A Critique of Prokaryotic Species Concepts

Papke, R. Thane

doi:10.1007/978-1-60327-853-9_22

Cited by 21 publications

(17 citation statements)

References 77 publications

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“…A similar observation was made for a set of Halorubrum isolates where the a single bop allele was found in >85% of the strains and this was interpreted as being in part the result of selection, which drove the allele to high frequency (Papke, 2009). This explanation is compatible with some of the genes examined within the T. uzonensis population.…”

Section: Discussionsupporting

confidence: 62%

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

Wagner¹,

Varghese²,

Hemme³

et al. 2013

Front. Microbiol.

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Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances.

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Section: Discussionsupporting

confidence: 62%

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

Wagner¹,

Varghese²,

Hemme³

et al. 2013

Front. Microbiol.

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“…This fact contradicts the assumption that the main trend in prokaryotic evolution is simplification of the genome of a particular individual compensated by complex interactions in the bacterial community (metagenome). 31 In the long run, oversimplification will kill the community.…”

Section: Discussionmentioning

confidence: 99%

Comparative Modeling of Coevolution in Communities of Unicellular Organisms: Adaptability and Biodiversity

Lashin

Суслов

Matushkin

2010

J. Bioinform. Comput. Biol.

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We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also present results of comparative modeling of stability, adaptability and biodiversity dynamics in populations of unicellular haploid organisms which form symbiotic ecosystems. The advantages and disadvantages of two evolutionary strategies of biota formation -a few generalists' taxa-based biota formation and biodiversity-based biota formation -are discussed.

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“…In the same way that interbreeding in animals results in the persistence of animal traits over time, bias in HGT partners in the microbial world is an important mechanism in creating biological coherence (Bapteste and Boucher 2009;Papke 2009). Perhaps it is time to embrace the fact that similarity as used in taxonomy and systematics is founded, not on a single evolutionary process, but on a panoply of forces of varying magnitude and consequence at different branches in the tree of life (Bapteste et al 2009).…”

Section: Hgt As a Force That Can Create Patterns Similar To Vertical mentioning

confidence: 98%

Natural taxonomy in light of horizontal gene transfer

2010

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We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns in microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied.

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A Critique of Prokaryotic Species Concepts

Cited by 21 publications

References 77 publications

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia

Comparative Modeling of Coevolution in Communities of Unicellular Organisms: Adaptability and Biodiversity

Natural taxonomy in light of horizontal gene transfer

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