these biodiversity generation processes, while the levels of genetic diversity can feed back and affect the level of species diversity, and vice versa. Therefore, biodiversity maintenance is a complex balance of processes and the biodiversity levels at any point in time may not be at equilibrium. A major concern for humans is that our activities are driving rapid losses of biodiversity, which outweigh by orders of magnitude the processes of biodiversity generation. A wide range of species and genetic diversity could be necessary for the provision of ecosystem functions and services (e.g., in maintaining the nutrient cycling, plant productivity, pollination, and pest control that underpin crop production). The importance of biodiversity becomes particularly marked over longer time periods, and especially under varying environmental conditions. In terms of biodiversity losses, there are natural processes that cause roughly continuous, low-level losses, but there is also strong evidence from fossil records for transient events in which exceptionally large loss of biodiversity has occurred. These major extinction episodes are thought to have been caused by various large-scale environmental perturbations, such as volcanic eruptions, sea-level falls, climatic changes, and asteroid impacts. From all these events, biodiversity has shown recovery over subsequent calmer periods, although the composition of higher-level evolutionary taxa can be significantly altered. In the modern era, biodiversity appears to be undergoing another mass extinction event, driven by large-scale human impacts. The primary mechanisms of biodiversity loss caused by humans vary over time and by geographic region, but they include overexploitation, habitat loss, climate change, pollution (e.g., nitrogen deposition), and the introduction of non-native species. It is worth noting that human activities may also lead to increases in biodiversity in some areas through species introductions and climatic changes, although these overall increases in species richness may come at the cost of loss of native species, and with uncertain effects on ecosystem service delivery. Genetic diversity is also affected by human activities, with many examples of erosion of diversity through crop and livestock breeding or through the decline in abundance of wild species populations. Significant future challenges are to develop better ways to monitor the drivers of biodiversity loss and biodiversity levels themselves, making use of new technologies, and improving coverage across geographic regions and taxonomic scope. Rather than treating biodiversity as a simple stock at equilibrium, developing a deeper understanding of the complex interactions—both between environmental drivers and between genetic and species diversity—is essential to manage and maintain the benefits that biodiversity delivers to humans, as well as to safeguard the intrinsic value of the Earth’s biodiversity for future generations.


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