Between the Balkans and the Baltic : phylogeography of a common vole mitochondrial DNA lineage limited to Central Europe

The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential `northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe

Elastic Theory of Defects in Toroidal Crystals

We report a comprehensive analysis of the ground state properties of axisymmetric toroidal crystals based on the elastic theory of defects on curved substrates. The ground state is analyzed as a function of the aspect ratio of the torus, which provides a non-local measure of the underlying Gaussian curvature, and the ratio of the defect core-energy to the Young modulus. Several structural features are discussed,including a spectacular example of curvature-driven amorphization in the limit of the aspect ratio approaching one. The outcome of the elastic theory is then compared with the results of a numerical study of a system of point-like particles constrained on the surface of a torus and interacting via a short range potential.Comment: 24 pages, 24 figure

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

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Abstract Background Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept. Results The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia. Conclusions The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa