Nuclear DNA phylogeny of the squirrels (Mammalia: Rodentia) and the evolution of arboreality from c-myc and RAG1

Although the family Sciuridae is large and well known, phylogenetic analyses are scarce. We report on a comprehensive molecular phylogeny for the family. Two nuclear genes (c-myc and RAG1) comprising approximately 4500 bp of data (most in exons) are applied for the first time to rodent phylogenetics. Parsimony, likelihood, and Bayesian analyses of the separate gene regions and combined data reveal five major lineages and refute the conventional elevation of the flying squirrels (Pteromyinae) to subfamily status. Instead, flying squirrels are derived from one of the tree squirrel lineages. C-myc indels corroborate the sequence-based topologies. The common ancestor of extant squirrels appears to have been arboreal, confirming the fossil evidence. The results also reveal an unexpected clade of mostly terrestrial squirrels with African and Holarctic centers of diversity. We present a revised classification of squirrels. Our results demonstrate the phylogenetic utility of relatively slowly evolving nuclear exonic data even for relatively recent clades.     

Mitochondrial phylogeny reveals differential modes of chromosomal evolution in the genus Tatera (Rodentia: Gerbillinae) in Africa

The African gerbils of the genus Tatera are widespread and abundant throughout sub-Saharan Africa. There is still today a certain controversy concerning the taxonomy of these rodents and very few attempts have been made to assess their systematic relationships. The present paper introduces findings based on the partial sequences of cytochrome b (495 bp) and the 16S rRNA (469 bp) mitochondrial genes of six (T. robusta, T. nigricauda, T. vicina, T. leucogaster, T. valida, and T. kempi) species together with two additional taxa. We also report the karyotypes of T. vicina and T. leucogaster. We propose that T. vicina should be considered as a valid species and show the monophyly of the robusta species group, with the exclusion of T. leucogaster. Our results show there is a different chromosomal evolutionary pattern within the two major lineages, which is recognizable through molecular phylogenetics. One is characterized by karyotype stability and the other by a considerable number of chromosomal rearrangements. The lineage divergence coincides with the formation of the East African Rift. The processes that led to the origin of the East African species seem to be related to the subsequent climatic changes, which caused cyclic contraction and expansion of the savannah biomes. Furthermore, geological activities that characterized East Africa during Plio-Pleistocene may also have contributed to lineage divergence.     

Phylogeny and evolutionary history of the Aplodontoidea (Mammalia: Rodentia)

Athough over a hundred species of fossil aplodontoids have been described since the extant species, Aplodontia rufa (the mountain beaver), was first described by Rafinesque in 1817, a thorough survey of the relationships among all the species in this clade has not been undertaken since McGrew's study in 1941. Here, a complete phylogenetic analysis of all published species of aplodontoids is used to reconstruct the evolutionary relationships within the clade, and to present an updated classification of the Aplodontoidea. Several of the traditionally recognized subfamilies are found to be paraphyletic, namely the Prosciurinae, the Allomyinae, and the Meniscomyinae. Others, however, including the Aplodontinae and the Mylagaulidae, appear to be monophyletic. These latter two taxa, which include all of the hypsodont members of the aplodontoid clade, seem to be sister taxa. The history of the aplodontoid clade shows several episodes of rapid diversification in the Early Oligocene, the Late Oligocene, and the Early to Middle Miocene. The Ansomyinae and Aplodontinae show comparatively low speciation rates. The patterns of change in morphology and evolutionary rates suggest a need for a more detailed study of the causes of diversification, extinction, and ecological change in this lineage.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 769–838.     

The gallbladder of the Capivara Hydrochoerus hydrochoeris (Mammalia: Rodentia)

The authors studied morphological and histochemically the mucopolysaccharides and proteins in the gallbladder tubular glands and epithelial cells of the capivara Hydrochoerus hydrochoeris. Based on the results the authors concluded: 1. the gallbladder single columnar epithelium consists of secretory, migrating, and goblet cells; 2. in the lamina propria are single coiled tubular glands; 3. goblet and tubular gland cells show neutral and sulphated mucopolysaccharides and sialic acid; 4. columnar cells show neutral mucopolysaccharides and protein radicals; 5. migrating cells show only protein radicals.     

Molecular Relationships Among Octodontidae (Mammalia: Rodentia: Caviomorpha)

We examined ten species of octodontid rodents and representatives of three outgroups in a complete 13 × 13 DNA-hybridization matrix. The results were indexed as differences in median melting-point depressions (T,_ms), symmetrized, subjected to phylogenetic analysis using FITCH, bootstrapped, and exhaustively taxon-jackknifed. Within Octodontidae, four clades were recovered with 100% bootstrap and complete jackknife support: Tympanoctomys barrerae with Octomys mimax, Octodontomys gliroides alone, Octodon spp., and Aconaemys spp. with Spalacopus cyanus; the latter two clades were closer to each other than either was to Octodontomys or Octomys-Tympanoctomys, but were slightly nearer to and united with Octodontomys, with 89% bootstrap support. However, relationships among the three Aconaemys species and Spalacopus were not completely resolved by our experiments. Ctenomys coyhaiquensis, Abrocoma bennetti, and Lagostomus maximus represented successive outgroups to Octodontidae, while one-way comparisons with Cavia porcellus and Microcavia australis suggested that these caviids are almost as distant from octodontoids as is the chinchilloid Lagostomus. When the data were suitably corrected for percentage hybridization and saturation, division of the distances by the rate previously determined for most amniotes (0.48%/myr) suggested that the basal divergence among the caviomorph rodents examined occurred about 59 myrbp, and that Octodontidae originated 40 myrbp and diversified into extant lineages beginning 14 myr ago. Calibration against the date of the earliest known caviomorph (late Eocene or about 37.5 myrbp) gave a rate of 0.75%/myr, which would suggest later dates for subsequent caviomorph cladogenesis. It is notable that, based respectively on the slower or faster rates, the tetraploid Tympanoctomys barrerae must have diverged from its sister-taxon Octomys mimax 10 or 6.5 myr ago.     

Comparison of climate space and phylogeny of Marmota (Mammalia: Rodentia) indicates a connection between evolutionary history and climate preference

Palaeobiologists have investigated the evolutionary responses to extinct organisms to climate change, and have also used extinct organisms to reconstruct palaeoclimates. There is evidence of a disconnection between climate change and evolution that suggest that organism may not be accurate paleoclimate indicators. Here, marmots (Marmota sp.) are used as a case study to examine whether similarity of climate preferences is correlated with evolutionary relatedness of species. This study tests for a relationship between phylogenetic distance and 'climate distance' of species with a clade. There should be a significant congruence between maximus likelihood distance and standardized Euclidian distance between climates if daughter species tend to say in environments similar to parent species. Marmots make a good test case because there are many extant species, their phylogenetics are well established and individual survival is linked to climatic factors. A Mantel test indicates a significant correlation between climate and phylogenetic distance matrices, but this relationship explains only a small fraction of the variance (regression R(2) = 0.114). These results that (i) closely related species of marmots tend to stay in similar environments; (ii) marmots may be more susceptible than may mammals to global climate change; and (iii) because of the considerable noise in this system, the correlation cannot be used for detailed palaeoclimate reconstruction.     

Taxonomic identity of Chionomys nivalis spitzenbergerae (Mammalia: Rodentia)

The most genetically divergent populations of the European snow vole Chionomys nivalis occupy the extreme eastern range of the Black Sea and the Caspian Sea. It was recently suggested that subspecies C. n. spitzenbergerae from the Central Taurus Mountains (Turkey) represents a highly divergent lineage of C. nivalis from the Alada? Range which induced us to address its status by examining topotype specimens. Two females karyotyped displayed 54 mitotic chromosomes of 25 acrocentric autosomal pairs. One of the smallest autosomal pairs was heteromorphic in both specimens, consisting of a submetacentric and an acrocentric chromosomes (NFa = 53). Cytochrome b sequences however unambiguously clustered both individuals with reference sequences from C. nivalis from Turkey. We conclude that a deviant haplotype from the Alada? Range does not represent C. n. spitzenbergerae. Its taxonomic identity was not resolved in our study. Further attention should be devoted to snow voles from Central Anatolia and Western Iran, which are characterized by cranial peculiarities.     

Evolutionary history of tree squirrels (Rodentia,Sciurini) based on multilocus phylogeny reconstruction

Pe?nerová, P. & Martínková, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. —Zoologica Scripta, 41, 211–219. Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d‐loop, and nuclear irbp, c‐myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans‐Pacific dispersal.     

Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

Background  

Phylogenetic comparative methods are often improved by complete phylogenies with meaningful branch lengths (e.g., divergence dates). This study presents a dated molecular supertree for all 34 world pinniped species derived from a weighted matrix representation with parsimony (MRP) supertree analysis of 50 gene trees, each determined under a maximum likelihood (ML) framework. Divergence times were determined by mapping the same sequence data (plus two additional genes) on to the supertree topology and calibrating the ML branch lengths against a range of fossil calibrations. We assessed the sensitivity of our supertree topology in two ways: 1) a second supertree with all mtDNA genes combined into a single source tree, and 2) likelihood-based supermatrix analyses. Divergence dates were also calculated using a Bayesian relaxed molecular clock with rate autocorrelation to test the sensitivity of our supertree results further.     

Chromosome studies in some members of the family Caviidae (Mammalia: Rodentia)

A study of the chromosomes of Cavia aperea and Galea musteloides has been made following the introduction into captivity of these two cavies from Argentina. The evolutionary relationships of the two genera have been considered, and the possible ancestry of C. porcellus from C. aperea was investigated in hybrids of the two species.     

Evolution of a dental character in the beaver Castor fiber L. (Mammalia: Rodentia)

Variation in morphology of beaver cheek teeth has been examined in respect of ontogeny, geographical variation and geological time. When the effects of ontogeny are taken into account, certain patterns of dental variation are found to be restricted in space and time. An isolated loop of enamel ubiquitously present in the lower third molars of European beavers from the present interglacial seems to be a "new" acquisition which is lacking in Recent Siberian and North American beavers, as well as in Western European specimens from earlier interglacials.
Whilst the genetic basis of such morphological details is presumed rather than established, they may be helpful in tracing past population movements and are also of potential stratigraphic importance. Changes in range associated with Pleistocene climatic oscillations have led to the "sudden" appearance of this and other castorid dental characters in the Western European fossil record. The morphological discontinuity in the fossil record should be taken as evidence of climatic change rather than evidence for the operation of a certain pattern of evolution.     

The phylogeny of the Rhinocerotoidea (Mammalia, Perissodactyla)

A new phylogeny of the Superfamily Rhinocerotoidea is proposed, based upon an analysis of shared derived characters of the skull, teeth and skeleton. Hyrachyus is considered the primitive sister-taxon of the three rhinocerotoid families (Amynodontidae, Hyracodontidae, Rhinocerotidae), and the amynodonts appear to be the sister-group of hyracodonts and rhinocerotids. The relationships of primitive hyracodonts and rhinocerotids are clarified. Menoceras and Pleuroceras (new Subfamily Menoceratinae) are removed from the Diceratheriinae, since they appear to be more closely related to higher rhinoceroses than they are to Diceratherium. Of the three major monophyletic groups of higher rhinocerotids (aceratherines, teleoceratines and rhinocerotines), the last two groups are more closely related to each other than either is to aceratherines. Toxotherium and Schizotheroides are tentatively removed from the Rhinocerotoidea and placed in the Lophiodontidae.     

Systematics and phylogeny of the cane rats (Rodentia: Thryonomyidae)

The family Thryonomyidae is known from the Eocene up to the present. Today, this group comprises just two closely related species, which are restricted to sub-Saharan Africa. However, various thryonomyids have been recorded in strata of Miocene age, when the group spread out of Africa eastward to southern Asia (Pakistan). A systematic revision and a cladistic analysis shows that 20 species can be referred to this family: Thryonomys swinderianus (Temninck), T. gregorianus (Thomas), Paraphiomys pigotti Andrews, P. occidentalis Lavocat, P. simonsi Wood, P. hopwoodi Lavocat, P. shipmani Denys et Jaeger, P. australis Mein, Pickford et Senut, P. roessneri Mein, Pickford et Senut, P. afarensis Geraads, Paraphiomys sp. nov. from Saudi Arabia López-Antoñanzas et Sen , P. renelavocati sp. nov. , Neosciuromys africanus Stromer, Apodecter stromeri Hopwood, Paraulacodus indicus Hinton, Paraulacodus johanesi Jaeger, Michaux et Sabatier, Gaudeamus aegyptius Wood, Epiphiomys coryndoni Lavocat, Kochalia geespei (de Bruijn et Hussain), Paraphiomys sp. nov. from Saudi Arabia, and Paraphiomys orangeus Mein et Pickford. The unresolved basal position of Sacaresia moyaeponsi with respect to Metaphiomys schaubi and the clade comprising the above-cited species, suggest that this taxon should not be allocated to the family Thryonomyidae. A phylogenetic definition of the family Thryonomyidae is proposed as an outcome of the phylogenetic analysis: Epiphiomys corindoni , Thryonomys swinderianus , their most recent common ancestor and all its descendants (node-based taxon).  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 423–444.     

The Iranian vole Microtus irani occurs in Lebanon (Mammalia: Rodentia)

We studied 1140 bp cytochrome b sequences of social voles from three localities in Lebanon. The results were compared with published sequences representing seven species of social voles. New sequences from Lebanon clustered with reference samples of two species: M. guentheri and M. irani. While M. guentheri was already reported for Lebanon, M. irani is a new addition to the fauna of Lebanon, and the third known record for the species. Animals were collected in two localities above Tripolis at 855 m and 1430 m a.s.l., respectively.     

Additions to the knowledge on fossil rodents of Uruguay (Mammalia: Rodentia)

Additions to the knowledge on fossil rodents of Uruguay (Mammalia: Rodentia). — This paper brings new information on fossil rodents of Uruguay. Four new species are described:Microcavia (M.) aua n. sp. (Caviidae),Ctenomys mesorhinus n. sp. (Octodontidae),Isostylomys intermedius n. sp. andIsostylomys magnus n. sp. (Dinomyidae), the latter from Argentina. Apart from this,Palmiramys waltheri Kraglievich, 1932, illustrated here for the first time, is considered a Lower Oligocene (Deseadan) ?Dasyproctidae. The first records for Uruguay ofEucardiodon cf.marshi (Ameghino) (Hydrochoeridae), and +Holochilus brasiliensis (Desmarest) are reported.     

Geomorphometric differences among four species of Microtus in Turkey (Mammalia: Rodentia)

In order to determine the phenotypic associations of four morphologically similar species of Microtus occurring in Turkey, we applied landmark-based shape analysis. The skulls of Microtus anatolicus, M. dogramacii, M. guentheri and M. levis (= M. rossiaemeridionalis) were found to differ significantly in terms of both size and shape. M. guentheri had the biggest skull, while M. levis had the smallest. Sexual dimorphism was found in the shape of the skull in M. dogramacii and M. levis. The tympanic bulla area is enlarged in M. anatolicus compared to the other species. Mahalanobis distances (the distance between a point and the group mean, taking into account the within-group covariance-variance matrix) confirm the distinction of the arvalis group (M. levis) and socialis group (Microtus anatolicus, M. dogramacii, M. guentheri).