Anatomical and phylogenetic investigation of the genera Alabastrina Kobelt, 1904, Siretia Pallary, 1926, and Otala Schumacher, 1817 (Stylommatophora, Helicidae).

This study presents new insights in the anatomy of genital organs of some large helicid gastropods from northern Africa. The genetic analysis with the markers COI, 16S, H3, and 5.8 S rRNA+ITS2 reveales a high support for Alabastrina and Otala as separate evolutionary lineages within the Otalini. The position of Siretia as another separate lineage within the Otalini is discussed. "Tingitanaminetteidecussata" clusters within the O.xanthodon clade and confirms that the genus Tingitana can be synonymised with Otala. The genus Alabastrina differs from all other known genera by possession of a penial appendix. This character state is also found in topotypic A.tistutensis. Examination of the twin penial papilla system in Otala recovers a reduction of the proximal penial papilla in O.punctata. The position of Helixmurcica as a separate subspecies of O.lactea is not supported, and it is here considered to be a synonym of the latter species.

An annotated checklist of mammals of Kenya.

Kenya has a rich mammalian fauna. We reviewed recently published books and papers including the six volumes of Mammals of Africa to develop an up-to-date annotated checklist of all mammals recorded from Kenya. A total of 390 species have been identified in the country, including 106 species of rodents, 104 species of bats, 63 species of even-toed ungulates (including whales and dolphins), 36 species of insectivores and carnivores, 19 species of primates, five species of elephant shrews, four species of hyraxes and odd-toed ungulates, three species of afrosoricids, pangolins, and hares, and one species of aardvark, elephant, sirenian and hedgehog. The number of species in this checklist is expected to increase with additional surveys and as the taxonomic status of small mammals (e.g., bats, shrews and rodents) becomes better understood.

Rediscovery of the type series of the Sacred Shrew, Sorex religiosus I. Geoffroy Saint-Hilaire, 1826, with additional notes on mummified shrews of ancient Egypt (Mammalia: Soricidae).

In 1826, Isidore Geoffroy Saint-Hilaire described the Sacred Shrew, Sorex religiosus [= Crocidura religiosa] from a series of 22 embalmed individuals that comprised a portion of the Italian archeologist Joseph Passalacqua's collection of Egyptian antiquities from an ancient necropolis near Thebes, central Egypt. Living members of the species were not discovered until the beginning of the 20th century and are currently restricted to the Nile Delta region, well north of the type locality. In 1968, the type series of S. religiosus was reported lost, and in 1978, a neotype was designated from among a small collection of modern specimens in the Natural History Museum, London. Our investigations have revealed, however, that the type series is still extant. Most of the specimens used by I. Geoffroy Saint-Hilaire to describe S. religiosus still form part of the Passalacqua Collection in the Ägyptisches Museum, Berlin, Germany. We summarize the taxonomic history of S. religiosus, review the history of the Passalacqua collection, and explain why the type series was thought to have been lost. We designate an appropriate lectotype from among the original syntypes of S. religiosus in the Ägyptisches Museum. Our examination of the shrew mummies in the Passalacqua collection also yielded a species previously unrecorded from either ancient or modern Egypt: Crocidura pasha Dollman, 1915. Its presence increases the number of soricid species embalmed in ancient Egypt to seven and provides additional evidence for a more diverse Egyptian shrew fauna in the archeological past. Finally, we provide details that will assist in better understanding the variety of mummification procedures used to preserve animals in ancient Egypt.

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa.

The spatial subdivision of species often plays a pivotal role in speciation. Across their entire range, species are rarely panmictic and crucial consequences of spatial subdivision are (1) random genetic drift including historical factors, (2) uniform selection, and (3) divergent selection. Each of these consequences may result in geographic variation and eventually reproductive isolation, but their relative importance in speciation is still unclear. In this study, we used a combination of genetic, morphological, and climatic data to obtain a comprehensive picture of differentiation among three closely related, parapatrically distributed taxa of the land snail genus Theba occurring along the Atlantic coasts of South Morocco and Western Sahara. We conducted Mantel and partial Mantel tests to relate phenotypic and genotypic variation of these species to geography and/or climate. As null hypothesis for an evolutionary scenario, we assumed nonadaptive speciation and expected a pattern of isolation by distance among taxa. Rejection of the null hypothesis would indicate isolation by environment due to adaptation. Generally, genetic drift plays an important role but is rarely considered as sole driver of speciation. It is the combination of drift and selection that predominantly drives speciation. This study, however, provides a potential example, in which nonadaptive speciation, that is, genetic drift, is apparently the main driver of shaping the diversity of Theba in NW Africa. Restriction of gene flow between populations caused by geographic isolation probably has played an important role. Climate oscillations during the Plio- and Pleistocene may have led to repeated ecological changes in NW Africa and disruptions of habitats promoting differentiation by geographic isolation. The inferred evolutionary scenario, however, did not fully explain the incongruence between the AFLP- and mtDNA-tree topologies. This incongruence might indicate past hybridization among the studied Theba forms.

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.

A redescription of the Long-tailed Nesokia, Nesokia bunnii, and designation of a neotype (Rodentia: Muridae).

Long-tailed Nesokia, Nesokia bunnii, is a large rat restricted to the Mesopotamian marshes in Basra Province in southern Iraq. The species is known from five museum vouchers collected between March 1974 and January 1977. The type and the paratype, deposited in the Natural History Research Centre and Museum, University of Baghdad, Iraq, were destroyed during War on Iraq in 2003. By studying morphological details on three museum specimens in the Senckenberg Institution, Frankfurt a. M., Germany, we show that N. bunnii is unique among the Bandicoot rats (Nesokia and Bandicota) in having (1) rufous dorsal pelage, (2) facial mask of rufous, dark brown, grey and whitish areas, (3) whitish belly which is clearly demarcated along flanks, (4) ventral hairs white to bases, (5) woolly underfur, (6) long front claws, and (7) large tail annulation. Similar to N. indica, but in contrast to Bandicota, N. bunnii displays short incisive foramina, posterior margin of hard palate which terminates at the level of the third molar, and robust, hypsodont and laminate molars which lack posterior cingula. To objectively define the taxon we designate a neotype, which was collected at Saraifa, 30 km north of Qurna, Iraq. Our study highlights the importance of museum collections in documenting biodiversity and the indifference of decision makers and international institutions regarding their safe future.

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.

Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa.

BACKGROUND: This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. RESULTS: The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. CONCLUSIONS: Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex.

Early and middle holocene hunter-gatherer occupations in western Amazonia: the hidden shell middens.

We report on previously unknown early archaeological sites in the Bolivian lowlands, demonstrating for the first time early and middle Holocene human presence in western Amazonia. Multidisciplinary research in forest islands situated in seasonally-inundated savannahs has revealed stratified shell middens produced by human foragers as early as 10,000 years ago, making them the oldest archaeological sites in the region. The absence of stone resources and partial burial by recent alluvial sediments has meant that these kinds of deposits have, until now, remained unidentified. We conducted core sampling, archaeological excavations and an interdisciplinary study of the stratigraphy and recovered materials from three shell midden mounds. Based on multiple lines of evidence, including radiocarbon dating, sedimentary proxies (elements, steroids and black carbon), micromorphology and faunal analysis, we demonstrate the anthropogenic origin and antiquity of these sites. In a tropical and geomorphologically active landscape often considered challenging both for early human occupation and for the preservation of hunter-gatherer sites, the newly discovered shell middens provide evidence for early to middle Holocene occupation and illustrate the potential for identifying and interpreting early open-air archaeological sites in western Amazonia. The existence of early hunter-gatherer sites in the Bolivian lowlands sheds new light on the region's past and offers a new context within which the late Holocene "Earthmovers" of the Llanos de Moxos could have emerged.

A new hero emerges: another exceptional mammalian spine and its potential adaptive significance.

The hero shrew's (Scutisorex somereni) massive interlocking lumbar vertebrae represent the most extreme modification of the vertebral column known in mammals. No intermediate form of this remarkable morphology is known, nor is there any convincing theory to explain its functional significance. We document a new species in the heretofore monotypic genus Scutisorex; the new species possesses cranial and vertebral features representing intermediate character states between S. somereni and other shrews. Phylogenetic analyses of DNA sequences support a sister relationship between the new species and S. somereni. While the function of the unusual spine in Scutisorex is unknown, it gives these small animals incredible vertebral strength. Based on field observations, we hypothesize that the unique vertebral column is an adaptation allowing these shrews to lever heavy or compressive objects to access concentrated food resources inaccessible to other animals.

Radiating on oceanic islands: patterns and processes of speciation in the land snail genus Theba (Risso 1826).

Island radiations have played a major role in shaping our current understanding of allopatric, sympatric and parapatric speciation. However, the fact that species divergence correlates with island size emphasizes the importance of geographic isolation (allopatry) in speciation. Based on molecular and morphological data, we investigated the diversification of the land snail genus Theba on the two Canary Islands of Lanzarote and Fuerteventura. Due to the geological history of both islands, this study system provides ideal conditions to investigate the interplay of biogeography, dispersal ability and differentiation in generating species diversity. Our analyses demonstrated extensive cryptic diversification of Theba on these islands, probably driven mainly by non-adaptive allopatric differentiation and secondary gene flow. In a few cases, we observed a complete absence of gene flow among sympatrically distributed forms suggesting an advanced stage of speciation. On the Jandía peninsula genome scans suggested genotype-environment associations and potentially adaptive diversification of two closely related Theba species to different ecological environments. We found support for the idea that genetic differentiation was enhanced by divergent selection in different environments. The diversification of Theba on both islands is therefore best explained by a mixture of non-adaptive and adaptive speciation, promoted by ecological and geomorphological factors.

Paleogenetic analyses reveal unsuspected phylogenetic affinities between mice and the extinct Malpaisomys insularis, an endemic rodent of the Canaries.

BACKGROUND: The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14(th) century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. CONCLUSION/SIGNIFICANCE: This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse.

Diet of the extinct Lava mouse Malpaisomys insularis from the Canary Islands: insights from dental microwear.

Malpaisomys insularis is a mouse-like rodent endemic to the eastern Canary Islands. It became extinct during the fourteenth century. It was a remarkable species living under hyperarid conditions. A dental microwear analysis was performed in order to determine its former diet. The elevated number of fine scratches found in Malpaisomys molars suggests that it consumed a significant part of Poaceae, grass consumption leaving the most distinctive features on dental wear facets. A graminivorous diet with a high amount of abrasive items is in agreement with the broad teeth of Malpaisomys, considered as adapted to grass consumption. However, in the absence of potential competitors over its native range, it is likely that Malpaisomys also foraged on dicots to meet higher nutrient and energetic requirements. The ecology of Malpaisomys is discussed from these results in the context of the desertic climatic conditions of the eastern Canary Islands and with a special concern on its small body size in contrast to other large-sized island murine species such as the giant rats of the central Canary Islands.

Evolutionary diversification of the genus Theba (Gastropoda: Helicidae) in space and time: a land snail conquering islands and continents.

Among oceanic islands, the Canary Islands offer exceptional opportunities for studying speciation processes due to their habitat diversity and well documented geological history. Based on a combined COI+ITS1 data set for more than 140 specimens, we studied the diversification of the land snail genus Theba on the Canary Islands and adjacent African and European continental areas. Phylogenetic analyses resulted in the recognition of 18 genetically distinct clades including at least three new species. Divergence time estimates suggested an evolution of Theba in the Canarian archipelago and an initial radiation on the three eastern-most islands during the Late Oligocene/Early Miocene. Despite the close proximity of NW Africa to the Canary Islands, the main mode of diversification was intra-archipelago speciation rather than independent colonization of the islands from the mainland. Notably, species from Morocco are nested among species from the Canary Islands, indicating re-colonization of the continent from the islands. The re-colonization of NW Africa occurred during the Middle Miocene and led to a remarkable continental radiation.

Body shape and life style of the extinct Balearic dormouse Hypnomys (Rodentia, Gliridae): new evidence from the study of associated skeletons.

Hypnomys is a genus of Gliridae (Rodentia) that occurred in the Balearic Islands until Late Holocene. Recent finding of a complete skeleton of the chronospecies H. morpheus (Late Pleistocene-Early Holocene) and two articulated skeletons of H. cf. onicensis (Late Pliocene) allowed the inference of body size and the calculation of several postcranial indexes. We also performed a Factorial Discriminant Analysis (FDA) in order to evaluate locomotory behaviour and body shape of the taxa. Using allometric models based on skull and tooth measurements, we calculated a body weight between 173 and 284 g for H. morpheus, and direct measurements of articulated skeletons yielded a Head and Body Length (HBL) of 179 mm and a Total Body Length of 295 mm for this species. In addition to the generally higher robustness of postcranial bones already recorded by previous authors, H. morpheus, similar to Canariomys tamarani, another extinct island species, displayed elongated zygopodium bones of the limbs and a wider distal humerus and femur than in an extant related taxon, Eliomys quercinus. Indexes indicated that Hypnomys was more terrestrial and had greater fossorial abilities than E. quercinus. This was also corroborated by a Discriminant Analysis, although no clear additional inference of locomotory abilities could be calculated.

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene.

The phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus.

Phylogeographical footprints of the Strait of Gibraltar and Quaternary climatic fluctuations in the western Mediterranean: a case study with the greater white-toothed shrew, Crocidura russula (Mammalia: Soricidae).

We used mitochondrial cyt b sequences to investigate the phylogenetic relationships of Crocidura russula (sensu lato) populations across the Strait of Gibraltar, western Europe, Maghreb, and the Mediterranean and Atlantic islands. This revealed very low genetic divergence between European and Moroccan populations. The application of a molecular clock previously calibrated for shrews suggested that the separation of European from Moroccan lineages occurred less than 60 000 bp, which is at least 5 million years (Myr) after the reopening of the Strait of Gibraltar. This means that an overwater dispersal event was responsible for the observed phylogeographical structure. In contrast, genetic analyses revealed that Moroccan populations were highly distinct from Tunisian ones. According to the molecular clock, these populations separated about 2.2 million years ago (Ma), a time marked by sharp alternations of dry and humid climates in the Maghreb. The populations of the Mediterranean islands Ibiza, Pantelleria, and Sardinia were founded from Tunisian populations by overwater dispersal. In conclusion, overwater dispersal across the Strait of Gibraltar, probably assisted by humans, is possible for small terrestrial vertebrates. Moreover, as in Europe, Quaternary climatic fluctuations had a major effect on the phylogeographical structure of the Maghreb biota.