Leonid A. Lavrenchenko

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa

BackgroundRodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete.ResultsWe performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene.ConclusionsWe discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.

A genetic study of natural hybridization between two forms of the common vole (Microtus arvalis) with the use of molecular and cytogenetic methods

222 Natural hybridization zones between earlier diverged populations provide broad opportunities for studying the gene flow dynamics and the consequences of disturbance of coadapted genomes [1]. The use of chromosome analysis methods in taxonomic studies of common voles of the Microtus arvalis group led to distinguishing karyologically discrete sibling species-the sibling vole M. rossiaemeridionalis (2 n = 54) and the common vole M. arvalis (2 n = 46) [2, 3]. The latter includes two karyomorphs differing both in the proportion of small acrocentric and metacentric chromosomes and the Y chromosome morphology: arvalis ( NF = 84) and obscurus ( NF = 72) [4–6]. These forms are widespread in the European part of Russia. They geographically replace one another [7] and are regarded by some authors as independent species [8]. A hybrid zone between them has been recently discovered in Vladimir oblast [9]. Until the end of 1990s, the karyotype remained the only criterion on the basis of which differential diagnostics of sibling species and karyomorphs of common voles could be performed. Recent data on the mitochondrial gene of cytochrome b (based primarily on samples of M. arvalis s. lat., collected outside of Russia) are indicative of a significant level of genetic differentiation between both M. rossiaemeridionalis and M. arvalis and the two karyomorphs of 46-chromosome voles [10]. The results of analysis of this gene showed that forms arvalis and obscurus are clearly distinct throughout their ranges, despite a certain level of their intraspecific differentiation [11]. The goal of this study was the search for a form-specific nuclear marker for common voles and the study of natural hybridization between forms obscurus and arvalis using cytogenetic and molecular-genetic methods. For the first time, the structure of the hybrid zone between these forms was studied using chromosome, nuclear, and mitochondrial markers. The results of this work revealed a fairly unusual combination of characteristics of this zone, such as an almost complete absence of “pure” representatives of initial parental forms and an obvious deficit of first-generation hybrids.

Genomic versus chromosomal polytypy in studies of mitochondrial and nuclear DNA markers in the Microtus arvalis group

Common voles of the Microtus arvalis group distributed over the territory of European Russia are represented by three karyotypic categories, i.e., sympatric sibling species with 2n = 46 and 54, and two allopatric karyoforms in one of them, 2n = 46. For each category, molecular markers were found. For two 46-chromosome forms (arvalis and obscurus), iDNA was for the first time studied in karyotyped and non-karyotyped specimens for a parapatric hybrid zone, where high diversity of intermediate karyotypes was recorded. Preferential migration of the mitochondrial markers in arvalis and significant differences in the cline width for chromosomal and nuclear markers in obscurus were shown. The hybrid zone examined exhibited unusual combination of such features as the practically complete absence of “pure” representatives of the original parental forms and a clear deficiency of the first generation hybrids. The mtDNA divergence for the arvalis and obscurus karyoforms (4.6%) is comparable to the lowest limit for interspecies differences within the large and complex genus Microtus.

The phylogeny and systematics of the endemic Ethiopian Lophuromys flavopunctatus species complex based upon random amplified polymorphic DNA (RAPD) analysis

Abstract Random amplified polymorphic DNA (RAPD) analysis was performed to clarify systematics and phylogenetic relationships within the Ethiopian endemic representatives of Lophuromys flavopunctatus species complex. Data were analysed by both phenetic (UPGMA) and phylogenetic (neighbor-joining (NJ) and maximum parsimony) procedures. NJ and maximum parsimony analyses yielded identical phylogenetic trees that demonstrate the basal position of L. melanonyx with L. brevicaudus splitting next and sister-group relationship for L. brunneus–L. chrysopus. This phylogenetic pattern is congruent with inferences from allozymes for the considered species suggesting early divergence of Afroalpine species and recent origin of forest taxa. Thus, the results demonstrate that RAPD-PCR might be a useful technique for phylogenetic analysis at the species levels in vertebrates. Controversial taxonomy of L. brevicaudus, L. brunneus and L. chrysopus is clarified, with their specific ranks confirmed on the basis of tree topology and genetic distances.

Phylogenetic position of a monotypic Ethiopian endemic rodent genus Megadendromus (Rodentia, Nesomyidae)

Abstract The taxonomic and phylogenetic position of the Nikolaus’s African climbing mouse (Megadendromus nikolausi), formerly known only from four specimens, remained for a long time ambiguous. Here, we report, for the first time, the phylogenetic analysis of this species using mitochondrial (cytochrome b) and nuclear (interphotoreceptor binding protein) gene sequences obtained from a new specimen recently caught in the Bale Mountains in south-eastern Ethiopia. Our analyses strongly suggest that the Nikolaus’s climbing mouse does not belong to a distinct monotypic genus, but to the genus Dendromus. The first karyotype description of this enigmatic Ethiopian endemic is presented. The diploid set comprises 18 pairs of bi-armed chromosomes, 2N=36, one of the lowest diploid numbers reported for the genus Dendromus (2N=30–52). Moreover, the phylogenetic analysis reveals that another very distinctive Ethiopian endemic, Dendromus lovati, sometimes placed in a subgenus Chortomys, occupies an internal position within Dendromus s.s. The results suggest that the Ethiopian Plateau is an important center of high diversity and adaptive radiation for the genus Dendromus. The conservation status of M. nikolausi is assessed.

Diversity of shrews in Ethiopia, with the description of two new species of Crocidura (Mammalia: Lipotyphla: Soricidae)

Two new species of white-toothed shrews, Crocidura afeworkbekelei and Crocidura yaldeni, are described from southern Ethiopia. Comparisons are made with other species of Crocidura known to occur in Ethiopia. A list of 28 species of shrews known from Ethiopia is provided, 10 of which (including both newly described species) are currently considered to be endemic to Ethiopia. The endemic shrew fauna consists of forest and montane species known to occur within the altitudinal range of 1200-4050 m a.s.l. The remarkable number of endemic species of Crocidura shows that the Ethiopian Plateau is an important centre of diversity and adaptive radiation of the genus. Current cytogenetic and molecular data support the monophyly of most species of Crocidura endemic to Ethiopia.

The role of hybrid zones in speciation: A case study on chromosome races of the house mouse Mus domesticus and common shrew Sorex araneus

Although diverse complexes of chromosome races are of rather rare occurrence in mammals, this does not reduce their importance to an insignificant phenomenon unworthy of studying as a unique case without direct analogy. Moreover, these complexes represent virtually ideal models for estimation of the impact of hybridization on the process of microevolution. The chromosome races are characterized by an almost zero level of molecular genetic differentiation and well-defined distinctions between them, which are usually associated only with chromosome rearrangements. This review shows the valuable contribution of the studies on Sorex araneus and Mus domesticus chromosome Robertsonian systems to our understanding of the varied impacts of hybridization on the speciation process. It particularly promotes a better understanding of evolutionary phenomena such as the “reinforcement” of reproductive isolation in secondary contact zones between divergent populations, speciation without geographic separation (“divergence with gene flow”), and “zonal raciation.”

Shrews (Crocidura spp.) endemic to Ethiopia: Recent adaptive radiation of an ancient lineage

57 Twenty-eight out of 30 species of the family Soricidae living in Ethiopia belong to the genus Crocidura. Eleven of them are endemic to this country; they are either forest (seven species) or mountain (four species) forms. All these endemic species of Crocidura have primitive characters of the cranial structure but exhibit a striking diversity of morphological characteristics within this, generally rather homogeneous, genus. Cytogenetic analysis that we performed earlier [1] showed that all karyologically studied Ethiopian endemics except C. macmillani (2 n = 28) (including C. bottegoides, C. glassi, C. thalia, C. harenna, C. lucina, Crocidura sp. A, and Crocidura sp. B) had structurally similar karyotypes (2 n = 36, NF = 52–56). The chromosome set of C. macmillani (2 n = 28, NFa = 52), which entirely consists of biarmed elements, is probably derivative of the 36-chromosome karyotype of the remaining Ethiopian endemics; it may have resulted from Robertsonian translocations of acrocentric chromosomes in this original karyotype. These results were rather unexpected, because the karyotypes of most African species of Crocidura have high diploid numbers (on average, 2 n = 50, NF > 60). In contrast, most representatives of this genus inhabiting the Palearctic region and Southeast Asia have karyotypes of 40 or fewer chromosomes and relatively low fundamental numbers [2]. Although African species of Crocidura are exceptionally numerous and karyologically diverse, only two taxa of Crocidura with 2 n = 36 are known to inhabit the Afrotropical region outside Ethiopia: C. cf. bottegi and C. luna (NF = 56) [2]. We demonstrated that these species live in Ethiopia too. Interestingly, the karyotype structures of C. canariensis (endemic to the Canary Islands), C. sicula (endemic to Sicily and Malta), and C. tarfayaensis inhabiting southwestern Morocco are almost identical to those of 36-chromosome Ethiopian endemics [3–6]. Note that the chromosome sets of these species are strikingly similar to the original, ancestral chromosome set of the genus Crocidura (2 n = 38, NF = 54–58, Xm, Yst) reconstructed on the basis of chromosome banding homeology [2]. Phylogenetic studies based on analyses of allozyme data [7] and combined mitochondrial and nuclear gene sequences (a total of 3577 bp) [8] have demonstrated that the genus Crocidura comprises two main clades corresponding to Eurasian and Afrotropical species.

An Assessment of the Systematics of the Genus Desmomys Thomas, 1910 (Rodentia: Muridae) Using Mitochondrial DNA Sequences

We analyzed two mitochondrial gene fragments to assess genetic divergence within the genus Desmomys endemic to Ethiopia and its phylogenetic relationships with related genera. The phylogenetic analysis supported the monophyly of the Arvicanthini-Otomyini group and revealed that Stochomys is clearly a member of Arvicanthini. Our study demonstrated that D. harringtoni and D. yaldeni belong to remarkably different mitochondrial lineages, the estimated divergence time between them is 4.10–5.38 Myr. Such early splitting of specialized forest dweller, D. yaldeni, from its sole congener supposes a more ancient formation of some elements of Ethiopian forest rodent fauna than is assumed today.

POSSIBLE KARYOLOGICAL AFFINITIES OF SMALL MAMMALS FROM NORTH OF THE ETHIOPIAN PLATEAU

Representatives of eight genera of Ethiopian rodents were collected and their chromosome characteristics were analyzed for the first time in the northern montane part of the country (between Tana Lake and Mt Guna, altitudes from 1800 to 3800 m a.s.l. at latitudes between 11–12° N). Even preliminary chromosome analysis gives rich empirical materials for the correction of current systematic definitions, interpretation of endemic taxa and evaluation of possible relationships with the already known karyotypic forms in Ethiopia and abroad. As a result of this study, four new karyotypes are manifested and five karyotypic descriptions already known for Ethiopian species are confirmed.