scholarly journals Ecological Insights from the Evolutionary History of Microbial Innovations

2017 ◽  
Author(s):  
Mario E. Muscarella ◽  
James P. O’Dwyer
Keyword(s):  
Evolutionary History ◽  
Selective Advantage ◽  
Ecological Function ◽  
Transition Rates ◽  
Independent Evidence ◽  
Resource Degradation ◽  
A Genome ◽  
Evolutionary Relatedness ◽  
History Of ◽  
Open Question

Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity. Because these organisms and their traits directly impact ecosystems and human health, a focus on functional traits has become increasingly common in microbial ecology. These trait-based approaches have the potential to link microbial communities and their ecological function. But an open question is how, why, and in what order microorganisms acquired the traits we observe in the present day. To address this, we reconstructed the evolutionary history of microbial traits using genomic data to understand the evolution, selective advantage, and similarity of traits in extant organisms and provide insights into the composition of genomes and communities. We used the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Using this reconstructed evolutionary history, we explored hypotheses related to the composition of genomes. We showed that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many evolutionarily labile genes while specialist genomes comprise more highly conserved functional genes. These findings suggest that generalist organisms do not build up and hoard an array of functions, but rather tend to experiment with functions related to environmental sensing, transport, and complex resource degradation. Our results provide a framework for understanding the evolutionary history of extant microorganisms, the origin and maintenanceof traits, and linking evolutionary relatedness and ecological function.

scholarly journals Recombination-aware phylogenomics unravels the complex divergence of hybridizing species.

2018 ◽  
Author(s):  
Gang Li ◽  
Henrique V. Figueiro ◽  
Eduardo Eizirik ◽  
William J. Murphy
Keyword(s):  
Gene Flow ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Selective Sweeps ◽  
A Genome ◽  
Chromosome Recombination ◽  
History Of ◽  
Lineage Divergence ◽  
Recurrent Patterns ◽  
Ancient Gene

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

scholarly journals Insights on the process of reciprocal gene loss in the duplicate DPL genes of rice

2019 ◽  
Author(s):  
Xun Xu ◽  
Song Ge ◽  
Fu-min Zhang
Keyword(s):  
Evolutionary History ◽  
Gene Loss ◽  
Diploid Species ◽  
Recent Common Ancestor ◽  
Duplicate Genes ◽  
Evolutionary Divergence ◽  
Dna Transposons ◽  
B Genome ◽  
A Genome ◽  
History Of

Abstract Background: Reciprocal gene loss (RGL) of duplicate genes is an important genetic resource of reproductive isolation, which is essential for speciation. In the past decades, various RGL patterns have been revealed, but RGL process is still poorly understood. The RGL of the duplicate DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2) gene can lead to BDM-type hybrid incompatibility between two rice subspecies. The evolutionary history of the duplicate genes, including their origin and mechanism of duplication as well as their evolutionary divergence after the duplication, remains unclear. In this study, we investigated the evolutionary history of the duplicate genes for gaining insights into the process of RGL.Results: We reconstructed phylogenetic relationships of DPL copies from all 15 diploid species representing six genome types of rice genus and then found that all the DPL copies from the latest diverged A- and B-genome gather into one monophyletic clade. Southern blot analysis also detected definitely two DPL copies only in A- and B-genome. High conserved collinearity can be observed between A- and B-genomic segments containing DPL1 and DPL2 respectively but not between DPL1 and DPL2 segments. Investigations of transposon elements indicated that DPL duplication is related to DNA transposons. Likelihood-based analyses with branch models showed a relaxation of selective constraint in DPL1 lineage but an enhancement in DPL2 lineage after DPL duplication. Sequence analysis also indicated that quite a few defective DPL1 can be found in 6 wild and cultivated species out of all 8 species of A-genome but only one defective DPL2 occurs in a cultivated rice subspecies. Conclusions: DPL duplication of rice originated in the recent common ancestor of A- and B-genome about 6.76 million years ago and the duplication was possibly caused by DNA transposons. The DPL1 is a redundant copy and has being in the process of pseudogenization, suggesting that artificial selection may play an important role in forming the RGL of DPLs between two rice subspecies during the domestication.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals Evidence of ancient papillomavirus recombination

2006 ◽  
Vol 87 (9) ◽  
pp. 2527-2531 ◽  
Author(s):  
Arvind Varsani ◽  
Eric van der Walt ◽  
Livio Heath ◽  
Edward P. Rybicki ◽  
Anna Lise Williamson ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Papillomavirus ◽  
Evolutionary History ◽  
Full Genome ◽  
Genome Sequences ◽  
Aids Epidemic ◽  
Immunodeficiency Virus ◽  
History Of ◽  
Hpv Types ◽  
Open Question

An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised human immunodeficiency virus patients are often co-infected with extraordinarily diverse mixtures of human papillomavirus (HPV) types. It is expected that these conditions may facilitate the emergence of HPV recombinants, some of which might have novel pathogenic properties. Here, a range of rigorous analyses is applied to full-genome sequences of papillomaviruses to provide convincing statistical and phylogenetic evidence that evolutionarily relevant papillomavirus recombination can occur.

scholarly journals A genome‐wide linkage map for the house sparrow ( Passer domesticus ) provides insights into the evolutionary history of the avian genome

2020 ◽  
Vol 20 (2) ◽  
pp. 544-559 ◽  
Author(s):  
Ingerid J. Hagen ◽  
Sigbjørn Lien ◽  
Anna M. Billing ◽  
Tore O. Elgvin ◽  
Cassandra Trier ◽  
...  
Keyword(s):  
Linkage Map ◽  
Evolutionary History ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Genome Wide ◽  
A Genome ◽  
Avian Genome ◽  
History Of

Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Hikmet Budak ◽  
Robert C Shearman ◽  
Ismail Dweikat
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
Specific Marker ◽  
Buchloe Dactyloides ◽  
A Genome ◽  
Organelle Genomes ◽  
History Of

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalograss evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.Key words: buffalograss, evolution, organelle genomes, turfgrass.

scholarly journals A genome map ofSalmonella entericaserovar Agona: numerous insertions and deletions reflecting the evolutionary history of a human pathogen

2009 ◽  
Vol 293 (2) ◽  
pp. 188-195 ◽  
Author(s):  
Fang Chen ◽  
Cornelis Poppe ◽  
Gui-Rong Liu ◽  
Yong-Guo Li ◽  
Yi-Hong Peng ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Human Pathogen ◽  
Insertions And Deletions ◽  
A Genome ◽  
Genome Map ◽  
History Of

Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 714-723 ◽  
Author(s):  
S J McKay ◽  
J Trautner ◽  
M J Smith ◽  
B F Koop ◽  
R H Devlin
Keyword(s):  
Growth Hormone ◽  
Evolutionary History ◽  
Sequence Divergence ◽  
Genome Doubling ◽  
Disomic Inheritance ◽  
A Genome ◽  
Gh Gene ◽  
Average Sequence Divergence ◽  
History Of ◽  
Homeologous Chromosomes

A defining character of the piscine family Salmonidae is autotetraploidy resulting from a genome-doubling event some 25–100 million years ago. Initially, duplicated genes may have undergone concerted evolution and tetrasomic inheritance. Homeologous chromosomes eventually diverged and the resulting reduction in recombination and gene conversion between paralogous genes allowed the re-establishment of disomic inheritance. Among extant salmonine fishes (e.g. salmon, trout, char) the growth hormone (GH) gene is generally represented by two functional paralogs, GH1 and GH2. Sequence analyses of salmonid GH genes from species of subfamilies Coregoninae (whitefish, ciscos) and Salmoninae were used to examine the evolutionary history of the duplicated GH genes. Two divergent GH gene paralogs were also identified in Coregoninae, but they were not assignable to the GH1 and GH2 categories. The average sequence divergence between the coregonine GH genes was more than twofold lower than the corresponding divergence between the salmonine GH1 and GH2. Phylogenetic analysis of the coregonine GH paralogs did not resolve their relationship to the salmonine paralogs. These findings suggest that disomic inheritance of two GH genes was established by different mechanisms in these two subfamilies.Key words: salmon, phylogeny, growth hormone, disomy, tetraploidy.

scholarly journals How many species of the aquatic sloth Thalassocnus (Xenarthra: Megatheriidae) were in Chile?: new evidences from the Bahía Inglesa Formation, with a reappraisal of their biochronological affinities

2019 ◽  
Vol 46 (3) ◽  
pp. 693
Author(s):  
Javiera Peralta-Prato ◽  
Andrés Solórzano
Keyword(s):  
Evolutionary History ◽  
Pacific Coast ◽  
Taxonomic Diversity ◽  
Morphological Description ◽  
Distal Fragment ◽  
Northern Chile ◽  
Late Neogene ◽  
History Of ◽  
Open Question

The aquatic sloth, Thalassocnus, is one of the most intriguing lineage of mammal known from the southern pacific coast of South America during the late Neogene. It was initially recognized in Perú, but recent paleontological surveys also recorded its presence in Chile. However, the determination of how many species of Thalassocnus were actually present in Chile remains as an open question. Here, we provide a detailed morphological description of an isolated distal fragment of humerus recovered at the Mina Fosforita member (ca. 7 Ma), Bahía Inglesa Formation (Atacama Region, northern Chile), which is referred to Thalassocnus. Morphological comparisons with others forms from Chile and Perú allow us to attribute the CPUC/C/557 specimen to Thalassocnus cf. T. natans, though some degree of intraspecific variation is acknowledged. The assessment of the stratigraphic provenance of the materials with previously assigned to Thalassocnus from the Bahía Inglesa, Horcón and Coquimbo formations, permits us to propose that the taxonomic diversity of Thalassocnus in Chile is unequivocal conformed by T. carolomartini, and T. natans. We also admitted the likely presence of T. antiquus and probably T. yaucensis. Futures discoveries of more complete specimens, and/or the detailed analysis of undescribed specimens from Chile will undoubtedly contribute to illustrate the evolutionary history of the Thalassocnus radiation in Chile.

scholarly journals Reconstructing the Evolutionary History of Chromosomal Races on Islands: A Genome-Wide Analysis of Natural House Mouse Populations

2020 ◽  
Vol 37 (10) ◽  
pp. 2825-2837 ◽  
Author(s):  
Paolo Franchini ◽  
Andreas F Kautt ◽  
Alexander Nater ◽  
Gloria Antonini ◽  
Riccardo Castiglia ◽  
...  
Keyword(s):  
House Mouse ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Large Scale ◽  
Chromosomal Races ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Demographic Patterns ◽  
Aeolian Archipelago

Abstract Chromosomal evolution is widely considered to be an important driver of speciation, as karyotypic reorganization can bring about the establishment of reproductive barriers between incipient species. One textbook example for genetic mechanisms of speciation are large-scale chromosomal rearrangements such as Robertsonian (Rb) fusions, a common class of structural variants that can drastically change the recombination landscape by suppressing crossing-over and influence gene expression by altering regulatory networks. Here, we explore the population structure and demographic patterns of a well-known house mouse Rb system in the Aeolian archipelago in Southern Italy using genome-wide data. By analyzing chromosomal regions characterized by different levels of recombination, we trace the evolutionary history of a set of Rb chromosomes occurring in different geographical locations and test whether chromosomal fusions have a single shared origin or occurred multiple times. Using a combination of phylogenetic and population genetic approaches, we find support for multiple, independent origins of three focal Rb chromosomes. The elucidation of the demographic patterns of the mouse populations within the Aeolian archipelago shows that an interplay between fixation of newly formed Rb chromosomes and hybridization events has contributed to shaping their current karyotypic distribution. Overall, our results illustrate that chromosome structure is much more dynamic than anticipated and emphasize the importance of large-scale chromosomal translocations in speciation.

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