scholarly journals Reconstructed evolutionary history of the yeast septins Cdc11 and Shs1

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Julie Takagi ◽  
Christina Cho ◽  
Angela Duvalyan ◽  
Yao Yan ◽  
Megan Halloran ◽  
...  
Keyword(s):  
Recent Common Ancestor ◽  
Subunit Structure ◽  
Terminal Position ◽  
Yeast Saccharomyces Cerevisiae ◽  
Evolutionary Pathway ◽  
Ancestral Gene ◽  
Most Recent Common Ancestor ◽  
Extension Domain ◽  
Evolutionary Variation ◽  
History Of

Abstract Septins are GTP-binding proteins conserved across metazoans. They can polymerize into extended filaments and, hence, are considered a component of the cytoskeleton. The number of individual septins varies across the tree of life—yeast (Saccharomyces cerevisiae) has seven distinct subunits, a nematode (Caenorhabditis elegans) has two, and humans have 13. However, the overall geometric unit (an apolar hetero-octameric protomer and filaments assembled there from) has been conserved. To understand septin evolutionary variation, we focused on a related pair of yeast subunits (Cdc11 and Shs1) that appear to have arisen from gene duplication within the fungal clade. Either Cdc11 or Shs1 occupies the terminal position within a hetero-octamer, yet Cdc11 is essential for septin function and cell viability, whereas Shs1 is not. To discern the molecular basis of this divergence, we utilized ancestral gene reconstruction to predict, synthesize, and experimentally examine the most recent common ancestor (“Anc.11-S”) of Cdc11 and Shs1. Anc.11-S was able to occupy the terminal position within an octamer, just like the modern subunits. Although Anc.11-S supplied many of the known functions of Cdc11, it was unable to replace the distinct function(s) of Shs1. To further evaluate the history of Shs1, additional intermediates along a proposed trajectory from Anc.11-S to yeast Shs1 were generated and tested. We demonstrate that multiple events contributed to the current properties of Shs1: (1) loss of Shs1–Shs1 self-association early after duplication, (2) co-evolution of heterotypic Cdc11–Shs1 interaction between neighboring hetero-octamers, and (3) eventual repurposing and acquisition of novel function(s) for its C-terminal extension domain. Thus, a pair of duplicated proteins, despite constraints imposed by assembly into a highly conserved multi-subunit structure, could evolve new functionality via a complex evolutionary pathway.

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 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 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 The Most Recent Common Ancestor of Modern Humans was Born in Eurasia

2020 ◽  
Author(s):  
vicente cabrera
Keyword(s):  
Human Evolution ◽  
Genome Sequencing ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
African Origin ◽  
Modern Humans ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
New Vision

Ancient DNA has given a new vision to the recent history of human evolution. However, by always relying on the information provided by whole genome sequencing, some relevant relationships between modern humans and its archaic relatives have been misinterpreted by hybridization and recombination causes. In contrast, the congruent phylogeny, obtained from non-recombinant uniparental markers, indicates that humans and Neanderthals are sister subspecies, and that the most recent common ancestor of modern humans was not of African origin but Eurasian.

scholarly journals The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3844 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y.W. Ho ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Ancestral State ◽  
Crown Group ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
The Tropics ◽  
Age Constraints

The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, withHemisquillaas the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.

Phylogeography and evolutionary history of hepatitis E virus genotype 3 in Argentina

2021 ◽  
Author(s):  
María B Pisano ◽  
Andrés C A Culasso ◽  
Nancy Altabert ◽  
Maribel G Martínez Wassaf ◽  
Silvia V Nates ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Recent Common Ancestor ◽  
Genotype 3 ◽  
Posterior Density ◽  
Virus Genotype ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Highest Posterior Density

Abstract Background Few studies about the evolutionary history of the hepatitis E virus (HEV) have been conducted. The aim of our work was to investigate and make inferences about the origin and routes of dispersion of HEV-3 in Argentina. Methods Phylogenetic, coalescent and phylogeographic analyses were performed using a 322-bp ORF2 genomic fragment of all HEV-3 sequences with known date and place of isolation published at GenBank until May 2018 (n=926), including 16 Argentinian sequences (isolated from pigs, water and humans). Results Phylogenetic analysis revealed two clades within HEV-3: abchij and efg. All Argentinian samples were grouped intermingled within clade 3abchij. The coalescent analysis showed that the most recent common ancestor for the clade 3abchij would have existed around the year 1967 (95% highest posterior density (HPD): 1963–1970). The estimated substitution rate was 1.01×10−2 (95%HPD: 9.3×10ˉ3–1.09×10ˉ2) substitutions/site/y, comparable with the rate previously described. The phylogeographic approach revealed a correspondence between phylogeny and place of origin for Argentinian samples, suggesting many HEV introductions in the country, probably from Europe and Japan. Conclusions This is the first evolutionary inference of HEV-3 that includes Argentinian strains, showing the circulation of many HEV-3 subtypes, obtained from different sources and places, with recent diversification processes. Accession numbers [KX812460], [KX812461], [KX812462], [KX812465], [KX812466], [KX812467], [KX812468], [KX812469].

scholarly journals Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe

2019 ◽  
Vol 5 (6) ◽  
pp. eaaw5873 ◽  
Author(s):  
Stéphane Peyrégne ◽  
Viviane Slon ◽  
Fabrizio Mafessoni ◽  
Cesare de Filippo ◽  
Mateja Hajdinjak ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Nuclear Dna ◽  
Population History ◽  
The Other ◽  
Genomic Sequences ◽  
Recent Common Ancestor ◽  
Mitochondrial Lineage ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Genetic Continuity

Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.

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