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Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F. MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour 2020; 20:892-905. [PMID: 32243090 PMCID: PMC7497042 DOI: 10.1111/1755-0998.13160] [Citation(s) in RCA: 462] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/21/2020] [Accepted: 03/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Alex Schomaker-Bastos
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jonathan Romiguier
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Francisco Prosdocimi
- Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
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Sartori C, Gianesella M, Pilastro A, Mantovani R, Armato L, Fiore E. Digit ratio and length asymmetry in calves' limbs. ZOOLOGY 2020; 140:125777. [PMID: 32248058 DOI: 10.1016/j.zool.2020.125777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
Abstract
This study considered possible sexual dimorphism in the relative lengths of the second, third and fourth digits (digit ratio), in calves. Furthermore, a different length of the bone structures of the third (3D) and of the fourth (4D) digits has been examined as an evolutionary adaptation to locomotion on soft ground. The length of the digital bones of the right fore-limb of 33 females and 15 male calves was measured in vivo using a portable X-ray machine. The vestigial structure of the second digit (2D), and 3D and 4D, from metacarpus to the third phalanx were considered in a mixed model, as well as some ratios between 2D and different parts of 3D or 4D (2D:3D and 2D:4D). A covariate for the mean finger length was considered for digit ratios to control for possible biases due to shape allometry. Shorter first phalanx and trotter were found in 3D than in 4D, and the reverse for the third phalanx. The 2D was significantly shorter in females, as well as the second phalanges of 3D and 4D. Significant sex differences in 2D:3D and 2D:4D were found for some digit parts of 3D and 4D and for the first phalanges of 3D:4D. These ratios were always shorter in females, in contrast to that found in most mammals. The asymmetry between 3D and 4D could mean a functional adaptation for locomotion. Sex differences in 2D:4D and 3D:4D were found, but with a reverse pattern than in most mammal species (males > females rather than males < females). In this regard digit ratio in calves was similar to that of Old World monkeys. This study is the first investigation of digit ratio in Ungulates, whose limbs differ from the limbs of most mammals, maintaining five digits. The reverse pattern of sex differences (digit ratios: males> females) could be due to the peculiar nature of the vestigial dewclaw of 2D and to the hormone patterns acting on this digit during development, but further research is required around this topic.
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Affiliation(s)
- Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - Matteo Gianesella
- Department of Animal Medicine, Productions and Health (MAPS), University of Padova, Padova, Italy
| | | | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Leonardo Armato
- Department of Animal Medicine, Productions and Health (MAPS), University of Padova, Padova, Italy
| | - Enrico Fiore
- Department of Animal Medicine, Productions and Health (MAPS), University of Padova, Padova, Italy
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Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns. Mol Phylogenet Evol 2020; 147:106785. [PMID: 32135306 DOI: 10.1016/j.ympev.2020.106785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/03/2020] [Accepted: 02/27/2020] [Indexed: 11/24/2022]
Abstract
The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns. Our results uncovered a high proportion of cryptic diversity and revealed numerous taxonomic complications, especially within the C. consobrinus, C. malayanus, and C. pubisulcus groups. Comparisons of pairwise genetic distances and a preliminary species delimitation analysis using the Automatic Barcode Gap Discovery (ABGD) method demonstrated that some wide-ranging species on Borneo likely comprise multiple distinct and deeply divergent lineages, each with more restricted distributional ranges. We also tested the prevailing biogeographic hypothesis of a single invasion from Borneo into the Philippines. Our analyses revealed that Philippine taxa were not monophyletic, but were likely derived from multiple separate invasions into the geopolitical areas comprising the Philippines. Although our investigation of Bornean Cyrtodactylus is the most comprehensive to-date, it highlights the need for expanded taxonomic sampling and suggests that our knowledge of the evolutionary history, systematics, and biogeography of Bornean Cyrtodactylus is far from complete.
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Pinheiro A, Águeda-Pinto A, Melo-Ferreira J, Neves F, Abrantes J, Esteves PJ. Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups. BMC Evol Biol 2019; 19:221. [PMID: 31791244 PMCID: PMC6889247 DOI: 10.1186/s12862-019-1547-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/25/2019] [Indexed: 01/12/2023] Open
Abstract
Background Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. Results In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima’s relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML’s branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). Conclusions Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.
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Affiliation(s)
- Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - Ana Águeda-Pinto
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,Center for Immunotherapy, Vaccines, and Virotherapy (CIVV), The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - José Melo-Ferreira
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, 4585-116, Gandra, Portugal
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Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol 2019; 17:e3000494. [PMID: 31800571 PMCID: PMC6892540 DOI: 10.1371/journal.pbio.3000494] [Citation(s) in RCA: 447] [Impact Index Per Article: 89.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 12/18/2022] Open
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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Affiliation(s)
- Nathan S. Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Jacob A. Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity & Global Change, Yale University, New Haven, Connecticut, United States of America
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Du Y, Wu S, Edwards SV, Liu L. The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life. BMC Evol Biol 2019; 19:203. [PMID: 31694538 PMCID: PMC6833305 DOI: 10.1186/s12862-019-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 10/21/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees. RESULTS The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming. CONCLUSIONS Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.
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Affiliation(s)
- Yan Du
- Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu 221116 People’s Republic of China
| | - Scott V. Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138 USA
| | - Liang Liu
- Liang Liu, Department of Statistics and Institute of Bioinformatics, University of Georgia, 310 Herty Drive, Athens, GA 30606 USA
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He C, Liang D, Zhang P. Asymmetric Distribution of Gene Trees Can Arise under Purifying Selection If Differences in Population Size Exist. Mol Biol Evol 2019; 37:881-892. [DOI: 10.1093/molbev/msz232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AbstractIncomplete lineage sorting (ILS) is an important factor that causes gene tree discordance. For gene trees of three species, under neutrality, random mating, and the absence of interspecific gene flow, ILS creates a symmetric distribution of gene trees: the gene tree that accords with the species tree has the highest frequency, and the two discordant trees are equally frequent. If the neutral condition is violated, the impact of ILS may change, altering the gene tree distribution. Here, we show that under purifying selection, even assuming that the fitness effect of mutations is constant throughout the species tree, if differences in population size exist among species, asymmetric distributions of gene trees will arise, which is different from the expectation under neutrality. In extremes, one of the discordant trees rather than the concordant tree becomes the most frequent gene tree. In addition, we found that in a real case, the position of Scandentia relative to Primate and Glires, the symmetry in the gene tree distribution can be influenced by the strength of purifying selection. In current phylogenetic inference, the impact of purifying selection on the gene tree distribution is rarely considered by researchers. This study highlights the necessity of considering this impact.
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Affiliation(s)
- Chong He
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Novel Polyomaviruses in Mammals from Multiple Orders and Reassessment of Polyomavirus Evolution and Taxonomy. Viruses 2019; 11:v11100930. [PMID: 31658738 PMCID: PMC6833039 DOI: 10.3390/v11100930] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/14/2022] Open
Abstract
As the phylogenetic organization of mammalian polyomaviruses is complex and currently incompletely resolved, we aimed at a deeper insight into their evolution by identifying polyomaviruses in host orders and families that have either rarely or not been studied. Sixteen unknown and two known polyomaviruses were identified in animals that belong to 5 orders, 16 genera, and 16 species. From 11 novel polyomaviruses, full genomes could be determined. Splice sites were predicted for large and small T antigen (LTAg, STAg) coding sequences (CDS) and examined experimentally in transfected cell culture. In addition, splice sites of seven published polyomaviruses were analyzed. Based on these data, LTAg and STAg annotations were corrected for 10/86 and 74/86 published polyomaviruses, respectively. For 25 polyomaviruses, a spliced middle T CDS was observed or predicted. Splice sites that likely indicate expression of additional, alternative T antigens, were experimentally detected for six polyomaviruses. In contrast to all other mammalian polyomaviruses, three closely related cetartiodactyl polyomaviruses display two introns within their LTAg CDS. In addition, the VP2 of Glis glis (edible dormouse) polyomavirus 1 was observed to be encoded by a spliced transcript, a unique experimental finding within the Polyomaviridae family. Co-phylogenetic analyses based on LTAg CDS revealed a measurable signal of codivergence when considering all mammalian polyomaviruses, most likely driven by relatively recent codivergence events. Lineage duplication was the only other process whose influence on polyomavirus evolution was unambiguous. Finally, our analyses suggest that an update of the taxonomy of the family is required, including the creation of novel genera of mammalian and non-mammalian polyomaviruses.
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Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Mol Phylogenet Evol 2019; 139:106539. [DOI: 10.1016/j.ympev.2019.106539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022]
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Sato JJ, Bradford TM, Armstrong KN, Donnellan SC, Echenique-Diaz LM, Begué-Quiala G, Gámez-Díez J, Yamaguchi N, Nguyen ST, Kita M, Ohdachi SD. Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements. Mol Phylogenet Evol 2019; 141:106605. [PMID: 31479732 DOI: 10.1016/j.ympev.2019.106605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 11/26/2022]
Abstract
The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages-Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.
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Affiliation(s)
- Jun J Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimuracho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan; School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Tessa M Bradford
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Kyle N Armstrong
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Lazaro M Echenique-Diaz
- Environmental Education Center, Miyagi University of Education, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Gerardo Begué-Quiala
- Unidad Presupuestada Parque Nacional Alejandro de Humboldt (CITMA), Calle Abogado 14 e/12 y 13 Norte, Guantanamo 95200, Cuba
| | - Jorgelino Gámez-Díez
- Estación Ecológica La Melba, Unidad Presupuestada Parque Nacional Alejandro de Humboldt, CITMA-Guantánamo, Cuba
| | - Nobuyuki Yamaguchi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, PO Box 2713, Doha, Qatar
| | - Son Truong Nguyen
- Institute of Ecology and Biological Resources and Graduate University of Science and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Masaki Kita
- Graduate School of Bioagricultural Sciences, Nagoya University Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Satoshi D Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Kita-19 Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence. Syst Biol 2019; 69:308-324. [DOI: 10.1093/sysbio/syz058] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 08/26/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complement regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inference. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, IC score calculation typically requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing taxa is high, the scores yielded by current approaches that adjust bipartition frequencies in partial gene trees differ substantially from each other and tend to be overestimates. To overcome these issues, we developed three new IC measures based on the frequencies of quartets, which naturally apply to both complete and partial trees. Comparison of our new quartet-based measures to previous bipartition-based measures on simulated data shows that: (1) on complete data sets, both quartet-based and bipartition-based measures yield very similar IC scores; (2) IC scores of quartet-based measures on a given data set with and without missing taxa are more similar than the scores of bipartition-based measures; and (3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in phylogenetic inference than bipartition-based measures. Additionally, the analysis of an empirical mammalian phylogenomic data set using our quartet-based measures reveals the presence of substantial levels of incongruence for numerous internal branches. An efficient open-source implementation of these quartet-based measures is freely available in the program QuartetScores (https://github.com/lutteropp/QuartetScores).
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Asher RJ, Smith MR, Rankin A, Emry RJ. Congruence, fossils and the evolutionary tree of rodents and lagomorphs. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190387. [PMID: 31417738 PMCID: PMC6689570 DOI: 10.1098/rsos.190387] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 05/10/2023]
Abstract
Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and Ischyromys rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support Ischyromys in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and Aplodontia from extinct, 'protrogomorph'-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.
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Affiliation(s)
- Robert J. Asher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Martin R. Smith
- Department of Earth Sciences, University of Durham, Durham, UK
| | - Aime Rankin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Robert J. Emry
- Department of Paleobiology, Smithsonian Institution, Washington, DC, USA
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63
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Gustafson GT, Alexander A, Sproul JS, Pflug JM, Maddison DR, Short AEZ. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecol Evol 2019; 9:6933-6948. [PMID: 31312430 PMCID: PMC6617817 DOI: 10.1002/ece3.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/10/2023] Open
Abstract
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open‐source UCE probe set for beetles of the suborder Adephaga.
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Affiliation(s)
- Grey T Gustafson
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
| | - Alana Alexander
- Biodiversity Institute University of Kansas Lawrence Kansas.,Department of Anatomy, School of Biomedical Sciences University of Otago Dunedin New Zealand
| | - John S Sproul
- Department of Integrative Biology Oregon State University Corvallis Oregon.,Department of Biology University of Rochester Rochester New York
| | - James M Pflug
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - David R Maddison
- Department of Integrative Biology Oregon State University Corvallis Oregon
| | - Andrew E Z Short
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas.,Biodiversity Institute University of Kansas Lawrence Kansas
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64
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D’Elía G, Fabre PH, Lessa EP. Rodent systematics in an age of discovery: recent advances and prospects. J Mammal 2019. [DOI: 10.1093/jmammal/gyy179] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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65
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Nyakatura JA. Early primate evolution: insights into the functional significance of grasping from motion analyses of extant mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John A Nyakatura
- AG Morphologie und Formengeschichte, Institut für Biologie, Humboldt Universität, Philippstraße, Berlin, Germany
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66
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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67
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Drukewitz SH, von Reumont BM. The Significance of Comparative Genomics in Modern Evolutionary Venomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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68
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Neves F, Águeda-Pinto A, Pinheiro A, Abrantes J, Esteves PJ. Strong selection of the TLR2 coding region among the Lagomorpha suggests an evolutionary history that differs from other mammals. Immunogenetics 2019; 71:437-443. [PMID: 30874861 DOI: 10.1007/s00251-019-01110-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Toll-like receptors (TLRs) are one of the first lines of defense against pathogens and are crucial for triggering an appropriate immune response. Among TLRs, TLR2 is functional in all vertebrates and has high ability in detecting bacterial and viral pathogen ligands. The mammals' phylogenetic tree of TLR2 showed longer branches for the Lagomorpha clade, raising the hypothesis that lagomorphs experienced an acceleration of the mutation rate. This hypothesis was confirmed by (i) Tajima's test of neutrality that revealed different evolutionary rates between lagomorphs and the remaining mammals with lagomorphs presenting higher nucleotide diversity; (ii) genetic distances were similar among lagomorphs and between lagomorphs and other mammals; and (iii) branch models reinforced the existence of an acceleration of the mutation rate in lagomorphs. These results suggest that the lagomorph TLR2 has been strongly involved in pathogen recognition, which probably caused a host-pathogen arms race that led to the observed acceleration of the mutation rate.
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Affiliation(s)
- Fabiana Neves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Águeda-Pinto
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Ana Pinheiro
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Joana Abrantes
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO-UP, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr.7, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal. .,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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69
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Grunstra NDS, Zachos FE, Herdina AN, Fischer B, Pavličev M, Mitteroecker P. Humans as inverted bats: A comparative approach to the obstetric conundrum. Am J Hum Biol 2019; 31:e23227. [PMID: 30810261 PMCID: PMC6492174 DOI: 10.1002/ajhb.23227] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES The narrow human birth canal evolved in response to multiple opposing selective forces on the pelvis. These factors cannot be sufficiently disentangled in humans because of the limited range of relevant variation. Here, we outline a comparative strategy to study the evolution of human childbirth and to test existing hypotheses in primates and other mammals. METHODS We combined a literature review with comparative analyses of neonatal and female body and brain mass, using three existing datasets. We also present images of bony pelves of a diverse sample of taxa. RESULTS Bats, certain non-human primates, seals, and most ungulates, including whales, have much larger relative neonatal masses than humans, and they all differ in their anatomical adaptations for childbirth. Bats, as a group, are particularly interesting in this context as they give birth to the relatively largest neonates, and their pelvis is highly dimorphic: Whereas males have a fused symphysis, a ligament bridges a large pubic gap in females. The resulting strong demands on the widened and vulnerable pelvic floor likely are relaxed by roosting head-down. CONCLUSIONS Parturition has constituted a strong selective force in many non-human placentals. We illustrated how the demands on pelvic morphology resulting from locomotion, pelvic floor stability, childbirth, and perhaps also erectile function in males have been traded off differently in mammals, depending on their locomotion and environment. Exploiting the power of a comparative approach, we present new hypotheses and research directions for resolving the obstetric conundrum in humans.
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Affiliation(s)
- Nicole D. S. Grunstra
- Department of Theoretical BiologyUniversity of ViennaViennaAustria
- Mammal CollectionNatural History Museum ViennaViennaAustria
| | - Frank E. Zachos
- Mammal CollectionNatural History Museum ViennaViennaAustria
- Department of Integrative ZoologyUniversity of ViennaViennaAustria
| | | | - Barbara Fischer
- Konrad Lorenz Institute for Evolution and Cognition ResearchKlosterneuburgAustria
| | - Mihaela Pavličev
- Cincinnati Children's Hospital Medical CenterCincinnatiOhio
- Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiOhio
- Department of PhilosophyUniversity of CincinnatiCincinnatiOhio
| | - Philipp Mitteroecker
- Department of Theoretical BiologyUniversity of ViennaViennaAustria
- Konrad Lorenz Institute for Evolution and Cognition ResearchKlosterneuburgAustria
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70
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Youlatos D, Widayati KA, Tsuji Y. Foot postures and grasping of free-ranging Sunda colugos (Galeopterus variegatus) in West Java, Indonesia. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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71
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ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements. Genes (Basel) 2019; 10:genes10030181. [PMID: 30813627 PMCID: PMC6471834 DOI: 10.3390/genes10030181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 11/16/2022] Open
Abstract
Studying parallel and convergent amino acid replacements in protein evolution is frequently used to assess adaptive evolution at the molecular level. Identifying parallel and convergent replacements involves multiple steps and computational routines, such as multiple sequence alignment, phylogenetic tree inference, ancestral state reconstruction, topology tests, and simulation of sequence evolution. Here, we present ProtParCon, a Python 3 package that provides a common interface for users to process molecular data and identify parallel and convergent amino acid replacements in orthologous protein sequences. By integrating several widely used programs for computational biology, ProtParCon implements general functions for handling multiple sequence alignment, ancestral-state reconstruction, maximum-likelihood phylogenetic tree inference, and sequence simulation. ProtParCon also contains a built-in pipeline that automates all these sequential steps, and enables quick identification of observed and expected parallel and convergent amino acid replacements under different evolutionary assumptions. The most up-to-date version of ProtParCon, including scripts containing user tutorials, the full API reference and documentation are publicly and freely available under an open source MIT License via GitHub. The latest stable release is also available on PyPI (the Python Package Index).
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72
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Contrasting patterns of coding and flanking region evolution in mammalian keratin associated protein-1 genes. Mol Phylogenet Evol 2018; 133:352-361. [PMID: 30599197 DOI: 10.1016/j.ympev.2018.12.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/15/2018] [Accepted: 12/26/2018] [Indexed: 12/17/2022]
Abstract
Mammalian genomes contain a number of duplicated genes, and sequence identity between these duplicates can be maintained by purifying selection. However, between-duplicate recombination can also maintain sequence identity between copies, resulting in a pattern known as concerted evolution where within-genome repeats are more similar to each other than to orthologous repeats in related species. Here we investigated the tandemly-repeated keratin-associated protein 1 (KAP1) gene family, KRTAP1, which encodes proteins that are important components of hair and wool in mammals. Comparison of eutherian mammal KRTAP1 gene repeats within and between species shows a strong pattern of concerted evolution. However, in striking contrast to the coding regions of these genes, we find that the flanking regions have a divergent pattern of evolution. This contrast in evolutionary pattern transitions abruptly near the start and stop codons of the KRTAP1 genes. We reveal that this difference in evolutionary patterns is not explained by conventional purifying selection, nor is it likely a consequence of codon adaptation or reverse transcription of KRTAP1-n mRNA. Instead, the evidence suggests that these contrasting patterns result from short-tract gene conversion events that are biased to the KRTAP1 coding region by selection and/or differential sequence divergence. This work demonstrates the power that gene conversion has to finely shape the evolution of repetitive genes, and provides another distinctive pattern of contrasting evolutionary outcomes that results from gene conversion. A greater emphasis on exploring the evolution of multi-gene eukaryotic families will reveal how common different contrasting evolutionary patterns are in gene duplicates.
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73
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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74
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Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Syst Biol 2018; 68:573-593. [DOI: 10.1093/sysbio/syy085] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fernando Alda
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Victor A Tagliacollo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Ipirianga, 04263-000, São Paulo, São Paulo, Brazil
| | - Maxwell J Bernt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Brandon T Waltz
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - William B Ludt
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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75
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Mclean BS, Bell KC, Allen JM, Helgen KM, Cook JA. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Syst Biol 2018; 68:298-316. [DOI: 10.1093/sysbio/syy064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Bryan S Mclean
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Department of Invertebrate Zoology, Smithsonian Institution National Museum of Natural History, P.O. Box 37012, MRC 163, Washington, DC 20013-7012, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Kristofer M Helgen
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
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76
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Hutterer R, Balete DS, Giarla TC, Heaney LR, Esselstyn JA. A new genus and species of shrew (Mammalia: Soricidae) from Palawan Island, Philippines. J Mammal 2018. [DOI: 10.1093/jmammal/gyy041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Rainer Hutterer
- Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | - Danilo S Balete
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, USA
| | - Thomas C Giarla
- Department of Biology, Siena College, 515 Loudon Road, Loudonville, NY, USA
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, USA
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, USA
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77
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Roberts WR, Roalson EH. Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes). AMERICAN JOURNAL OF BOTANY 2018; 105:726-740. [PMID: 29702729 DOI: 10.1002/ajb2.1058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The Neotropical Gesneriaceae is a lineage known for its colorful and diverse flowers, as well as an extensive history of intra- and intergeneric hybridization, particularly among Achimenes (the magic flowers) and other members of subtribe Gloxiniinae. Despite numerous studies seeking to elucidate the evolutionary relationships of these lineages, relatively few have sought to infer specific patterns of gene flow despite evidence of widespread hybridization. METHODS To explore the utility of phylogenomic data for reassessing phylogenetic relationships and inferring patterns of gene flow among species of Achimenes, we sequenced 12 transcriptomes. We used a variety of methods to infer the species tree, examine gene tree discordance, and infer patterns of gene flow. KEY RESULTS Phylogenomic analyses resolve clade relationships at the crown of the lineage with strong support. In contrast to previous analyses, we recovered strong support for several new relationships despite a significant amount of gene tree discordance. We present evidence for at least two introgression events between two species pairs that share pollinators, and suggest that the species status of Achimenes admirabilis be reexamined. CONCLUSIONS Our study demonstrates the utility of transcriptome data for phylogenomic analyses, and inferring patterns of gene flow despite gene tree discordance. Moreover, these data provide another example of prevalent interspecific gene flow among Neotropical plants that share pollinators.
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Affiliation(s)
- Wade R Roberts
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, 99164-1030, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
| | - Eric H Roalson
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, 99164-1030, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
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78
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Kay RF. 100 years of primate paleontology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:652-676. [DOI: 10.1002/ajpa.23429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Richard F. Kay
- Department of Evolutionary Anthropology and Division of Earth and Ocean Sciences; Duke University; Durham North Carolina 27708
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79
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Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018; 45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.
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Affiliation(s)
- Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - James W D King
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander J Nash
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
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