Abstract
BackgroundThe rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people.ResultsWe focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations.ConclusionsAlthough geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.
Highlights
The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity
Assessment of linkage disequilibrium The admixture model implemented in STRUCTURE assigns individual genomes to populations under the assumption that all polymorphic sites within the genomes are in linkage equilibrium
We tested the degree of linkage equilibrium that is evident within begomovirus genomes using LIAN 3.4 to calculate a standardized index of association between genome sites (ISA)
Summary
The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. The study of genome-wide patterns of sequence variation within and between closely related virus species can be used to efficiently infer the fine-scale genetic structures of virus populations. Information on population structures - that pertaining to stratification and admixture (i.e. gene flow) - is valuable in a variety of situations These include the establishment of sensible species/subspecies/strain classification criteria, the detection of geographical or biological barriers to gene flow, and the identification of demographic, epidemiological. A seventh group of Sweet potato-infecting viruses (swepoviruses) is found in both the Old and New Worlds [20] This phylogenetic sub-division of the begomoviruses broadly corresponds with their geographical distributions [20] except that the divergent legumovirus and swepovirus [20,21] lineages occur alongside other distantly related begomovirus groups
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