Mediterranean populations of the lesser white-toothed shrew (Crocidura suaveolens group): an unexpected puzzle of Pleistocene survivors and prehistoric introductions

Multilocus Analysis of Phylogenetic Relationships in the Crocidura suaveolens Sensu Lato Species Complex: A Comparison with Mitochondrial Data

Multilocus analysis was for the first time used to study the phylogeny of the Crocidura suaveolens s. l. species complex. Sequencing data for 16 nuclear genes indicated that several distinct forms exist within the species complex. The structure of the complex did generally not contradict its mitochondrial phylogeny. Siberian shrew showed certain specificity of the nuclear genome, but the degree of its genetic differentiation did not correspond to the species level. Relationships of Crocidura aff. suaveolens from South Gansu and Sichuan with other forms of the species complex were clarified. Shrews from Buryatia and Khentei also belong to this form, but their mtDNA apparently introgressed from C. shantungensis in the past. Hybridization of C. suaveolens s. str. with C. aff. suaveolens and C. güeldenstaedtii occurred recently. Due to multiple introgression events in the history of C. suaveolens s. l., a far larger set of loci is necessary for the analysis of the phylogenetic relationships between its forms.

In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel

Caves have long been recognized as a window into the mechanisms of diversification and convergent evolution, due to the unique conditions of isolation and life in the dark. These lead to adaptations and reduce dispersal and gene flow, resulting in high levels of speciation and endemism. The Israeli cave arachnofauna remains poorly known, but likely represents a rich assemblage. In a recent survey, we found troglophilic funnel-web spiders of the genus Tegenaria in 26 caves, present mostly at the cave entrance ecological zone. In addition, we identified at least 14 caves inhabited by troglobitic Tegenaria, which are present mostly in the twilight and dark ecological zones. Ten of the caves, located in the north and center of Israel, are inhabited by both troglophilic and troglobitic Tegenaria. These spiders bear superficial phenotypic similarities but differ in the levels of eye reduction and pigmentation. To test whether these taxa constitute separate species, as well as understand their relationships to epigean counterparts, we conducted a broad geographic sampling of cave-dwelling Tegenaria in Israel and Palestine, using morphological and molecular evidence. Counterintuitively, our results show that the troglobitic Tegenaria we studied are distantly related to the troglophilic Tegenaria found at each of the cave entrances we sampled. Moreover, seven new troglobitic species can be identified based on genetic differences, eye reduction level, and features of the female and male genitalia. Our COI analysis suggest that the Israeli troglobitic Tegenaria species are more closely related to eastern-Mediterranean congeners than to the local sympatric troglophile Tegenaria species, suggesting a complex biogeographic history.

Environmental implications of Ptolemaic Period rodents and shrews from the Sacred Falcon Necropolis at Quesna, Egypt (Mammalia: Muridae and Soricidae)

BACKGROUND

Assemblages of mummified and preserved animals in necropoleis of Ptolemaic Period Egypt (ca. 332-30 BC) document some aspects of the ceremonial and religious practices of the ancient Egyptians, but study of these animal remains can also provide insight into the local environments in which the animals and humans lived.

RESULTS

Excavations of the Sacred Falcon Necropolis at Quesna in the Nile Delta have yielded many thousands of animal remains, mostly of raptors, but also of a lesser number of small, wild mammals. Among the latter, we identified four species of murid rodents (Rodentia: Muridae) and five species of shrews (Eulipotyphla: Soricidae). The soricids are of particular interest because they represent a more diverse assemblage of species than occurs in the delta today. They include one species, Crocidura gueldenstaedtii (Pallas, 1811), that no longer occurs in the delta and another, C. fulvastra (Sundevall, 1843), that is now extirpated from Egypt.

CONCLUSIONS

The coexistence of this diverse small mammal community suggests that a greater availability and variety of mesic habitats were present during the Ptolemaic Period than occur there now. The local mammal faunas recovered at Quesna and other well-studied ancient Egyptian sites together provide evidence of a richer, more complex regional environment along the Nile Valley. They also provide important insight regarding the biogeography of the individual species comprising the faunas and about the extent of faunal turnover since the Ptolemaic Period.

Phylogeography of the White-Toothed Shrews Crocidura suaveolens and Crocidura sibirica: Searching for the Geographical Homeland

Abstract

We studied the polymorphism of the cytb gene in two forms of the Lesser White-toothed Shrew species complex: Crocidura suaveolens s. stricto and C. sibirica. The haplotypes of C. sibirica are found to be very similar to those of Crocidura suaveolens. They do not belong to a distinct haplogroup. The molecular diversity of the populations in the Asian part of the range is higher than in Eastern Europe. For the combined sample from Asia and Europe together, we revealed a significant signal of population expansion. Analysis of the expansion time showed that the Asian territory was colonized earlier (before the last glacial maximum) than the Eastern Europe (at the very end of the Late Pleistocene and in the early Holocene). The results of the ancestral area reconstruction are consistent with the hypothesis of a Middle Asian origin of the C. suaveolens/C. sibirica group, recent colonization of Inner Asia and later penetration into Eastern Europe.

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our study provides a comparative population genomic analysis of the effects of neutral processes on a classical island‐mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

A new addition to the embalmed fauna of ancient Egypt: Güldenstaedt's White-toothed Shrew, Crocidura gueldenstaedtii (Pallas, 1811) (Mammalia: Eulipotyphla: Soricidae)

The Falcon Necropolis at Quesna in the Nile Delta of Egypt is considered to have been founded by the priest Djedhor, the Saviour, of Athribis (Tell Atrib in modern Benha) at the beginning of the Ptolemaic Period. Recent excavations here have revealed abundant avian remains from mummies dedicated to the ancient Egyptian god Horus Khenty-Khety. Among the few mammal remains from the site are five species of shrews (Eulipotyphla: Soricidae), including some that we identified as Güldenstaedt's White-toothed Shrew, Crocidura gueldenstaedtii (Pallas, 1811). Discovery of this species at Quesna increases the number of shrews recovered from ancient Egyptian archaeological sites to eight species. Crocidura gueldenstaedtii no longer occurs in the Nile Delta, and its presence in a diverse shrew fauna at Quesna that includes one other extirpated species, Crocidura fulvastra (Sundevall, 1843), supports the hypothesis of a moister regional environment 2000-3000 years ago. Inadvertently preserved local faunas, such as that from Quesna, can provide valuable information about ancient environments and subsequent turnover in faunal communities.

A taxonomic revision of fat dormice, genus Glis (Rodentia)

We address in this study the taxonomic status of the two major phylogenetic lineages of fat dormice, genus Glis. These lineages show unique mutations at 43 positions of the cytochrome b alignment and are classified as two distinct species, the European fat dormouse Glis glis (Linnaeus, C. [1766]. Systema naturae per regna tria naturae, secundum classes, ordines, genera, species, cum characteribus, differentiis synonymis, locis, Vol. 1. Laurentii Salvii, Holmiae [Stockholm]) and the Iranian fat dormouse Glis persicus (Erxleben, I.C.P. [1777]. Systema regni animalis per classes, ordines, genera, species, varietates cum synonymia et historia animalium. Classis I. Mammalia. Impensis Weygandianis, Lipsia [Leipzig]). The European dormouse is widespread in Europe, Asia Minor and the Caucasus, while the Iranian dormouse occupies the southern Caspian coast in Iran. Ranges are presumably delimited in Azerbaijan by rivers Kura and Aras. The two species differ categorically in size of the glans penis, size and shape of the baculum and in width of the posterior extension of the premaxilla. The Iranian fat dormouse has on average a more blackish distal half of the tail, a higher count for abdominal nipples, and a longer maxillary tooth-row. Intraspecific structuring in G. glis indicates a taxonomic complexity which is not yet understood and requires a comprehensive systematic revision. To define the nominal taxon objectively we designate voucher PMS 27369 (Slovenian Museum of Natural History) as the neotype for G. glis, therefore restricting the type locality for the species to Mt. Krim in Slovenia.

Using a blind test to assess the discriminant power of morphological traits to distinguish between similar shrew species

The Canary Islands are home to a large variety of endemic fauna. The Canary shrew (Crocidura canariensis) has a distribution restricted to Fuerteventura, Lanzarote and the islets of Lobos and Montaña Clara. One of the main threats to the insular fauna is the arrival of exotic species. The greater white-toothed shrew (Crocidura russula) is an easily transportable animal and a potential competitor for C. canariensis. Therefore, C. russula should be taken into account in the management protocols for invasive species. One of the most easily applicable techniques for detecting shrews is the analysis of pellets. This study aims to assess which morphological characters are diagnostic and easy to use when identifying both species of shrews. For this purpose, a blind specific assignment has been made using seven previously described characters and another three added in the present study. The results show that the observer’s experience did not improve the correct identification rate and that only three of the evaluated characters have a high discriminant capacity. Finally, it was found that the combined use of the maximum number of characters and the identification by two independent observers reduces the probability of making a mistake in the determination to minimum values.

Molecular relationships of the Israeli shrews (Eulipotyphla: Soricidae) based on cytochrome b sequences

The number of shrew species in Israel has been and still is the subject of debate. In this work we used for the first time a molecular marker, the cytochrome b gene, to investigate the number and identity of shrew species in Israel. Our molecular results confirmed the presence of four species: Crocidura leucodon, Crocidura suaveolens gueldenstaedtii, Crocidura ramona, and Suncus etruscus. The C. ramona sequences were found to differ from all other Crocidura species sequenced to date, supporting its status as a distinct species. Whether it is conspecific with Crocidura portali (described in 1920 from Israel and usually synonymized with C. suaveolens), will require additional study. The sequences of Israeli C. suaveolens were found to be very similar to those of Iran, Turkey, and Georgia (i.e., C. suaveolens gueldenstaedtii), in agreement with previous studies. The Israeli C. leucodon sequences, however, formed a distinct clade among C. leucodon. Finally, the S. etruscus sequences clustered with sequences from France, Italy, and Iran.

Genomic Characterization of the Novel Bartonella refiksaydamii sp. Isolated from the Blood of a Crocidura suaveolens (Pallas, 1811)

Bartonella species are reemerging infectious agents that are transmitted by arthropod vectors among animals and/or humans. At least 13 of the 35 currently recognized Bartonella species are pathogenic for humans. Most of the pathogenic species, except Bartonella quintana and Bartonella bacilliformis, are zoonotic agents with animal reservoirs, including cats, dogs, coyotes, foxes, cattle, and rodents. In this study, a novel Bartonella species was isolated from the blood of a Crocidura suaveolens (Pallas, 1811) Lesser shrew that was captured in the Bartın region of Northwestern Turkey. The strain, RSKK 19006, was characterized using whole-genome sequencing and comparison, multilocus sequence typing (gltA, rpoB, ssrA, nuoG, and 16S rRNA) and internal transcribed spacer sequencing, electron microscopy scanning, biochemical tests, and MALDI-TOF MS (matrix assisted laser desorption ionization-time of flight mass spectrometry). This novel Bartonella is a Gram-negative, rod-shaped, microaerophilic bacterium and has neither flagella nor pilus. As a consequence, we propose to name this new species Bartonella refiksaydamii sp. nov. in Bartonella genus. The zoonotic potential of this novel Bartonella species is as yet unknown.

A river runs through it: tree frog genomics supports the Dead Sea Rift as a rare phylogeographical break

Phylogeographical breaks can be viewed as regional hotspots of diversity where the genetic integrity of incipient species is put to the test. We focus on an understudied species transition from the Middle East, namely the Dead Sea Rift in the Levant region, which presumably divided the tree frogs Hyla savignyi and H. felixarabica. Combining multilocus genetic analyses (mitochondrial DNA and RAD-sequencing) with ecological niche modelling, we test whether the rift effectively acts as a biogeographical barrier preventing this pair from admixing and merging. The answer is yes: despite weak signs of introgression, all parapatric populations were assigned to either species without cyto-nuclear discordance. Yet, the projected distributions under present and glacial conditions largely overlapped in the area, meaning their current parapatric ranges do not represent an ecological transition. Instead, we hypothesize that H. savignyi and H. felixarabica are maintained apart by limited opportunities for dispersal across the barren Jordan Valley, combined with advanced reproductive isolation. Therefore, the Dead Sea Rift may represent a rare phylogeographical break, and we encourage international efforts to assess its contribution to the rich biodiversity of the Middle East.

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

Background

Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs.

Results

We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids.

Conclusions

The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1179-0) contains supplementary material, which is available to authorized users.

Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis)

Hotspots of intraspecific genetic diversity, which are of primary importance for the conservation of species, have been associated with glacial refugia, that is areas where species survived the Quaternary climatic oscillations. However, the proximate mechanisms generating these hotspots remain an open issue. Hotspots may reflect the long-term persistence of large refugial populations; alternatively, they may result from allopatric differentiation between small and isolated populations, that later admixed. Here, we test these two scenarios in a widely distributed species of tree frog, Hyla orientalis, which inhabits Asia Minor and southeastern Europe. We apply a fine-scale phylogeographic survey, combining fast-evolving mitochondrial and nuclear markers, with a dense sampling throughout the range, as well as ecological niche modelling, to understand what shaped the genetic variation of this species. We documented an important diversity centre around the Black Sea, composed of multiple allopatric and/or parapatric diversifications, likely driven by a combination of Pleistocene climatic fluctuations and complex regional topography. Remarkably, this diversification forms a ring around the Black Sea, from the Caucasus through Anatolia and eastern Europe, with terminal forms coming into contact and partially admixing in Crimea. Our results support the view that glacial refugia generate rather than host genetic diversity and can also function as evolutionary melting pots of biodiversity. Moreover, we report a new case of ring diversification, triggered by a large, yet cohesive dispersal barrier, a very rare situation in nature. Finally, we emphasize the Black Sea region as an important centre of intraspecific diversity in the Palearctic with implications for conservation.

Description of a new endemic species of shrew (Mammalia, Soricomorpha) from PrÍncipe Island (Gulf of Guinea)

São Tomé and Príncipe are unique islands off the Gulf of Guinea on account of the high degree of endemism in these areas due to isolation. These islands are known to harbor, among others, two species of shrews of the genus

Back to the suture: the distribution of intraspecific genetic diversity in and around anatolia

The effect of ice ages in speciation and diversification is well established in the literature. In Europe, the Iberian, the Italian and the Balkan peninsulas comprise the main glacial refugia, where the subsequent re-population of Europe started. Though not studied as extensively, Anatolia has also been hinted to be a potential glacial refugium for Europe, and with its proximity to the Caucasus and the Middle East at the same time, has potential to exhibit high levels of intraspecific diversity. The more ubiquitous use and cheaper availability of molecular methods globally now makes it possible to better understand molecular ecology and evolution of the fauna and flora in the genetically understudied regions of the world, such as Anatolia. In this review, the molecular genetic studies undertaken in Anatolia in the last decade, for 29 species of plants and animals, are examined to determine general phylogeographic patterns. In this regard, two major patterns are observed and defined, showing genetic breaks within Anatolia and between Anatolia and the Balkans. A third pattern is also outlined, which suggests Anatolia may be a center of diversity for the surrounding regions. The patterns observed are discussed in terms of their relevance to the location of suture zones, postglacial expansion scenarios, the effect of geographic barriers to gene flow and divergence time estimates, in order to better understand the effect of the geological history of Anatolia on the evolutionary history of the inhabitant species. In view of the current state of knowledge delineated in the review, future research directions are suggested.

Phylogeography of the Middle Eastern tree frogs (Hyla, Hylidae, Amphibia) as inferred from nuclear and mitochondrial DNA variation, with a description of a new species

Evolutionary relationships of the tree frogs from the Middle East and the demographic histories of their populations were studied using a combination of mitochondrial and nuclear genes. Hyla savignyi and neighboring populations of H. orientalis (former eastern populations of H. arborea) were the main focus taxa. Within H. savignyi, a deep phylogenetic divergence dated about 8.4Ma was discovered. Southern populations from Yemen, Jordan, southern Syria and extreme north-eastern Israel are hereby described as a new species, H. felixarabica sp. nov. Our study points to a biogeographic connection of the south-western Arabian Peninsula and southern Levant and to the importance of the Dead Sea Rift as a historical barrier geographically separating the new species from H. savignyi. Major genetic breaks revealed within species (H. felixarabica: Yemen vs. Jordan-Syria; H. savignyi sensu stricto: Levant vs. Turkey-Iran) are probably connected to climate changes during the Plio-Pleistocene boundary, while the finer phylogeographic structuring probably resulted from the Quaternary climate oscillations. The Cypriote population of H. savignyi originated from southern Anatolia relatively recently. Hyla orientalis from the southern Black Sea region seems to be genetically quite uniform, although two phylogeographic units with western Turkish and Caucasus-Caspian affinities might be detected. Hyla savignyi and H. orientalis carry signals of population expansions dated to the middle to late Pleistocene, while populations of H. felixarabica seem to have rather been constant in size, which might indicate more stable climatic conditions in the southern regions during the Quaternary.

Quaternary history and contemporary patterns in a currently expanding species

Background

Quaternary climatic oscillations had dramatic effects on species evolution. In northern latitudes, populations had to survive the coldest periods in refugial areas and recurrently colonized northern regions during interglacials. Such a history usually results in a loss of genetic diversity. Populations that did not experience glaciations, in contrast, probably maintained most of their ancestral genetic diversity. These characteristics dramatically affected the present-day distribution of genetic diversity and may influence the ability of species to cope with the current global changes. We conducted a range-wide study of mitochondrial genetic diversity in the pine processionary moth (Thaumetopoea pityocampa/T. wilkinsoni complex, Notodontidae), a forest pest occurring around the Mediterranean Basin and in southern Europe. This species is responding to the current climate change by rapid natural range expansion and can also be accidentally transported by humans. Our aim was to assess if Quaternary climatic oscillations had a different effect across the species' range and to determine if genetic footprints of contemporary processes can be identified in areas of recent introduction.

Results

We identified three main clades that were spatially structured. In most of Europe, the genetic diversity pattern was typical for species that experienced marked glaciation cycles. Except in refugia, European populations were characterized by the occurrence of one main haplotype and by a strong reduction in genetic diversity, which is expected in regions that were rapidly re-colonized when climatic conditions improved. In contrast, all other sub-clades around the Mediterranean Basin occurred in limited parts of the range and were strongly structured in space, as is expected in regions in which the impact of glaciations was limited. In such places, genetic diversity was retained in most populations, and almost all haplotypes were endemic. This pattern was extreme on remote Mediterranean islands (Crete, Cyprus, Corsica) where highly differentiated, endemic haplotypes were found. Recent introductions were typified by the existence of closely-related haplotypes in geographically distant populations, which is difficult to detect in most of Europe because of a lack of overall genetic structure.

Conclusion

In regions that were not prone to marked glaciations, recent moth introductions/expansions could be detected due to the existence of a strong spatial genetic structure. In contrast, in regions that experienced the most intense Quaternary climatic oscillations, the natural populations are not genetically structured, and contemporary patterns of population expansion remain undetected.

Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae)

We sequenced 1077 bp of the mitochondrial cytochrome b gene and 511 bp of the nuclear Apolipoprotein B gene in bicoloured shrew (Crocidura leucodon, Soricidae) populations ranging from France to Georgia. The aims of the study were to identify the main genetic clades within this species and the influence of Pleistocene climatic variations on the respective clades. The mitochondrial analyses revealed a European clade distributed from France eastwards to north-western Turkey and a Near East clade distributed from Georgia to Romania; the two clades separated during the Middle Pleistocene. We clearly identified a population expansion after a bottleneck for the European clade based on mitochondrial and nuclear sequencing data; this expansion was not observed for the eastern clade. We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea.