ConSpeciFix: classifying prokaryotic species based on gene flow
نویسندگان
چکیده
منابع مشابه
On the origin of prokaryotic species.
The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call "species" is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept -- by which is meant a genetic and ecological theory of speciation -- might best expl...
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Species are commonly thought to be evolutionarily independent in a way that populations within a species are not. In recent years, studies that seek to identify evolutionarily independent lineages (i.e., to delimit species) using genetic data have typically adopted multispecies coalescent approaches that assume that evolutionary independence is formed by the differential sorting of ancestral al...
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A defining feature of species is that their constituting populations are connected by gene flow. However, interspecific gene flow (introgression) can affect species integrity. If some genome components were less prone to introgression than others, they should be particularly suitable to delimitate species. Recent simulation studies have predicted a negative correlation between intra- and inters...
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Engineering of synthetic gene circuits is a rapidly growing discipline, currently dominated by prokaryotic transcription networks, which can be easily rearranged or rewired to give different output behaviours. In this review, we examine both a rational and a combinatorial design of such networks and discuss progress on using in vitro evolution techniques to obtain functional systems. Moving bey...
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Most current methods for inferring species-level phylogenies under the coa-lescent model assume that no gene flow occurs following speciation. Several studies have examined the impact of gene flow (e.g., Eckert and Carstens (2008); Chung and Ané (2011); Leaché et al. (2014); Solís-Lemus et al. (2016)) and of ancestral population structure (DeGeorgio and Rosenberg, 2016) on the performance of sp...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2018
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bty400