Large scale diversity reassessment, evolutionary history, and taxonomic revision of the green macroalgae family Udoteaceae (Bryopsidales, Chlorophyta)

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Download Full-text

New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences

Viruses ◽

10.3390/v10110586 ◽

2018 ◽

Vol 10 (11) ◽

pp. 586 ◽

Cited By ~ 5

Author(s):

Tomaž Zorec ◽

Denis Kutnjak ◽

Lea Hošnjak ◽

Blanka Kušar ◽

Katarina Trčko ◽

...

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Nk Cell ◽

Molluscum Contagiosum ◽

Molluscum Contagiosum Virus ◽

Genome Sequences ◽

Viral Interference ◽

Genomic Landscape ◽

Genetic Landscape ◽

Common Skin

Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and the causative agent of molluscum contagiosum (MC), a common skin disease. Although it is an important and frequent human pathogen, its genetic landscape and evolutionary history remain largely unknown. In this study, ten novel complete MCV genome sequences of the two most common MCV genotypes were determined (five MCV1 and five MCV2 sequences) and analyzed together with all MCV complete genomes previously deposited in freely accessible sequence repositories (four MCV1 and a single MCV2). In comparison to MCV1, a higher degree of nucleotide sequence conservation was observed among MCV2 genomes. Large-scale recombination events were identified in two newly assembled MCV1 genomes and one MCV2 genome. One recombination event was located in a newly identified recombinant region of the viral genome, and all previously described recombinant regions were re-identified in at least one novel MCV genome. MCV genes comprising the identified recombinant segments have been previously associated with viral interference with host T-cell and NK-cell immune responses. In conclusion, the two most common MCV genotypes emerged along divergent evolutionary pathways from a common ancestor, and the differences in the heterogeneity of MCV1 and MCV2 populations may be attributed to the strictness of the constraints imposed by the host immune response.

Download Full-text

Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmen Neosadocus Mello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae)

10.1101/2021.03.25.436954 ◽

2021 ◽

Author(s):

Daniel Castro Pereira ◽

Elen A. Peres ◽

Ricardo Pinto-da-Rocha

Keyword(s):

Atlantic Forest ◽

Reproductive Strategies ◽

Evolutionary History ◽

Taxonomic Revision ◽

Brazilian Atlantic Forest ◽

Nuclear Markers ◽

Physiological Constraints ◽

Male Polymorphism ◽

Female Holotype ◽

Molecular Phylogenetic

Neosadocus harvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution about Neosadocus includes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species' diversity in a phylogeographical framework. Our results show that Neosadocus is a monophyletic group and comprises four species: N. bufo, N. maximus, N. robustus and N. misandrus (which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism in N. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work: Bunoweyhia variabilis Mello-Leitão, 1935 = Neosadocus bufo (Mello-Leitão, 1926); and Bunoweyhia minor Mello-Leitão, 1935 = Neosadocus maximus (Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.

Download Full-text

Evolutionary heritage influences Amazon tree ecology

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1587 ◽

2016 ◽

Vol 283 (1844) ◽

pp. 20161587 ◽

Cited By ~ 21

Author(s):

Fernanda Coelho de Souza ◽

Kyle G. Dexter ◽

Oliver L. Phillips ◽

Roel J. W. Brienen ◽

Jerome Chave ◽

...

Keyword(s):

Life History ◽

Evolutionary History ◽

Large Scale ◽

Phylogenetic Signal ◽

Life History Strategies ◽

Relative Importance ◽

Life History Variation ◽

Trait Variation ◽

Closed Canopy ◽

Repeated Evolution

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change.

Download Full-text

RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽

10.1186/s43008-020-00040-0 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Yi Li ◽

Lan Jiang ◽

Ke Wang ◽

Hai-Jun Wu ◽

Rui-Heng Yang ◽

...

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Its Region ◽

Wide Distribution ◽

Specific Primers ◽

Ophiocordyceps Sinensis ◽

Single Genome ◽

History Of ◽

Geographic Populations ◽

Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

Download Full-text

Not all written in stone: interdisciplinary syntheses in echinoderm paleontology

Canadian Journal of Zoology ◽

10.1139/z00-217 ◽

2001 ◽

Vol 79 (7) ◽

pp. 1209-1231 ◽

Cited By ~ 16

Author(s):

Rich Mooi

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Body Wall ◽

Developmental Trajectories ◽

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Primary Target ◽

The Past ◽

Broad Scale

The fossil record of the Echinodermata is relatively complete, and is represented by specimens retaining an abundance of features comparable to that found in extant forms. This yields a half-billion-year record of evolutionary novelties unmatched in any other major group, making the Echinodermata a primary target for studies of biological change. Not all of this change can be understood by studying the rocks alone, leading to synthetic research programs. Study of literature from the past 20 years indicates that over 1400 papers on echinoderm paleontology appeared in that time, and that overall productivity has remained almost constant. Analysis of papers appearing since 1990 shows that research is driven by new finds including, but not restricted to, possible Precambrian echinoderms, bizarre new edrioasteroids, early crinoids, exquisitely preserved homalozoans, echinoids at the K-T boundary, and Antarctic echinoids, stelleroids, and crinoids. New interpretations of echinoderm body wall homologies, broad-scale syntheses of embryological information, the study of developmental trajectories through molecular markers, and the large-scale ecological and phenotypic shifts being explored through morphometry and analyses of large data sets are integrated with study of the fossils themselves. Therefore, recent advances reveal a remarkable and continuing synergistic expansion in our understanding of echinoderm evolutionary history.

Download Full-text

Shedding new light on opsin evolution

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1819 ◽

2011 ◽

Vol 279 (1726) ◽

pp. 3-14 ◽

Cited By ~ 140

Author(s):

Megan L. Porter ◽

Joseph R. Blasic ◽

Michael J. Bok ◽

Evan G. Cameron ◽

Thomas Pringle ◽

...

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Current Model ◽

Expression Patterns ◽

Model Organisms ◽

Biological Functions ◽

Site Specific ◽

History Of ◽

Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

Download Full-text

Taxonomic revision of Croton section Cleodora (Euphorbiaceae)

Phytotaxa ◽

10.11646/phytotaxa.121.1.1 ◽

2013 ◽

Vol 121 (1) ◽

pp. 1 ◽

Cited By ~ 7

Author(s):

MARIA BEATRIZ ROSSI CARUZO ◽

INÊS CORDEIRO

Keyword(s):

South America ◽

Central America ◽

Geographic Distribution ◽

Evolutionary History ◽

Taxonomic Revision ◽

Current Understanding ◽

Eastern Brazil ◽

Critical Revision ◽

Species Descriptions ◽

Degree Of Overlap

Croton section Cleodora is a Neotropical section disjunctly distributed in Mexico and Central America, northern and northwestern South America, and eastern Brazil. Eighteen species are recognized as belonging to the section, which is characterized mainly by an arborescent or shrubby habit, presence of clear or reddish latex, leaves with a pair of basilaminar or acropetiolar glands, pistillate flowers sepals with some degree of overlap, and 4-fid or multifid styles united at the base or above, usually forming a crown. We conduct a critical revision of Croton section Cleodora, congruent with the current understanding of its evolutionary history. We provide here an identification key for the two recognized subsections (Croton subsection Sphaerogyni and C. subsection Spruceani) and their species. Descriptions, illustrations, comments about taxonomy, habitat, geographic distribution and phenological information are provided for each species. Six lectotypes are here designated.

Download Full-text

Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmen Neosadocus Mello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae)

PLoS ONE ◽

10.1371/journal.pone.0249746 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0249746

Author(s):

Daniel Castro-Pereira ◽

Elen A. Peres ◽

Ricardo Pinto-da-Rocha

Keyword(s):

Atlantic Forest ◽

Reproductive Strategies ◽

Evolutionary History ◽

Taxonomic Revision ◽

Brazilian Atlantic Forest ◽

Nuclear Markers ◽

Physiological Constraints ◽

Male Polymorphism ◽

Female Holotype ◽

Molecular Phylogenetic

Neosadocus harvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution about Neosadocus includes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species’ diversity in a phylogeographical framework. Our results show that Neosadocus is a monophyletic group and comprises four species: N. bufo, N. maximus, N. robustus and N. misandrus (which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism in N. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work: “Bunoweyhia” variabilis Mello-Leitão, 1935 = Neosadocus bufo (Mello-Leitão, 1926); and “Bunoweyhia” minor Mello-Leitão, 1935 = Neosadocus maximus (Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.

Download Full-text

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

10.1101/777623 ◽

2019 ◽

Cited By ~ 3

Author(s):

Roberto Lozano ◽

Elodie Gazave ◽

Jhonathan P.R. dos Santos ◽

Markus Stetter ◽

Ravi Valluru ◽

...

Keyword(s):

Comparative Genomics ◽

Evolutionary History ◽

Large Scale ◽

Evolutionary Dynamics ◽

Deleterious Mutation ◽

Genomic Variation ◽

Evolutionary Analysis ◽

Deleterious Mutations ◽

Maize Population ◽

Whole Genome Resequencing

AbstractSorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the “domestication cost” hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding.

Download Full-text