Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

Abstract The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.

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Evolution of primate orphan proteins

Biochemical Society Transactions ◽

10.1042/bst0370778 ◽

2009 ◽

Vol 37 (4) ◽

pp. 778-782 ◽

Cited By ~ 17

Author(s):

Macarena Toll-Riera ◽

Robert Castelo ◽

Nicolás Bellora ◽

M. Mar Albà

Keyword(s):

Related Species ◽

Sequence Divergence ◽

Orphan Genes ◽

Closely Related Species ◽

Protein Coding ◽

Rapid Sequence ◽

Adaptive Processes ◽

Mechanisms Of Formation ◽

Novel Protein

Genomes contain a large number of genes that do not have recognizable homologues in other species. These genes, found in only one or a few closely related species, are known as orphan genes. Their limited distribution implies that many of them are probably involved in lineage-specific adaptive processes. One important question that has remained elusive to date is how orphan genes originate. It has been proposed that they might have arisen by gene duplication followed by a period of very rapid sequence divergence, which would have erased any traces of similarity to other evolutionarily related genes. However, this explanation does not seem plausible for genes lacking homologues in very closely related species. In the present article, we review recent efforts to identify the mechanisms of formation of primate orphan genes. These studies reveal an unexpected important role of transposable elements in the formation of novel protein-coding genes in the genomes of primates.

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Wickerhamiella allomyrinae f.a., sp. nov., a yeast species isolated from the gut of the rhinoceros beetle Allomyrina dichotoma

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.068403-0 ◽

2014 ◽

Vol 64 (Pt_11) ◽

pp. 3856-3861 ◽

Cited By ~ 6

Author(s):

Yong-Cheng Ren ◽

Yun Wang ◽

Liang Chen ◽

Tao Ke ◽

Feng-Li Hui

Keyword(s):

Related Species ◽

Nature Reserve ◽

Yeast Species ◽

Novel Species ◽

Sequence Divergence ◽

Rrna Gene ◽

The Novel ◽

Closely Related Species ◽

Rhinoceros Beetle ◽

Lsu Rrna Gene

Two strains representing Wickerhamiella allomyrinae f.a., sp. nov. were isolated from the gut of Allomyrina dichotoma (Coleoptera: Scarabeidae) collected from the Baotianman National Nature Reserve, Nanyan, Henan Province, China. Sequence analyses of the D1/D2 domains of the LSU rRNA gene revealed that this novel species was located in the Wickerhamiella clade (Saccharomycetes, Saccharomycetales), with three described species of the genus Candida, namely Candida musiphila, Candida spandovensis and Candida sergipensis, as the most closely related species. The novel species differed from these three species by 9.3–9.8 % sequence divergence (35–45 nt substitutions) in the D1/D2 sequences. The species could also be distinguished from the closely related species, C. musiphila, C. spandovensis and C. sergipensis, by growth on vitamin-free medium and at 37 °C. The type strain is Wickerhamiella allomyrinae sp. nov. NYNU 13920T ( = CICC 33031T = CBS 13167T).

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Molecular identification of animal isolates ofEchinococcus granulosusfrom Iran using four mitochondrial genes

Journal of Helminthology ◽

10.1017/s0022149x1100071x ◽

2011 ◽

Vol 86 (4) ◽

pp. 485-492 ◽

Cited By ~ 23

Author(s):

M. Rostami Nejad ◽

N. Taghipour ◽

Z. Nochi ◽

E. Nazemalhosseini Mojarad ◽

S.R. Mohebbi ◽

...

Keyword(s):

Molecular Markers ◽

Related Species ◽

Mitochondrial Genes ◽

12S Rrna ◽

Rrna Gene ◽

Sequence Evolution ◽

Closely Related Species ◽

12S Rrna Gene ◽

Complete Sequences ◽

Animal Isolates

AbstractMitochondrial genes have more power than nuclear genes in reconstructing phylogenetic relationships among closely related species because of their faster sequence evolution. The aim of this study was to use the complete or near-complete sequences from three mitochondrial genes (cox1,nad1andatp6) and partial sequences of the 12S rRNA gene to infer relationships among isolates ofEchinococcus granulosusfrom Iran. Two hundred and twenty-nine isolates ofE. granulosuswere collected from cattle, camels, sheep, buffalo and goats from different geographical areas. Most individuals were found to possess the G1 genotype but some of the camel samples belonged to the G6 genotype. Newly designed primers forcox1,nad1andatp6genes amplified bands of 1830, 708 and 1157 bp for the G1 genotype and 1856, 705, 1054 bp for the G6 genotype, respectively. The result of this survey showed thatatp6andnad1genes are good molecular markers for identifyingE. granulosusisolates from a range of hosts in Iran.

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Phylogeny of Vibrio cholerae Based onrecA Sequence

Infection and Immunity ◽

10.1128/iai.68.12.7180-7185.2000 ◽

2000 ◽

Vol 68 (12) ◽

pp. 7180-7185 ◽

Cited By ~ 37

Author(s):

O. Colin Stine ◽

Shanmuga Sozhamannan ◽

Qing Gou ◽

Siqen Zheng ◽

J. Glenn Morris ◽

...

Keyword(s):

Vibrio Cholerae ◽

Related Species ◽

Horizontal Transfer ◽

Vibrio Parahaemolyticus ◽

Vibrio Vulnificus ◽

Sequence Divergence ◽

Closely Related Species ◽

O Antigen

ABSTRACT We sequenced a 705-bp fragment of the recA gene from 113 Vibrio cholerae strains and closely related species. One hundred eighty-seven nucleotides were phylogenetically informative, 55 were phylogenetically uninformative, and 463 were invariant. Not unexpectedly, Vibrio parahaemolyticus and Vibrio vulnificus strains formed out-groups; we also identified isolates which resembled V. cholerae biochemically but which did not cluster with V. cholerae. In many instances, V. cholerae serogroup designations did not correlate with phylogeny, as reflected by recA sequence divergence. This observation is consistent with the idea that there is horizontal transfer of O-antigen biosynthesis genes among V. cholerae strains.

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Divergence and introgression among the virilis group of Drosophila

10.1101/2022.01.11.475832 ◽

2022 ◽

Author(s):

Leeban Yusuf ◽

Venera Tyukmaeva ◽

Anneli Hoikkala ◽

Michael G Ritchie

Keyword(s):

Gene Flow ◽

Related Species ◽

De Novo ◽

Phylogenetic Reconstruction ◽

Sequence Divergence ◽

Sexual Isolation ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Closely Related Species ◽

Virilis Group

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains around a dozen species that are geographically widespread and show varying levels of pre-zygotic and post-zygotic isolation. Here, we utilize de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and much more recent gene flow between closely-related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and may be related to the evolution of sexual isolation. We suggest that gene flow between closely-related species has potentially had an impact on lineage-specific adaptation and the evolution of reproductive barriers. Our results show how ancient and recent introgression confuse phylogenetic reconstruction, and suggest that shared variation can facilitate adaptation and speciation.

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Urban colonization is driven by a mixture of evolutionarily conserved and labile traits

10.1101/2020.01.20.912170 ◽

2020 ◽

Author(s):

David A. Duchene ◽

Carolina Pardo-Diaz ◽

Maider Iglesias-Carrasco

Keyword(s):

Opposite Direction ◽

Related Species ◽

Urban Areas ◽

Large Data ◽

Passerine Birds ◽

Data Set ◽

Closely Related Species ◽

Successful Strategy ◽

Large Data Set ◽

Evolutionarily Conserved

AbstractUrbanization is a fast and dramatic transformation of habitat that generally forces native fauna into novel ecological challenges. The biological prerequisites necessary to establish in urban areas have been widely studied, but the macroevolutionary characteristics of traits that allow urban colonization remain poorly understood. Urban colonization might be facilitated by traits that are evolutionarily conserved and which lead to a diversity of closely related species. Alternatively, urban colonization might be associated with labile traits that frequently arise and are lost. In a large data set from passerine birds, we find that urban colonization has a signal of highly labile traits, despite many traits associated with colonization being highly conserved. Urban colonization is associated with traits that allow faster speciation than non-urban-colonizing counterparts, and more frequently transition to non-urban trait states than in the opposite direction. Overall, the traits that facilitate urban colonization are a mix of highly conserved and labile traits and appear to provide an evolutionarily successful strategy.

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Strategies for quantitative RNA-seq analyses among closely related species

10.1101/297408 ◽

2018 ◽

Cited By ~ 2

Author(s):

Swati Parekh ◽

Beate Vieth ◽

Christoph Ziegenhain ◽

Wolfgang Enard ◽

Ines Hellmann

Keyword(s):

Related Species ◽

Sequence Divergence ◽

Model Organisms ◽

Easy Access ◽

Test Case ◽

Rna Seq ◽

Closely Related Species ◽

Common Reference ◽

Genome Assemblies ◽

Relative Differences

AbstractWith the growing appreciation for the role of regulatory differences in evolution, researchers need to reliably quantify expression levels within and among species. However, for non-model organisms genome assemblies and annotations are often not available or have inferior quality, biasing the inference of expression changes to an unknown extent. Here, we explore the possibility to map RNA-seq reads from diverged species to one high quality reference genome. As test case, we used a small primate phylogeny ranging from Human to Marmoset spanning 12% nucleotide divergence. To distinguish the effect of sequence divergence and genome quality, we used in silico evolved genomes and existing genomes to simulate RNA-seq reads. These were then mapped to the genome of origin (self-mapping) as well as to one common reference (cross-mapping) to infer the quantification biases. We find that the bias due to cross-mapping is small for the closely related great apes (≤ 4% divergence), and preferable to self-mapping given current genome qualities. For closely related species, cross-mapping provides easy access, high power and a well controlled false discovery rate for both; the analysis of intra-species expression differences as well as the detection of relative differences between species. If divergence increases, so that a substantial fraction of reads exceeds the limits of the mapper used, we find that gene-specific corrections and effect-size cutoffs can limit the bias before self-mapping becomes unavoidable. In summary, for the first time we systematically quantify biases in cross-species RNA-seq studies, providing guidance to best practices for these important evolutionary studies.

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Revision of Pazala Moore, 1888: The Graphium (Pazala) mandarinus (Oberthür, 1879) Group, with Treatments of Known Taxa and Descriptions of New Species and New Subspecies (Lepidoptera: Papilionidae)

Zootaxa ◽

10.11646/zootaxa.4441.3.1 ◽

2018 ◽

Vol 4441 (3) ◽

pp. 401 ◽

Cited By ~ 3

Author(s):

SHAO-JI HU ◽

ADAM M. COTTON ◽

FABIEN L. CONDAMINE ◽

KUANG DUAN ◽

RONG-JIANG WANG ◽

...

Keyword(s):

New Species ◽

Related Species ◽

Morphological Analysis ◽

Divergence Time ◽

Species Level ◽

Molecular Dating ◽

Closely Related Species ◽

New Subspecies ◽

Western Yunnan

The previously recognised closely related species Graphium (Pazala) mandarinus (Oberthür, 1879) and G. (P.) sichuanica (Koiwaya, 1993) are shown to comprise seven species as a result of both molecular and morphological analysis. Molecular dating analysis is also performed on the mandarinus group in order to investigate the divergence time of the taxa. Two taxa, G. (P.) garhwalica (Katayama, 1988) stat. nov. and G. (P.) paphus (de Nicéville, 1886) stat. nov., are raised from subspecific to specific status; G. (P.) hoeneanus Cotton & Hu nom. nov., stat. rev. is separated from sichuanica at species level; and two previously unrecognised new species, G. (P.) daiyuanae Hu, Zhang & Cotton sp. nov. and G. (P.) confucius Hu, Duan & Cotton sp. nov. are described from Vietnam and China respectively, the latter being sympatric with nominate G. (P.) mandarinus. The identity of the lectotype of G. (P.) mandarinus is confirmed and a lectotype is designated for the taxon Papilio Glycerion Gray, 1831. A new subspecies of G. (P.) mandarinus is described from western Yunnan and northern Myanmar, G. (P.) mandarinus stilwelli Cotton & Hu ssp. nov.

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