1
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Nagasawa K, Kitano T. Pseudogenization of the Hair-Related Genes PADI3 and S100A3 in Cetaceans and Hippopotamus amphibius. J Mol Evol 2023; 91:745-760. [PMID: 37787841 DOI: 10.1007/s00239-023-10133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Hair-related genes in mammals play important roles in the development and maintenance of hair and other keratinous structures in mammals. The peptidyl arginine deiminase 3 (PADI3) gene encodes an enzyme that catalyzes the conversion of arginine residues to citrulline. The S100 calcium binding protein A3 (S100A3) gene encodes a protein that is highly expressed in the hair cuticle and contains arginine residues that are converted to citrullines by PADI enzymes. In this study, we investigated the pseudogenization events of PADI3 and S100A3 in cetaceans and Hippopotamus amphibius. We found that PADI3 underwent three independent pseudogenization events during cetacean evolution, in baleen whales, toothed cetaceans other than Physeter catodon, and P. catodon. Notably, the entire PADI3 gene is absent in the baleen whales. Pseudogenization of S100A3 occurred independently in cetaceans and H. amphibius. Interestingly, we found that in cetaceans S100A3 underwent pseudogenization before PADI3, suggesting that differential selection pressures were acting on the two genes. Our findings provide valuable insights into the molecular evolution of these genes in cetaceans and hippopotamuses, highlighting their importance for understanding the evolution of hair-related genes.
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Affiliation(s)
- Kyomi Nagasawa
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-Cho, Hitachi, Ibaraki, 316-8511, Japan
| | - Takashi Kitano
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-Cho, Hitachi, Ibaraki, 316-8511, Japan.
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2
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Doronina L, Ogoniak L, Schmitz J. Homoplasy of Retrotransposon Insertions in Toothed Whales. Genes (Basel) 2023; 14:1830. [PMID: 37761970 PMCID: PMC10531181 DOI: 10.3390/genes14091830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18-0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany;
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Lynn Ogoniak
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany;
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, 48149 Münster, Germany;
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3
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SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics. Genes (Basel) 2022; 13:genes13060989. [PMID: 35741751 PMCID: PMC9223172 DOI: 10.3390/genes13060989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/31/2022] Open
Abstract
Currently, the insertions of SINEs (and other retrotransposed elements) are regarded as one of the most reliable synapomorphies in molecular systematics. The methodological mainstream of molecular systematics is the calculation of nucleotide (or amino acid) sequence divergences under a suitable substitution model. In contrast, SINE insertion analysis does not require any complex model because SINE insertions are unidirectional and irreversible. This straightforward methodology was named the “SINE method,” which resolved various taxonomic issues that could not be settled by sequence comparison alone. The SINE method has challenged several traditional hypotheses proposed based on the fossil record and anatomy, prompting constructive discussions in the Evo/Devo era. Here, we review our pioneering SINE studies on salmon, cichlids, cetaceans, Afrotherian mammals, and birds. We emphasize the power of the SINE method in detecting incomplete lineage sorting by tracing the genealogy of specific genomic loci with minimal noise. Finally, in the context of the whole-genome era, we discuss how the SINE method can be applied to further our understanding of the tree of life.
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4
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Skovrind M, Louis M, Westbury MV, Garilao C, Kaschner K, Castruita JAS, Gopalakrishnan S, Knudsen SW, Haile JS, Dalén L, Meshchersky IG, Shpak OV, Glazov DM, Rozhnov VV, Litovka DI, Krasnova VV, Chernetsky AD, Bel'kovich VM, Lydersen C, Kovacs KM, Heide-Jørgensen MP, Postma L, Ferguson SH, Lorenzen ED. Circumpolar phylogeography and demographic history of beluga whales reflect past climatic fluctuations. Mol Ecol 2021; 30:2543-2559. [PMID: 33825233 DOI: 10.1111/mec.15915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/28/2022]
Abstract
Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analysed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas) sampled across their circumpolar range, and four nuclear genomes, covering both the Atlantic and the Pacific Arctic region. We found four well-differentiated mitochondrial lineages, which were established before the onset of the last glacial expansion ~110 thousand years ago. Our findings suggested these lineages diverged in allopatry, reflecting isolation of populations during glacial periods when the Arctic sea-shelf was covered by multiyear sea ice. Subsequent population expansion and secondary contact between the Atlantic and Pacific Oceans shaped the current geographic distribution of lineages, and may have facilitated mitochondrial introgression. Our demographic reconstructions based on both mitochondrial and nuclear genomes showed markedly lower population sizes during the Last Glacial Maximum (LGM) compared to the preceding Eemian and current Holocene interglacial periods. Habitat modelling similarly revealed less suitable habitat during the LGM (glacial) than at present (interglacial). Together, our findings suggested the association between climate, population size, and available habitat in belugas. Forecasts for year 2100 showed that beluga habitat will decrease and shift northwards as oceans continue to warm, putatively leading to population declines in some beluga populations. Finally, we identified vulnerable populations which, if extirpated as a consequence of ocean warming, will lead to a substantial decline of species-wide haplotype diversity.
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Affiliation(s)
| | - Marie Louis
- GLOBE Institute, University of Copenhagen, Denmark
| | | | | | - Kristin Kaschner
- Department of Biometry and Environmental System Analysis, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | | | | | - Steen Wilhelm Knudsen
- NIVA Denmark Water Research, Copenhagen, Denmark.,Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - James S Haile
- Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Ilya G Meshchersky
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow, Russia
| | - Olga V Shpak
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow, Russia
| | - Dmitry M Glazov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow, Russia
| | - Viatcheslav V Rozhnov
- A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Science, Moscow, Russia
| | - Dennis I Litovka
- Office of Governor and Government of the Chukotka Autonomous Okrug, Anadyr, Russia
| | - Vera V Krasnova
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, Russia
| | - Anton D Chernetsky
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, Russia
| | | | | | | | - Mads Peter Heide-Jørgensen
- Natural History Museum of Denmark, University of Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Lianne Postma
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
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5
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Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans. Mol Biol Rep 2020; 48:315-322. [PMID: 33296067 DOI: 10.1007/s11033-020-06048-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/28/2020] [Indexed: 10/22/2022]
Abstract
The Ganges river dolphin, Platanista gangetica gangetica is one of the endangered cetaceans. Due to increasing anthropogenic activities, it has faced a significant reduction in distribution range since the late 1800s and has even gone extinct from most of the early localities. The investigation of complete mitogenome holds significant relevance for identifying evolutionary relationships and monitoring the endangered species. Herein, we report and characterize for the first time the 16,319 bp complete mitochondrial genome of P. g. gangetica. It comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The genome composition was A + T biased (59.6%) and exhibited a positive AT-skew (0.104) and negative GC-skew (- 0.384). All the genes were encoded on the heavy strand, except eight tRNAs and the ND6 gene. In the CR, an 18 bp tandem repeat sequence was observed. Our Bayesian Inference (BI) and Maximum Likelihood (ML) based phylogenetic analysis indicated that studied river dolphins were polyphyletic and the placement of Platanista was to be more basal than other river dolphins (Lipotes, Inia and Pontoporia). The pairwise genetic distance of Platanista with other cetaceans was varied, with an overall close affinity with whales. The model-based BI and ML phylogenetic analysis indicated that Platanista clustering with Ziphiidae with high to moderate supportive values (PP/BP = 98/68). The results of this study provide insights important for the conservation genetics and further evolutionary studies of the freshwater river dolphins.
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6
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McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
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}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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7
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Hildebrandt E, Penzes JJ, Gifford RJ, Agbandje-Mckenna M, Kotin RM. Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors. Virus Evol 2020; 6:veaa043. [PMID: 32913662 PMCID: PMC7474932 DOI: 10.1093/ve/veaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.
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Affiliation(s)
- Evin Hildebrandt
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
| | - Judit J Penzes
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Genomics & Bioinformatics, Sir Michael Stoker Building Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Mavis Agbandje-Mckenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert M Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
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8
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Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets. J Hered 2019; 111:147-168. [DOI: 10.1093/jhered/esz076] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
DNA sequence alignments have provided the majority of data for inferring phylogenetic relationships with both concatenation and coalescent methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroelement insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroelement insertions satisfy the “no intralocus-recombination” assumption of summary coalescent methods because they are singular events and better approximate neutrality relative to DNA loci commonly sampled in phylogenomic studies. Retroelements have traditionally been analyzed with parsimony, distance, and network methods. Here, we analyze retroelement data sets for vertebrate clades (Placentalia, Laurasiatheria, Balaenopteroidea, Palaeognathae) with 2 ILS-aware methods that operate by extracting, weighting, and then assembling unrooted quartets into a species tree. The first approach constructs a species tree from retroelement bipartitions with ASTRAL, and the second method is based on split-decomposition with parsimony. We also develop a Quartet-Asymmetry test to detect hybridization using retroelements. Both ILS-aware methods recovered the same species-tree topology for each data set. The ASTRAL species trees for Laurasiatheria have consecutive short branch lengths in the anomaly zone whereas Palaeognathae is outside of this zone. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both ILS-aware methods resolved balaeonopterids as paraphyletic. Application of the Quartet-Asymmetry test to this data set detected 19 different quartets of species for which historical introgression may be inferred. Evidence for introgression was not detected in the other data sets.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - Erin K Molloy
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
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9
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Minato T, Unno M, Kitano T. Evolution of S100A3 and PAD3, two important genes for mammalian hair. Gene 2019; 713:143975. [PMID: 31302167 DOI: 10.1016/j.gene.2019.143975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
Abstract
Hair is one of the defining characteristics of mammals. The hair shaft has a two-layer structure comprising the cortex, which is the inner layer and is composed of cortical cells, and the cuticle, which is the outermost layer. S100 calcium-binding protein A3 (S100A3) is expressed at high levels in the human hair cuticle. Arginine 51 of S100A3 protein is citrullinated specifically by peptidylarginine deiminase 3 (PAD3), and this citrullination is related to maturation of the cuticle. However, the detailed evolutionary processes of S100A3 and PAD3 during mammalian evolution are unknown. Here, we show that nonsynonymous changes in S100A3 accelerated in the common ancestral branch of mammals, probably as a result of positive selection that returned after the acquisition of hair cuticle-specific function in mammals. Later, pseudogenisation or nonfunctionalisation of S100A3 and PAD3 occurred in some species, such as the cetaceans. Our results show that positive selection and relaxation of the functional constraints of genes played important roles in the evolution of mammalian hair.
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Affiliation(s)
- Tadashi Minato
- Department of Chemistry and Life Sciences, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Masaki Unno
- Department of Chemistry and Life Sciences, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Takashi Kitano
- Department of Chemistry and Life Sciences, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan.
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10
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Ohishi K, Maruyama T, Seki F, Takeda M. Marine Morbilliviruses: Diversity and Interaction with Signaling Lymphocyte Activation Molecules. Viruses 2019; 11:E606. [PMID: 31277275 PMCID: PMC6669707 DOI: 10.3390/v11070606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 01/08/2023] Open
Abstract
Epidemiological reports of phocine distemper virus (PDV) and cetacean morbillivirus (CeMV) have accumulated since their discovery nearly 30 years ago. In this review, we focus on the interaction between these marine morbilliviruses and their major cellular receptor, the signaling lymphocyte activation molecule (SLAM). The three-dimensional crystal structure and homology models of SLAMs have demonstrated that 35 residues are important for binding to the morbillivirus hemagglutinin (H) protein and contribute to viral tropism. These 35 residues are essentially conserved among pinnipeds and highly conserved among the Caniformia, suggesting that PDV can infect these animals, but are less conserved among cetaceans. Because CeMV can infect various cetacean species, including toothed and baleen whales, the CeMV-H protein is postulated to have broader specificity to accommodate more divergent SLAM interfaces and may enable the virus to infect seals. In silico analysis of viral H protein and SLAM indicates that each residue of the H protein interacts with multiple residues of SLAM and vice versa. The integration of epidemiological, virological, structural, and computational studies should provide deeper insight into host specificity and switching of marine morbilliviruses.
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Affiliation(s)
- Kazue Ohishi
- Faculty of Engineering, Tokyo Polytechnic University, 1583, Iiyama, Atsugi, Kanagawa 243-0297, Japan.
| | - Tadashi Maruyama
- School of Marine Biosciences, Kitasato University, 1-15-1, Kitazato, Minami, Sagamihara, Kanagawa 252-0373, Japan
| | - Fumio Seki
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama, Tokyo 208-0011, Japan
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11
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Casanova EL, Switala AE, Dandamudi S, Hickman AR, Vandenbrink J, Sharp JL, Feltus FA, Casanova MF. Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. Autism Res 2019; 12:860-869. [PMID: 31025836 DOI: 10.1002/aur.2112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 03/22/2019] [Accepted: 04/06/2019] [Indexed: 11/09/2022]
Abstract
Previous research on autism risk (ASD), developmental regulatory (DevReg), and central nervous system (CNS) genes suggests they tend to be large in size, enriched in nested repeats, and mutation intolerant. The relevance of these genomic features is intriguing yet poorly understood. In this study, we investigated the feature landscape of these gene groups to discover structural themes useful in interpreting their function, developmental patterns, and evolutionary history. ASD, DevReg, CNS, housekeeping, and whole genome control (WGC) groups were compiled using various resources. Multiple gene features of interest were extracted from NCBI/UCSC Bioinformatics. Residual variation intolerance scores, Exome Aggregation Consortium pLI scores, and copy number variation data from Decipher were used to estimate variation intolerance. Gene age and protein-protein interactions (PPI) were estimated using Ensembl and EBI Intact databases, respectively. Compared to WGC: ASD, DevReg, and CNS genes are longer, produce larger proteins, maintain greater numbers/density of conserved noncoding elements and transposable elements, produce more transcript variants, and are comparatively variation intolerant. After controlling for gene size, mutation tolerance, and clinical association, ASD genes still retain many of these same features. In addition, we also found that ASD genes that are extremely mutation intolerant have larger PPI networks. These data support many of the recent findings within the field of autism genetics but also expand our understanding of the evolution of these broad gene groups, their potential regulatory complexity, and the extent to which they interact with the cellular network. Autism Res 2019, 12: 860-869. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Autism risk genes are more ancient compared to other genes in the genome. As such, they exhibit physical features related to their age, including long gene and protein size and regulatory sequences that help to control gene expression. They share many of these same features with other genes that are expressed in the brain and/or are associated with prenatal development.
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Affiliation(s)
- Emily L Casanova
- Department of Biomedical Sciences, University of South Carolina, Greenvile, South Carolina.,Department of Pediatrics, Prisma Health System, Greenville, South Carolina
| | - Andrew E Switala
- Department of Bioengineering, University of Louisville, Louisville, Kentucky
| | - Srini Dandamudi
- Department of Statistics, Colorado State University, Fort Collins, Colorado
| | - Allison R Hickman
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Joshua Vandenbrink
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana
| | - Julia L Sharp
- Department of Statistics, Colorado State University, Fort Collins, Colorado
| | - Frank Alex Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Manuel F Casanova
- Department of Biomedical Sciences, University of South Carolina, Greenvile, South Carolina.,Department of Pediatrics, Prisma Health System, Greenville, South Carolina
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12
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Kundu S, Sharma G, Balakrishnan S, Tyagi K, Chandra K, Kumar V. DNA barcoding identified two endangered dolphins: threats on living aquatic mammals in India. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1536467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shantanu Kundu
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Gopal Sharma
- 2Gangetic Plains Regional Centre, Zoological Survey of India, Patna, India
| | | | - Kaomud Tyagi
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
- 2Gangetic Plains Regional Centre, Zoological Survey of India, Patna, India
- 3Marine Aquarium and Research Centre, Zoological Survey of India, Digha, India
| | - Vikas Kumar
- 1Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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13
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Márquez S, Pagano AS, Mongle CS, Albertine KH, Laitman JT. The Nasal Complex of a Semiaquatic Artiodactyl, the Moose (Alces alces): Is it a Good Evolutionary Model for the Ancestors of Cetaceans? Anat Rec (Hoboken) 2018; 302:667-692. [DOI: 10.1002/ar.24022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/17/2018] [Accepted: 09/23/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Samuel Márquez
- Departments of Cell Biology and OtolaryngologySUNY Downstate Medical Center Brooklyn New York
| | - Anthony S. Pagano
- Department of Medical SciencesHackensack‐Meridian School of Medicine at Seton Hall University Nutley New Jersey
| | - Carrie S. Mongle
- Interdepartmental Program in Anthropological SciencesStony Brook University Stony Brook New York
| | - Kurt H. Albertine
- Department of PediatricsUniversity of Utah School of Medicine Salt Lake City Utah
| | - Jeffrey T. Laitman
- Departments of Medical Education and Otolaryngology, Icahn School of Medicine at Mount SinaiCenter for Anatomy & Functional Morphology New York New York
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14
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Isogai Y, Imamura H, Nakae S, Sumi T, Takahashi KI, Nakagawa T, Tsuneshige A, Shirai T. Tracing whale myoglobin evolution by resurrecting ancient proteins. Sci Rep 2018; 8:16883. [PMID: 30442991 PMCID: PMC6237822 DOI: 10.1038/s41598-018-34984-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.
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Affiliation(s)
- Yasuhiro Isogai
- Department of Pharmaceutical Engineering, Toyama Prefectural University, Imizu, Toyama, 939-0398, Japan.
| | - Hiroshi Imamura
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Setsu Nakae
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Tomonari Sumi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan
| | - Ken-Ichi Takahashi
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Taro Nakagawa
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan
| | - Antonio Tsuneshige
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| | - Tsuyoshi Shirai
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-Cho, Nagahama, Shiga, 526-0829, Japan.
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15
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Lambert O, Auclair C, Cauxeiro C, Lopez M, Adnet S. A close relative of the Amazon river dolphin in marine deposits: a new Iniidae from the late Miocene of Angola. PeerJ 2018; 6:e5556. [PMID: 30225172 PMCID: PMC6139015 DOI: 10.7717/peerj.5556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
Background A few odontocetes (echolocating toothed cetaceans) have been able to independently colonize freshwater ecosystems. Although some extant species of delphinids (true dolphins) and phocoenids (porpoises) at least occasionally migrate upstream of large river systems, they have close relatives in fully marine regions. This contrasts with the three odontocete families only containing extant species with a strictly freshwater habitat (Iniidae in South America, the recently extinct Lipotidae in China, and Platanistidae in southeast Asia). Among those, the fossil record of Iniidae includes taxa from freshwater deposits of South America, partly overlapping geographically with the extant Amazon river dolphin Inia geoffrensis, whereas a few marine species from the Americas were only tentatively referred to the family, leaving the transition from a marine to freshwater environment poorly understood. Methods Based on a partial odontocete skeleton including the cranium, discovered in late Miocene (Tortonian-Messinian) marine deposits near the estuary of the Cuanza River, Angola, we describe a new large iniid genus and species. The new taxon is compared to other extinct and extant iniids, and its phylogenetic relationships with the latter are investigated through cladistic analysis. Results and Discussion The new genus and species Kwanzacetus khoisani shares a series of morphological features with Inia geoffrensis, including the combination of a frontal boss with nasals being lower on the anterior wall of the vertex, the laterally directed postorbital process of the frontal, the anteroposterior thickening of the nuchal crest, and robust teeth with wrinkled enamel. As confirmed (although with a low support) with the phylogenetic analysis, this makes the new taxon the closest relative of I. geoffrensis found in marine deposits. The geographic provenance of K. khoisani, on the eastern coast of South Atlantic, suggests that the transition from the marine environment to a freshwater, Amazonian habitat may have occurred on the Atlantic side of South America. This new record further increases the inioid diversity during the late Miocene, a time interval confirmed here as the heyday for this superfamily. Finally, this first description of a Neogene cetacean from inland deposits of western sub-Saharan Africa reveals the potential of this large coastal area for deciphering key steps of the evolutionary history of modern cetaceans in the South Atlantic.
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Affiliation(s)
- Olivier Lambert
- D.O. Terre et Histoire de la Vie, Institut royal des Sciences naturelles de Belgique, Brussels, Belgium
| | - Camille Auclair
- ISEM, Université de Montpellier, Montpellier, France.,Sardent, France
| | - Cirilo Cauxeiro
- Faculdade de Ciências, Universidade Agostinho Neto, Luanda, Angola.,Geosciences, Université de Montpellier, Montpellier, France
| | - Michel Lopez
- Geosciences, Université de Montpellier, Montpellier, France
| | - Sylvain Adnet
- ISEM, Université de Montpellier, Montpellier, France
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16
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Mancia A. On the revolution of cetacean evolution. Mar Genomics 2018; 41:1-5. [PMID: 30154054 DOI: 10.1016/j.margen.2018.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 01/13/2023]
Abstract
The order of Cetacea with 88 species including Odontoceti (or toothed whales) and Mysticeti (or baleen whales) is the most specialized and diversified group of mammals. The blue whale with a maximum recorded length of 29.9 m for 173 t of weight is the largest animal known to have ever existed, and any dolphin's brain is most powerful and complex than any other brain in the animal kingdom, second only to primate's. Nevertheless, Cetacea are mammals that re-entered the oceans only a little over 50 million years ago, a relatively short time on the evolutionary scale. During this time cetaceans and humans have developed marked morphological and behavioral differences, yet their genomes show a high level of similarity. This present review is focused on the description and significance of newly accessible cetacean genome tools and information, and their relevance in the study of the evolution of successful phenotypic adaptations associated to mammal's marine existence, and their applicability to the unresolved disease mechanisms in humans.
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Affiliation(s)
- Annalaura Mancia
- University of Ferrara, Department of Life Sciences and Biotechnology, Ferrara 44121, Italy.
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17
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Santos BF, Perrard A. Testing the Dutilleul syndrome: host use drives the convergent evolution of multiple traits in parasitic wasps. J Evol Biol 2018; 31:1430-1439. [PMID: 29957856 DOI: 10.1111/jeb.13343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022]
Abstract
Common life-history aspects among independent lineages often result in the repeated evolution of suites of adaptive traits, or 'syndromes'. Such syndromes can be key avenues to understand relationships between morphological and ecological traits, but are rarely tested due to insufficient trait shift repetitions. We use a hyperdiverse lineage to investigate the evolution of a syndrome. Cryptine ichneumonid wasps that parasitize insects concealed in hard substrates display several traits that are putative adaptations to that end. Using a phylogenetic framework from a combined multigene molecular and morphological data set with 308 cryptine species, we tested whether these traits were part of a morphofunctional syndrome related to host use. Ancestral state estimations show multiple origins for six investigated traits, which are correlated to each other and to the use of deeply concealed hosts, suggesting adaptation. Putatively adaptive traits showed a much stronger link among themselves than with an assemblage of 49 other morphological traits. However, estimation of the order of evolution in adaptive traits showed no structured pattern. The results indicate that the challenge of attacking deeply concealed hosts induced the repeated evolution of a 'Dutilleul syndrome', named after the 'walker-through-walls' character from French literature. They also point towards a dynamic scenario in the evolution of complex functional systems. These findings highlight the power of morphology to illuminate poorly known aspects of natural history, and how hyperdiverse lineages can be used to understand the evolution of complex traits.
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Affiliation(s)
- Bernardo F Santos
- Department of Entomology, National Museum of Natural History, Washington, DC, USA
| | - Adrien Perrard
- Université Paris Diderot, Sorbonne Université, CNRS, IRD, INRA, Institute of Ecology and Environmental Sciences, iEES-Paris, Paris, France
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18
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Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence. ISME JOURNAL 2018; 12:2518-2531. [PMID: 29942073 DOI: 10.1038/s41396-018-0199-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022]
Abstract
Since the discovery of the human pathogen Helicobacter pylori, various other Helicobacter species have been identified in the stomach of domesticated and wild mammals. To better understand the evolutionary history of these ecologically similar but genetically distinct species, we analyzed 108 gastric Helicobacter genomes and included 54 enterohepatic Helicobacter genomes for comparison purposes. An admixture analysis supported the presence of an ecological barrier, preventing the genetic exchange between the gastric and enterohepatic Helicobacter species, and unraveled many gene flow events within and across species residing in the stomach. As pets can be colonized by multiple gastric Helicobacter species, the genetic exchange between the canine and feline strains was evident, with H. heilmannii and H. bizzozeronii showing the highest interspecies recombination. An admixture between H. pylori (in particular, the ancestral African strains), H. acinonychis from wild felines and H. cetorum from marine mammals was also identified. Because these latter species do not share the same host, this phenomenon is most likely a remaining signal of shared ancestry. A reconstruction of the time of divergence of the gastric Helicobacter spp. revealed that the domestic animal-related Helicobacter species evolved in parallel with H. pylori and its two closest relatives (H. acinonychis and H. cetorum), rather than together.
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19
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Mattiucci S, Cipriani P, Levsen A, Paoletti M, Nascetti G. Molecular Epidemiology of Anisakis and Anisakiasis: An Ecological and Evolutionary Road Map. ADVANCES IN PARASITOLOGY 2018. [PMID: 29530312 DOI: 10.1016/bs.apar.2017.12.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review addresses the biodiversity, biology, distribution, ecology, epidemiology, and consumer health significance of the so far known species of Anisakis, both in their natural hosts and in human accidental host populations, worldwide. These key aspects of the Anisakis species' biology are highlighted, since we consider them as main driving forces behind which most of the research in this field has been carried out over the past decade. From a public health perspective, the human disease caused by Anisakis species (anisakiasis) appears to be considerably underreported and underestimated in many countries or regions around the globe. Indeed, when considering the importance of marine fish species as part of the everyday diet in many coastal communities around the globe, there still exist significant knowledge gaps as to local epidemiological and ecological drivers of the transmission of Anisakis spp. to humans. We further identify some key knowledge gaps related to Anisakis species epidemiology in both natural and accidental hosts, to be filled in light of new 'omic' technologies yet to be fully developed. Moreover, we suggest that future Anisakis research takes a 'holistic' approach by integrating genetic, ecological, immunobiological, and environmental factors, thus allowing proper assessment of the epidemiology of Anisakis spp. in their natural hosts, in human populations, and in the marine ecosystem, in both space and time.
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20
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Gabler MK, Gay DM, Westgate AJ, Koopman HN. Microvascular characteristics of the acoustic fats: Novel data suggesting taxonomic differences between deep and shallow-diving odontocetes. J Morphol 2017; 279:458-471. [DOI: 10.1002/jmor.20782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Molly K. Gabler
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - D. Mark Gay
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - Andrew J. Westgate
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - Heather N. Koopman
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
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21
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Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia. Cladistics 2016; 33:295-332. [DOI: 10.1111/cla.12170] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Affiliation(s)
- John Gatesy
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert W. Meredith
- Department of Biology and Molecular Biology Montclair State University Montclair NJ 07043 USA
| | - Jan E. Janecka
- Department of Biological Sciences Duquesne University Pittsburgh PA 15282 USA
| | - Mark P. Simmons
- Department of Biology Colorado State University Fort Collins CO 80523 USA
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA
| | - Mark S. Springer
- Department of Biology University of California Riverside CA 92521 USA
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22
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Zhang X, Lin W, Zhou R, Gui D, Yu X, Wu Y. Low Major Histocompatibility Complex Class II Variation in the Endangered Indo-Pacific Humpback Dolphin (Sousa chinensis): Inferences About the Role of Balancing Selection. J Hered 2016; 107:143-52. [PMID: 26787544 PMCID: PMC5994972 DOI: 10.1093/jhered/esv138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/04/2015] [Indexed: 11/13/2022] Open
Abstract
It has been widely reported that the major histocompatibility complex (MHC) is under balancing selection due to its immune function across terrestrial and aquatic mammals. The comprehensive studies at MHC and other neutral loci could give us a synthetic evaluation about the major force determining genetic diversity of species. Previously, a low level of genetic diversity has been reported among the Indo-Pacific humpback dolphin (Sousa chinensis) in the Pearl River Estuary (PRE) using both mitochondrial marker and microsatellite loci. Here, the expression and sequence polymorphism of 2 MHC class II genes (DQB and DRB) in 32 S. chinensis from PRE collected between 2003 and 2011 were investigated. High ratios of non-synonymous to synonymous substitution rates, codon-based selection analysis, and trans-species polymorphism (TSP) support the hypothesis that balancing selection acted on S. chinensis MHC sequences. However, only 2 haplotypes were detected at either DQB or DRB loci. Moreover, the lack of deviation from the Hardy-Weinberg expectation at DRB locus combined with the relatively low heterozygosity at both DQB locus and microsatellite loci suggested that balancing selection might not be sufficient, which further suggested that genetic drift associated with historical bottlenecks was not mitigated by balancing selection in terms of the loss of MHC and neutral variation in S. chinensis. The combined results highlighted the importance of maintaining the genetic diversity of the endangered S. chinensis.
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Affiliation(s)
| | - Wenzhi Lin
- *These authors contributed equally to the work
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23
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Kuramoto T, Nishihara H, Watanabe M, Okada N. Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis. Genome Biol Evol 2015; 7:3180-9. [PMID: 26527652 PMCID: PMC4700946 DOI: 10.1093/gbe/evv213] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution.
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Affiliation(s)
- Tae Kuramoto
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Maiko Watanabe
- Division of Microbiology, National Institute of Health Sciences, Setagaya, Tokyo, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan Foundation for Advancement of International Science, Tsukuba, Ibaraki, Japan Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
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24
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Pyenson ND, Vélez-Juarbe J, Gutstein CS, Little H, Vigil D, O’Dea A. Isthminia panamensis, a new fossil inioid (Mammalia, Cetacea) from the Chagres Formation of Panama and the evolution of 'river dolphins' in the Americas. PeerJ 2015; 3:e1227. [PMID: 26355720 PMCID: PMC4562255 DOI: 10.7717/peerj.1227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/13/2015] [Indexed: 11/28/2022] Open
Abstract
In contrast to dominant mode of ecological transition in the evolution of marine mammals, different lineages of toothed whales (Odontoceti) have repeatedly invaded freshwater ecosystems during the Cenozoic era. The so-called 'river dolphins' are now recognized as independent lineages that converged on similar morphological specializations (e.g., longirostry). In South America, the two endemic 'river dolphin' lineages form a clade (Inioidea), with closely related fossil inioids from marine rock units in the South Pacific and North Atlantic oceans. Here we describe a new genus and species of fossil inioid, Isthminia panamensis, gen. et sp. nov. from the late Miocene of Panama. The type and only known specimen consists of a partial skull, mandibles, isolated teeth, a right scapula, and carpal elements recovered from the Piña Facies of the Chagres Formation, along the Caribbean coast of Panama. Sedimentological and associated fauna from the Piña Facies point to fully marine conditions with high planktonic productivity about 6.1-5.8 million years ago (Messinian), pre-dating the final closure of the Isthmus of Panama. Along with ecomorphological data, we propose that Isthminia was primarily a marine inhabitant, similar to modern oceanic delphinoids. Phylogenetic analysis of fossil and living inioids, including new codings for Ischyrorhynchus, an enigmatic taxon from the late Miocene of Argentina, places Isthminia as the sister taxon to Inia, in a broader clade that includes Ischyrorhynchus and Meherrinia, a North American fossil inioid. This phylogenetic hypothesis complicates the possible scenarios for the freshwater invasion of the Amazon River system by stem relatives of Inia, but it remains consistent with a broader marine ancestry for Inioidea. Based on the fossil record of this group, along with Isthminia, we propose that a marine ancestor of Inia invaded Amazonia during late Miocene eustatic sea-level highs.
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Affiliation(s)
- Nicholas D. Pyenson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Departments of Mammalogy and Paleontology, Burke Museum of Natural History and Culture, Seattle, WA, USA
| | - Jorge Vélez-Juarbe
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Carolina S. Gutstein
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Comisión de Patrimonio Natural, Consejo de Monumentos Nacionales, Santiago, Chile
| | - Holly Little
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Dioselina Vigil
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Aaron O’Dea
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
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25
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Yamamoto Y, Akamatsu T, da Silva VMF, Yoshida Y, Kohshima S. Acoustic characteristics of biosonar sounds of free-ranging botos (Inia geoffrensis) and tucuxis (Sotalia fluviatilis) in the Negro River, Amazon, Brazil. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2015; 138:687-693. [PMID: 26328686 DOI: 10.1121/1.4926440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Odontoceti emit broadband high-frequency clicks on echolocation for orientation or prey detection. In the Amazon Basin, two odontoceti species, boto (Amazon River dolphin, Inia geoffrensis) and tucuxi (Sotalia fluviatilis), live sympatrically. The acoustic characteristics of the echolocation clicks of free-ranging botos and tucuxis were measured with a hydrophone array consisting of a full-band and an acoustic event recorder (A-tag). The clicks of the two species were short-duration broadband signals. The apparent source level was 201 dB 1 μPa peak-to-peak at 1 m in the botos and 181 dB 1 μPa peak-to-peak at 1 m in the tucuxis, and the centroid frequency was 82.3 kHz in the botos and 93.1 kHz in the tucuxis. The high apparent source level and low centroid frequency are possibly due to the difference in body size or sound production organs, especially the nasal structure, the sound source of clicks in odontoceti.
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Affiliation(s)
- Yukiko Yamamoto
- National Research Institute of Fisheries Engineering, Fisheries Research Agency, 7620-7, Hasaki, Kamisu-shi, Ibaraki 314-0408, Japan
| | - Tomonari Akamatsu
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Vera M F da Silva
- Aquatic Mammals Laboratory (LMA), National Institute of Amazonian Research, Avenue André Araújo, 2.936, Petrópolis, Manaus, Amazonas 69067-375, Brasil
| | - Yayoi Yoshida
- Department of Marine Biology, Tokai University, 3-20-1 Orido, Shimizu, Shizuoka 424-8610, Japan
| | - Shiro Kohshima
- Wildlife Research Center of Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto 606-8203, Japan
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Caballero S, Duchêne S, Garavito MF, Slikas B, Baker CS. Initial Evidence for Adaptive Selection on the NADH Subunit Two of Freshwater Dolphins by Analyses of Mitochondrial Genomes. PLoS One 2015; 10:e0123543. [PMID: 25946045 PMCID: PMC4422622 DOI: 10.1371/journal.pone.0123543] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 03/04/2015] [Indexed: 01/31/2023] Open
Abstract
A small number of cetaceans have adapted to an entirely freshwater environment, having colonized rivers in Asia and South America from an ancestral origin in the marine environment. This includes the ‘river dolphins’, early divergence from the odontocete lineage, and two species of true dolphins (Family Delphinidae). Successful adaptation to the freshwater environment may have required increased demands in energy involved in processes such as the mitochondrial osmotic balance. For this reason, riverine odontocetes provide a compelling natural experiment in adaptation of mammals from marine to freshwater habitats. Here we present initial evidence of positive selection in the NADH dehydrogenase subunit 2 of riverine odontocetes by analyses of full mitochondrial genomes, using tests of selection and protein structure modeling. The codon model with highest statistical support corresponds to three discrete categories for amino acid sites, those under positive, neutral, and purifying selection. With this model we found positive selection at site 297 of the NADH dehydrogenase subunit 2 (dN/dS>1.0,) leading to a substitution of an Ala or Val from the ancestral state of Thr. A phylogenetic reconstruction of 27 cetacean mitogenomes showed that an Ala substitution has evolved at least four times in cetaceans, once or more in the three ‘river dolphins’ (Families Pontoporidae, Lipotidae and Inidae), once in the riverine Sotalia fluviatilis (but not in its marine sister taxa), once in the riverine Orcaella brevirostris from the Mekong River (but not in its marine sister taxa) and once in two other related marine dolphins. We located the position of this amino acid substitution in an alpha-helix channel in the trans-membrane domain in both the E. coli structure and Sotalia fluviatilis model. In E. coli this position is located in a helix implicated in a proton translocation channel of respiratory complex 1 and may have a similar role in the NADH dehydrogenases of cetaceans.
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Affiliation(s)
- Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
- * E-mail:
| | - Sebastian Duchêne
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
- School of Biological Sciences, The University of Sydney, NSW, Australia
| | - Manuel F. Garavito
- Grupo de Investigaciones en Bioquímica y Biología Molecular de Parásitos, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
| | - Beth Slikas
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America
| | - C. Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Hatfield Marine Science Center, Oregon State University, Newport, Oregon, United States of America
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Marx FG, Fordyce RE. Baleen boom and bust: a synthesis of mysticete phylogeny, diversity and disparity. ROYAL SOCIETY OPEN SCIENCE 2015; 2:140434. [PMID: 26064636 PMCID: PMC4448876 DOI: 10.1098/rsos.140434] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 03/03/2015] [Indexed: 05/23/2023]
Abstract
A new, fully dated total-evidence phylogeny of baleen whales (Mysticeti) shows that evolutionary phases correlate strongly with Caenozoic modernization of the oceans and climates, implying a major role for bottom-up physical drivers. The phylogeny of 90 modern and dated fossil species suggests three major phases in baleen whale history: an early adaptive radiation (36-30 Ma), a shift towards bulk filter-feeding (30-23 Ma) and a climate-driven diversity loss around 3 Ma. Evolutionary rates and disparity were high following the origin of mysticetes around 38 Ma, coincident with global cooling, abrupt Southern Ocean eutrophication and the development of the Antarctic Circumpolar Current (ACC). Subsequently, evolutionary rates and disparity fell, becoming nearly constant after approximately 23 Ma as the ACC reached its full strength. By contrast, species diversity rose until 15 Ma and then remained stable, before dropping sharply with the onset of Northern Hemisphere glaciation. This decline coincided with the final establishment of modern mysticete gigantism and may be linked to glacially driven variability in the distribution of shallow habitats or an increased need for long-distance migration related to iron-mediated changes in glacial marine productivity.
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Affiliation(s)
- Felix G. Marx
- Department of Geology, University of Otago, Dunedin 9054, New Zealand
- Department of Geology and Palaeontology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - R. Ewan Fordyce
- Department of Geology, University of Otago, Dunedin 9054, New Zealand
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Wang J, Yu X, Hu B, Zheng J, Xiao W, Hao Y, Liu W, Wang D. Physicochemical evolution and molecular adaptation of the cetacean osmoregulation-related gene UT-A2 and implications for functional studies. Sci Rep 2015; 5:8795. [PMID: 25762239 PMCID: PMC4357013 DOI: 10.1038/srep08795] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 02/04/2015] [Indexed: 12/15/2022] Open
Abstract
Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf. Our findings suggest that the UT-A2 protein shows folding similar to that of dvUT and UT-B, whereas some variations occurred in the functional So and Si regions of the selectivity filter. Additionally, several regions of the cetacean UT-A2 protein have experienced molecular adaptations. We suggest that positive-destabilizing selection could contribute to adaptations by influencing its biochemical and conformational character. The conservation of amino acid residues within the selectivity filter of the urea conduction pore is likely to be necessary for urea conduction, whereas the non-conserved amino acid replacements around the entrance and exit of the conduction pore could potentially affect the activity, which could be interesting target sites for future mutagenesis studies.
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Affiliation(s)
- Jingzhen Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - Xueying Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bo Hu
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Jinsong Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wuhan Xiao
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Yujiang Hao
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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Butti C, Janeway CM, Townshend C, Wicinski BA, Reidenberg JS, Ridgway SH, Sherwood CC, Hof PR, Jacobs B. The neocortex of cetartiodactyls: I. A comparative Golgi analysis of neuronal morphology in the bottlenose dolphin (Tursiops truncatus), the minke whale (Balaenoptera acutorostrata), and the humpback whale (Megaptera novaeangliae). Brain Struct Funct 2014; 220:3339-68. [PMID: 25100560 DOI: 10.1007/s00429-014-0860-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/25/2014] [Indexed: 12/12/2022]
Abstract
The present study documents the morphology of neurons in several regions of the neocortex from the bottlenose dolphin (Tursiops truncatus), the North Atlantic minke whale (Balaenoptera acutorostrata), and the humpback whale (Megaptera novaeangliae). Golgi-stained neurons (n = 210) were analyzed in the frontal and temporal neocortex as well as in the primary visual and primary motor areas. Qualitatively, all three species exhibited a diversity of neuronal morphologies, with spiny neurons including typical pyramidal types, similar to those observed in primates and rodents, as well as other spiny neuron types that had more variable morphology and/or orientation. Five neuron types, with a vertical apical dendrite, approximated the general pyramidal neuron morphology (i.e., typical pyramidal, extraverted, magnopyramidal, multiapical, and bitufted neurons), with a predominance of typical and extraverted pyramidal neurons. In what may represent a cetacean morphological apomorphy, both typical pyramidal and magnopyramidal neurons frequently exhibited a tri-tufted variant. In the humpback whale, there were also large, star-like neurons with no discernable apical dendrite. Aspiny bipolar and multipolar interneurons were morphologically consistent with those reported previously in other mammals. Quantitative analyses showed that neuronal size and dendritic extent increased in association with body size and brain mass (bottlenose dolphin < minke whale < humpback whale). The present data thus suggest that certain spiny neuron morphologies may be apomorphies in the neocortex of cetaceans as compared to other mammals and that neuronal dendritic extent covaries with brain and body size.
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Affiliation(s)
- Camilla Butti
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Box 1639, One Gustave L. Levy Place, New York, NY, 10029, USA.
| | - Caroline M Janeway
- Laboratory of Quantitative Neuromorphology, Psychology, Colorado College, 14 E. Cache La Poudre, Colorado Springs, CO, 80903, USA
| | - Courtney Townshend
- Laboratory of Quantitative Neuromorphology, Psychology, Colorado College, 14 E. Cache La Poudre, Colorado Springs, CO, 80903, USA
| | - Bridget A Wicinski
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Box 1639, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Joy S Reidenberg
- Center for Anatomy and Functional Morphology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Sam H Ridgway
- National Marine Mammal Foundation, 2240 Shelter Island Drive, San Diego, CA, 92106, USA
| | - Chet C Sherwood
- Department of Anthropology, The George Washington University, 2110 G Street NW, Washington, DC, 20052, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Box 1639, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Bob Jacobs
- Laboratory of Quantitative Neuromorphology, Psychology, Colorado College, 14 E. Cache La Poudre, Colorado Springs, CO, 80903, USA
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Kelley TC, Higdon JW, Ferguson SH. Large testes and brain sizes in odontocetes (order Cetacea, suborder Odontoceti): the influence of mating system on encephalization. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2014-0044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Little is known about their mating systems, but odontocetes may utilize the same types of mating systems as terrestrial mammals. Species with relatively large testes are likely to be polygynandrous, while species with smaller testes and greater sexual size dimorphism (SSD) are predicted to be polygynous. The “Machiavellian intelligence or sexual conflict” hypothesis predicts that polygynadrous species also evolved larger brains both to coerce conspecifics to mate and to resist mating attempts by undesirable mates. The “costly tissue” hypothesis predicts that species investing heavily in testes invest less in brain tissue and vice versa to conserve energy. Residual testes and brain mass measurements were used to test the sexual conflict and costly tissue hypotheses in 40 species of odontocetes. Correlations were performed on both raw data and independent contrasts to control for phylogeny. There was a significant positive correlation between residual testes mass and SSD in both data sets, and between residual testes mass and residual brain mass in the non-phylogenetically controlled data set. Results indicate a negative relationship between increased testes masses and SSD in odontocetes. There was no support for the costly tissue hypothesis. Support for Machiavellian intelligence or sexual conflict hypothesis was found only when phylogenetic effects were not considered.
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Affiliation(s)
- Trish C. Kelley
- Department of Environment and Geography, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Jeff W. Higdon
- Higdon Wildlife Consulting, 912 Ashburn Street, Winnipeg, MB R3G 3C9, Canada
| | - Steven H. Ferguson
- Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB R3T 2N6, Canada
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Walters-Conte KB, Johnson DLE, Johnson WE, O’Brien SJ, Pecon-Slattery J. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms. BMC Evol Biol 2014; 14:137. [PMID: 24947429 PMCID: PMC4084570 DOI: 10.1186/1471-2148-14-137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/11/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed. RESULTS We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. CONCLUSIONS We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement.
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Affiliation(s)
- Kathryn B Walters-Conte
- Department of Biology, American University, 101 Hurst Hall 4440 Massachusetts Ave, Washington, DC 20016, USA
| | - Diana LE Johnson
- Department of Biological Sciences, The George Washington University, 2036 G St, Washington, DC 20009, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Stephen J O’Brien
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41 A, Sredniy Avenue St., Petersburg 199034, Russia
| | - Jill Pecon-Slattery
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
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One Species or Two? Vicariance, Lineage Divergence and Low mtDNA Diversity in Geographically Isolated Populations of South Asian River Dolphin. J MAMM EVOL 2014. [DOI: 10.1007/s10914-014-9265-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gutstein CS, Cozzuol MA, Pyenson ND. The Antiquity of Riverine Adaptations in Iniidae (Cetacea, Odontoceti) Documented by a Humerus from the Late Miocene of the Ituzaingó Formation, Argentina. Anat Rec (Hoboken) 2014; 297:1096-102. [DOI: 10.1002/ar.22901] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 01/15/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Carolina Simon Gutstein
- Departamento de Biología Red Paleontológica U Chile Laboratorio de Ontogenia y Filogenia Facultad de Ciencias; Universidad de Chile; Las Palmeras 3425 Ñuñoa Santiago Chile
- Department of Paleobiology National Museum of Natural History; Smithsonian Institution; Washington District of Columbia
| | - Mario Alberto Cozzuol
- Departamento de Zoologia Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Av. Antônio Carlos, 6627, Pampulha 31270-910 Belo Horizonte Minas Gerais Brasil
| | - Nicholas D. Pyenson
- Department of Paleobiology National Museum of Natural History; Smithsonian Institution; Washington District of Columbia
- Departments of Mammalogy and Paleontology; Burke Museum of Nature and Culture; Seattle Washington
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Gatesy J, Geisler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, McGowen MR. A phylogenetic blueprint for a modern whale. Mol Phylogenet Evol 2012; 66:479-506. [PMID: 23103570 DOI: 10.1016/j.ympev.2012.10.012] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/10/2012] [Accepted: 10/12/2012] [Indexed: 11/16/2022]
Abstract
The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.
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Affiliation(s)
- John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA.
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Xu S, Chen Y, Cheng Y, Yang D, Zhou X, Xu J, Zhou K, Yang G. Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans. Proc Biol Sci 2012; 279:4433-40. [PMID: 22977148 DOI: 10.1098/rspb.2012.1729] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The enlargement of cetacean brain size represents an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. One candidate gene associated with brain size evolution is the abnormal spindle-like microcephaly associated (ASPM), as mutations in this gene cause severe reductions in the cortical size of humans. Here, we investigated the ASPM gene in representative cetacean lineages and previously published sequences from other mammals to test whether the expansion of the cetacean brain matched adaptive ASPM evolution patterns. Our analyses yielded significant evidence of positive selection on the ASPM gene during cetacean evolution, especially for the Odontoceti and Delphinoidea lineages. These molecular patterns were associated with two major events of relative brain size enlargement in odontocetes and delphinoids. It is of particular interest to find that positive selection was restricted to cetaceans and primates, two distant lineages both characterized by a massive expansion of brain size. This result is suggestive of convergent molecular evolution, although no site-specific convergence at the amino acid level was found.
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Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, People's Republic of China
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Yu W, Xu J, Wu Y, Yang G. A comparative study of mammalian diversification pattern. Int J Biol Sci 2012; 8:486-97. [PMID: 22457604 PMCID: PMC3314190 DOI: 10.7150/ijbs.3982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/11/2012] [Indexed: 11/06/2022] Open
Abstract
Although mammals have long been regarded as a successful radiation, the diversification pattern among the clades is still poorly known. Higher-level phylogenies are conflicting and comprehensive comparative analyses are still lacking. Using a recently published supermatrix encompassing nearly all extant mammalian families and a novel comparative likelihood approach (MEDUSA), the diversification pattern of mammalian groups was examined. Both order- and family-level phylogenetic analyses revealed the rapid radiation of Boreoeutheria and Euaustralidelphia in the early mammalian history. The observation of a diversification burst within Boreoeutheria at approximately 100 My supports the Long Fuse model in elucidating placental diversification progress, and the rapid radiation of Euaustralidelphia suggests an important role of biogeographic dispersal events in triggering early Australian marsupial rapid radiation. Diversification analyses based on family-level diversity tree revealed seven additional clades with exceptional diversification rate shifts, six of which represent accelerations in net diversification rate as compared to the background pattern. The shifts gave origin to the clades Muridae+Cricetidae, Bovidae+Moschidae+Cervidae, Simiiformes, Echimyidae, Odontoceti (excluding Physeteridae+Kogiidae+Platanistidae), Macropodidae, and Vespertilionidae. Moderate to high extinction rates from background and boreoeutherian diversification patterns indicate the important role of turnovers in shaping the heterogeneous taxonomic richness observed among extant mammalian groups. Furthermore, the present results emphasize the key role of extinction on erasing unusual diversification signals, and suggest that further studies are needed to clarify the historical radiation of some mammalian groups for which MEDUSA did not detect exceptional diversification rates.
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Affiliation(s)
- Wenhua Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Guzmán-Verri C, González-Barrientos R, Hernández-Mora G, Morales JA, Baquero-Calvo E, Chaves-Olarte E, Moreno E. Brucella ceti and brucellosis in cetaceans. Front Cell Infect Microbiol 2012; 2:3. [PMID: 22919595 PMCID: PMC3417395 DOI: 10.3389/fcimb.2012.00003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 01/12/2012] [Indexed: 01/18/2023] Open
Abstract
Since the first case of brucellosis detected in a dolphin aborted fetus, an increasing number of Brucella ceti isolates has been reported in members of the two suborders of cetaceans: Mysticeti and Odontoceti. Serological surveys have shown that cetacean brucellosis may be distributed worldwide in the oceans. Although all B. ceti isolates have been included within the same species, three different groups have been recognized according to their preferred host, bacteriological properties, and distinct genetic traits: B. ceti dolphin type, B. ceti porpoise type, and B. ceti human type. It seems that B. ceti porpoise type is more closely related to B. ceti human isolates and B. pinnipedialis group, while B. ceti dolphin type seems ancestral to them. Based on comparative phylogenetic analysis, it is feasible that the B. ceti ancestor radiated in a terrestrial artiodactyl host close to the Raoellidae family about 58 million years ago. The more likely mode of transmission of B. ceti seems to be through sexual intercourse, maternal feeding, aborted fetuses, placental tissues, vertical transmission from mother to the fetus or through fish or helminth reservoirs. The B. ceti dolphin and porpoise types seem to display variable virulence in land animal models and low infectivity for humans. However, brucellosis in some dolphins and porpoises has been demonstrated to be a severe chronic disease, displaying significant clinical and pathological signs related to abortions, male infertility, neurobrucellosis, cardiopathies, bone and skin lesions, strandings, and death.
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Affiliation(s)
- Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad NacionalHeredia, Costa Rica
| | | | | | - Juan-Alberto Morales
- Cátedra de Patología, Escuela de Medicina Veterinaria, Universidad NacionalHeredia, Costa Rica
| | - Elías Baquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad NacionalHeredia, Costa Rica
| | - Esteban Chaves-Olarte
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad NacionalHeredia, Costa Rica
- Facultad de Microbiología, Centro de Investigación en Enfermedades Tropicales, Universidad de Costa RicaSan José, Costa Rica
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad NacionalHeredia, Costa Rica
- Instituto Clodomiro Picado, Universidad de Costa RicaSan José, Costa Rica
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Cunha HA, Moraes LC, Medeiros BV, Lailson-Brito J, da Silva VMF, Solé-Cava AM, Schrago CG. Phylogenetic status and timescale for the diversification of Steno and Sotalia dolphins. PLoS One 2011; 6:e28297. [PMID: 22163290 PMCID: PMC3233566 DOI: 10.1371/journal.pone.0028297] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022] Open
Abstract
Molecular data have provided many insights into cetacean evolution but some unsettled issues still remain. We estimated the topology and timing of cetacean evolutionary relationships using bayesian and maximum likelihood analyses of complete mitochondrial genomes. In order to clarify the phylogenetic placement of Sotalia and Steno within the Delphinidae, we sequenced three new delphinid mitogenomes. Our analyses support three delphinid clades: one joining Steno and Sotalia (supporting the revised subfamily Stenoninae); another placing Sousa within the Delphininae; and a third, the Globicephalinae, which includes Globicephala, Feresa, Pseudorca, Peponocephala and Grampus. We also conclude that Orcinus does not belong in the Globicephalinae, but Orcaella may be part of that subfamily. Divergence dates were estimated using the relaxed molecular clock calibrated with fossil data. We hypothesise that the timing of separation of the marine and Amazonian Sotalia species (2.3 Ma) coincided with the establishment of the modern Amazon River basin.
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Affiliation(s)
- Haydée A. Cunha
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Mamíferos Aquáticos e Bioindicadores, Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas C. Moraes
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruna V. Medeiros
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Lailson-Brito
- Laboratório de Mamíferos Aquáticos e Bioindicadores, Faculdade de Oceanografia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vera M. F. da Silva
- Laboratório de Mamíferos Aquáticos, Instituto Nacional de Pesquisas da Amazônia, Amazonas, Brazil
| | - Antonio M. Solé-Cava
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos G. Schrago
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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Walters-Conte KB, Johnson DLE, Allard MW, Pecon-Slattery J. Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact. J Hered 2011; 102 Suppl 1:S2-10. [PMID: 21846743 DOI: 10.1093/jhered/esr051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.
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40
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Chen Z, Xu S, Zhou K, Yang G. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences. BMC Evol Biol 2011; 11:314. [PMID: 22029548 PMCID: PMC3219603 DOI: 10.1186/1471-2148-11-314] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 10/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. RESULTS An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. CONCLUSIONS Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.
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Affiliation(s)
- Zhuo Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Evidence for positive selection on the leptin gene in Cetacea and Pinnipedia. PLoS One 2011; 6:e26579. [PMID: 22046310 PMCID: PMC3203152 DOI: 10.1371/journal.pone.0026579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 09/29/2011] [Indexed: 01/21/2023] Open
Abstract
The leptin gene has received intensive attention and scientific investigation for its importance in energy homeostasis and reproductive regulation in mammals. Furthermore, study of the leptin gene is of crucial importance for public health, particularly for its role in obesity, as well as for other numerous physiological roles that it plays in mammals. In the present work, we report the identification of novel leptin genes in 4 species of Cetacea, and a comparison with 55 publicly available leptin sequences from mammalian genome assemblies and previous studies. Our study provides evidence for positive selection in the suborder Odontoceti (toothed whales) of the Cetacea and the family Phocidae (earless seals) of the Pinnipedia. We also detected positive selection in several leptin gene residues in these two lineages. To test whether leptin and its receptor evolved in a coordinated manner, we analyzed 24 leptin receptor gene (LPR) sequences from available mammalian genome assemblies and other published data. Unlike the case of leptin, our analyses did not find evidence of positive selection for LPR across the Cetacea and Pinnipedia lineages. In line with this, positively selected sites identified in the leptin genes of these two lineages were located outside of leptin receptor binding sites, which at least partially explains why co-evolution of leptin and its receptor was not observed in the present study. Our study provides interesting insights into current understanding of the evolution of mammalian leptin genes in response to selective pressures from life in an aquatic environment, and leads to a hypothesis that new tissue specificity or novel physiologic functions of leptin genes may have arisen in both odontocetes and phocids. Additional data from other species encompassing varying life histories and functional tests of the adaptive role of the amino acid changes identified in this study will help determine the factors that promote the adaptive evolution of the leptin genes in marine mammals.
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Dornburg A, Brandley MC, McGowen MR, Near TJ. Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea). Mol Biol Evol 2011; 29:721-36. [PMID: 21926070 DOI: 10.1093/molbev/msr228] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.
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Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, USA.
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Toward the resolution of an explosive radiation—A multilocus phylogeny of oceanic dolphins (Delphinidae). Mol Phylogenet Evol 2011; 60:345-57. [DOI: 10.1016/j.ympev.2011.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 04/15/2011] [Accepted: 05/03/2011] [Indexed: 11/22/2022]
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Pyenson ND, Sponberg SN. Reconstructing Body Size in Extinct Crown Cetacea (Neoceti) Using Allometry, Phylogenetic Methods and Tests from the Fossil Record. J MAMM EVOL 2011. [DOI: 10.1007/s10914-011-9170-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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45
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Ray DA, Batzer MA. Reading TE leaves: new approaches to the identification of transposable element insertions. Genome Res 2011; 21:813-20. [PMID: 21632748 PMCID: PMC3106314 DOI: 10.1101/gr.110528.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.
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Affiliation(s)
- David A. Ray
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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Geisler JH, McGowen MR, Yang G, Gatesy J. A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea. BMC Evol Biol 2011; 11:112. [PMID: 21518443 PMCID: PMC3114740 DOI: 10.1186/1471-2148-11-112] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 04/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. RESULTS We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. CONCLUSIONS The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.
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Affiliation(s)
- Jonathan H Geisler
- Department of Anatomy, New York College of Osteopathic Medicine, New York Institute of Technology, Northern Boulevard, Old Westbury, NY,11568, USA
| | - Michael R McGowen
- Department of Biology, Spieth Hall, University of California, Riverside, CA, 92521, US
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - John Gatesy
- Department of Biology, Spieth Hall, University of California, Riverside, CA, 92521, US
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Yu L, Peng D, Liu J, Luan P, Liang L, Lee H, Lee M, Ryder OA, Zhang Y. On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes. BMC Evol Biol 2011; 11:92. [PMID: 21477367 PMCID: PMC3088541 DOI: 10.1186/1471-2148-11-92] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 04/10/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems. RESULTS The combined nuclear intron and mt genome analyses both robustly support that Taxidiinae diverged first, followed by Melinae. Lutrinae and Mustelinae are grouped together in all analyses with strong supports. The position of Helictidinae, however, is enigmatic because the mt genome analysis places it to the clade uniting Lutrinae and Mustelinae, whereas the nuclear intron analysis favors a novel view supporting a closer relationship of Helictidinae to Martinae. This finding emphasizes a need to add more data and include more taxa to resolve this problem. In addition, the molecular dating provides insights into the time scale of the origin and diversification of the Mustelidae subfamilies. Finally, the phylogenetic performances and limits of nuclear introns and mt genes are discussed in the context of Mustelidae phylogeny. CONCLUSION Our study not only brings new perspectives on the previously obscured phylogenetic relationships among Mustelidae subfamilies, but also provides another example demonstrating the effectiveness of nuclear non-coding loci for reconstructing evolutionary histories in a group that has undergone rapid bursts of speciation.
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Affiliation(s)
- Li Yu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Dan Peng
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Jiang Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Pengtao Luan
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
| | - Lu Liang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and Coll. of Vet. Med., Seoul National Univ., Seoul 151-742, South Korea
| | - Muyeong Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and Coll. of Vet. Med., Seoul National Univ., Seoul 151-742, South Korea
| | - Oliver A Ryder
- San Diego Zoo's Institute for Conservation Research, Escondido, CA, USA 92027-7000
| | - Yaping Zhang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, PR, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
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48
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Modular organizations of novel cetacean papillomaviruses. Mol Phylogenet Evol 2011; 59:34-42. [DOI: 10.1016/j.ympev.2010.12.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 12/02/2010] [Accepted: 12/22/2010] [Indexed: 11/20/2022]
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49
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Zhou X, Xu S, Yang Y, Zhou K, Yang G. Phylogenomic analyses and improved resolution of Cetartiodactyla. Mol Phylogenet Evol 2011; 61:255-64. [PMID: 21315162 DOI: 10.1016/j.ympev.2011.02.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 01/29/2011] [Accepted: 02/03/2011] [Indexed: 11/26/2022]
Abstract
The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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Klimpel S, Kuhn T, Busch MW, Karl H, Palm HW. Deep-water life cycle of Anisakis paggiae (Nematoda: Anisakidae) in the Irminger Sea indicates kogiid whale distribution in north Atlantic waters. Polar Biol 2011. [DOI: 10.1007/s00300-010-0946-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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