A Morphological Basis for Assessing the Phylogeny of the Tenrecoidea (Mammalia, Lipotyphla)

A phylogenetic analysis of 35 mammalian taxa focusing on the lipotyphlan family Tenrecidae, based on 193 morphological character states across 71 characters, is undertaken to test several hypotheses of lipotyphlan relationships, including monophyly of the Lipotyphla, Tenrecidae, Malagasy Tenrecidae, and Caribbean Lipotyphla. Explicit tests of these hypotheses are central to understanding larger issues concerning Malagasy and Caribbean biogeography, in addition to mammalian phylogeny. Methodologically, several different parameters are created with which to determine the sensitivity of resulting clades to initial assumptions about a posteriori character weighting, missing data, and multistate character ordering. Clades produced by this data set that appear despite perturbations in these parameters and that are supported by other confidence-assessment techniques contradict Malagasy tenrecid monophyly and the association of soricids with the Caribbean taxon Solenodon. Results regarding tenrecid and lipotyphlan monophyly are more ambiguous and depend on certain assumptions regarding treatment of character ordering, weighting, and missing data. An alternative phylogeny supporting an African mammal clade receives no support from the data set discussed herein.     

Phylogeny and conservation priorities of afrotherian mammals (Afrotheria,Mammalia)

Kuntner, M., May‐Collado, L. J. & Agnarsson, I. (2010). Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia). —Zoologica Scripta, 40, 1–15. Phylogenies play an increasingly important role in conservation biology providing a species‐specific measure of biodiversity – evolutionary distinctiveness (ED) or phylogenetic diversity (PD) – that can help prioritize conservation effort. Currently, there are many available methods to integrate phylogeny and extinction risk, with an ongoing debate on which may be best. However, the main constraint on employing any of these methods to establish conservation priorities is the lack of detailed species‐level phylogenies. Afrotheria is a recently recognized clade grouping anatomically and biologically diverse placental mammals: elephants and mammoths, dugong and manatees, hyraxes, tenrecs, golden moles, elephant shrews and aardvark. To date, phylogenetic studies have focused on understanding higher level relationships among the major groups within Afrotheria. Here, we provide a species‐level phylogeny of Afrotheria based on nine molecular loci, placing nearly 70% of the extant afrotherian species (50) and five extinct species. We then use this phylogeny to assess conservation priorities focusing on the widely used evolutionary distinctiveness and global endangeredness (EDGE) method and how that compares to the more recently developed PD framework. Our results support the monophyly of Afrotheria and its sister relationship to Xenarthra. Within Afrotheria, the basal division into Afroinsectiphilia (aardvark, tenrecs, golden moles and elephant shrews) and Paenungulata (hyraxes, dugongs, manatees and elephants) is supported, as is the monophyly of all afrotherian families: Elephantidae, Procaviidae, Macroscelididae, Chrysochloridae, Tenrecidae, Trichechidae and Dugongidae. Within Afroinsectiphilia, we recover the most commonly proposed topology (Tubulidentata sister to Afroscoricida plus Macroscelidea). Within Paenungulata, Sirenia is sister to Hyracoidea plus Proboscidea, a controversial relationship supported by morphology. Within Proboscidea, the mastodon is sister to the remaining elephants and the woolly mammoth sister to the Asian elephant, while both living elephant genera, Loxodonta and Elephas are paraphyletic. Top ranking evolutionarily unique species always included the aardvark, followed by several species of elephant shrews and tenrecs. For conservation priorities top ranking species always included the semi‐aquatic Nimba otter shrew, some poorly known species, such as the Northern shrew tenrec, web‐footed tenrec, giant otter shrew and Giant golden mole, as well as high profile conservation icons like Asian elephant, dugong and the three species of manatee. Conservation priority analyses were broadly congruent between the EDGE and PD methodologies. However, for certain species EDGE overestimates conservation urgency as it, unlike PD, fails to account for the status of closely related, but less threatened, species. Therefore, PD offers a better guide to conservation decisions.     

Effects of altitudinal change on the auditory bulla in Ochotona daurica (Mammalia, Lagomorpha)

The lengths and widths of body parts are influenced to a considerable extent by the environment. Along with increasing altitude, wings of arthropods degenerated or even disappeared so that a trend of degeneration on their acoustic systems appeared. We measured 131 adult skulls of daurian pikas, Ochotona daurica , in order to know whether the degeneration will happen in mammals. Our results show that both the size and relative size of auditory bulla of daurian pikas were negatively correlated with altitude and this change was significant. However, the ear length showed an opposite trend. We suggest that lower oxygen concentration, constantly strong winds and lack of resources at high altitude are responsible for the decrease in the size of the auditory bulla. Besides thermoregulation for large different temperatures of day and night in high altitude, larger external ears of the pika help detect the direction of the predator and could compensate for a relatively small bulla.     

Comparative Endocranial Anatomy,Encephalization, and Phylogeny of Notoungulata (Placentalia,Mammalia)

Journal of Mammalian Evolution - Cranial endocasts are one of the most direct tools available to obtain information about the endocranial cavity of fossil mammals, but few anatomical comparisons...     

Enamel microstructure ofTribosphenomys (Mammalia,glires): Character analysis and systematic implications

Enamel distribution on the upper and lower incisors ofTribosphenomys minutus (from Late Paleocene-Early Eocene of Inner Mongolia of China) is typically rodent-like, i.e., primarily confined to the anterior surface throughout these transversely compressed, evergrowing teeth. AlthoughTribosphenomys incisor enamel is differentiated into two layers, it does not possess Hunter-Schreger bands (HSB). The incisor and molar enamels are radial in type, a condition regarded as either an autapomorph or a primtive retention forTribosphenomys. Character polarities concerning enamel thickness, enamel layer number, HSB, enamel types, and functional and phylogenetic implications of the enamel structures are discussed. Overall, enamel microstructural evolution at high taxonomic levels within Glires displays considerably more homoplasy than generally appreciated. A phylogenetic definition of Rodentia is proposed.Tribosphenomys is the sister-group of a taxon here named Rodentia, and thus is not itself a member of the order, from a systematic viewpoint.     

Tooth Root Morphology in the Early Pliocene African Bear Agriotherium africanum (Mammalia, Carnivora, Ursidae) and its Implications for Feeding Ecology

Tooth root surface areas serve as proxies for bite force potentials, and by extension, dietary specialization in extant carnivorans. Here, we investigate the feeding ecology of the extinct large-bodied ursid Agriotherium africanum, by comparing its root surface areas (reconstructed with the aid of computed tomography and three-dimensional image processing) and bite force estimates, with those of extant carnivorans. Results show that in absolute terms, canine and carnassial bite forces, as well as root surface areas were highest in A. africanum. However, when adjusted for skull size, A. africanum’s canine roots were smaller than those of extant solitary predators. With teeth being the limiting factor in the masticatory system, low canine root surface areas suggest that A. africanum would have struggled to bring down large vertebrate prey. Its adjusted carnassial root sizes were found to be smaller than those of extant hard object feeders and the most carnivorous tough object feeders, but larger than those of extant omnivorous ursids and Ursus maritimus. This and the fact that it displayed its highest postcanine root surface areas in the carnassial region (rather than the most distal tooth in the tooth row) suggest that A. africanum consumed more vertebrate tissue than extant omnivorous ursids. With an apparent inability to routinely bring down large prey or to consume mechanically demanding skeletal elements, its focus was most likely on tough tissue, which it acquired by actively scavenging the carcasses of freshly dead/freshly killed animals. Mechanically less demanding skeletal elements would have been a secondary food source, ingested and processed mainly in association with muscle and connective tissue.     

不同食性哺乳动物及人的牙釉质微结构对比研究

根据动物食性将搜集于西藏、新疆、江苏和吉林4省和自治区16种哺乳动物的581颗牙齿分为食草、杂食和食肉3类,设计了录像-截图-测量-定标4步微米量级牙釉质结构测量方法,测量得到牙釉质的颊面厚度和舌面厚度比、臼齿外轮廓平均牙釉质厚度比等牙釉质分布规律,观测到不同哺乳动物釉柱的组装直径均在100 μm 左右,但柱间晶体的宽度不同,发现3类哺乳动物牙釉柱与釉牙本质界夹角的规律:人和食肉动物狗的釉柱角度最大,接近90°,杂食动物猪釉柱角度约为70°,而食草动物釉柱角度在54°～68°之间.研究表明,不同食性哺乳动物牙齿外在和内在结构都和其生物力学功能密切相关,牙釉质的异型结构是使得釉质具有优异的力学性能的优化结构模式.     

The Entotympanic of Pangolins and the Phylogeny of the Pholidota (Mammalia)

Entotympanics are independent elements present in the auditory bullae of various eutherians. An entotympanic has been reported for extant pangolins of the Order Pholidota, but the actual distribution of this element remains uncertain, in part, because it is a small, loosely attached structure that is often lost in macerated skulls. Consequently, it is unknown whether or not the entotympanic characterizes Pholidota primitively or has evolved within the group. This report addresses the morphology and distribution of the entotympanic among living and extinct pholidotans. An entotympanic occurs in the African pangolins Manis gigantea, M. temminckii, and in one specimen of M. tricuspis. In each, it is a small, nodular bone that occupies a distinct fossa primarily on the basioccipital, the presence of which allows us to assess the occurrence of an entotympanic even in specimens in which the bone has fallen out. Both the entotympanic and the basioccipital facet are lacking in the four remaining extant pangolin species and in the late Eocene pangolin Patriomanis. To assess the significance of this entotympanic distribution, a phylogenetic analysis of extant pangolins plus Patriomanis based on 67 cranial characters was performed. Four different outgroup analyses all resulted in the same single most parsimonious tree, in which the three extant Asian pangolins form a monophyletic clade and the four extant African pangolins fall into a paraphyletic assemblage. Optimization of the entotympanic distribution onto this tree results in two patterns, dependent on the outgroup choice. If Patriomanis is the sole outgroup to the extant pangolins, the entotympanic arises within pangolins as a synapomorphy of Manis gigantea and M. temminckii, convergently acquired in some M. tricuspis. If Xenarthra and Palaeanodonta are employed as outgroups, the entotympanic optimization is ambiguous: the pattern is either as above or the entotympanic is present primitively within Pholidota and lost secondarily in Patriomanis and a clade comprising M. tricuspis, M. tetradactyla, and the Asian forms.     

The South American Gomphotheres (Mammalia, Proboscidea, Gomphotheriidae): Taxonomy, Phylogeny, and Biogeography

The taxonomic history of South American Gomphotheriidae is very complex and controversial. Three species are currently recognized: Amahuacatherium peruvium, Cuvieronius hyodon, and Notiomastodon platensis. The former is a late Miocene gomphothere whose validity has been questioned by several authors. The other two, C. hyodon and N. platensis, are Quaternary taxa in South America, and they have distinct biogeographic patterns: Andean and lowland distributions, respectively. South American gomphotheres became extinct at the end of the Pleistocene. We conducted a phylogenetic analysis of Proboscidea including the South American Quaternary gomphotheres, which resulted in two most parsimonious trees. Our results support a paraphyletic Gomphotheriidae and a monophyletic South American gomphothere lineage: C. hyodon and N. platensis. The late Miocene gomphothere record in Peru, Amahuacatherium peruvium, seems to be a crucial part of the biogeography and evolution of the South American gomphotheres.     

Phylogeny of rodentia (Mammalia) inferred from the nuclear-encoded gene IRBP

The order Rodentia includes nearly half of all living mammalian species. Phylogenetic relationships among 22 species of rodents were investigated by use of a 1.2-kb region from exon 1 of the single-copy nuclear gene IRBP. IRBP has been extensively used for study of interordinal phylogeny in mammals, which allowed inclusion of 50 outgroup species, representing every eutherian order plus seven marsupials. Several clades were strongly supported, regardless of analytical method or inclusion/exclusion of data. These include a monophyletic Muroidea, with a clade including Spalax and Rhizomys as the first divergence; a clade uniting Zapus with Dipus, but excluding Sicista; a monophyletic Myodonta (Muroidea plus Dipodidae); and a clade including Aplodontidae as sister to Sciuridae. One bipartition, separating Hystricognathi and Geomyoidea from the remaining rodents, is strongly supported in all analyses that include third-position sites but almost completely absent from analyses that exclude third-position sites. A combination of nonstationary nucleotide composition and branch length effects may be causing all methods examined (including those using the LogDet distance) to support an incorrect conclusion when third-position sites are analyzed together with first- and second-position sites.     

The Phylogeny of Living and Extinct Pangolins (Mammalia, Pholidota) and Associated Taxa: A Morphology Based Analysis

The present study was undertaken in order to effect a comprehensive phylogenetic analysis of the order Pholidota, examining seven of the eight currently recognized extant species (absent is Manis culionensis, formerly recognized as a subspecies of Manis javanica) and nearly all the well-known fossil taxa, and employing a wide range of osteological characters from the entire skeleton. In addition, the relationship of pangolins to several putative early Tertiary relatives, including palaeanodonts and the enigmatic “edentate” Eurotamandua joresi, were investigated. The goal of the study was to improve understanding of the systematics and the biogeographic and evolutionary history of the pangolins. A computer-based cladistic analysis of phylogenetic relationships among seven extant species of pangolins, five extinct pangolin species (including all but one of the well-preserved taxa), as well as Eurotamandua and two genera of metacheiromyid palaeanodonts, Palaeanodon and Metacheiromys, was performed based upon 395 osteological characteristics of the skull and postcranial skeleton. Characters were polarized via comparison to the following successive outgroups: the basal feliform carnivoran Nandinia binotata and the hedgehog Erinaceus sp., a eulipotyphlan laursiatherian placental. A revised classification is presented based on the results of the analysis. The results support the monophyly of Pholidota and Palaeanodonta by providing new anatomical characters that can serve to diagnose a pangolin/palaeanodont clade, termed here Pholidotamorpha. Pholidota is defined so as to include all living and fossil pangolins, including all three taxa of middle Eocene “edentates” from the Messel fauna of Germany, among them Eurotamandua joresi. The results do not support the monophyly of the remaining two Messel “edentates” originally placed in the same genus Eomanis, which is restricted to the type species Eomanis waldi. Euromanis, new genus, is named with Eomanis krebsi Storch and Martin, 1994, as the type species, to form a new combination Euromanis krebsi (Storch and Martin, 1994). The analysis strongly supports the monophyly of a crown clade of pangolins diagnosed by many anatomical synapomorphies, the family Manidae. This crown clade is sister to the family Patriomanidae, which includes two Tertiary taxa, Patriomanis americana and Cryptomanis gobiensis, within the superfamily Manoidea. The relationship of the Tertiary European pangolin Necromanis to these two families is unresolved. Within Manidae, the extant species are divided into three well-supported, monophyletic genera, Manis for the Asian pangolins, Smutsia for the African ground pangolins, and Phataginus for the African tree pangolins. The latter two form a monophyletic African assemblage, the subfamily Smutsiinae. The biogeographic implications of this phylogeny are examined. A European origin for Pholidota is strongly indicated. The fossil record of pangolins would seem to support a European origin for the modern forms, with subsequent dispersal into sub-Saharan African and then to southern Asia, and the phylogeny produced in this analysis is consistent with such a scenario.     

Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)

The round-eared sengis or elephant-shrews (genus Macroscelides) exhibit striking pelage variation throughout their ranges. Over ten taxonomic names have been proposed to describe this variation, but currently only two taxa are recognized (M. proboscideus proboscideus and M. p. flavicaudatus). Here, we review the taxonomic history of Macroscelides, and we use data on the geographic distribution, morphology, and mitochondrial DNA sequence to evaluate the current taxonomy. Our data support only two taxa that correspond to the currently recognized subspecies M. p. proboscideus and M. p. flavicaudatus. Mitochondrial haplotypes of these two taxa are reciprocally monophyletic with over 13% uncorrected sequence divergence between them. PCA analysis of 14 morphological characters (mostly cranial) grouped the two taxa into non-overlapping clusters, and body mass alone is a relatively reliable distinguishing character throughout much of Macroscelides range. Although fieldworkers were unable to find sympatric populations, the two taxa were found within 50 km of each other, and genetic analysis showed no evidence of gene flow. Based upon corroborating genetic data, morphological data, near sympatry with no evidence of gene flow, and differences in habitat use, we elevate these two forms to full species.     

Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange

The Procyonidae (Mammalia: Carnivora) have played a central role in resolving the controversial systematics of the giant and red pandas, but phylogenetic relationships of species within the family itself have received much less attention. Cladistic analyses of morphological characters conducted during the last two decades have resulted in topologies that group ecologically and morphologically similar taxa together. Specifically, the highly arboreal and frugivorous kinkajou (Potos flavus) and olingos (Bassaricyon) define one clade, whereas the more terrestrial and omnivorous coatis (Nasua), raccoons (Procyon), and ringtails (Bassariscus) define another clade, with the similar-sized Nasua and Procyon joined as sister taxa in this latter group. These relationships, however, have not been tested with molecular sequence data. We examined procyonid phylogenetics based on combined data from nine nuclear and two mitochondrial gene segments totaling 6534bp. We were able to fully resolve relationships within the family with strongly supported and congruent results from maximum parsimony, maximum likelihood, minimum evolution, and Bayesian analyses. We identified three distinct lineages within the family: a (Nasua, Bassaricyon) clade, a (Bassariscus, Procyon) clade, and a Potos lineage, the last of which is sister to the other two clades. These findings, which are in strong disagreement with prior fossil and morphology-based assessments of procyonid relationships, reemphasize the morphological and ecological flexibility of these taxa. In particular, morphological similarities between unrelated genera possibly reflect convergence associated with similar lifestyles and diets rather than ancestry. Furthermore, incongruence between the molecular supermatrix and a morphological character matrix comprised mostly of dental characters [Baskin, J.A., 2004. Bassariscus and Probassariscus (Mammalia, Carnivora, Procyonidae) from the early Barstovian (Middle Miocene). J. Vert. Paleo. 24, 709-720] may be due to non-independence among atomized dental characters that does not take into account the high developmental genetic correlation of these characters. Finally, molecular divergence dating analyses using a relaxed molecular clock approach suggest that intergeneric and intrageneric splits in the Procyonidae mostly occurred in the Miocene. The inferred divergence times for intrageneric splits for several genera whose ranges are bisected by the Panamanian Isthmus is significant because they suggest diversification well precedes the Great American Interchange, which has long been considered a primary underlying mechanism for procyonid evolution.     

A Total Evidence Phylogeny of the Arctoidea (Carnivora: Mammalia): Relationships Among Basal Taxa

A total evidence phylogenetic analysis was performed for 14 extant and 18 fossil caniform genera using a data matrix of 5.6 kbp of concatenated sequence data from six independent loci and 80 morphological characters from the cranium and dentition. Maximum parsimony analysis recovered a single most parsimonious cladogram (MPC). The topology of the extant taxa in the MPC agreed with previous molecular phylogenies. Phylogenetic positions for fossil taxa indicate that several taxa previously described as early members of extant families (e.g., Bathygale and Plesictis) are likely stem taxa at the base of the Arctoidea. Taxa in the “Paleomustelidae” were found to be paraphyletic, but a monophyletic Oligobuninae was recovered within this set of taxa. This clade was closely related to the extant genera Gulo and Martes, therefore, nested within the extant radiation of the family Mustelidae. This analysis provides a resolution to several discrepancies between phylogenies considering either fossil taxa or extant taxa separately, and provides a framework for incorporating fossil and extant taxa into comprehensive combined evidence analyses.     

The Phylogeny of the Myrmecophagidae (Mammalia, Xenarthra, Vermilingua) and the Relationship of Eurotamandua to the Vermilingua

A cladistic investigation of the phylogenetic relationships among the three extant anteater genera and the three undoubted extinct myrmecophagid genera is performed based upon osteological characteristics of the skull and postcranial skeleton. One hundred seven discrete morphological characters are analyzed using the computer program PAUP. Characters are polarized via comparison to the successive xenarthran outgroups Tardigrada (represented by the living sloth Bradypus) and Cingulata (represented by the recent armadillos Dasypus and Euphractus). The analysis results in a single most-parsimonious tree (TL = 190, CI = 0.699, RI = 0.713). The tree corroborates the monophyly of the subfamilies Cyclopinae and Myrmecophaginae, the former including the extant Cyclopes and the Pliocene genus Palaeomyrmidon. Within the Myrmecophaginae the Miocene genus Protamandua is the sister taxon to a clade including the remaining three genera. The recent Tamandua is in turn the sister taxon to the extant Myrmecophaga plus the Pliocene genus Neotamandua. Contrary to the suggestions of recent authors, weak support is provided for the taxonomic distinctiveness of the latter genus from the recent Myrmecophaga. The monophyly of the Myrmecophagidae is supported by 15 unequivocal synapomorphies. The monophyly of the Cyclopinae and Myrmecophaginae is supported by 3 and 13 unambiguous synapomorphies, respectively. The enigmatic Eocene genus Eurotamandua, from the Messel fauna of Germany, is coded for the 107 morphological characters above and included in two subsequent PAUP analyses. The palaeanodont Metacheiromys is also added to these two analyses as a nonxenarthran outgroup to test for the possibility that Eurotamandua lies outside the Xenarthra. In the first analysis, Eurotamandua is constrained a priori to membership in the Vermilingua. The single most-parsimonious tree (TL = 224, CI = 0.618) that results places Eurotamandua as the sister group to the remaining anteater genera, contra Storch and Habersetzer's (1991) assignment of Eurotamandua to the vermilinguan subfamily Myrmecophaginae. Eurotamandua shares six unequivocal synapomorphies with other anteaters, including the absence of teeth and the presence of a lateral tuberosity on the fifth metatarsal. The remaining vermilinguans are united by 11 unequivocal synapomorphies, plus an additional 10 ambiguous synapomorphies. In the second analysis, the position of Eurotamandua is unconstrained. The resulting single most-parsimonious tree (TL = 219, CI = 0.632) places Eurotamandua outside Vermilingua as the sister group to the Pilosa (Vermilingua plus Bradypus). The monophyly of this node is supported by four unambiguous synapomorphies in the unconstrained analysis. Further manipulation of this second analysis shows that placement of Eurotamandua as the sister group to the Xenarthra or to the Palaeanodonta adds three steps to the shortest tree but is more parsimonious than its placement as a sister group to the Vermilingua is the previous analysis. The addition of pangolins to the analysis does little to alter the major phylogenetic conclusions of the study. The allocation of Eurotamandua to the Xenarthra, but as a sister group to the Pilosa, is a novel arrangement which leaves open the biogeographic question of how a xenarthran reached Western Europe during the Eocene.     

The 'Ice Worm' - the Immature Stages,Phylogeny and Biology of the Glacier Midge Zelandochlus (Diptera: Chironomidae)

The previously unknown female and larva for the New Zealand glacier midge, Zealandochlus latipalpis Brundin are described for the first time, and the pupa described more fully than previously. Unlike the male, which is brachypterous, the female has large wings possessing traces of a vein between R₁ and R₄₊₅ uniquely for the subfamily Podonominae. The larvae, known locally as ice-worms, live in meltwater pools and ice caves of the Franz Joseph and Fox glaciers, New Zealand. Cladistic analysis of this highly autapomorphic species results in an unresolved trichotomy Zelandochlus + Parochlus + Podonomus, which is no advance on the suggestion made by Brundin (1966) concerning the relationships. Information is too scanty on many species of the putative related genera, but additional morphological features indicate that there may be a sister group relationship with part of Parochlus.     

Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.