OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

<p>Abstract</p> <p>Background</p> <p>Molecular sequence data have become the standard in modern day phylogenetics. In particular, several long-standing questions of mammalian evolutionary history have been recently resolved thanks to the use of molecular characters. Yet, most studies have focused on only a handful of standard markers. The availability of an ever increasing number of whole genome sequences is a golden mine for modern systematics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels.</p> <p>Description</p> <p>The EnsEMBL database was used to determine a set of orthologous genes from 12 available complete mammalian genomes. As targets for possible amplification and sequencing in additional taxa, more than 3,000 exons of length > 400 bp have been selected, among which 118, 368, 608, and 674 are respectively retrieved for 12, 11, 10, and 9 species. A bioinformatic pipeline has been developed to provide evolutionary descriptors for these candidate markers in order to assess their potential phylogenetic utility. The resulting OrthoMaM (Orthologous Mammalian Markers) database can be queried and alignments can be downloaded through a dedicated web interface <url>http://kimura.univ-montp2.fr/orthomam</url>.</p> <p>Conclusion</p> <p>The importance of marker choice in phylogenetic studies has long been stressed. Our database centered on complete genome information now makes possible to select promising markers to a given phylogenetic question or a systematic framework by querying a number of evolutionary descriptors. The usefulness of the database is illustrated with two biological examples. First, two potentially useful markers were identified for rodent systematics based on relevant evolutionary parameters and sequenced in additional species. Second, a complete, gapless 94 kb supermatrix of 118 orthologous exons was assembled for 12 mammals. Phylogenetic analyses using probabilistic methods unambiguously supported the new placental phylogeny by retrieving the monophyly of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria. Muroid rodents thus do not represent a basal placental lineage as it was mistakenly reasserted in some recent phylogenomic analyses based on fewer taxa. We expect the OrthoMaM database to be useful for further resolving the phylogenetic tree of placental mammals and for better understanding the evolutionary dynamics of their genomes, i.e., the forces that shaped coding sequences in terms of selective constraints.</p

The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

BACKGROUND: Mitochondrial and nuclear genes have generally been employed for different purposes in molecular systematics, the former to resolve relationships within recently evolved groups and the latter to investigate phylogenies at a deeper level. In the case of rapid and recent evolutionary radiations, mitochondrial genes like cytochrome b (CYB) are often inefficient for resolving phylogenetic relationships. One of the best examples is illustrated by Arvicolinae rodents (Rodentia; Muridae), the most impressive mammalian radiation of the Northern Hemisphere which produced voles, lemmings and muskrats. Here, we compare the relative contribution of a nuclear marker – the exon 10 of the growth hormone receptor (GHR) gene – to the one of the mitochondrial CYB for inferring phylogenetic relationships among the major lineages of arvicoline rodents. RESULTS: The analysis of GHR sequences improves the overall resolution of the Arvicolinae phylogeny. Our results show that the Caucasian long-clawed vole (Prometheomys schaposnikowi) is one of the basalmost arvicolines, and confirm that true lemmings (Lemmus) and collared lemmings (Dicrostonyx) are not closely related as suggested by morphology. Red-backed voles (Myodini) are found as the sister-group of a clade encompassing water vole (Arvicola), snow vole (Chionomys), and meadow voles (Microtus and allies). Within the latter, no support is recovered for the generic recognition of Blanfordimys, Lasiopodomys, Neodon, and Phaiomys as suggested by morphology. Comparisons of parameter estimates for branch lengths, base composition, among sites rate heterogeneity, and GTR relative substitution rates indicate that CYB sequences consistently exhibit more heterogeneity among codon positions than GHR. By analyzing the contribution of each codon position to node resolution, we show that the apparent higher efficiency of GHR is due to their third positions. Although we focus on speciation events spanning the last 10 million years (Myr), CYB sequences display highly saturated codon positions contrary to the nuclear exon. Lastly, variable length bootstrap predicts a significant increase in resolution of arvicoline phylogeny through the sequencing of nuclear data in an order of magnitude three to five times greater than the size of GHR exon 10. CONCLUSION: Our survey provides a first resolved gene tree for Arvicolinae. The comparison of CYB and GHR phylogenetic efficiency supports recent assertions that nuclear genes are useful for resolving relationships of recently evolved animals. The superiority of nuclear exons may reside both in (i) less heterogeneity among sites, and (ii) the presence of highly informative sites in third codon positions, that evolve rapidly enough to accumulate synapomorphies, but slow enough to avoid substitutional saturation

Systematics of hairy armadillos and the taxonomic status of the Andean hairy armadillo (<i>Chaetophractus nationi</i>)

Hairy armadillos constitute an ecologically homogeneous and morphologically similar group with currently 5 species classified in the subfamily Euphractinae. Among them, the Andean hairy armadillo Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae) is a small, endangered armadillo that has long been suspected to represent a high-altitude variant of Chaetophractus vellerosus. Here, we report the 1st phylogenetic systematics assessment of hairy armadillos using morphological and molecular analyses of all described species with focus on the status of the Andean hairy armadillo. Multivariate analyses of shape variation based on 3-dimensional landmark coordinates of skulls allowed a clear differentiation of each species with the exception of C. vellerosus and C. nationi, within which only a latitudinal and/or altitudinal gradient in size was apparent. Moreover, analyses of mitochondrial DNA control region (D-loop) revealed a single C. nationi haplotype that appeared to be identical with a C. vellerosus haplotype from Argentina. Identical sequences in C. vellerosus and C. nationi were also observed for 3 of the 5 non-coding nuclear markers investigated. Based on these data, we propose that C. nationi should be considered as a synonym of C. vellerosus. However, this taxonomic change should not preclude the protection of the high-altitude Bolivian populations that are steadily declining because of their overexploitation for traditional purposes. Finally, phylogenetic analyses of euphractine armadillos based on a combination of 6 non-coding nuclear markers and 2 nuclear exons suggest the paraphyly of the genus Chaetophractus, with C. vellerosus being more closely related to Zaedyus pichiy than to C. villosus.Los armadillos peludos constituyen un grupo ecológicamente homogéneo y morfológicamente similar que actualmente consiste de 5 especies clasificadas en la subfamilia Euphractinae. Una de ellas, el quirquincho Andino Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae), es un pequeño armadillo amenazado de extinción del cual se ha sospechado durante mucho tiempo que representa una variedad de altitud de Chaetophractus vellerosus. Aquí reportamos la primera evaluación sistemática filogenética de armadillos peludos utilizando análisis morfológicos y moleculares de todas las especies descritas, poniendo un especial enfoque en el estado del quirquincho Andino. Los análisis multivariados de la forma basados en landmarks tridimensionales de cráneos, permitieron distinguir claramente las especies, con la excepción de C. vellerosus y C. nationi en los cuales sólo se halló un gradiente latitudinal y/o altitudinal en el tamaño. Además, los análisis de la región control del ADN mitocondrial (D-loop) mostraron un solo haplotipo de C. nationi, que fue idéntico a un haplotipo de C. vellerosus de Argentina. También se observaron secuencias idénticas para C. vellerosus y C. nationi en 3 de los 5 marcadores nucleares no codificantes analizados. A partir de estos resultados proponemos que C. nationi sea considerado sinónimo de C. vellerosus. Sin embargo, este cambio taxonómico no debe excluir la protección de las poblaciones altoandinas de Bolivia que están sufriendo una reducción continua debido a su sobreexplotación para fines tradicionales. Finalmente, los análisis filogenéticos de los armadillos eufractinos basados en una combinación de 6 marcadores nucleares no codificantes y 2 exones nucleares sugieren la parafilia del género Chaetophractus, Siendo C. vellerosus relacionado mas estrechamente con Zaedyus pichiy que con C. villosus.Facultad de Ciencias Naturales y Muse

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

<p>Abstract</p> <p>Background</p> <p>Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.</p> <p>Results</p> <p>Thirty new complete 18S rRNA sequences were acquired from previously unsampled tunicate species, with special focus on groups presenting high evolutionary rate. The updated 18S rRNA dataset has been aligned with respect to the constraint on homology imposed by the rRNA secondary structure. A probabilistic framework of phylogenetic reconstruction was adopted to accommodate the particular evolutionary dynamics of this ribosomal marker. Detailed Bayesian analyses were conducted under the non-parametric CAT mixture model accounting for site-specific heterogeneity of the evolutionary process, and under RNA-specific doublet models accommodating the occurrence of compensatory substitutions in stem regions. Our results support the division of tunicates into three major clades: 1) Phlebobranchia + Thaliacea + Aplousobranchia, 2) Appendicularia, and 3) Stolidobranchia, but the position of Appendicularia could not be firmly resolved. Our study additionally reveals that most Aplousobranchia evolve at extremely high rates involving changes in secondary structure of their 18S rRNA, with the exception of the family Clavelinidae, which appears to be slowly evolving. This extreme rate heterogeneity precluded resolving with certainty the exact phylogenetic placement of Aplousobranchia. Finally, the best fitting secondary-structure and CAT-mixture models suggest a sister-group relationship between Salpida and Pyrosomatida within Thaliacea.</p> <p>Conclusion</p> <p>An updated phylogenetic framework for tunicates is provided based on phylogenetic analyses using the most realistic evolutionary models currently available for ribosomal molecules and an unprecedented taxonomic sampling. Detailed analyses of the 18S rRNA gene allowed a clear definition of the major tunicate groups and revealed contrasting evolutionary dynamics among major lineages. The resolving power of this gene nevertheless appears limited within the clades composed of Phlebobranchia + Thaliacea + Aplousobranchia and Pyuridae + Styelidae, which were delineated as spots of low resolution. These limitations underline the need to develop new nuclear markers in order to further resolve the phylogeny of this keystone group in chordate evolution.</p

Systematics of hairy armadillos and the taxonomic status of the Andean hairy armadillo (<i>Chaetophractus nationi</i>)

Hairy armadillos constitute an ecologically homogeneous and morphologically similar group with currently 5 species classified in the subfamily Euphractinae. Among them, the Andean hairy armadillo Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae) is a small, endangered armadillo that has long been suspected to represent a high-altitude variant of Chaetophractus vellerosus. Here, we report the 1st phylogenetic systematics assessment of hairy armadillos using morphological and molecular analyses of all described species with focus on the status of the Andean hairy armadillo. Multivariate analyses of shape variation based on 3-dimensional landmark coordinates of skulls allowed a clear differentiation of each species with the exception of C. vellerosus and C. nationi, within which only a latitudinal and/or altitudinal gradient in size was apparent. Moreover, analyses of mitochondrial DNA control region (D-loop) revealed a single C. nationi haplotype that appeared to be identical with a C. vellerosus haplotype from Argentina. Identical sequences in C. vellerosus and C. nationi were also observed for 3 of the 5 non-coding nuclear markers investigated. Based on these data, we propose that C. nationi should be considered as a synonym of C. vellerosus. However, this taxonomic change should not preclude the protection of the high-altitude Bolivian populations that are steadily declining because of their overexploitation for traditional purposes. Finally, phylogenetic analyses of euphractine armadillos based on a combination of 6 non-coding nuclear markers and 2 nuclear exons suggest the paraphyly of the genus Chaetophractus, with C. vellerosus being more closely related to Zaedyus pichiy than to C. villosus.Los armadillos peludos constituyen un grupo ecológicamente homogéneo y morfológicamente similar que actualmente consiste de 5 especies clasificadas en la subfamilia Euphractinae. Una de ellas, el quirquincho Andino Chaetophractus nationi (Xenarthra, Cingulata, Dasypodidae), es un pequeño armadillo amenazado de extinción del cual se ha sospechado durante mucho tiempo que representa una variedad de altitud de Chaetophractus vellerosus. Aquí reportamos la primera evaluación sistemática filogenética de armadillos peludos utilizando análisis morfológicos y moleculares de todas las especies descritas, poniendo un especial enfoque en el estado del quirquincho Andino. Los análisis multivariados de la forma basados en landmarks tridimensionales de cráneos, permitieron distinguir claramente las especies, con la excepción de C. vellerosus y C. nationi en los cuales sólo se halló un gradiente latitudinal y/o altitudinal en el tamaño. Además, los análisis de la región control del ADN mitocondrial (D-loop) mostraron un solo haplotipo de C. nationi, que fue idéntico a un haplotipo de C. vellerosus de Argentina. También se observaron secuencias idénticas para C. vellerosus y C. nationi en 3 de los 5 marcadores nucleares no codificantes analizados. A partir de estos resultados proponemos que C. nationi sea considerado sinónimo de C. vellerosus. Sin embargo, este cambio taxonómico no debe excluir la protección de las poblaciones altoandinas de Bolivia que están sufriendo una reducción continua debido a su sobreexplotación para fines tradicionales. Finalmente, los análisis filogenéticos de los armadillos eufractinos basados en una combinación de 6 marcadores nucleares no codificantes y 2 exones nucleares sugieren la parafilia del género Chaetophractus, Siendo C. vellerosus relacionado mas estrechamente con Zaedyus pichiy que con C. villosus.Facultad de Ciencias Naturales y Muse

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals

DATA AVAILABILITY : Draft genomes (Manis culionensis, M. crassicaudata, Phataginus tetradactyla, Smutsia temminckii) and the hybrid assembled, annotated reference genome with associated metadata (S. gigantea) are available in the GenBank Nucleotide Database (BioProject: PRJNA795390). The associated sequence read data have also been deposited in Genbank (SRA: SRR17702824-SRR17702828) for the aforementioned genomes (except for S. temminckii). The accession numbers or links for all accessed genomic data are listed in supplementary table S1, Supplementary Material online. A database containing the list genes ranked by diversity amongst all eight pangolin species has been deposited at Zenodo and is publicly available (supplementary Database S1, Supplementary Material online: https://doi.org/10.5281/zenodo.7517409). All original code in the form of custom scripts for processing the genomics data in this study have also been deposited at Zenodo and are publicly available (Custom scripts 1–3: https://doi.org/10.5281/zenodo.7517409). Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.The Agence Nationale de la Recherche, European Research Council, Mohamed bin Zayed Species Conservation Fund, the National Research Foundation of South Africa and the National Natural Science Foundation of China.https://academic.oup.com/mbehj2024Mammal Research InstituteZoology and EntomologySDG-15:Life on lan

T2-weighted cardiovascular magnetic resonance in acute cardiac disease

Cardiovascular magnetic resonance (CMR) using T2-weighted sequences can visualize myocardial edema. When compared to previous protocols, newer pulse sequences with substantially improved image quality have increased its clinical utility. The assessment of myocardial edema provides useful incremental diagnostic and prognostic information in a variety of clinical settings associated with acute myocardial injury. In patients with acute chest pain, T2-weighted CMR is able to identify acute or recent myocardial ischemic injury and has been employed to distinguish acute coronary syndrome (ACS) from non-ACS as well as acute from chronic myocardial infarction