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Maier W, Tröscher A, Ruf I. The orbitotemporal region and the mandibular joint in the skull of shrews (Soricidae, Mammalia). VERTEBRATE ZOOLOGY 2022. [DOI: 10.3897/vz.72.e90840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Modern phylogenetics place the Soricidae (shrews) into the order Lipotyphla, which belongs to the relatively new superorder clade Laurasiatheria. Their most derived skull feature is the unusual position and shape of the jaw articulation: Whereas in all other mammals the glenoid region of the squamosum is more or less tightly attached to the otic capsule or petrosal, respectively, in the soricids it is attached to the nasal capsule. This new position of the jaw articulation becomes possible by the posterior extension of the nasal capsule and the rostral shift of the glenoid fossa. By the study of dated postnatal ontogenetic stages of Crocidura russula and Sorex araneus, we show that the glenoid part of the squamosal becomes fixed to the nasal capsule by the ossified alae orbitalis and temporalis. The ala orbitalis is displaced laterally by the expanded cupula nasi posterior; this posterior expansion is well documented by the lamina terminalis, which incorporates parts of the palatinum and alisphenoid. Both alae consist largely of ‘Zuwachsknochen’ (‘appositional bone’) and are then named orbitosphenoid and alisphenoid. By the forward move of the pars glenoidea and of the alisphenoid, the foramen lacerum medium (‘fenestra piriformis’) also expands rostrally. Functionally, the forward shift of the jaw joint helps to keep the incisal biting force high. Biomechanically the jaws can be considered as a tweezer, and the rostral position of the jaw joints makes the interorbital pillar and the shell-like walls of the facial skull a lever for the highly specialized incisal dentition.
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Arnold P, Hagemann J, Gilissen E, Hofreiter M. Otter shrew mitogenomes (Afrotheria, Potamogalidae) reconstructed from historical museum skins. Mitochondrial DNA B Resour 2022. [DOI: 10.1080/23802359.2022.2122747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Patrick Arnold
- Evolutionary and Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Justus Hagemann
- Evolutionary and Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Emmanuel Gilissen
- Department of African Zoology, Royal Museum for Central Africa, Tervuren, Belgium
- Laboratory of Histology and Neuropathology, School of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Hofreiter
- Evolutionary and Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Neely BA, Palmblad M. Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics. J Proteome Res 2021; 20:4640-4645. [PMID: 34523928 PMCID: PMC8491155 DOI: 10.1021/acs.jproteome.1c00528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Science is full of
overlooked and undervalued research waiting
to be rediscovered. Proteomics is no exception. In this perspective,
we follow the ripples from a 1960 study of Zuckerkandl, Jones, and
Pauling comparing tryptic peptides across animal species. This pioneering
work directly led to the molecular clock hypothesis and the ensuing
explosion in molecular phylogenetics. In the decades following, proteins
continued to provide essential clues on evolutionary history. While
technology has continued to improve, contemporary proteomics has strayed
from this larger biological context, rarely comparing species or asking
how protein structure, function, and interactions have evolved. Here
we recombine proteomics with molecular phylogenetics, highlighting
the value of framing proteomic results in a larger biological context
and how almost forgotten research, though technologically surpassed,
can still generate new ideas and illuminate our work from a different
perspective. Though it is infeasible to read all research published
on a large topic, looking up older papers can be surprisingly rewarding
when rediscovering a “gem” at the end of a long citation
chain, aided by digital collections and perpetually helpful librarians.
Proper literature study reduces unnecessary repetition and allows
research to be more insightful and impactful by truly standing on
the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/)
as dataset MSV000087993.
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Affiliation(s)
- Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina 29412, United States
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Yazhini A, Srinivasan N, Sandhya S. Signatures of conserved and unique molecular features in Afrotheria. Sci Rep 2021; 11:1011. [PMID: 33441654 PMCID: PMC7806701 DOI: 10.1038/s41598-020-79559-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/07/2020] [Indexed: 11/09/2022] Open
Abstract
Afrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.
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Affiliation(s)
- Arangasamy Yazhini
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Narayanaswamy Srinivasan
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
| | - Sankaran Sandhya
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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Averianov AO, Lopatin AV. High-level systematics of placental mammals: Current status of the problem. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014090039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Patzke N, LeRoy A, Ngubane NW, Bennett NC, Medger K, Gravett N, Kaswera-Kyamakya C, Gilissen E, Chawana R, Manger PR. The distribution of doublecortin-immunopositive cells in the brains of four afrotherian mammals: the Hottentot golden mole (Amblysomus hottentotus), the rock hyrax (Procavia capensis), the eastern rock sengi (Elephantulus myurus) and the four-toed sengi (Petrodromus tetradactylus). BRAIN, BEHAVIOR AND EVOLUTION 2014; 84:227-41. [PMID: 25377859 DOI: 10.1159/000367934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/28/2014] [Indexed: 11/19/2022]
Abstract
Adult neurogenesis in the mammalian brain is now a widely accepted phenomenon, typically occurring in two forebrain structures: the subgranular zone (SGZ) of the hippocampal dentate gyrus and the subventricular zone (SVZ). Until recently, the majority of studies have focused on laboratory rodents, and it is under debate whether the process of adult neurogenesis occurs outside of the SGZ and the SVZ in other mammalian species. In the present study, we investigated potential adult neurogenetic sites in the brains of two elephant shrews/sengis, a golden mole and a rock hyrax, all members of the superorder Afrotheria. Doublecortin (DCX) immunoreactivity was used as a proxy to visualise adult neurogenesis, which is expressed in neuronal precursor cells and immature neurons. In all four species, densely packed DCX-positive cells were present in the SVZ, from where cells appear to migrate along the rostral migratory stream towards the olfactory bulb (OB). DCX-immunopositive cells were present in the granular cell layer and the glomerular layer of the OB. In the hippocampus, DCX-immunopositive cells were observed in the SGZ and in the granular layer of the dentate gyrus, with DCX-immunopositive processes extending into the molecular layer. In addition to these well-established adult neurogenic regions, DCX-immunopositive cells were also observed in layer II of the neocortex and the piriform cortex. While the present study reveals a similar pattern of adult neurogenesis to that reported previously in other mammals, further studies are needed to clarify if the cortical DCX-immunopositive cells are newly generated neurons or cells undergoing cortical remodelling.
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Affiliation(s)
- Nina Patzke
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Ekdale EG. Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals. PLoS One 2013; 8:e66624. [PMID: 23805251 PMCID: PMC3689836 DOI: 10.1371/journal.pone.0066624] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 05/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported. PRINCIPAL FINDINGS The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha. SIGNIFICANCE The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear.
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Affiliation(s)
- Eric G. Ekdale
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Paleontology, San Diego Natural History Museum, San Diego, California, United States of America
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Calvey T, Patzke N, Kaswera C, Gilissen E, Bennett NC, Manger PR. Nuclear organisation of some immunohistochemically identifiable neural systems in three Afrotherian species—Potomogale velox, Amblysomus hottentotus and Petrodromus tetradactylus. J Chem Neuroanat 2013; 50-51:48-65. [DOI: 10.1016/j.jchemneu.2013.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 01/23/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022]
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9
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Kuntner M, May-Collado LJ, Agnarsson I. Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00452.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Shape and size variations in the cranium of elephant-shrews: a morphometric contribution to a phylogenetic debate. ZOOMORPHOLOGY 2007. [DOI: 10.1007/s00435-007-0053-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Redi CA, Garagna S, Zuccotti M, Capanna E. Genome size: a novel genomic signature in support of Afrotheria. J Mol Evol 2007; 64:484-7. [PMID: 17479346 DOI: 10.1007/s00239-006-0237-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 01/08/2007] [Indexed: 11/26/2022]
Abstract
Molecular phylogenetic analyses suggest an emerging phylogeny for the extant Placentalia (eutherian) that radically departs from morphologically based constructions of the past. Placental mammals are partitioned into four supraordinal clades: Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. Afrotheria form an endemic African clade that includes elephant shrews, golden moles, tenrecs, aardvarks, hyraxes, elephants, dugongs, and manatees. Datamining databases of genome size (GS) shows that till today just one afrotherian GS has been evaluated, that of the aardvark Orycteropus afer. We show that the GSs of six selected representatives across the Afrotheria supraordinal group are among the highest for the extant Placentalia, providing a novel genomic signature of this enigmatic group. The mean GS value of Afrotheria, 5.3 +/- 0.7 pg, is the highest reported for the extant Placentalia. This should assist in planning new genome sequencing initiatives.
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12
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Mason MJ, Lucas SJ, Wise ER, Stein RS, Duer MJ. Ossicular density in golden moles (Chrysochloridae). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2006; 192:1349-57. [PMID: 16944164 DOI: 10.1007/s00359-006-0163-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 08/02/2006] [Accepted: 08/06/2006] [Indexed: 11/25/2022]
Abstract
The densities of middle ear ossicles of golden moles (family Chrysochloridae, order Afrosoricida) were measured using the buoyancy method. The internal structure of the malleus was examined by high-resolution computed tomography, and solid-state NMR was used to determine relative phosphorus content. The malleus density of the desert golden mole Eremitalpa granti (2.44 g/cm3) was found to be higher than that reported in the literature for any other terrestrial mammal, whereas the ossicles of other golden mole species are not unusually dense. The increased density in Eremitalpa mallei is apparently related both to a relative paucity of internal vascularization and to a high level of mineralization. This high density is expected to augment inertial bone conduction, used for the detection of seismic vibrations, while limiting the skull modifications needed to accommodate the disproportionately large malleus. The mallei of the two subspecies of E. granti, E. g. granti and E. g. namibensis, were found to differ considerably from one another in both size and shape.
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Affiliation(s)
- Matthew J Mason
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.
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13
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Mcnab BK. The evolution of energetics in eutherian “insectivorans”: an alternate approach. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/bf03192663] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Hunter JP, Janis CM. Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia. J MAMM EVOL 2006. [DOI: 10.1007/s10914-006-9006-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Nishihara H, Satta Y, Nikaido M, Thewissen JGM, Stanhope MJ, Okada N. A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 2005; 22:1823-33. [PMID: 15930154 DOI: 10.1093/molbev/msi179] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.
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Affiliation(s)
- Hidenori Nishihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005; 6:361-75. [PMID: 15861208 DOI: 10.1038/nrg1603] [Citation(s) in RCA: 908] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to several fundamental evolutionary questions. However, challenges for the future have also been revealed. The very nature of the evolutionary history of organisms and the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult, if not impossible, to resolve with confidence.
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Affiliation(s)
- Frédéric Delsuc
- Canadian Institute for Advanced Research, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
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Sillitoe RV, Marzban H, Larouche M, Zahedi S, Affanni J, Hawkes R. Conservation of the architecture of the anterior lobe vermis of the cerebellum across mammalian species. PROGRESS IN BRAIN RESEARCH 2005; 148:283-97. [PMID: 15661197 DOI: 10.1016/s0079-6123(04)48022-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Roy V Sillitoe
- Department of Cell Biology & Anatomy, and Genes and Development Research Group, Faculty of Medicine, The University of Calgary, 3330 Hospital Drive N.W., Calgary, AB T2N 4N1, Canada
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Mason MJ. Functional morphology of the middle ear in Chlorotalpa golden moles (Mammalia, Chrysochloridae): predictions from three models. J Morphol 2004; 261:162-74. [PMID: 15216521 DOI: 10.1002/jmor.10235] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The ossicular apparatus of golden moles in the genus Chlorotalpa has received comparatively little attention in the literature, although the malleus is known to be intermediate in size between the "unmodified" malleus of Amblysomus and the hypertrophied mallei found in some other golden moles. In the present study, the middle ear structures of three Chlorotalpa species (C. duthieae, C. sclateri, and C. arendsi) are described. Measurements of middle ear structures were applied into three existing models of middle ear function. The predictions from the models suggest that the airborne hearing of Chlorotalpa species is limited to relatively low frequencies, but the impedance transformation by the middle ear apparatus is expected to be reasonably efficient. The sensitivity of the middle ear apparatus to inertial bone conduction is intermediate between that predicted for Amblysomus and that predicted for species with hypertrophied mallei. Hearing in fossorial mammals may be limited by factors other than the middle ear apparatus: the predictions for Chlorotalpa must therefore be treated with caution. However, a consideration of the "intermediate" middle ear morphology of Chlorotalpa species sheds some light on the origin of ossicular hypertrophy in golden moles. The limited enlargement of the malleus seen in Chlorotalpa is expected to have improved seismic sensitivity by bone conduction significantly at low frequencies, while airborne hearing might not have been adversely affected.
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Affiliation(s)
- Matthew J Mason
- University of Cambridge, Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK.
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19
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Robinson TJ, Fu B, Ferguson-Smith MA, Yang F. Cross-species chromosome painting in the golden mole and elephant-shrew: support for the mammalian clades Afrotheria and Afroinsectiphillia but not Afroinsectivora. Proc Biol Sci 2004; 271:1477-84. [PMID: 15306319 PMCID: PMC1691750 DOI: 10.1098/rspb.2004.2754] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cross-species painting (fluorescence in situ hybridization) with 23 (human Homo sapiens (HSA)) chromosome-specific painting probes (HSA 1-22 and the X) was used to delimit regions of homology on the chromosomes of the golden mole (Chrysochloris asiaticus) and elephant-shrew (Elephantulus rupestris). A cladistic interpretation of our data provides evidence of two unique associations, HSA 1/19p and 5/21/3, that support Afrotheria. The recognition of HSA 5/3/21 expands on the 3/21 synteny originally designated as an ancestral state for all eutherians. We have identified one adjacent segment combination (HSA2/8p/4) that is supportive of Afroinsectiphillia (aardvark, golden mole, elephant-shrew). Two segmental combinations (HSA 10q/17 and HSA 3/20) unite the aardvark and elephant-shrews as sister taxa. The finding that segmental syntenies in evolutionarily distant taxa can improve phylogenetic resolution suggests that they may be useful for testing sequence-based phylogenies of the early eutherian mammals. They may even suggest clades that sequence trees are not recovering with any consistency and thus encourage the search for additional rare genomic changes among afrotheres.
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Affiliation(s)
- T J Robinson
- Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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Robinson TJ, Seiffert ER. Afrotherian origins and interrelationships: new views and future prospects. Curr Top Dev Biol 2004; 63:37-60. [PMID: 15536013 DOI: 10.1016/s0070-2153(04)63002-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Terence J Robinson
- Evolutionary Genomics Group, Department of Zoology, University of Stellenbosch, Matieland 7602, South Africa
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21
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Murata Y, Nikaido M, Sasaki T, Cao Y, Fukumoto Y, Hasegawa M, Okada N. Afrotherian phylogeny as inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2003; 28:253-60. [PMID: 12878462 DOI: 10.1016/s1055-7903(03)00035-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Afrotheria is a huge assemblage of various mammals encompassing six orders that were once classified as distantly related groups. This superordinal relationship may have resulted from the break-up of Gondowanaland followed by the isolation of the African continent between 105 and 40 million years ago. Although the monophyly of Afrotheria is well supported by recent molecular studies, the interrelationships within afrotherian mammals remain unclarified. In this study, we determined the sequence of the complete mitochondrial genomes of hyrax, golden mole, and elephant shrew. These sequences were compared with those of other eutherians to analyze the phylogenetic relationships among afrotherians and, in particular, those among paenungulates. Our mitochondrial genome analysis supports the monophyly of Tethytheria.
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Affiliation(s)
- Yumie Murata
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, Japan
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22
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Nikaido M, Cao Y, Harada M, Okada N, Hasegawa M. Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol Phylogenet Evol 2003; 28:276-84. [PMID: 12878464 DOI: 10.1016/s1055-7903(03)00120-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We sequenced the complete mitochondrial (mt) genomes of three insectivores: the long-eared hedgehog Hemiechinus auritus, the Japanese mole Mogera wogura, and the greater Japanese shrew-mole Urotrichus talpoides. These mtDNA data together with other previously sequenced mtDNAs were analyzed using a maximum likelihood method to infer their phylogenetic relationships among eutherians. Previous mitochondrial protein analyses used a simple model that did not consider site-heterogeneity, and Erinaceoidea (hedgehogs and moonrats) was placed at the basal eutherian position that is separated from Soricoidea (shrews) and Talpoidea (moles), suggesting the exclusion of the Erinaceoidea-Eulipotyphla tree. By including the new mtDNA sequences and introducing site-heterogeneity into the model, the Erinaceoidea-Eulipotyphla tree emerges as the best tree or as a tree with a log-likelihood score indistinguishable from that of the best tree. However, this conclusion depends on species sampling in Erinaceoidea, demonstrating the importance of both species sampling and use of an appropriate substitution model when inferring phylogenetic relationships.
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Affiliation(s)
- Masato Nikaido
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Yang F, Alkalaeva EZ, Perelman PL, Pardini AT, Harrison WR, O'Brien PCM, Fu B, Graphodatsky AS, Ferguson-Smith MA, Robinson TJ. Reciprocal chromosome painting among human, aardvark, and elephant (superorder Afrotheria) reveals the likely eutherian ancestral karyotype. Proc Natl Acad Sci U S A 2003; 100:1062-6. [PMID: 12552116 PMCID: PMC298726 DOI: 10.1073/pnas.0335540100] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Indexed: 11/18/2022] Open
Abstract
The Afrotheria, a supraordinal grouping of mammals whose radiation is rooted in Africa, is strongly supported by DNA sequence data but not by their disparate anatomical features. We have used flow-sorted human, aardvark, and African elephant chromosome painting probes and applied reciprocal painting schemes to representatives of two of the Afrotherian orders, the Tubulidentata (aardvark) and Proboscidea (elephants), in an attempt to shed additional light on the evolutionary affinities of this enigmatic group of mammals. Although we have not yet found any unique cytogenetic signatures that support the monophyly of the Afrotheria, embedded within the aardvark genome we find the strongest evidence yet of a mammalian ancestral karyotype comprising 2n = 44. This karyotype includes nine chromosomes that show complete conserved synteny to those of man, six that show conservation as single chromosome arms or blocks in the human karyotype but that occur on two different chromosomes in the ancestor, and seven neighbor-joining combinations (i.e., the synteny is maintained in the majority of species of the orders studied so far, but which corresponds to two chromosomes in humans). The comparative chromosome maps presented between human and these Afrotherian species provide further insight into mammalian genome organization and comparative genomic data for the Afrotheria, one of the four major evolutionary clades postulated for the Eutheria.
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Affiliation(s)
- F Yang
- Centre for Veterinary Science, University of Cambridge, Cambridge CB3 0ES, United Kingdom
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LAVOUÉ SÉBASTIEN, SULLIVAN JOHNP, HOPKINS CARLD. Phylogenetic utility of the first two introns of the S7 ribosomal protein gene in African electric fishes (Mormyroidea: Teleostei) and congruence with other molecular markers. Biol J Linn Soc Lond 2003. [DOI: 10.1046/j.1095-8312.2003.00170.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Helgen K. Major mammalian clades: a review under consideration of molecular and palaeontological evidence. Mamm Biol 2003. [DOI: 10.1078/1616-5047-1610057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Madsen O, Willemsen D, Ursing BM, Arnason U, de Jong WW. Molecular evolution of the mammalian alpha 2B adrenergic receptor. Mol Biol Evol 2002; 19:2150-60. [PMID: 12446807 DOI: 10.1093/oxfordjournals.molbev.a004040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The alpha 2B adrenergic receptor (A2AB) is a heptahelical G protein-coupled receptor for catecholamines. We compared the almost complete coding region (about 1,175 bp) of the A2AB gene from 48 mammalian species, including eight newly determined sequences, representing all the 18 eutherian and two marsupial orders. Comparison of the encoded proteins reveals that residues thought to be involved in agonist binding are highly conserved, as are the regions playing a role in G protein-coupling. The three extracellular loops are generally more variable than the transmembrane domains and two of the intracellular loops, indicating a lower functional constraint. However, the greatest variation is observed in the very long, third intracellular loop, where only a few residues and a polyglutamyl tract are preserved. Although this polyglutamyl domain displays a great variation in length, its presence in all described A2ABs confirms its proposed role in agonist-dependent phosphorylation of the third intracellular loop. Phylogenetic analyses of the A2AB data set, including Bayesian methods, recognized the superordinal clades Afrotheria, Laurasiatheria, and Euarchontoglires, in agreement with recent molecular evidence, albeit with lower support. Within Afrotheria, A2AB strongly supports the paenungulate clade and the association of the continental African otter shrew with Malagasy tenrecs. Among Laurasiatheria, A2AB confirms the nesting of whales within the artiodactyls, as a sister group to hippopotamus. Within the Euarchontoglires, there is constant support for rodent monophyly.
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Affiliation(s)
- Ole Madsen
- Department of Biochemistry 161, University of Nijmegen, 6500 HB Nijmegen, The Netherlands
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27
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Delsuc F, Scally M, Madsen O, Stanhope MJ, de Jong WW, Catzeflis FM, Springer MS, Douzery EJP. Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting. Mol Biol Evol 2002; 19:1656-71. [PMID: 12270893 DOI: 10.1093/oxfordjournals.molbev.a003989] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Extant xenarthrans (armadillos, anteaters and sloths) are among the most derived placental mammals ever evolved. South America was the cradle of their evolutionary history. During the Tertiary, xenarthrans experienced an extraordinary radiation, whereas South America remained isolated from other continents. The 13 living genera are relics of this earlier diversification and represent one of the four major clades of placental mammals. Sequences of the three independent protein-coding nuclear markers alpha2B adrenergic receptor (ADRA2B), breast cancer susceptibility (BRCA1), and von Willebrand Factor (VWF) were determined for 12 of the 13 living xenarthran genera. Comparative evolutionary dynamics of these nuclear exons using a likelihood framework revealed contrasting patterns of molecular evolution. All codon positions of BRCA1 were shown to evolve in a strikingly similar manner, and third codon positions appeared less saturated within placentals than those of ADRA2B and VWF. Maximum likelihood and Bayesian phylogenetic analyses of a 47 placental taxa data set rooted by three marsupial outgroups resolved the phylogeny of Xenarthra with some evidence for two radiation events in armadillos and provided a strongly supported picture of placental interordinal relationships. This topology was fully compatible with recent studies, dividing placentals into the Southern Hemisphere clades Afrotheria and Xenarthra and a monophyletic Northern Hemisphere clade (Boreoeutheria) composed of Laurasiatheria and Euarchontoglires. Partitioned likelihood statistical tests of the position of the root, under different character partition schemes, identified three almost equally likely hypotheses for early placental divergences: a basal Afrotheria, an Afrotheria + Xenarthra clade, or a basal Xenarthra (Epitheria hypothesis). We took advantage of the extensive sampling realized within Xenarthra to assess its impact on the location of the root on the placental tree. By resampling taxa within Xenarthra, the conservative Shimodaira-Hasegawa likelihood-based test of alternative topologies was shown to be sensitive to both character and taxon sampling.
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Affiliation(s)
- Frédéric Delsuc
- Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l'Evolution, Université Montpellier II, Montpellier, France
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Künzle H, Radtke-Schuller S, von Stebut B. Parabrachio-cortical connections with the lateral hemisphere in the madagascan hedgehog tenrec: prominent projections to layer 1, weak projections from layer 6. Brain Res Bull 2002; 57:705-19. [PMID: 11927376 DOI: 10.1016/s0361-9230(01)00784-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The present study was undertaken to further characterize and subdivide the rhinal cortex (insular and perirhinal areas) in the hedgehog tenrec (Echinops telfairi), a placental mammal with a rather low encephalisation index. Injections of wheat germ agglutinin-horseradish peroxidase into the dorsolateral pontine tegmentum revealed a prominent layer 1 projection to several rhinal target areas, while the rhinal cortex only stained weakly for the calcitonin gene-related peptide. Among the regions retrogradely labeled following tracer injections into the rhinal cortex, the parabrachial nucleus was considered the main origin of the tegmento-cortical projection. This conclusion was based on the circumscribed pattern of termination, as well as the differences noted between the pattern of anterograde labeling and the pattern obtained by thyrosine hydroxylase immunohistochemistry. The tracer injections into the dorsolateral tegmentum also revealed numerous retrogradely labeled cells in the layer 5 of the dorsomedial frontal cortex. In contrast, the rhinal cortex only showed few labeled cells and most of these cells were located in the layer 6/7. A comparison with other species indicates that the tenrec's parabrachial nucleus gives rise to the most extensive cortical projections but receives the least prominent input from the lateral cerebral hemisphere. The layer 6/7 projection may be a common mammalian feature but it is overshadowed by the layer 5 projection in higher mammals.
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Affiliation(s)
- Heinz Künzle
- Institute of Anatomy, Ludwig Maximilians University, Pettenkoferstrasse 11, D-80336 Munich, Germany.
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Abstract
Recent analyses of nucleotide sequence data suggest that living placental mammals belong to one of four superorders. The early divergence of these groups was followed by long periods of geographical isolation, due to the break up of continental land masses, allowing for convergent evolution of similar traits in different superorders. As an example, the transition from epitheliochorial to haemochorial placentation occurred independently in bats, rodents, anthropoid primates, armadillos and others. A group of ancient African mammals is suggested by the molecular data, but is not fully supported by morphological evidence. The hypothesis is, however, consistent with some of the data on fetal membranes, suggesting that it would be worthwhile to study the early development of tenrecs, golden moles and elephant shrews. Analyses of fetal membrane traits that group the tarsiers with anthropoid primates, and separate them from the lemurs, are challenged by the molecular data. Other relatives of the primates seem to include tree shrews and flying lemurs, and little is known about the fetal membranes of the latter group. Comparative studies of placental function normally are confined to primates, rodents, lagomorphs and domestic animals: the biological diversity represented by mammals that evolved in ancient Africa and South America is not represented. Therefore, future comparative studies should strive to include species such as the rock hyrax and the armadillo.
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Affiliation(s)
- A M Carter
- Department of Physiology and Pharmacology, University of Southern Denmark, Winsloewparken 21, DK-5000 Odense, Denmark.
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31
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Affiliation(s)
- S B Hedges
- Department of Biology, Institute of Molecular Evolutionary Genetics, and Astrobiology Research Center, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA.
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