Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100042).Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.

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Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

Molecular Biology and Evolution ◽

10.1093/molbev/msaa067 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2192-2196 ◽

Cited By ~ 2

Author(s):

Jonathan Rolland ◽

Dolph Schluter ◽

Jonathan Romiguier

Keyword(s):

Life History ◽

Evolutionary Biology ◽

Life History Traits ◽

Deleterious Mutation ◽

Purifying Selection ◽

Synonymous Substitution ◽

Deleterious Mutations ◽

Data Set ◽

Terrestrial Vertebrates ◽

Genome Data

Abstract Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.

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Lacking conservation genomics in the giant Galápagos tortoise

10.1101/101980 ◽

2017 ◽

Cited By ~ 1

Author(s):

Etienne Loire ◽

Nicolas Galtier

Keyword(s):

Evolutionary Biology ◽

Population Genomics ◽

Conservation Policy ◽

Population Substructure ◽

Conservation Practices ◽

Conservation Genomics ◽

Current Conservation ◽

Data Set ◽

Peer Community ◽

Ngs Data

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100031).Conservation policy in the giant Galápagos tortoise, an iconic endangered animal, has been assisted by genetic markers for ∼15 years: a dozen loci have been used to delineate thirteen (sub)species, between which hybridization is prevented. Here, comparative reanalysis of a previously published NGS data set reveals a conflict with traditional markers. Genetic diversity and population substructure in the giant Galápagos tortoise are found to be particularly low, questioning the genetic relevance of current conservation practices. Further examination of giant Galapagos tortoise population genomics is critically needed.

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Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

10.1101/615633 ◽

2019 ◽

Author(s):

Hong-Rui Zhang ◽

Ran Wei ◽

Qiao-Ping Xiang ◽

Xian-Chun Zhang

Keyword(s):

Substitution Rate ◽

Gc Content ◽

Synonymous Substitution ◽

Morphological Characters ◽

Phylogenetic Position ◽

Basal Clade ◽

Phylogenetic Framework ◽

Phylogenomic Analyses ◽

The Stability

AbstractSelaginellaceae has been repeatedly proved as monophyly by previous studies with only one genus being recognized. However, the subgeneric classification has been debated during the recent decades. Furthermore, phylogenetic position of the newly identified sanguinolenta group has not been resolved, varying depending on the datasets and analysis methods. We carried out the phylogenomic analyses of twenty-six species from Selaginellaceae with ten species being newly sequenced and three species representing the sanguinolenta group. Four of the ten newly sequenced plastomes are assembled into the complete molecules, whereas the other six species are only assembled into five to sixteen contigs owing to high numbers of repeats. The phylogenetic framework from our study is basically congruent with the subgeneric classification of Weststrand and Korall (2016b). The position of sanguinolenta group was resolved as the basal clade in subg. Stachygynandrum, which support the position β proposed by Weststrand and Korall (2016a), also supported by the morphological characters of dimorphic vegetative leaves, monomorphic sporophylls and intermixed sporangial arrangements. Both values of dS, dN and GC content in Selaginellaceae plastomes were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). The correlation analysis showed that the elevated synonymous substitution rate was significantly correlated with the high GC content in Selaginellaceae. Besides, the values of dS and dN differs significantly between branches in the phylogenetic tree of Selaginellaceae. We propose that both high GC content and the extensive RNA editing sites contributed to the elevated substitution rate in Selaginellaceae, and all of these three factors could influence the stability of phylogenetic topology of Selaginellaceae.

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Visualization of Cartilage from Knee Joint Magnetic Resonance Images and Quantitative Assessment to Study the Effect of Age, Gender and Body Mass Index (BMI) in Progressive Osteoarthritis (OA)

Current Medical Imaging Formerly Current Medical Imaging Reviews ◽

10.2174/1573405614666181018123251 ◽

2019 ◽

Vol 15 (6) ◽

pp. 565-572

Author(s):

Mallikarjunaswamy Shivagangadharaiah Matada ◽

Mallikarjun Sayabanna Holi ◽

Rajesh Raman ◽

Sujana Theja Jayaramu Suvarna

Keyword(s):

Body Mass Index ◽

Magnetic Resonance ◽

Knee Joint ◽

Body Mass ◽

3D Visualization ◽

Cartilage Degradation ◽

Magnetic Resonance Images ◽

Cartilage Thickness ◽

Knee Joints ◽

Data Set

Background: Osteoarthritis (OA) is a degenerative disease of joint cartilage affecting the elderly people around the world. Visualization and quantification of cartilage is very much essential for the assessment of OA and rehabilitation of the affected people. Magnetic Resonance Imaging (MRI) is the most widely used imaging modality in the treatment of knee joint diseases. But there are many challenges in proper visualization and quantification of articular cartilage using MRI. Volume rendering and 3D visualization can provide an overview of anatomy and disease condition of knee joint. In this work, cartilage is segmented from knee joint MRI, visualized in 3D using Volume of Interest (VOI) approach. Methods: Visualization of cartilage helps in the assessment of cartilage degradation in diseased knee joints. Cartilage thickness and volume were quantified using image processing techniques in OA affected knee joints. Statistical analysis is carried out on processed data set consisting of 110 of knee joints which include male (56) and female (54) of normal (22) and different stages of OA (88). The differences in thickness and volume of cartilage were observed in cartilage in groups based on age, gender and BMI in normal and progressive OA knee joints. Results: The results show that size and volume of cartilage are found to be significantly low in OA as compared to normal knee joints. The cartilage thickness and volume is significantly low for people with age 50 years and above and Body Mass Index (BMI) equal and greater than 25. Cartilage volume correlates with the progression of the disease and can be used for the evaluation of the response to therapies. Conclusion: The developed methods can be used as helping tool in the assessment of cartilage degradation in OA affected knee joint patients and treatment planning.

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Journal of Cotton Research ◽

10.1186/s42397-021-00090-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Teame Gereziher MEHARI ◽

Yanchao XU ◽

Richard Odongo MAGWANGA ◽

Muhammad Jawad UMER ◽

Joy Nyangasi KIRUNGU ◽

...

Keyword(s):

Drought Stress ◽

Gossypium Hirsutum ◽

Abiotic Stresses ◽

Substitution Rate ◽

Synonymous Substitution ◽

Synonymous Substitution Rate ◽

Drought Tolerant ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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Body mass data set for 1317 bird and 270 mammal species from Colombia

Ecology ◽

10.1002/ecy.3273 ◽

2020 ◽

Author(s):

David Ocampo ◽

Kevin G. Borja‐Acosta ◽

Julián Lozano‐Flórez ◽

Sebastián Cifuentes‐Acevedo ◽

Enrique Arbeláez‐Cortés ◽

...

Keyword(s):

Body Mass ◽

Mammal Species ◽

Data Set ◽

Mass Data

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Vanishing GC-Rich Isochores in Mammalian Genomes

Genetics ◽

10.1093/genetics/162.4.1837 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1837-1847 ◽

Cited By ~ 6

Author(s):

Laurent Duret ◽

Marie Semon ◽

Gwenaël Piganeau ◽

Dominique Mouchiroud ◽

Nicolas Galtier

Keyword(s):

Gc Content ◽

Synonymous Substitution ◽

Equilibrium Analysis ◽

Large Excess ◽

Substitution Pattern ◽

Origin And Evolution ◽

Evolutionary Force ◽

Mammalian Genomes ◽

Human Polymorphism ◽

Probability Of Fixation

AbstractTo understand the origin and evolution of isochores—the peculiar spatial distribution of GC content within mammalian genomes—we analyzed the synonymous substitution pattern in coding sequences from closely related species in different mammalian orders. In primate and cetartiodactyls, GC-rich genes are undergoing a large excess of GC → AT substitutions over AT → GC substitutions: GC-rich isochores are slowly disappearing from the genome of these two mammalian orders. In rodents, our analyses suggest both a decrease in GC content of GC-rich isochores and an increase in GC-poor isochores, but more data will be necessary to assess the significance of this pattern. These observations question the conclusions of previous works that assumed that base composition was at equilibrium. Analysis of allele frequency in human polymorphism data, however, confirmed that in the GC-rich parts of the genome, GC alleles have a higher probability of fixation than AT alleles. This fixation bias appears not strong enough to overcome the large excess of GC → AT mutations. Thus, whatever the evolutionary force (neutral or selective) at the origin of GC-rich isochores, this force is no longer effective in mammals. We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals.

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Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

Zootaxa ◽

10.11646/zootaxa.4286.1.4 ◽

2017 ◽

Vol 4286 (1) ◽

pp. 93 ◽

Cited By ~ 18

Author(s):

OLGA KLISHKO ◽

MANUEL LOPES-LIMA ◽

ELSA FROUFE ◽

ARTHUR BOGAN ◽

LYUDMILA VASILIEV ◽

...

Keyword(s):

Freshwater Mussel ◽

Integrated Approach ◽

Molecular Data ◽

Coi Gene ◽

Data Set ◽

Widespread Species ◽

Molecular Analyses ◽

Morphological Variations ◽

Mtdna Coi ◽

Morphological And Molecular Data

The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio, in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus. Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al. (2004) and Bogatov & Kijashko (2016).

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