Morphometric and morphological delineation of southern African species of Aethomys (Rodentia: Muridae)

Five species of African rock rats, Aethomys namaquensis, A. granti, A. silindensis, A. nyikae and A. chrysophilus, have to date been recognized in southern Africa. While the first three species are craniometrically well-delineated, morphometric analysis of cytogenetically known and other specimens of A. chrysophilus revealed that it comprises two sympatric, morphologically similar species, the nominate species and the newly recognized A. ineptus. This is in agreement with observations on cranial morphology and earlier investigations involving cytogenetics, protein electrophoresis, and gross sperm and bacular morphology. Contrary to published reports, the Central African A. nyikae does not extend into southern Africa, and the single previous record from eastern Zimbabwe is probably based on a misidentification.     

Phylogeography of spiny mice (genus Acomys, Rodentia: Muridae) from the south-western margin of the Sahara with taxonomic implications

The present study aims to depict the overall pattern of Acomys history in south-western Sahara. We tested the specific predictions that: (1) several mitochondrial clades can be identified and that they coincide with the described species; (2) successive phases of desert expansion and contraction during the last 3 Myr have resulted in several phases of demographic expansion and population fragmentation in Acomys ; and (3) isolation-by-distance occurs. The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene and D-loop) were addressed in a survey of 90 individuals of Acomys from 38 localities. Our phylogeographical analyses show a strong genetic structure within western Saharan Acomys , with several phylogroups displaying non-overlapping geographic distributions. Restricted gene flow with isolation-by-distance was recorded and a signal of population expansion was detected within several clades. We suggest that during arid or semi-arid paleoclimatic periods, when large sandy areas were present, Acomys was restricted to rocky massifs, whereas, in more humid periods, when savannah and/or steppe habitat prevailed, this species was able to disperse and to survive outside rocky areas because food resources were abundant. Based on a comprehensive sampling and the use of an integrative approach (i.e. combining cytogenetic, molecular and morphological data), we firmly propose that Acomys airensis should be considered as a junior synonym of Acomys chudeaui .  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 29–46.     

Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.     

Rapid chromosomal evolution in the mesic four‐striped grass rat Rhabdomys dilectus (Rodentia,Muridae) revealed by mtDNA phylogeographic analysis

The mesic four‐striped grass rat Rhabdomys dilectus De Winton, 1897 is distributed in mesic regions of southern and eastern Africa. We carried out a molecular and chromosomal study of the northernmost populations of the species to provide insight into the subspecific boundaries identified within the species and to describe its genetic structure in Eastern Africa. Maximum likelihood, maximum parsimony and neighbour‐joining methods were used to construct phylogenetic relationships among all the haplotypes belonging to the large part of the species range. Times of divergences were estimated assuming a relaxed molecular clock with two calibration points. We identified three well‐supported clades within R. dilectus. One basal clade corresponding to Rhabdomys d. chakae (2n = 48) is found in South Africa. Two additional sister clades corresponding to R. d. dilectus (2n = 48 and 2n = 46) are allopatrically distributed in southern and northern parts of the species range. Genetic divergence among the three clades is relatively high (ranges 4.2–5.7%). A very divergent new karyotype 2n = 38, FNa = 60 was found in two high‐altitude populations on Mt. Meru and Mt. Kilimanjaro. The karyotype differences consist in three Robertsonian fusions and one whole‐arm reciprocal translocation. Interestingly, the mtDNA phylogeny does not match with the diploid numbers. In fact, the 2n = 38 specimens form a monophyletic group within a clade that includes specimens with the 2n = 46 karyotype that appears as paraphyletic. We estimated the new karyotype originated in peripatric condition during the last phases of the Pleistocene. This study confirms the importance of chromosomal analysis in detecting taxonomic units and cryptic diversity in rodents.     

Species delimitation in the Acomys cahirinus–dimidiatus complex (Rodentia, Muridae) inferred from chromosomal and morphological analyses

Our earlier chromosome banding studies of Acomys cahirinus and Acomys dimidiatus (the latter long considered to be a subspecies of the former) revealed that, despite very close diploid numbers (36 vs. 38), these taxa possess sharply different karyotypes and undoubtedly belong to different species. In this context, the taxonomic status and the relationship between the two chromosomal forms in Sinai (2 n  = 36) and Israel (2 n  = 38), chromosomally homozygous across a vast range except for a very narrow hybrid zone, remain poorly documented. Neither of these forms have previously been studied by chromosome banding; thus, the exact nature of chromosomal differences as well as the species to which these forms should be assigned remain unknown. Here, we present the data on comparative G-banding analysis and morphometrics of Acomys from Israel, Sinai, and Saudi Arabia, and a hybrid obtained in laboratory crosses between latter two. The analysis revealed that karyotype of Acomys from Israel is identical to that of Acomys from Saudi Arabia and both are different from that of Acomys from Sinai by one Robertsonian fusion. Therefore, karyotypically, all three are very different from A. cahirinus . It follows from the study that Sinai and probably Arabian peninsula and Minor Asia must be excluded from geographical distribution of A. cahirinus , which is limited from West Sahara to Egypt along Nile river (except Sinai). Furthermore, the synthesis of chromosomal and recent molecular data suggests a phylogeographical scenario explaining the modern distribution of Acomys in the Sinai and Arabian peninsulas and permits the update of the taxonomic status of these populations.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 203–214.     

Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia: Muridae) in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Lemniscomys striatus and to evaluate the relative roles of ecological change, habitat patchiness, rivers and geological barriers in structuring patterns of diversity. Location Sub‐Saharan Africa. Methods The extent of phylogeographic patterns and molecular genetic diversity (cytochrome b gene) were addressed in a survey of 128 individuals of L. striatus from 42 localities. Using maximum parsimony, maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intraspecific relationships and tested hypotheses for historical patterns of gene flow within L. striatus. Results Our results identified four major geographical clades within L. striatus: a West African clade, a Benin‐Nigeria clade, a Central African clade, and an East African clade. Several subclades were identified within these four major clades. Restricted gene flow with isolation by distance was recorded, which is congruent with the low dispersal ability of such a small murid rodent. No clear signal of population expansion was detected within clades or subclades. Main conclusions The western rift system and the Volta and Niger rivers may have acted as long‐term extrinsic barriers to gene flow, resulting in the emergence of the four main clades of L. striatus. The observed pattern of mitochondrial variation observed within each clade probably results from late Pleistocene climatic and vegetation changes: during adverse conditions (forest expansion), L. striatus may have survived only in refugia, and then experienced range expansion under favourable conditions (savanna expansion).     

Taxonomic hypotheses regarding the genus Gerbillus (Rodentia,Muridae, Gerbillinae) based on molecular analyses of museum specimens

Methodological improvements now allow routine analyses of highly degraded DNA samples as found in museum specimens. Using these methods could be useful in studying such groups as rodents of the genus Gerbillus for which i) the taxonomy is still highly debated, ii) collection of fresh specimens may prove difficult. Here we address precise taxonomic questions using a small portion of the cytochrome b gene obtained from 45 dry skin/skull museum samples (from 1913 to 1974) originating from two African and three Asian countries. The specimens were labelled Gerbillus gerbillus, Gerbillus andersoni, Gerbillus nanus, Gerbillus amoenus, Gerbillus perpallidus and Gerbillus pyramidum, and molecular results mostly confirmed these assignations. The close relationship between Gerbillus nanus (Asian origin) and Gerbillus amoenus (African origin) confirmed that they represent vicariant sibling species which differentiated in allopatry on either side of the Red Sea. In the closely related Gerbillus perpallidus and Gerbillus pyramidum, specimens considered as belonging to one Gerbillus pyramidum subspecies (Gerbillus pyramidum floweri) appeared closer to Gerbillus perpallidus suggesting that they (Gerbillus pyramidum floweri and Gerbillus perpallidus) may represent a unique species, distributed on both sides of the Nile River, for which the correct name should be Gerbillus floweri. Furthermore, the three other Gerbillus pyramidum subspecies grouped together with no apparent genetic structure suggesting that they may not yet represent genetically differentiated lineages. This study confirms the importance of using these methods on museum samples, which can open new perspectives in this particular group as well as in other groups of interest.     

Phylogeny and phylogeography of squirrel monkeys (genus Saimiri) based on cytochrome b genetic analysis

Squirrel monkeys (genus Saimiri) are distributed over a wide area encompassing the Amazon Basin: French Guiana, Suriname, and Guyana, together with Western Panama and Western Costa Rica. The genus Saimiri includes a complex of species and subspecies displaying considerable morphological variation. Taxonomic and systematic studies have identified, in this genus, one to seven species comprising up to 16 subspecies. The phylogenetic relationships between these taxa are poorly understood. Molecular markers have yielded a consistent framework for the systematics of Central and South American Saimiri, identifying four distinct clades: S. oerstedii, S. sciureus, S. boliviensis, and S. ustus. Here, we reconsider the phylogenetic and biogeographic history of Saimiri on the basis of mitochondrial (mtDNA) sequence data, focusing mostly on individuals originating from the Amazon Basin. We studied 32 monkeys with well‐defined geographic origins and inferred the phylogenetic relationships between them on the basis of full‐length cytochrome b gene nucleotide sequences. The high level of gene diversity observed (0.966) is consistent with the high level of behavioral and morphological variation observed across the geographic range of the genus: 20 mtDNA haplotypes were identified with a maximum divergence of 4.81% between S. b. boliviensis and S. ustus. In addition to confirming the existence of the four clades previously identified on the basis of molecular characters, we suggest several new lineages, including S. s. macrodon, S. s. albigena, S. s. cassiquiarensis, and S. s. collinsi. We also propose new patterns of dispersion and diversification for the genus Saimiri, and discuss the contribution of certain rivers and forest refuges to its structuring. Am. J. Primatol. 72:242–253, 2010. © 2009 Wiley‐Liss, Inc.     

The molecular phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae) clarifies rodent host–hantavirus associations

Several species of the genus Oligoryzomys are natural hosts of different hantavirus genotypes affecting humans. The systematics of the genus is confusing, which complicates the identification of the rodent host and hence the potential endemic areas of hantavirus pulmonary syndrome. In this study, we analyse molecular data to infer phylogenetic relationships among Central and South American specimens of Oligoryzomys, and compare our results with previously published data on karyotypic, geographic distribution and host–virus associations to solve contradictory taxonomic reports. We identified 25 clades, each one corresponding to a different putative species. The phylogenetic trees show that Oligoryzomys longicaudatus is strongly related to the Oligoryzomys flavescens complex, which comprises four clades; Oligoryzomys nigripes is related to Oligoryzomys stramineus, Oligoryzomys vegetus is related to Oligoryzomys fulvescens from Central America, and Oligoryzomys brendae is the sister species of Oligoryzomys aff. destructor. We identified the following rodent host–hantavirus genotype relationships: O. longicaudatus–Andes; O. flavescens ‘West'–Bermejo; O. flavescens ‘East'–Lechiguanas; O. nigripes–Juquitiba; Oligoryzomys microtis–Rio Mamore and Rio Mamore‐3; Oligoryzomys chacoensis–Oran; Oligoryzomys costaricencis–Choclo; Oligoryzomys delicatus–Maporal; Oligoryzomys utiaritensis–Castelo dos Sonhos; Oligoryzomys sp. RT2012–Rio Mamore‐4; Oligoryzomys sp. (and not Oligoryzomys fornesi)–Anajatuba. This work, besides contributing to the development of prevention programmes for hantavirus epidemiology in Latin America, represents a comprehensive update of the systematics of the genus Oligoryzomys. © 2014 The Linnean Society of London     

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.     

Phylogeny and historical demography of economically important rodents of the genus Arvicanthis (Mammalia: Muridae) from the Nile Valley: of mice and men

The present study clarified the taxonomy, phylogeny and historical demography of semicommensal Nile rats ( Arvicanthis ) from the Nile Valley in Sudan. Nile rats are important crop pests and zoonotic disease reservoirs and are closely associated with agricultural settlements in the Nile Valley. Phylogenetic analysis of the complete cytochrome b gene (1140 bp) of 23 individuals from six localities in Sudan (from two previously recognized species, Arvicanthis niloticus and Arvicanthis testicularis ), supported the existence of only a single species, A. niloticus , from the Nile Valley. Historical demography of the Sudanese Nile Valley population inferred from mismatch coefficients indicated that an exponential population expansion event occurred approximately 144 000–288 000 years ago, corresponding in time with early human expansion and colonization from Africa to the Middle East, Europe, and the world. The inferred high level of gene flow and large size of Sudanese Nile populations of A. niloticus is consistent with historically recent (300 years ago) exponential human population growth and intense agricultural activity inferred from archaeological and historical evidence. Two African Arvicanthis clades were well supported by the broader phylogenetic analysis: (1) A. niloticus , Arvicanthis abyssinicus and Arvicanthis neumanni and (2) Arvicanthis rufinus and Arvicanthis ansorgei from western Africa. Within the first clade, divergence between lineages of A. niloticus s.s. from west and north-east Africa (8.9%) suggests specific recognition, but sampling of geographically intermediate localities is required. Based on hypothesized palaeodrainage and palaeoclimatic patterns, we propose a simple model for speciation of Arvicanthis in Africa.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 641–655.     

Comparative gastrointestinal morphology of three small mammalian insectivores: Acomys spinosissimus (Rodentia), Crocidura cyanea (Eulipotyphla), and Amblysomus hottentotus (Afrosoricida)

The gastrointestinal morphology was investigated in three mammalian insectivorous species, namely Acomys spinosissimus, Crocidura cyanea, and Amblysomus hottentotus. The aim of the study was to provide a comprehensive morphological comparison between the different species and to explore whether anatomical gastrointestinal adaptations are associated with the insectivorous diet of these species. The shape, proportional length, and proportional surface areas of the different gastrointestinal regions were recorded and compared in the three insectivores. Hematoxylin and Eosin (H&E) and Alcian Blue/Periodic Acid Schiff (AB/PAS) were used for morphological assessment. In all three species, the stomach was simple and uncompartmentalized. The internal aspect of the stomach in A. spinosissimus was hemi‐glandular, containing stratified squamous epithelium in the fundus, with glandular epithelium in the body and pyloric region. However, C. cyanea and A. hottentotus had wholly glandular stomachs. Paneth cells were not observed in the intestinal tracts of C. cyanea and A. hottentotus. Acomys spinosissimus was the only species studied that had a cecum. The proximal colonic region of A. spinosissimus had V‐shaped mucosal folds. Histologically, C. cyanea had villi throughout the entire gastrointestinal tract (GIT), whereas for A. hottentotus villi were not present in the most distal gastrointestinal regions. In both C. cyanea and A. hottentotus, longitudinal mucosal folds were present in the distal part of the colon. The GITs of C. cyanea and A. hottentotus showed little morphological differentiation namely, a simple, glandular stomach and the lack of a cecum. J. Morphol., 2013. © 2013 Wiley Periodicals, Inc.     

A new genus and species of long-clawed mouse (Rodentia: Muridae) from temperate rainforests of Chile

Morphological comparisons of long-clawed mice in southern South America reveal the existence of four genera, only three of which are named. The fourth genus is described and compared with Geoxus, Chelemys and Notiomys. External, cranial and dental characters indicate that the new mouse is most closely related to Geoxus , the raton topo or mole mouse. Geoxus and the new form may be distinguished using both qualitative and quantitative characters. The incipient specializations of the new mouse for fossorial life suggest that it represents an early offshoot along the line leading to the more highly specialized Geoxus. Discovery of a new mammalian genus in Chile, where naturalists have been active for more than two centuries, indicates the importance of continued biological surveys, even in ostensibly well-studied regions. The new mouse reinforces the strong differentiation of faunas inhabiting southern beech ( Nothofagus ) forests in South America, where generic endemism of rodents and marsupials reaches 67%.     

Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): evidence for introgression and incomplete lineage sorting

Although mitochondrial DNA markers have several properties that make them suitable for phylogeographic studies, they are not free of difficulties. Phylogeographic inferences within and between closely related species can be mislead by introgression and retention of ancestral polymorphism. Here we combine different phylogenetic, phylogeographic, and population genetic methods to extract the maximum information from the Liolaemus darwinii complex. We estimate the phylogeographic structure of L. darwinii across most of its distributional range, and we then estimate relationships between L. darwinii and the syntopic species L. laurenti and L. grosseorum. Our results suggest that range expansion of these lineages brought them into secondary contact in areas where they are presently in syntopy. Here we present the first evidence for introgression in lizards from temperate South America (of L. danwinii mitochondrial DNA into L. laurenti and L. grosseorum), and for incomplete lineage sorting (between L. darwinii and L. laurenti). We show that a combination of methods can provide additional support for inferences derived from any single method and thus provide more robust interpretations and narrow the range of plausible hypotheses about mechanisms and processes of divergence. Additional studies are needed in this group of lizards and in other codistributed groups to determine if Pleistocene climatic changes could be a general factor influencing the evolutionary history of a regional biota.     

Chromosomal and molecular characterization of Aethomys kaiseri from Zambia and Aethomys chrysophilus from Tanzania (Rodentia, Muridae)

Aethomys is a common and widespread rodent genus in the African savannas and grasslands. However, its systematics and taxonomy are still unclear as no study has covered the entire range. In fact it might not be a monophyletic genus and perhaps should be split into two subgenera, Micaelamys and Aethomys. In this paper, we present findings based on the cytogenetics and the entire cytochrome b sequence of two species from Zambia (A. kaiseri) and Tanzania (A. chrysophilus), and we compare them with the sequences of a South African species (A. namaquensis) and other allied muroid genera. Comparison of the banded chromosomes revealed complete G-band homology between the autosomes of the two species. However, the X and Y chromosomes clearly differ in size and in C- and G-banding, being much larger in A. kaiseri. Comparison of the cytochrome b sequences places the separation between A. kaiseri and A. chrysophilus at 4.49 Mya, a period of intense speciation in other African muroids. The resulting phylogeny strongly supports the idea of a paraphyletic group, suggesting the need to elevate the previously described subgenera to the genus rank.     

Phylogeography of Mus (Nannomys) minutoides (Rodentia,Muridae) in West Central African savannahs: singular vicariance in neighbouring populations

We studied the phylogeography of the strict savannah pygmy mice Mus (Nannomys) minutoides in West Central Africa. A total of 846 base pairs of the cytochrome b sequence were obtained for 66 individuals collected in Gabon, Cameroon, Republic of Congo and Central African Republic. These sequences were compared to those of M. minutoides from other African countries and to eight other species of the genus Mus. We performed maximum likelihood, Bayesian and nested clade analyses, as well as neutrality tests and time estimates. We show that M. minutoides is a well‐differentiated monophyletic species that separated from other pygmy mice 1.17 Myr ago. A distinct West Central African M. minutoides clade diverged early from the other African populations of the species, with a more recent common ancestor dating 0.14 Myr. West Central African populations are globally homogeneous, despite the present fragmentation of savannahs by the rain forest. However, our analyses show an unexpected vicariance between geographically close savannahs, embedded in the rain forest in Central Gabon. One of these populations is genetically more similar to very distant peripheral populations than to three closely neighbouring populations situated on both sides of the Ogooué River. A non‐river geographical barrier probably persisted in this area, durably isolating these local populations. This hypothesis about the history of the savannah landscape should be testable through the biogeographical analysis of other strict savannah small mammal species.