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Robert J. Asher - One of the best experts on this subject based on the ideXlab platform.
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Dental Eruption and Growth in Hyracoidea (Mammalia, Afrotheria)
Journal of Vertebrate Paleontology, 2017Co-Authors: Robert J. Asher, Erik R. Seiffert, Rodolphe Tabuce, Lionel Hautier, Gf Gunnell, David Pattinson, Hesham M. SallamAbstract:ABSTRACT We investigated dental homologies, development, and growth in living and fossil hyracoids and tested if hyracoids and other mammals show correlations between eruption patterns, gestation time, and age at maturity. Unlike living species, fossil hyracoids simultaneously possess replaced P1 and canine teeth. Fossil species also have shorter crowns, an I3/i3, I2, and a hypoconulid on m3. Prenatal specimens of the living Procavia capensis and Heterohyrax brucei show up to three tooth buds posterior to dI1 and anterior to the seven upper cheek teeth that consistently erupt; erupted teeth include an anterior premolar but not a canine. Most lower cheek teeth finish eruption during growth in hyracoids, not after growth as in most other Afrotherians. All hyracoids show the m1 at (lower) or near (upper) the beginning of eruption of permanent teeth; M3/m3 is the last permanent tooth to erupt. The living P. capensis erupts most lower antemolar loci before m2. In contrast, fossil hyraxes erupt lower antemolars...
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Dental eruption and growth in Hyracoidea (Mammalia, Afrotheria)
2017Co-Authors: Robert J. Asher, Erik R. Seiffert, Rodolphe Tabuce, Lionel Hautier, Gf Gunnell, David Pattinson, Hesham M. SallamAbstract:We investigated dental homologies, development, and growth in living and fossil hyracoids and tested if hyracoids and other mammals show correlations between eruption patterns, gestation time, and age at maturity. Unlike living species, fossil hyracoids simultaneously possess replaced P1 and canine teeth. Fossil species also have shorter crowns, an I3/i3, I2, and a hypoconulid on m3. Prenatal specimens of the living Procavia capensis and Heterohyrax brucei show up to three tooth buds posterior to dI1 and anterior to the seven upper cheek teeth that consistently erupt; erupted teeth include an anterior premolar but not a canine. Most lower cheek teeth finish eruption during growth in hyracoids, not after growth as in most other Afrotherians. All hyracoids show the m1 at (lower) or near (upper) the beginning of eruption of permanent teeth; M3/m3 is the last permanent tooth to erupt. The living P. capensis erupts most lower antemolar loci before m2. In contrast, fossil hyraxes erupt lower antemolars after m2. Although the early eruption of antemolars correlates with increased gestation time and age at maturity in primates and Tupaia (i.e., ‘Schultz's rule’), and although modern hyraxes resemble some anthropoid primates in exhibiting long gestation and eruption of antemolars at or before molars, eruption patterns do not significantly covary with either life history parameter among Afrotherians sampled so far. However, we do observe a shift in eruption timing and crown height in Procavia relative to fossil hyracoids, mirroring observations recently made for other ungulate-grade mammals. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Asher, R. J., G. F. Gunnell, E. R. Seiffert, D. Pattinson, R. Tabuce, L. Hautier, and H. M. Sallam. 2017. Dental eruption and growth in Hyracoidea (Mammalia, Afrotheria). Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1317638.
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2016Co-Authors: Lionel Hautier, Nigel C Bennett, Hermien Viljoen, Lauren Howard, Michel C. Milinkovitch, Athanasia C. Tzika, Anjali Goswami, Robert J. AsherAbstract:1 Consensus on placental mammal phylogeny is fairly recent compared to that for vertebrates as a whole. A stable phylogenetic hypothesis enables investigation into the possibility that placental clades differ from one another in terms of their development. Here, we focus on the sequence of skeletal ossification as a possible source of developmental distinctiveness in "northern " (Laurasiatheria and Euarchontoglires) vs. "southern " (Afrotheria and Xenarthra) placental clades. Previous analyses of mammalian ossification sequences have mainly focused on marsupials, monotremes, and northern placentals. We contribute data on cranial and postcranial ossification events during growth in Afrotheria, including elephants, hyraxes, golden moles, tenrecs, sengis, and aardvarks, and also draw on data for Xenarthra. We use three different techniques to quantify sequence heterochrony: continuous method, sequence-ANOVA and event-paring/Parsimov. By controlling for ties and taking into account results that all methods support, we show that Afrotherian
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Jaw anatomy of Potamogale velox (Tenrecidae, Afrotheria) with a focus on cranial arteries and the coronoid canal in mammals
PeerJ, 2016Co-Authors: Robert J. Brocklehurst, Nick Crumpton, Evie Button, Robert J. AsherAbstract:Afrotheria is a strongly supported clade within placental mammals, but morphological synapomorphies for the entire group have only recently come to light. Soft tissue characters represent an underutilized source of data for phylogenetic analysis, but nonetheless provide features shared by some or all members of Afrotheria. Here, we investigate the developmental anatomy of Potamogale velox (Tenrecidae) with histological and computerized tomographic data at different ontogenetic ages, combined with osteological data from other mammals, to investigate patterns of cranial arterial supply and the distribution of the coronoid canal. Potamogale is atypical among placental mammals in exhibiting a small superior stapedial artery, a primary supply of the posterior auricular by the posterior stapedial artery, and the development of vascular plexuses (possibly with relevance for heat exchange) in the posterior and dorsal regions of its neck. In addition, the posterior aspect of Meckel’s cartilage increases its medial deflection in larger embryonic specimens as the mandibular condyle extends mediolaterally during embryogenesis. We also map the distribution of the coronoid canal across mammals, and discuss potential confusion of this feature with alveoli of the posterior teeth. The widespread distribution of the coronoid canal among living and fossil proboscideans, sirenians, and hyracoids supports previous interpretations that a patent coronoid canal is a synapomorphy of paenungulates, but not Afrotherians as a whole.
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DO1:10.1080/10635150500433649 Tenrec Phylogeny and the Noninvasive Extraction of Nuclear DNA
2015Co-Authors: Robert J. Asher, Michael HofreiterAbstract:Abstract.—Due in part to scarcity of material, no published study has yet cladistically addressed the systematics of living and fossil Tenrecidae (Mammalia, Afrotheria). Using a noninvasive technique for sampling nuclear DNA from museum specimens, we investigate the evolution of the Tenrecidae and assess the extent to which tenrecids fit patterns of relationships proposed for other terrestrial mammals on Madagascar. Application of several tree-reconstruction techniques on sequences of the nuclear growth hormone receptor gene and morphological data for all recognized tenrecid genera supports monophyly of Malagasy tenrecids to the exclusion of the two living African genera. However, both parsimony and Bayesian methods favor a close relationship between fossil African tenrecs and the Malagasy Geogale, supporting the hypothesis of island paraphyly, but not polyphyly. More generally, the noninvasive extraction technique can be applied with minimal risk to rare/unique specimens and, by better utilizing museum collections for genetic work, can greatly mitigate field expenses and disturbance of natural populations. [Afrotheria; DNA; fossils; Madagascar; museums; phylogeny; Tenrecs.] With the exception of a single genus of shrew (Sun-cus), insectivoran-grade mammals from Madagascar are members of the family Tenrecidae (Eisenberg and Gould, 1970; Olson and Goodman, 2003). This group of placental mammals consists of eight genera endemi
Terence J Robinson - One of the best experts on this subject based on the ideXlab platform.
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Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Guillaume Cornelis, Terence J Robinson, François Catzeflis, Michel C. Milinkovitch, Athanasia C. Tzika, Cécile Vernochet, Sébastien Malicorne, Sylvie Souquere, Steven M. Goodman, Gérard PierronAbstract:Syncytins are fusogenic envelope (env) genes of retroviral origin that have been captured for a function in placentation. Syncytins have been identified in Euarchontoglires (primates, rodents, Leporidae) and Laurasiatheria (Carnivora, ruminants) placental mammals. Here, we searched for similar genes in species that retained characteristic features of primitive mammals, namely the Malagasy and mainland African Tenrecidae. They belong to the superorder Afrotheria, an early lineage that diverged from Euarchotonglires and Laurasiatheria 100 Mya, during the Cretaceous terrestrial revolution. An in silico search for env genes with full coding capacity within a Tenrecidae genome identified several candidates, with one displaying placenta-specific expression as revealed by RT-PCR analysis of a large panel of Setifer setosus tissues. Cloning of this endogenous retroviral env gene demonstrated fusogenicity in an ex vivo cell–cell fusion assay on a panel of mammalian cells. Refined analysis of placental architecture and ultrastructure combined with in situ hybridization demonstrated specific expression of the gene in multinucleate cellular masses and layers at the materno–fetal interface, consistent with a role in syncytium formation. This gene, which we named “syncytin-Ten1,” is conserved among Tenrecidae, with evidence of purifying selection and conservation of fusogenic activity. To our knowledge, it is the first syncytin identified to date within the ancestrally diverged Afrotheria superorder.
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phylogenetic relationships of elephant shrews Afrotheria macroscelididae
Journal of Zoology, 2011Co-Authors: H A Smit, Malcolm A Fergusonsmith, Fengtang Yang, Jansen B Van Vuuren, P C M Obrien, Terence J RobinsonAbstract:Elephant-shrews or sengis (Macroscelidea, Afrotheria) are grouped into two subfamilies, Rhynchocyoninae with a single genus and four species, and Macroscelidinae represented by three genera and 13 species. Our current understanding of the evolutionary relationships within this group is largely based on a molecular phylogeny that suffers from incomplete species representation. We present the first complete phylogeny (with the exception of the recently described East African Rhynchocyon udzungwensis) for Macroscelidea based on mitochondrial and nuclear markers. Novel cytogenetic characters as well as previously described allozyme variation and various morphological features are evaluated and mapped to the molecular topology. Our analyses indicate that Elephantulus is paraphyletic, and that Petrodromus and Macroscelides should be subsumed in Elephantulus. A relaxed Bayesian dating approach supports the hypothesis that an arid-adapted Macroscelidinae lineage dispersed from east Africa at ∼11.5 MYA via an African arid corridor to south-western Africa. The timing of speciation within the east African Rhynchocyoninae (8–10 MYA) is coincidental with the diversification of some other forest specialists. In turn, divergence within the Macroscelidinae coincides with major aridification events across Africa.
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Sex chromosomes of basal placental mammals
Chromosoma, 2007Co-Authors: Paul D. Waters, Aurora Ruiz-herrera, Gauthier Dobigny, Montserrat Garcia Caldès, Terence J RobinsonAbstract:Placental (eutherian) mammals are currently classified into four superordinal clades (Afrotheria, Xenarthra, Laurasiatheria and Supraprimates) of which one, the Afrotheria (a unique lineage of African origin), is generally considered to be basal. Therefore, Afrotheria provide a pivotal evolutionary link for studying fundamental differences between the sex chromosomes of human/mouse (both representatives of Supraprimates and the index species for studies of sex chromosomes) and those of the distantly related marsupials. In this study, we use female fibroblasts to investigate classical features of X chromosome inactivation including replication timing of the X chromosomes and Barr body formation. We also examine LINE-1 accumulation on the X chromosomes of representative Afrotherians and look for evidence of a pseudoautosomal region (PAR). Our results demonstrate that asynchronous replication of the X chromosomes is common to Afrotheria, as with other mammals, and Barr body formation is observed across all Placentalia, suggesting that mechanisms controlling this evolved before their radiation. Finally, we provide evidence of a PAR (which marsupials lack) and demonstrate that LINE1 is accumulated on the Afrotherian and xenarthran X, although this is probably not due to transposition events in a common ancestor, but rather ongoing selection to retain recently inserted LINE1 on the X.
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Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies.
BMC evolutionary biology, 2007Co-Authors: Aurora Ruiz-herrera, Terence J RobinsonAbstract:Background: Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria). Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of Afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three Afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results: We described 29 fragile sites in the aardvark (OAF) genome, 27 in the golden mole (CAS), and 35 in the elephant-shrew (EED) genome. We show that fragile sites are conserved among Afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA) genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica) and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion: We provide evidence that (i) the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii) that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals) and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii) that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared by all Paenungulata.
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Afrotherian origins and interrelationships: new views and future prospects.
Current topics in developmental biology, 2004Co-Authors: Terence J Robinson, Erik R. SeiffertAbstract:Publisher Summary This chapter discusses a number of issues related to Afrotherian origins and interrelationships. Particular attention is given to the apparent conflict between molecular and morphological evidence for Afrotherian monophyly and the evolutionary or interpretive bases underlying the apparent absence of morphological characters. The phylogenetic position and time of origin of Afrotheria, the implications they hold for competing views of a southern versus northern origin for Afrotherians, and other extant placental mammals are discussed. Representative species of the six orders of mammals comprising the Afrotheria are: (1) elephant, (2) manatee, (3) hyrax, (4) golden mole, (5) elephant-shrews, and (6) aardvark. The recognition of Afrotherian monophyly has exposed a number of unique phylogenetic patterns in the morphology and physiology of the peculiar mammals. Phylogenetic analyses of mitochondrial genomes often support a nested placement for Afrotheria within Placentalia. The chapter concludes that the possible inability of sequence data to conclusively resolve many of the evolutionary relationships within Afrotheria and propose that an emphasis on the identification of so-called rare genomic changes (RGCs) may ultimately provide the most convincing resolution of Afrotherian supraordinal phylogeny.
Roscoe Stanyon - One of the best experts on this subject based on the ideXlab platform.
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RESEARCH ARTICLE Open Access Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for
2016Co-Authors: Nathália F Azevedo, Roscoe Stanyon, Marta Svartman, Andrea Manchester, Nádia De Moraes-barros, Angela M Vianna-morganteAbstract:Background: Xenarthra (sloths, armadillos and anteaters) represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results: Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5
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The Chromosomes of Afrotheria and Their Bearing on Mammalian Genome Evolution
Cytogenetic and genome research, 2012Co-Authors: Marta Svartman, Roscoe StanyonAbstract:Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orde
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chromosome painting in the manatee supports Afrotheria and paenungulata
BMC Evolutionary Biology, 2007Co-Authors: Margaret E Kellogg, Thomas R Dennis, Brian A. Gray, Roberto T Zori, Peter M Mcguire, Sandra Burkett, Gary Stone, Roscoe StanyonAbstract:Background Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two Afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee.
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Chromosome painting in the manatee supports Afrotheria and Paenungulata
BMC Evolutionary Biology, 2007Co-Authors: Margaret E Kellogg, Thomas R Dennis, Brian A. Gray, Roberto T Zori, Peter M Mcguire, Sandra Burkett, Gary Stone, Roscoe StanyonAbstract:Background Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two Afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee. Results The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19. Conclusion There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link Afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If Afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking Afrotherian taxa.
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The Ancestral Eutherian Karyotype Is Present in Xenarthra
PLoS genetics, 2006Co-Authors: Marta Svartman, Gary Stone, Roscoe StanyonAbstract:Molecular studies have led recently to the proposal of a new super-ordinal arrangement of the 18 extant Eutherian orders. From the four proposed super-orders, Afrotheria and Xenarthra were considered the most basal. Chromosome-painting studies with human probes in these two mammalian groups are thus key in the quest to establish the ancestral Eutherian karyotype. Although a reasonable amount of chromosome-painting data with human probes have already been obtained for Afrotheria, no Xenarthra species has been thoroughly analyzed with this approach. We hybridized human chromosome probes to metaphases of species (Dasypus novemcinctus, Tamandua tetradactyla, and Choloepus hoffmanii) representing three of the four Xenarthra families. Our data allowed us to review the current hypotheses for the ancestral Eutherian karyotype, which range from 2n = 44 to 2n = 48. One of the species studied, the two-toed sloth C. hoffmanii (2n = 50), showed a chromosome complement strikingly similar to the proposed 2n = 48 ancestral Eutherian karyotype, strongly reinforcing it.
Ole Madsen - One of the best experts on this subject based on the ideXlab platform.
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Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses
BMC Evolutionary Biology, 2008Co-Authors: Céline Poux, Ole Madsen, Wilfried W De Jong, Julian Glos, Miguel VencesAbstract:Background Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec , Echinops , Setifer and Hemicentetes ; Oryzorictinae: Oryzorictes , Limnogale and Microgale ; Geogalinae: Geogale ). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed. Results Within Afrotheria the vast majority of the nodes received a high support, including the grouping of hyrax with sea cow and the monophyly of both Afroinsectivora (Macroscelidea + Afrosoricida) and Afroinsectiphillia (Tubulidentata + Afroinsectivora). Strongly supported relationships were also recovered among all tenrec genera, allowing us to firmly establish the grouping of Geogale with Oryzorictinae, and to confirm the previously hypothesized nesting of Limnogale within the genus Microgale . The timeline of Malagasy tenrec diversification does not reflect a fast adaptive radiation after the arrival on Madagascar, indicating that morphological specializations have appeared over the whole evolutionary history of the family, and not just in a short period after colonization. In our analysis, age estimates at the root of a clade became older with increased taxon sampling of that clade. Moreover an augmentation of data partitions resulted in older age estimates as well, whereas standard deviations increased when more extreme partition schemes were used. Conclusion Our results provide as yet the best resolved gene tree comprising all Malagasy tenrec genera, and may lead to a revision of tenrec taxonomy. A timeframe of tenrec evolution built on the basis of this solid phylogenetic framework showed that morphological specializations of the tenrecs may have been affected by environmental changes caused by climatic and/or subsequent colonization events. Analyses including various taxon sampling and data partitions allow us to point out some possible pitfalls that may lead to biased results in molecular dating; however, further analyses are needed to corroborate these observations.
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Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree.
Molecular phylogenetics and evolution, 2003Co-Authors: Wilfried W De Jong, Marjon A.m. Van Dijk, Céline Poux, Guido Kappé, Teun Van Rheede, Ole MadsenAbstract:Abstract Despite the availability of large molecular data sets, the position of the root of the eutherian tree remains a controversial issue. Depending on source data, taxon sampling and analytical approach, the root can be placed at either Afrotheria, Xenarthra, Afrotheria + Xenarthra, or murid rodents. We explored the phylogenetic potential of indels in four nuclear protein-coding genes (SCA1, PRNP, TNFα, and HspB3) with regard to a possible rooting at the murid branch. According to parsimony principles, five indels were interpreted to contradict such a rooting, and one indel to support it. The results illustrate that indels, despite the occurrence of homoplasy, can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.
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Resolving mammalian relationships with molecules
2003Co-Authors: Ole MadsenAbstract:The aim of the present study was to gain a deeper knowledge about the phylogenetic relationships amongst extant mammals, as derived from extensive molecular data sets. Analyses of molecular data gave strong evidence for dividing placental (eutherian) mammals into four major groups. One of these groups, Afrotheria, includes morphologically very distinct mammals such as elephants, sea cows, hyraxes, aardvarks, elephant shrews and two endemic African insectivores: tenrecs and golden moles. Inclusion of golden moles and tenrecs in Afrotheria leads to the conclusion that the present order Insectivora should be divided into two groups, one with African origin and one with Laurasian origin. These two groups of insectivores have originated and evolved independently, showing remarkable parallel adaptive radiations at the morphological level. Most notable are the morphological convergences of Erinaceidae (hedgehogs) versus Echinops (Madagascar 'hedgehogs'); Soricidae (shrews) versus Microgale (shrewlike tenrecs); and Talpidae (moles) versus Chrysochloridae (golden moles). Further, molecular clock estimations suggested that the radiation of the different Afrotheria, which all have African origin, occurred during Africa's isolation in mid Cretaceous to early Cenozoic. In conclusion, a well resolved eutherian tree has been obtained, which displays new and surprising relationships which have never been recognized by morphological or paleontological data
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Molecular Evolution of the Mammalian Alpha 2B Adrenergic Receptor
Molecular biology and evolution, 2002Co-Authors: Ole Madsen, Diederik Willemsen, Björn M. Ursing, Ulfur Arnason, Wilfried W De JongAbstract: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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Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting.
Molecular Biology and Evolution, 2002Co-Authors: Frédéric Delsuc, Michael J. Stanhope, Ole Madsen, Mark Scally, Wilfried W De Jong, Mark S. Springer, François M Catzeflis, Emmanuel DouzeryAbstract: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.
Wilfried W De Jong - One of the best experts on this subject based on the ideXlab platform.
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Molecular phylogeny and divergence times of Malagasy tenrecs: Influence of data partitioning and taxon sampling on dating analyses
BMC Evolutionary Biology, 2008Co-Authors: Céline Poux, Ole Madsen, Wilfried W De Jong, Julian Glos, Miguel VencesAbstract:Background Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec , Echinops , Setifer and Hemicentetes ; Oryzorictinae: Oryzorictes , Limnogale and Microgale ; Geogalinae: Geogale ). The diversity of their morphology and incomplete taxon sampling made it difficult until now to resolve phylogenies based on either morphology or molecular data for this group. Therefore, in order to delineate the evolutionary history of this family, phylogenetic and dating analyses were performed on a four nuclear genes dataset (ADRA2B, AR, GHR and vWF) including all Malagasy tenrec genera. Moreover, the influence of both taxon sampling and data partitioning on the accuracy of the estimated ages were assessed. Results Within Afrotheria the vast majority of the nodes received a high support, including the grouping of hyrax with sea cow and the monophyly of both Afroinsectivora (Macroscelidea + Afrosoricida) and Afroinsectiphillia (Tubulidentata + Afroinsectivora). Strongly supported relationships were also recovered among all tenrec genera, allowing us to firmly establish the grouping of Geogale with Oryzorictinae, and to confirm the previously hypothesized nesting of Limnogale within the genus Microgale . The timeline of Malagasy tenrec diversification does not reflect a fast adaptive radiation after the arrival on Madagascar, indicating that morphological specializations have appeared over the whole evolutionary history of the family, and not just in a short period after colonization. In our analysis, age estimates at the root of a clade became older with increased taxon sampling of that clade. Moreover an augmentation of data partitions resulted in older age estimates as well, whereas standard deviations increased when more extreme partition schemes were used. Conclusion Our results provide as yet the best resolved gene tree comprising all Malagasy tenrec genera, and may lead to a revision of tenrec taxonomy. A timeframe of tenrec evolution built on the basis of this solid phylogenetic framework showed that morphological specializations of the tenrecs may have been affected by environmental changes caused by climatic and/or subsequent colonization events. Analyses including various taxon sampling and data partitions allow us to point out some possible pitfalls that may lead to biased results in molecular dating; however, further analyses are needed to corroborate these observations.
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Indels in protein-coding sequences of Euarchontoglires constrain the rooting of the eutherian tree.
Molecular phylogenetics and evolution, 2003Co-Authors: Wilfried W De Jong, Marjon A.m. Van Dijk, Céline Poux, Guido Kappé, Teun Van Rheede, Ole MadsenAbstract:Abstract Despite the availability of large molecular data sets, the position of the root of the eutherian tree remains a controversial issue. Depending on source data, taxon sampling and analytical approach, the root can be placed at either Afrotheria, Xenarthra, Afrotheria + Xenarthra, or murid rodents. We explored the phylogenetic potential of indels in four nuclear protein-coding genes (SCA1, PRNP, TNFα, and HspB3) with regard to a possible rooting at the murid branch. According to parsimony principles, five indels were interpreted to contradict such a rooting, and one indel to support it. The results illustrate that indels, despite the occurrence of homoplasy, can be convincing sources of independent molecular evidence to distinguish between alternative phylogenetic hypotheses.
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Molecular Evolution of the Mammalian Alpha 2B Adrenergic Receptor
Molecular biology and evolution, 2002Co-Authors: Ole Madsen, Diederik Willemsen, Björn M. Ursing, Ulfur Arnason, Wilfried W De JongAbstract: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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Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting.
Molecular Biology and Evolution, 2002Co-Authors: Frédéric Delsuc, Michael J. Stanhope, Ole Madsen, Mark Scally, Wilfried W De Jong, Mark S. Springer, François M Catzeflis, Emmanuel DouzeryAbstract: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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Molecular Evidence for the Major Clades of Placental Mammals
Journal of Mammalian Evolution, 2001Co-Authors: Mark Scally, Michael J. Stanhope, Ole Madsen, Christophe J Douady, Wilfried W De Jong, Mark S. SpringerAbstract:Higher-level relationships among placental mammals, as well as the historical biogeography of this group against the backdrop of continental fragmentation and reassembly, remain poorly understood. Here, we analyze two independent molecular data sets that represent all placental orders. The first data set includes six genes (A2AB, IRBP, vWF, 12S rRNA, tRNA valine, 16S rRNA; total = 5.71 kb) for 26 placental taxa and two marsupials; the second data set includes 2.95 kb of exon 11 of the BRCA1 gene for 51 placental taxa and four marsupials. We also analyzed a concatenation of these data sets (8.66 kb) for 26 placentals and one marsupial. Unrooted and rooted analyses were performed with parsimony, distance methods, maximum likelihood, and a Bayesian approach. Unrooted analyses provide convincing support for a fundamental separation of placental orders into groups with southern and northern hemispheric origins according to the current fossil record. On rooted trees, one or both of these groups are monophyletic depending on the position of the root. Maximum likelihood and Bayesian analyses with the BRCA1 and combined 8.66 kb data sets provide strong support for the monophyly of the northern hemisphere group (Boreoeutheria). Boreoeutheria is divided into Laurasiatheria (Carnivora + Cetartiodactyla + Chiroptera + Eulipotyphla + Perissodactyla + Pholidota) and Euarchonta (Dermoptera + Primates + Scandentia) + Glires (Lagomorpha + Rodentia). The southern hemisphere group is either monophyletic or paraphyletic, depending on the method of analysis used. Within this group, Afrotheria (Proboscidea + Sirenia + Hyracoidea + Tubulidentata + Macroscelidea + Afrosoricida) is monophyletic. A unique nine base-pair deletion in exon 11 of the BRCA1 gene also supports Afrotheria monophyly. Given molecular dates that suggest that the southern hemisphere group and Boreoeutheria diverged in the Early Cretaceous, a single trans-hemispheric dispersal event may have been of fundamental importance in the early history of crown-group Eutheria. Parallel adaptive radiations have subsequently occurred in the four major groups: Laurasiatheria, Euarchonta + Glires, Afrotheria, and Xenarthra.
