scholarly journals xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria

2017 ◽  
Author(s):  
Eliot C Bush ◽  
Anne E Clark ◽  
Carissa A DeRanek ◽  
Alexander Eng ◽  
Juliet Forman ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genomic Island ◽  
Gene Families ◽  
Enteric Bacteria ◽  
Genomic Islands ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
History Of ◽  
Multiple Strains

AbstractBackgroundGenomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based and comparative have been developed to identify them. Some of these methods are explicitly designed to work in single strains, while others make use of multiple strains. In general, existing methods do not identify islands in the context of the phylogeny in which they evolved. Even multiple strain approaches are best suited to identifying genomic islands that are present in one strain but absent in others. They do not automatically recognize islands which are shared between some strains in the clade or determine the branch on which these islands inserted within the phylogenetic tree.ResultsWe have developed a software package, xenoGI, that identifies genomic islands and maps their origin within a clade of closely related bacteria, determining which branch they inserted on. It takes as input a set of sequenced genomes and a tree specifying their phylogenetic relationships. Making heavy use of synteny information, the package builds gene families in a species-tree-aware way, and then attempts to combine into islands those families whose members are adjacent and whose most recent common ancestor is shared. The package provides a variety of text-based analysis functions, as well as the ability to export genomic islands into formats suitable for viewing in a genome browser. We demonstrate the capabilities of the package with several examples from enteric bacteria, including an examination of the evolution of the acid fitness island in the genus Escherichia. In addition we use output from simulations and a set of known genomic islands from the literature to show that xenoGI can accurately identify genomic islands and place them on a phylogenetic tree.ConclusionsxenoGI is an effective tool for studying the history of genomic island insertions in a clade of microbes. It identifies genomic islands, and determines which branch they inserted on within the phylogenetic tree for the clade. Such information is valuable because it helps us understand the adaptive path that has produced living species. Given the large and growing number of sequenced microbial genomes, this sort of analysis will become increasingly useful in the future.

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

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

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.

scholarly journals Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

scholarly journals Age and rate of diversification of the Hawaiian silversword alliance (Compositae)

1998 ◽  
Vol 95 (16) ◽  
pp. 9402-9406 ◽  
Author(s):  
Bruce G. Baldwin ◽  
Michael J. Sanderson
Keyword(s):  
Common Ancestor ◽  
Error Variance ◽  
Diversification Rate ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Sequence Evolution ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Fossil Records ◽  
Fossil Data

Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an “external” calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 ± 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (≤5.1 ± 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 ± 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.

scholarly journals Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event

2005 ◽  
Vol 79 (3) ◽  
pp. 1595-1604 ◽  
Author(s):  
Leen Vijgen ◽  
Els Keyaerts ◽  
Elien Moës ◽  
Inge Thoelen ◽  
Elke Wollants ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Complete Genome ◽  
Recent Common Ancestor ◽  
Human Coronavirus ◽  
Transmission Event ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
Clock Analysis ◽  
Group 2 ◽  
Molecular Clock Analysis

ABSTRACT Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10−4 nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

scholarly journals A closer look at pupil diversity and evolution in frogs and toads

2021 ◽  
Vol 288 (1957) ◽  
pp. 20211402
Author(s):  
Nadia G. Cervino ◽  
Agustín J. Elias-Costa ◽  
Martín O. Pereyra ◽  
Julián Faivovich
Keyword(s):  
Life Histories ◽  
Activity Patterns ◽  
Diel Activity ◽  
Recent Common Ancestor ◽  
Evolutionary Patterns ◽  
Most Recent Common Ancestor ◽  
Diel Activity Patterns ◽  
History Of ◽  
Ecological Versatility

The eyes of frogs and toads (Anura) are among their most fascinating features. Although several pupil shapes have been described, the diversity, evolution, and functional role of the pupil in anurans have received little attention. Studying photographs of more than 3200 species, we surveyed pupil diversity, described their morphological variation, tested correlation with adult habits and diel activity, and discuss major evolutionary patterns considering iris anatomy and visual ecology. Our results indicate that the pupil in anurans is a highly plastic structure, with seven main pupil shapes that evolved at least 116 times during the history of the group. We found no significant correlation between pupil shape, adult habits, and diel activity, with the exception of the circular pupil and aquatic habits. The vertical pupil arose at least in the most-recent common ancestor of Anura + Caudata, and this morphology is present in most early-diverging anuran clades. Subsequently, a horizontal pupil, a very uncommon shape in vertebrates, evolved in most neobatrachian frogs. This shape evolved into most other known pupil shapes, but it persisted in a large number of species with diverse life histories, habits, and diel activity patterns, demonstrating a remarkable functional and ecological versatility.

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 Diversity and Paleodemography of the Addax (Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1236
Author(s):  
Elisabeth Hempel ◽  
Michael V. Westbury ◽  
José H. Grau ◽  
Alexandra Trinks ◽  
Johanna L. A. Paijmans ◽  
...  
Keyword(s):  
Population Size ◽  
Population History ◽  
Phylogeographic Structure ◽  
Recent Common Ancestor ◽  
Mitochondrial Genomes ◽  
Effective Population ◽  
Mammal Species ◽  
Human Disturbances ◽  
Most Recent Common Ancestor ◽  
History Of

Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.

scholarly journals Early Archean origin of Photosystem II

2017 ◽  
Author(s):  
Tanai Cardona ◽  
Patricia Sánchez-Baracaldo ◽  
A. William Rutherford ◽  
Anthony W. D. Larkum
Keyword(s):  
Photosystem Ii ◽  
Reaction Center ◽  
Water Oxidation ◽  
Photochemical Reaction ◽  
Early Stage ◽  
Oxygenic Photosynthesis ◽  
Recent Common Ancestor ◽  
Molecular Clocks ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractPhotosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of Eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale we hypothesize that this early Archean photosystem was capable of water oxidation and had already evolved some level of protection against the formation of reactive oxygen species, which would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.

scholarly journals Population Genetic Analysis of the DARC Locus (Duffy) Reveals Adaptation from Standing Variation Associated with Malaria Resistance in Humans

2016 ◽  
Author(s):  
Kimberly F. McManus ◽  
Angela Taravella ◽  
Brenna Henn ◽  
Carlos D. Bustamante ◽  
Martin Sikora ◽  
...  
Keyword(s):  
Plasmodium Vivax ◽  
Evolutionary History ◽  
Sub Saharan Africa ◽  
Recent Common Ancestor ◽  
Human Populations ◽  
Selection Coefficient ◽  
Population Genetic Analysis ◽  
Most Recent Common Ancestor ◽  
Standing Variation ◽  
History Of

AbstractThe human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of its strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of a locus under positive selection in humans.Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human and great ape genomes, to analyze the fine scale population structure of DARC. We estimate the time to most recent common ancestor (TMRCA) of the FY*O mutation to be 42 kya (95% CI: 34–49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011–0.18), which is among the strongest estimated in the genome. We estimate the TMRCA of the FY*A mutation to be 57 kya (95% CI: 48–65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause.Author SummaryInfectious diseases have undoubtedly played an important role in ancient and modern human history. Yet, there are relatively few regions of the genome involved in resistance to pathogens that have shown a strong selection signal. We revisit the evolutionary history of a gene associated with resistance to the most common malaria-causing parasite, Plasmodium vivax, and show that it is one of regions of the human genome that has been under strongest selective pressure in our evolutionary history (selection coefficient: 5%). Our results are consistent with a complex evolutionary history of the locus involving selection on a mutation that was at a very low frequency in the ancestral African population (standing variation) and a large differentiation between European, Asian and African populations.

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

PeerJ ◽  
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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