scholarly journals Evolution of the extracytoplasmic function σ factor protein family

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Daniela Pinto ◽  
Rute R da Fonseca
Keyword(s):  
Soil Bacteria ◽  
Scientific Community ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Σ Factor ◽  
History Of ◽  
Promoter Specificity ◽  
Partner Proteins ◽  
Relevant Gene ◽  
Recent Duplication

Abstract Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF σ factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF σ factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF σ factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated σ factor. At last, we also demonstrate horizontal transfer of ECF σ factors between soil bacteria.

Rhizobial plasmids — replication, structure and biological role

2012 ◽  
Vol 7 (4) ◽  
pp. 571-586 ◽  
Author(s):  
Andrzej Mazur ◽  
Piotr Koper
Keyword(s):  
Genome Organization ◽  
Soil Bacteria ◽  
Evolutionary History ◽  
Bacterial Genome ◽  
Biological Role ◽  
Genome Architecture ◽  
Genomic Knowledge ◽  
History Of ◽  
Cryptic Plasmids ◽  
Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

scholarly journals Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9980
Author(s):  
José J. Nuñez ◽  
Elkin Y. Suárez-Villota ◽  
Camila A. Quercia ◽  
Angel P. Olivares ◽  
Jack W. Sites Jr
Keyword(s):  
Population Structure ◽  
Species Distribution ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Glacial Refugia ◽  
Species Distribution Modelling ◽  
Wood Frog ◽  
Type I ◽  
Distribution Modelling ◽  
History Of

Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.

scholarly journals Darwin wasps: a new name heralds renewed efforts to unravel the evolutionary history of Ichneumonidae

2019 ◽  
Vol 1 ◽  
pp. ec01006 ◽  
Author(s):  
Seraina Klopfstein ◽  
Bernardo F. Santos ◽  
Mark R. Shaw ◽  
Mabel Alvarado ◽  
Andrew M.R. Bennett ◽  
...  
Keyword(s):  
Scientific Community ◽  
Evolutionary History ◽  
Charles Darwin ◽  
Current Knowledge ◽  
Parasitoid Wasp ◽  
Pivotal Role ◽  
Species Discovery ◽  
New Name ◽  
The Family ◽  
History Of

The parasitoid wasp family Ichneumonidae is arguably one of the groups for which current knowledge lags most strongly behind their enormous diversity. In a five-day meeting in Basel (Switzerland) in June 2019, 22 researchers from 14 countries met to discuss the most important issues in ichneumonid research, including increasing the speed of species discovery, resolving higher-level relationships, and studying the radiation of these parasitoids onto various host groups through time. All agreed that it is time to advertise ichneumonid research more broadly in the scientific community and thereby attract young talents to this group for which specialists are sorely lacking. In order to popularize the group, we here suggest a new name for the family, “Darwin wasps”, to reflect the pivotal role they played in convincing Charles Darwin that not all of creation could have been created by a benevolent god. We hope that the name catches on, and that Darwin wasps start buzzing more loudly across all disciplines of biology.

scholarly journals Evolution of 14-3-3 Proteins in Angiosperm Plants: Recurring Gene Duplication and Loss

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2724
Author(s):  
Yulia V. Mikhaylova ◽  
Roman K. Puzanskiy ◽  
Maria F. Shishova
Keyword(s):  
Gene Duplication ◽  
Evolutionary History ◽  
Basal Angiosperm ◽  
Physiological Processes ◽  
Gene Duplication And Loss ◽  
Duplication Events ◽  
History Of ◽  
Angiosperm Species ◽  
Opposite Manner ◽  
Recent Duplication

14-3-3 proteins are key regulatory factors in plants and are involved in a broad range of physiological processes. We addressed the evolutionary history of 14-3-3s from 46 angiosperm species, including basal angiosperm Amborella and major lineage of monocotyledons and eudicotyledons. Orthologs of Arabidopsis isoforms were detected. There were several rounds of duplication events in the evolutionary history of the 14-3-3 protein family in plants. At least four subfamilies (iota, epsilon, kappa, and psi) formed as a result of ancient duplication in a common ancestor of angiosperm plants. Recent duplication events followed by gene loss in plant lineage, among others Brassicaceae, Fabaceae, and Poaceae, further shaped the high diversity of 14-3-3 isoforms in plants. Coexpression data showed that 14-3-3 proteins formed different functional groups in different species. In some species, evolutionarily related groups of 14-3-3 proteins had coexpressed together under certain physiological conditions, whereas in other species, closely related isoforms expressed in the opposite manner. A possible explanation is that gene duplication and loss is accompanied by functional plasticity of 14-3-3 proteins.

scholarly journals Native <i>Dreissena</i> freshwater mussels in the Balkans: in and out of ancient lakes

2010 ◽  
Vol 7 (10) ◽  
pp. 3051-3065 ◽  
Author(s):  
T. Wilke ◽  
R. Schultheiß ◽  
C. Albrecht ◽  
N. Bornmann ◽  
S. Trajanovski ◽  
...  
Keyword(s):  
Native Species ◽  
Evolutionary History ◽  
Environmental Changes ◽  
Substantial Part ◽  
Ancient Lakes ◽  
Lake Ohrid ◽  
The Balkans ◽  
History Of ◽  
Limited Gene Flow ◽  
Time Frames

Abstract. The Balkans is a biogeographically highly diverse region and a worldwide hotspot of endemic freshwater diversity. A substantial part of this diversity is attributed to well recognized and potential ancient lakes in its southwestern part. However, despite considerable research efforts, faunal relationships among those lakes are not well understood. Therefore, genetic information from native representatives of the mussel genus Dreissena is here used to test the biogeographical zonation of the southwestern Balkans, to relate demographic changes to environmental changes, to assess the degree of eco-insularity, to reconstruct their evolutionary history, and to explore the potential of native taxa for becoming invasive. Phylogeographical and population genetic analyses indicate that most studied populations belong to two native species: D. presbensis (including the distinct genetic subgroup from Lake Ohrid, "D. stankovici") and D. blanci. In addition, the first confirmed record of invasive D. polymorpha in the southwestern Balkan is presented. The distribution of native Dreissena spp. generally coincides with the biogeographical zonations previously suggested based on fish data. However, there is disagreement on the assignment of the ancient lakes in the area to respective biogeographical regions. The data for Lake Ohrid are not conclusive. A closer biogeographical connection to lakes of the Vardar region and possibly the northern Ionian region is, however, suggested for Lake Prespa. The reconstruction of the evolutionary history of Dreissena spp. suggests that populations underwent demographic and spatial expansions in the recent past. Expansions started around 320 000–300 000 years ago in "D. stankovici", 160 000–140 000 years ago in D. blanci, and 110 000–70 000 years ago in D. presbensis. These time frames are discussed within the context of available paleogeological data for lakes Ohrid and Prespa. It is suggested that regional environmental changes may have had pronounced effects on the population histories of native Dreissena spp., though the high buffer capacity of Lake Ohrid may have lessened these effects in "D. stankovici". In addition, local events influencing individual lakes had very likely considerable effects on the demographic histories of Dreissena spp. as well. The observed patterns of immigration and emigration in and out of ancient lakes may suggest that limited gene flow enabled the survival of few isolated subpopulations and that later on eco-insularity (selective advantages of locally adopted groups) may have prevented excessive hybridization and sympatry of closely related taxa. As for the potential invasiveness of native Dreissena spp., the inferred spatial expansions are not human-mediated and all taxa still appear to be restricted to their native ranges. A concern, however, is that today D. presbensis and D. blanci also occur in artificial water bodies, and that invasive D. polymorpha has reached the area.

scholarly journals Untangling the Evolutionary History of European Bison (Bison bonasus)

2018 ◽  
Author(s):  
Ayla L. van Loenen ◽  
Emilia Hofman-Kamińska ◽  
Kieren J. Mitchell ◽  
Bastien Llamas ◽  
Hervé Bocherens ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Environmental Changes ◽  
Population History ◽  
Mitochondrial Genomes ◽  
European Bison ◽  
Bison Bonasus ◽  
Anthropogenic Pressures ◽  
Eurasian Continent ◽  
History Of ◽  
Rapid Environmental Change

ABSTRACTEuropean bison (Bison bonasus) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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