Faculty Opinions recommendation of Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence.

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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Systematics and biogeography of the “Metacryphaeus group” Calmoniidae (Trilobita, Devonian), with comments on adaptive radiations and the geological history of the Malvinokaffric Realm

Journal of Paleontology ◽

10.1017/s0022336000024902 ◽

1993 ◽

Vol 67 (4) ◽

pp. 549-570 ◽

Cited By ~ 27

Author(s):

Bruce S. Lieberman

Keyword(s):

New Species ◽

South African ◽

Evolutionary History ◽

Geological History ◽

Parsimony Analysis ◽

Evolutionary Patterns ◽

The Family ◽

History Of ◽

Adaptive Radiations ◽

Rapid Diversification

Phylogenetic parsimony analysis was used to classify the Siegenian–Eifelian “Metacryphaeus group” of the family Calmoniidae. Thirty-eight exoskeletal characters for 16 taxa produced a shortest-length cladogram with a consistency index of 0.49. A classification based on retrieving the structure of this cladogram recognizes nine genera: Typhloniscus Salter, Plesioconvexa n. gen., Punillaspis Baldis and Longobucco, Eldredgeia n. gen., Clarkeaspis n. gen., Malvinocooperella n. gen., Wolfartaspis Cooper, Plesiomalvinella Lieberman, Edgecombe, and Eldredge (used to represent the malvinellid clade), and Metacryphaeus Reed. The malvinellid clade is most closely related to a revised monophyletic Metacryphaeus. Typhloniscus is the basal member of the “Metacryphaeus group,” and the monotypic Wolfartaspis is sister to the clade containing the malvinellids and Metacryphaeus. Six new species are diagnosed: Punillaspis n. sp. A, “Clarkeaspis” gouldi, Clarkeaspis padillaensis, Malvinocooperella pregiganteus, Metacryphaeus curvigena, and Metacryphaeus branisai. Primitively, this group has South African and Andean affinities, and its evolutionary history suggests rapid diversification. In addition, evolutionary patterns in this group, and the distribution of character reversals, call into question certain notions about the nature of adaptive radiations. The distributions of taxa may answer questions about the number of marine transgressive/regressive cycles in the Emsian–Eifelian of the Malvinokaffric Realm.

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Evolution of the vertebrate globin gene family

Hemoglobin ◽

10.1093/oso/9780198810681.003.0005 ◽

2018 ◽

pp. 94-123

Author(s):

Jay F. Storz

Keyword(s):

Whole Genome Duplication ◽

Evolutionary History ◽

Functional Divergence ◽

Globin Gene ◽

Globin Genes ◽

Tandem Gene Duplication ◽

Animal Evolution ◽

Phylogenetic Reconstructions ◽

Duplication Events ◽

History Of

Chapter 5 provides an overview of the evolutionary history of the globin gene superfamily and places the evolution of vertebrate-specific globins in phylogenetic context. The duplication and functional divergence of globin genes has promoted key physiological innovations in respiratory gas transport and other physiological functions during animal evolution. A combination of both tandem gene duplication and whole-genome duplication contributed to the diversification of vertebrate globins. Phylogenetic reconstructions arrange vertebrate globins into those that derive from vertebrate-specific duplications (cytoglobin, globin E, globin Y, and the independently derived myoglobin-like and hemoglobin-like genes of jawed vertebrates and jawless fishes [lampreys and hagfish]) and those that derive from far more ancient duplication events that predate the divergence between deuterostomes and protostomes (androglobin, globin X, and neuroglobin). Tracing the evolutionary history of deuterostome globins reveals evidence for the repeated culling of ancestral diversity, followed by lineage-specific diversification of surviving gene lineages via repeated rounds of duplication and divergence.

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Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

PeerJ ◽

10.7717/peerj.9861 ◽

2020 ◽

Vol 8 ◽

pp. e9861

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis E. Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Marine Bacteria ◽

Evolutionary History ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Demethylation Pathway ◽

History Of ◽

New Gene ◽

Enzymatic Adaptation

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes

10.1101/2020.01.13.903906 ◽

2020 ◽

Author(s):

Sumanth Kumar Mutte ◽

Dolf Weijers

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Regulatory Proteins ◽

Protein Oligomerization ◽

Evolutionary Patterns ◽

Fundamental Process ◽

History Of ◽

Pb1 Domain ◽

Origin Of Eukaryotes ◽

Considerable Complexity

ABSTRACTProtein oligomerization is a fundamental process to build complex functional modules. Domains that facilitate the oligomerization process are diverse and widespread in nature across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is functionally (relatively) well understood in the animal kingdom. However, beyond animals, neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear how these relate to animal PB1 proteins.To address this question, we utilized large transcriptome datasets along with the proteomes of a broad range of species. We discovered eight PB1 domain-containing protein families in plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. Tertiary structural models of these plant PB1 families, combined with Random Forest based classification, indicated family-specific differences attributed to the length of PB1 domain and the proportion of β-sheets.This study identifies novel PB1 families and reveals considerable complexity in the protein oligomerization potential at the origin of eukaryotes. The newly identified relationships provide an evolutionary basis to understand the diverse functional interactions of key regulatory proteins carrying PB1 domains across eukaryotic life.

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MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

GigaScience ◽

10.1093/gigascience/giab036 ◽

2021 ◽

Vol 10 (5) ◽

Cited By ~ 1

Author(s):

Mengni Liu ◽

Jianyu Chen ◽

Xin Wang ◽

Chengwei Wang ◽

Xiaolong Zhang ◽

...

Keyword(s):

Phylogenetic Trees ◽

Evolutionary History ◽

Cancer Evolution ◽

Evolutionary Patterns ◽

Evolutionary Trajectory ◽

Wide Range ◽

Heterogeneous Features ◽

History Of ◽

Somatic Alterations ◽

Tumor Biopsies

Abstract Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.

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A Comprehensive Comparative Phylogenomics and Demographic Evolutionary History of the SARS-CoV-2

10.20944/preprints202005.0332.v1 ◽

2020 ◽

Author(s):

Özgül Doğan ◽

Ertan Mahir Korkmaz ◽

Mahir Budak ◽

Battal Çıplak ◽

Hasan Hüseyin Başıbüyük

Keyword(s):

Evolutionary History ◽

Demographic History ◽

Amino Acid Sequences ◽

Neutral Evolution ◽

Genomic Evolution ◽

Evolutionary Patterns ◽

Network Analyses ◽

Genome Data ◽

History Of

A new form of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) causing a recent pandemic outbreak possesses a linear positive ss-RNA genome with a length of 29,903 nt. Here, the genomes of SARS-CoV-2 from 821 samples were characterised for its better understanding of the genomic and evolutionary patterns. The phylogeny of SARS-CoV-2 was reconstructed using concatenated dataset consisting of all peptide encoding sequences under Bayesian Inference (BI) and Maximum Likelihood (ML) approaches. Comparison of all peptide encoding sequences reveals high divergence of amino acid sequences proportional to divergence of nucleotides, indicating that the viral genomic evolution has not been strictly neutral. The most part of the genome was under neutral evolution, however, the specific sites for peptide encoding sequences were evolved under positive selection. As well as providing reliable evidence on transmission routes of the SARS-CoV-2 outbreak, the phylogenetics and network analyses suggest the sample reported from Guangdong province is likely ancestor of the pandemic virus form. The overall substitution rate of SARS-CoV-2 genome was estimated to be 1.65 x 10-3 per site per year, falling within the range for previously reported RNA viruses. Median estimation of tMRCA from Bayesian coalescent analyses corresponds to 10 September 2019. The exponential growth rate (r), doubling time (Td) and R0 were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. These findings convincingly emphasise that the use of more comprehensive genome data improves robustness and also enhances understanding of the demographic history of the outbreak.

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Insights Into the Evolutionary History of the Subfamily Orthotrichoideae (Orthotrichaceae, Bryophyta): New and Former Supra-Specific Taxa So Far Obscured by Prevailing Homoplasy

Frontiers in Plant Science ◽

10.3389/fpls.2021.629035 ◽

2021 ◽

Vol 12 ◽

Author(s):

Isabel Draper ◽

Ricardo Garilleti ◽

Juan Antonio Calleja ◽

Maren Flagmeier ◽

Vicente Mazimpaka ◽

...

Keyword(s):

Evolutionary History ◽

New Genus ◽

Phylogenetic Reconstruction ◽

Morphological Characters ◽

Generic Level ◽

Evolutionary Patterns ◽

Molecular Phylogenetic ◽

History Of ◽

Epiphytic Communities ◽

Main Components

Mosses of the subfamily Orthotrichoideae represent one of the main components of the cryptogam epiphytic communities in temperate areas. During the last two decades, this taxonomical group has undergone an extensive revision that has led to its rearrangement at the generic level. However, their phylogenetic relationships and inferences on the evolutionary patterns that have driven the present diversity have little advanced. In this study, we present a dated molecular phylogenetic reconstruction at the subfamily level, including 130 samples that represent the 12 genera currently recognized within the subfamily, and the analysis of four molecular markers: ITS2, rps4, trnG, and trnL-F. We also analyze 13 morphological characters of systematic value to infer their origin and diagnostic utility within the subfamily. The phylogenetic reconstruction yields three main clades within the subfamily, two of which correspond to the tribe Zygodonteae, and one to Orthotricheae. Within Zygodonteae, the genus Zygodon results to be a polyphyletic artificial assembly, and we propose to separate a new genus named Australoria. Conversely, our results do not support the separation of Pentastichella and Pleurorthotrichum at the genus level and we therefore propose to include Pleurorthotrichum in Pentastichella. Regarding Orthotricheae, our analyses clearly allow the distinction of two subtribes: Orthotrichinae and Lewinskyinae. Within the latter, Ulota results a polyphyletic entity, and therefore we propose the segregation of a separate new genus named Atlantichella. Dating analyses allow us to conclude that the split of the tribes within Orthotrichoideae dates from the Middle Jurassic, while the diversification of Orthotrichum and Zygodon probably started during the Late Cretaceous. However, most of the extant genera of this subfamily seem to be younger, and apparently its highest diversification burst took place during the Oligocene. Finally, the analysis of the morphological traits reveals that most of the characters previously used to separate genera and here tested are homoplastic, which has hindered the taxonomical and systematic proposals for decades. However, even if there are no exclusive characters, all of the genera can be defined by the combination of a few characters.

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Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation

Genome Biology ◽

10.1186/s13059-021-02467-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Abraham Morales-Cruz ◽

Jonas A. Aguirre-Liguori ◽

Yongfeng Zhou ◽

Andrea Minio ◽

Summaira Riaz ◽

...

Keyword(s):

Evolutionary History ◽

Introgressive Hybridization ◽

Ecological Niches ◽

Evolutionary Patterns ◽

Adaptive Introgression ◽

Reference Genome Assembly ◽

Abiotic Stressors ◽

Bioclimatic Variables ◽

Species Pairs ◽

History Of

Abstract Background Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. Results By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce’s disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. Conclusions Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.

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