Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae : Murinae : Otomyini) : revision of the Otomys typus complex

We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.Nous avons combiné un ensemble de données, biogéographiques craniodentaires, morphométriques (linéaires et géométriques; 233 crânes), cytogénétiques (caryotypes de 18 individus) et moléculaires (ADN mitochondrial: 44 séquences de cytochrome b et 21 séquences de 12 rRNA) afin d’évaluer les délimitations d'espèces au sein d’Otomys typus s.l. (Muridae: Murinae: Otomyini), un complexe d’espèces distribué à travers les zones alpestres de l'Éthiopie et d'Afrique de l'Est. Nos résultats 1) confirment le statut spécifique d'O. dartmouthi, O. jacksoni, O. orestes et O. uzungwensis, des formes dont la synonymie avec typus s.l. a récemment été infirmée, 2) soutiennent l'élévation au statut d’espèce de quatre autres formes alpestres (O. fortior, O. helleri, O. thomasi et O. zinki), 3) permettent d’identifier trois nouvelles espèces supplémentaires (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.), et 4) nous permettent de redéfinir O. typus s.s. comme une espèce restreinte à certaines montagnes à l'ouest de la Vallée du Rift en Éthiopie (les montagnes Simien et Guna au nord, s'étendant aux pays montagneux du bord occidental de la vallée du Rift). L'interprétation phylogénétique des séquences de cytochrome b démontre clairement que la forme alpestre autrefois incluse dans O. typus s.l. est apparue de façon indépendante à de hautes altitudes sur plusieurs massifs montagneux en Afrique de l'Est et du Nord-Est. Bien que généralement adaptées à la végétation de haute altitude, de telles espèces alpestres sont écologiquement distinctes les unes des autres. Les différentiations morphométrique, génétique et écologique au sein des populations regroupées de façon incorrecte sous les noms O. tropicalis et O. typus reflètent plus parcimonieusement une diversification régionale suivant des gradients altitudinaux, plutôt qu’unecolonisation multiple, successive par différentes formes ancestrales d'Afrique du Sud, comme supposé antérieurement. Bien qu'incomplètes et préliminaires, les données obtenues pour O. tropicalis indiquent qu’il constitue aussi un complexe d'espèces. Plusieurs lignes de recherche sont envisagées afin de réévaluer son statut polyphylétique. Nos résultats, ajoutés à d'autres études taxinomiques récentes d'Otomys, élèvent sensiblement le niveau d'endémisme en l'Afrique de l'Est et soulignent l’importancedes hautes terres de l'est de l'Afrique dans la diversification continentale des Otomyini.We gratefully acknowledge the financial assistance of the Smithsonian Institution Short Term Visitor Award (in 2006), and a South African National Research Foundation Grant (between 2005 and 2007), which allowed P.J.T. to visit and study important North American and European museum collections of Otomys.http://www.mapress.com/zootaxa/nf201

The naked truth:a comprehensive clarification and classification of current 'myths' in naked mole-rat biology

The naked mole-rat (Heterocephalus glaber) has fascinated zoologists for at least half a century. It has also generated considerable biomedical interest not only because of its extraordinary longevity, but also because of unusual protective features (e.g. its tolerance of variable oxygen availability), which may be pertinent to several human disease states, including ischemia/reperfusion injury and neurodegeneration. A recent article entitled 'Surprisingly long survival of premature conclusions about naked mole-rat biology' described 28 'myths' which, those authors claimed, are a 'perpetuation of beautiful, but falsified, hypotheses' and impede our understanding of this enigmatic mammal. Here, we re-examine each of these 'myths' based on evidence published in the scientific literature. Following Braude et al., we argue that these 'myths' fall into four main categories: (i) 'myths' that would be better described as oversimplifications, some of which persist solely in the popular press; (ii) 'myths' that are based on incomplete understanding, where more evidence is clearly needed; (iii) 'myths' where the accumulation of evidence over the years has led to a revision in interpretation, but where there is no significant disagreement among scientists currently working in the field; (iv) 'myths' where there is a genuine difference in opinion among active researchers, based on alternative interpretations of the available evidence. The term 'myth' is particularly inappropriate when applied to competing, evidence-based hypotheses, which form part of the normal evolution of scientific knowledge. Here, we provide a comprehensive critical review of naked mole-rat biology and attempt to clarify some of these misconceptions

A contribution to the systematics of Desmomys Thomas, 1910 (Rodentia, Muridae) with the description of a new species

Volume: 50Start Page: 313End Page: 32

Crocidura yaldeni Lavrenchenko, Voyta & Hutterer, 2016, sp. nov.

<i>Crocidura yaldeni</i> sp. nov. <p>Figs. 7 A, 8A, 9A, 10; Table 2.</p> <p> <i>Crocidura</i> sp. B: Bannikova <i>et al</i>., 2001: 56.</p> <p> <i>Crocidura</i> sp. B: Bannikova <i>et al</i>., 2005: 47.</p> <p> <i>Crocidura</i> sp. B: Lavrenchenko <i>et al</i>., 2009: 57.</p> <p> <b>Holotype</b>. ZMMU S-165342; adult male, dry skin and skull; collector's number 30; collected by L.A. Lavrenchenko on 16 April 1997.</p> <p> <b>Type locality</b>. Beletta Forest, south-western Ethiopia, 07º34'N, 036º31'E, 1900 m a.s.l.</p> <p> <b>Paratypes</b>. ZMMU S-165340 (adult female, dry skin and skull, collector's number 20); ZMMU S-165341 (adult male, dry skin and skull, collector's number 28); ZMMU S-165343 (adult male, dry skin and skull, collector's number 35; Fig. 8 A); all three specimens from the type locality collected by L.A. Lavrenchenko between 13 and 19 April 1997.</p> <p> <b>Diagnosis</b>. A large-sized, greyish-brown <i>Crocidura</i> similar in external measurements (HB, TL) to <i>C. thalia</i> but slightly larger, on average, in cranial size (Table 2). Distinguished from the latter species by the following features: moderately longer hindfoot and claws; relatively uniformly colored tail; bristle hairs of tail bicolored and longer; skull large; nasal aperture wide; dorsal profile of skull looks concave at the midpoint and, slightly convex above the upper tooth row (Fig. 8, A); upper first incisor with a hook-like apex; lingual outline of the second upper molar with a distinct symmetric incision (Fig. 9, A1-a); second and third upper molar in firmly contact (Fig. 9, A1-b); occlusal outline of the third upper molar more undulated (Fig. 9, A1-c); hypoconulids of the lower molars visible in medial view (Fig 9, A2-d); postcingulid of m3 forming a notch (Fig. 9, A3-e).</p> <p> <b>Description</b>. Large-sized <i>Crocidura</i> (head and body length 84.0– 99.5 mm; here regarded as large-sized shrew in comparison to examined species) with a moderately long tail, ranging between 62.2–77.6% of head and body length. Dorsal pelage grey-brown with pale ochre shades (differs from <i>C. thalia</i> in slightly less intensive shades); dorsal hairs grey at base, brown at tip. Ventral pelage blackish-grey with pale ochre wash; ventral hairs dark grey at base, pale-yellowish at tip. Dorsal surface of fore- and hindfoot brownish. Tail uniformly colored, dark grey-brown above and brown below. Bristle hairs are long, dark-grey at base, pale-grey at tip, and present along the full length of the tail.</p> <p> Skull (Fig. 8, A) with a long rostrum and wide braincase. The rostral part is distinctly inflated (similar to <i>C. thalia</i> and differs from others Ethiopian endemic and Afromontane-Afroalpine species). The nasal aperture is wide; the posterior margin of the aperture has no medial tip. The dorsal outline of the orbital parts is slightly flexed. The lateral profile of the braincase is slightly angulated (Fig. 8, A-a). The nuchal crests are well-developed; their postero-lateral ends are prolonged and joint with noticeable paraoccipital processes (Fig. 8, A-pp). The sagittal crest is faint (in adult specimens); the temporal line is clearly recognizable. Mandible with broad body; its lower margin running in a shallow convex inward curve; body achieving its maximum depth below p4–m3. Coronoid spicule massive. External temporal fossa well-developed and wide. Angular process with hooked tip (Fig. 8, A).</p> <p>First upper incisor (I1) is robust; the apex (partly worn) is comparably long and hooked. The talon is welldeveloped, with distinct lingual ridge (lingual cingulum). The posterior ridge of the talon apex is stronglydeveloped. Lateral cingulum is weak and extending dorsally about 3/4 of I1 base height, with a faint bulge on the inferior part. Upper antemolars (A1–A3) are well-spaced, with a weak buccal cingulum and postero-buccal small cuspules. The upper first antemolar (A1) is very large; basal prominence of the anterior ridge is absent. The upper second antemolar (A2) is smallest, approximately 1/3 the height of A1, and 3/4 the height of A3. The upper third antemolar (A3) with straight buccal outline; the posterior edge is not strongly curved and connected with P4. The parastyle of the fourth upper premolar (P4) is well defined (tip partly worn); the upper margin (lateral view) is undulated and distinctly concave above parastyle and main cusp (Fig. 9, A4-f); three-quarters of the crown base is surrounded by a cingulum (Fig. 9, A4-g). The upper molars (M1–M2) are comparably wide. The lingual edge of the upper second molar (M2) has a well-developed and symmetrically curved incision (Fig. 9, A1-a). The upper third molar (M3) is relatively long and wide, in close contact with M2 (Fig. 9, A1-b), posterior edge is undulated (Fig. 9, A1-c).</p> <p>The first lower incisor (i1) is wide at base, with a blunt tip; the tooth is partly worn in all specimens, and therefore the denticulation of the cutting ridge is unknown. The second incisor (a1) is elongated, approximately 1/3 of the lower border of the tooth is in contact with i1; its posterior border is considerably (about 1/4) overlapped by the fourth lower premolar (p4); the postero-lateral ridge has a bulge. The basal prominence on the anterior ridge of p4 is present but indistinct, the lingual cusp (metaconid) is small. The hypoconulids of the lower molars (m1-m3) are well-developed and visible from the medial side of the teeth (Fig. 9, A2-d). The postcingulid of the lower third molar (m3) forms a visible notch buccal to the entoconid (Fig. 9, A3-e).</p> <p> The chromosomal set of <i>C. yaldeni</i> <b>sp. nov.</b> (2n = 36, NFa = 52) comprises 4 pairs of metacentric, 5 pairs of subtelocentric and 8 pairs of acrocentric autosomes. The X-chromosome is large metacentric; the Y-chromosome is small subtelocentric.</p> <p> <b>Variation</b>. Specimens of the type series are uniformly colored. In external and skull measurements S-165340 (female) is slightly smaller (HB = 84.0 mm, vs. 94.0– 99.5 mm in males). The qualitative characters are relatively homogeneous.</p> <p> <b>Comparisons</b>. This is a large-sized shrew, comparable in external size (HB, TL) to <i>C. thalia</i>, but slightly larger in cranial size (Table 2). It is substantially larger than the following Ethiopian Afromontane–Afroalpine species: <i>C. bottegoides,</i> <i>C.</i> cf. <i>bottegi</i> <i>,</i> <i>C.</i> cf. <i>hildegardeae</i> <i>, C. harenna, C. phaeura, C. parvipes, C. afeworkbekelei</i> <b>sp. nov.</b>, <i>C. lucina, C. macmillani, C. baileyi,</i> and <i>C. glassi.</i> The values of CI for all mentioned species range between 14.3–24.51 mm. The new species is considerably smaller than the other Ethiopian <i>Crocidura</i> species found in the Afromontane–Afroalpine biozones: <i>C. zaphiri</i> (HB = 105 mm, CI unknown; Churchfield & Jenkins, 2013a), and <i>C. olivieri</i> (CI = 32.0– 34.3 mm; Churchfield & Hutterer, 2013).</p> <p> The first PCA (see above, and Fig. 7 A) revealed significant differences between the groups of smaller, medium-sized and larger shrews along significant PC 1. Therefore, a further PCA was performed on two larger species and <i>C. glassi</i>.</p> <p> The third PCA (Fig. 10) of all 25 cranial and mandibular linear measurements reveals that the smaller <i>C. glassi</i> is clearly separated from the larger <i>C. thalia</i> and <i>C. yaldeni</i> <b>sp. nov.</b> along PC 1. This statistically significant axis accounted for 91.49% of the total variance and is most correlated with measures of the general size of the skull and mandible, such as CI (<i>r</i> = 0.674), PL (<i>r</i> = 0.316), MBL (<i>r</i> = 0.297) and COR (<i>r</i> = 2.788). The second component accounted only for a small percentage of the total variance (2.78%), and therefore was not significant. The PC 2 is most positively correlated with cranial width (PGW, <i>r</i> = 0.576; ZYG, <i>r</i> = 0.349; GW, <i>r</i> = 0.261). As can be seen from Fig. 10, <i>C. thalia</i> and <i>C. yaldeni</i> <b>sp. nov.</b> are clearly distinguished along the first two principal components. The difference between the two species along the first axis reflects the larger average size of <i>C. yaldeni</i> <b>sp. nov.</b>, while the second component is associated with changes in skull shape.</p> <p> Detailed comparison between similar in size species: <i>C. yaldeni</i> <b>sp. nov.</b> differs from <i>C. thalia</i> in: smaller P4s/ d, M3s/d; bigger M2L, M3W, M3L, UML, ZYG, PGW, LML; longer hindfoot and claws (Table 2); the uniformly colored tail (tail of <i>C. thalia</i> is mottled with brown and pale ochre); the bicolored and longer bristle hairs of tail; more massive I1; more compact upper antemolars row; stronger developed incision on lingual edge of the M2 (Fig. 9, A1-a vs. B1); the expression of hypoconulids on the lower molars (Fig. 9, A2-d).</p> <p> The standard karyotype is identical to that of two related species, <i>C. thalia</i> and <i>C. glassi</i> (Lavrenchenko <i>et al</i>., 1997). Phylogenetic analyses based upon repetitive DNA elements (taxonomic DNA fingerprint) and inter-SINE- PCR (IS-PCR) revealed that genetic distances between <i>C. yaldeni</i> <b>sp. nov.</b> and its two closest relatives, <i>C. thalia</i> and <i>C. glassi,</i> fell within the range usually recorded for interspecific genetic differentiation within <i>Crocidura</i> (Bannikova <i>et al</i>., 2001; Bannikova <i>et al</i>., 2005). The former analysis strongly supported that <i>C. yaldeni</i> <b>sp. nov.</b> is a sister species to <i>C. thalia</i>; in the latter analysis <i>C. thalia</i> and <i>C. glassi</i> had a tendency to form a clade against <i>C.</i></p> <p> <i>yaldeni</i> <b>sp. nov.</b> The phylogenetic analysis of an extended set of <i>Crocidura</i> species using mitochondrial cytochrome b gene sequences (Lavrenchenko et al., 2009) revealed that <i>C. yaldeni</i> <b>sp. nov.</b> and <i>C. macmillani</i> form the most basal branch of the group of Ethiopian endemics (including <i>C. glassi</i>, <i>C. thalia</i>, <i>C. lucina</i> and <i>C. baileyi</i>), whereas <i>C. thalia</i> appears as sister to <i>C. glassi</i>.</p> <p> <b>Distribution</b>. The new species has been found only in the Beletta Forest (07º34'N, 36º31'E, 1900 m a.s.l.). We failed to trap <i>C. yaldeni</i> <b>sp. nov.</b> in any other site of this forest and other humid Afromontane forest blocks of SW Ethiopia: the Sheko Forest (07°04'N, 35°30'E, 1930 m a.s.l.), the Dushi Area of the Godare Forest (07°21'N, 35°13'E, 1200 m a.s.l.), the Meti Area of the Godare Forest (07°17'N, 35°16'E, 1370 m a.s.l.) and the Inegawa Forest (07°25'N, 35°24'E, 2340 m a.s.l.). Therefore, the currently known distribution range of this new species is extremely small.</p> <p> <b>Habitat</b>. All four specimens of <i>C. yaldeni</i> <b>sp. nov.</b> were captured in the riverine variant of humid Afromontane forest on the bank of the small river (trees: <i>Schefflera abyssinica</i>, <i>Croton macrostacis</i>, <i>Allophylus abyssinicus</i>, <i>Aningeria altissima</i>, <i>Malacanta</i> <i>alnifolia</i>, <i>Phoenix reclinata</i>, <i>Brucea antiderinterica</i>, <i>Polyscias fulva</i>; small trees: <i>Vepris dainelii</i>, <i>Teclea nobilis</i>, <i>Dracaena afromontana</i>, <i>D. fragrans</i>; shrubs: <i>Coffea arabica</i>, <i>Canthium oligocarpum</i>, <i>Galiniera coffeoides</i>; climbers: <i>Embelia schimperi</i>, <i>Phychotria neglecta</i>; ferns: <i>Pteris dentatum</i>, <i>Asplenium sandersoni</i>, <i>Pleopeltis</i> sp.; herbs: <i>Afromomum</i> sp.). Three rodent species, <i>Lophuromys chrysopus</i> Osgood, <i>Mus mahomet</i> Rhoads, and <i>Stenocephalemys albipes</i> (Rueppell) were also collected at the same trapping site. All individuals of the new shrew were caught in Sherman live traps placed on the ground no more than 1 m from the river bank. Probably the very restricted range of <i>C. yaldeni</i> <b>sp. nov.</b> is associated with yet unknown habitat requirements, presumably more specific than 'river edge'. However, no morphological adaptations to some specific life style (including semi-aquatic adaptations) were observed.</p> <p> <b>Etymology</b>. The new species is named in honor of the late Dr. Derek W. Yalden (1940-2013), who has contributed greatly to our knowledge on Ethiopian small mammals (Fig. 11). As the vernacular name for the new species we propose Beletta Shrew.</p>Published as part of <i>Lavrenchenko, Leonid A., Voyta, Leonid L. & Hutterer, Rainer, 2016, Diversity of shrews in Ethiopia, with the description of two new species of Crocidura (Mammalia: Lipotyphla: Soricidae) in Zootaxa 4196 (1)</i>, DOI: 10.11646/zootaxa.4196.1.2, <a href="http://zenodo.org/record/167667">http://zenodo.org/record/167667</a&gt

Diversity and conservation of Ethiopian mammals: what have we learned in 30 years?

For over thirty years, the Mammal Research Group of Joint Ethio-Russian Biological Expedition (JERBE) studied diversity and evolution of Ethiopian mammals. The goal of the present paper is to review the most interesting results of the study and to summarize the present-day knowledge of the highly endemic mammalian fauna of Ethiopia. The obtained data revealed that the species diversity and the level of endemism of the Ethiopian small mammals could be far higher than was suspected before. One order, one family, four genera and 10 species were detected for the first time. Species rank of seven rodent taxa previously held in taxonomic synonymy was confirmed, all these newly recognized species were re-described. Eleven new endemic species were described de novo. In addition, 20 species of small mammals, belonging to 11 genera, were identified as new to science and await formal description. Totally, according to our obviously incomplete list, the Ethiopian mammal fauna consists of 311 species, and 55 of them are at present considered to be endemic to the country. The level of mammalian endemism in Ethiopia is much higher than in other African countries. Many of the endemic small mammals are potentially threatened because of their extremely limited distribution ranges and habitat destruction through agricultural expansion. In view of the fast habitat destruction in the country, taxonomic and evolutionary studies on Ethiopian small mammals are especially important and urgent. There is a high risk that some unknown endemic species will become extinct before they can be described and studied.Keywords/phrases: Conservation, Diversity, Endemism, Mammals, New specie

Three new karyotypes extend a Robertsonian fan in Ethiopian spiny mice of the genus Acomys I. Geoffroy, 1838 (Mammalia, Rodentia)

Three new karyotypes (2n=40, 44, 52) are described revealing what are probably new cryptic species of Ethiopian spiny mice. Two other diploid numbers have already been reported for the country (2n=36 and 68) and, overall, the five known karyotypic forms constitute a common lineage differentiated by a Robertsonian process. Such arrays of karyotypic forms are known as a ‘Robertsonian fan’. This view of the situation in Ethiopian Acomys I. Geoffroy, 1838 is based on standard chromosomal morphology that reveals a constant FN (68) and needs further investigation of chromosome homology by differential staining and/or molecular cytogenetic techniques as well as further molecular phylogenetic analysis

Notes on the bats (Chiroptera) collected by the joint Ethiopian-Russian biological expedition, with remarks on their systematics, distribution, and ecology

Volume: 52Start Page: 127End Page: 14

Uncovering the diversity of endemic Ethiopian fauna: complete mitochondrial genomes of four Lophuromys species (Rodentia, Muridae)

Complete mitochondrial genomes of four species of Ethiopian speckled brush-furred rats Lophuromys (L. chrysopus, L. menageshae, L. melanonyx, and L. simensis) were assembled for the first time. We provide data concerning the sequencing, assembly, and annotation of the obtained mitogenomes; compare two widely used circular-genome annotation tools (MITOS and MitoZ), and discuss relevant points concerning relationships within both Ethiopian Lophuromys and the Muridae family

Mitogenomics of the endemic Ethiopian rats: looking for footprints of adaptive evolution in sky islands

International audienc