Dataset Information

Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America.

ABSTRACT: Disentangling the historical evolutionary processes that contribute to patterns of phenotypic and genetic variation is important for understanding contemporary patterns of both traits of interest and genetic diversity of a species. Ipomoea hederacea is a self-compatible species whose geographic origin is contested, and previous work suggests that although there are signals of adaptation (significant leaf shape and flowering time clines), no population structure or neutral genetic differentiation of I. hederacea populations was detected. Here, we use DNA sequence data to characterize patterns of genetic variation to establish a more detailed understanding of the current and historical processes that may have generated the patterns of genetic variation in this species. We resequenced ca. 5000 bp across 7 genes for 192 individuals taken from 24 populations in North America. Our results indicate that North American I. hederacea populations are ubiquitously genetically depauperate, and patterns of nucleotide diversity are consistent with population expansion. Contrary to previous findings, we discovered significant population subdivision and isolation-by-distance, but genetic structure was spatially discontinuous, potentially implicating long-distance dispersal. We further found significant genetic differentiation at sequenced loci but nearly fourfold stronger differentiation at the leaf shape locus, strengthening evidence that the leaf shape locus is under divergent selection. We propose that North American I. hederacea has experienced a recent founder event, and/or population dynamics are best described by a metapopulation model (high turnover and dispersal), leading to low genetic diversity and a patchy genetic distribution.

SUBMITTER: Campitelli BE

PROVIDER: S-EPMC4132172 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature

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Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America.

Campitelli Brandon E BE Stinchcombe John R JR

G3 (Bethesda, Md.) 20140603 8

Disentangling the historical evolutionary processes that contribute to patterns of phenotypic and genetic variation is important for understanding contemporary patterns of both traits of interest and genetic diversity of a species. Ipomoea hederacea is a self-compatible species whose geographic origin is contested, and previous work suggests that although there are signals of adaptation (significant leaf shape and flowering time clines), no population structure or neutral genetic differentiation ...[more]

PMID: 24898709

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Project description:The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribunyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach.IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.

Dataset Information

Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America.

Publications

Population dynamics and evolutionary history of the weedy vine Ipomoea hederacea in North America.

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