Molecular systematics and biodiversity of the Cryptotis mexicanus group (Eulipotyphla: Soricidae): two new species from Honduras supported

Small-eared shrews of the genus Cryptotis (Mammalia: Eulipotyphla: Soricidae) are widespread in the northern Neotropics. Systematic studies of these shrews over the past two decades have revealed previously undocumented morphological and species diversity, resulting in a quadrupling of the number of recognized species. Unfortunately, a small proportion of the species in the genus have been included in molecular phylogenetic studies, and evolutionary relationships within the genus are incompletely known. Traditionally, species have been assigned to four or five morphologically defined ‘species groups’, but tests of the monophyly of some of these groups show weak support and relationships amongst species groups remain somewhat speculative. The largest species group is the C. mexicanus group inhabiting Mexico and northern Central America. We studied sequences from mitochondrial cytochrome-b and 16S genes, as well as nuclear ApoB and BRCA1 genes from 22 species of Cryptotis, including 15 species in the C. mexicanus group. Our combined analysis shows that the C. goldmani subgroup is very weakly supported as monophyletic; however, the C. mexicanus group as a whole is not monophyletic. Our molecular phylogenetic analyses confirm the distinctiveness of two newly described species (C. celaque and C. mccarthyi) from isolated highlands of western Honduras and illustrate their relationship with other species formerly considered part of a widespread C. goodwini.     

Recombinogenic Telomeres in Diploid Sorex granarius (Soricidae,Eulipotyphla) Fibroblast Cells

The telomere structure in the Iberian shrew Sorex granarius is characterized by unique, striking features, with short arms of acrocentric chromosomes carrying extremely long telomeres (up to 300 kb) with interspersed ribosomal DNA (rDNA) repeat blocks. In this work, we investigated the telomere physiology of S. granarius fibroblast cells and found that telomere repeats are transcribed on both strands and that there is no telomere-dependent senescence mechanism. Although telomerase activity is detectable throughout cell culture and appears to act on both short and long telomeres, we also discovered that signatures of a recombinogenic activity are omnipresent, including telomere-sister chromatid exchanges, formation of alternative lengthening of telomeres (ALT)-associated PML-like bodies, production of telomere circles, and a high frequency of telomeres carrying marks of a DNA damage response. Our results suggest that recombination participates in the maintenance of the very long telomeres in normal S. granarius fibroblasts. We discuss the possible interplay between the interspersed telomere and rDNA repeats in the stabilization of the very long telomeres in this organism.     

A new southern distribution limit for Sorex mirabilis Ognev, 1937 (Eulipotyphla,Soricidae)

Sorex mirabilis, a small insectivorous mammal, is a very rare, poorly known species distributed at high latitudes and altitudes of northeastern Asia. The occurrence of this species in the Republic of Korea was known from late 1990s. We found a new specimen from a location of a 50′ lower latitude and 400 m lower altitude than the previously known locations of the first record in the Republic of Korea. This finding may imply that S. mirabilis is distributed in a wider range than previously considered and that their distribution might be related to eoreumgols, or ice valleys, where there are potential insular refugia due to micro-meteorological characteristics.     

Molecular taxonomy of Crocidura species (Eulipotyphla: Soricidae) in a key biogeographical region for African shrews,Nigeria

The taxonomy of African shrew species is still unresolved due to their conserved morphology. This also affects knowledge concerning their geographic distribution. In Nigeria, using mitochondrial Cytochrome b gene sequences, we carried out a survey for shrews from the genus Crocidura across various ecological zones to determine taxa that are present and also to assess their phylogeographic structure. Our analyses include 183 specimens collected with Sherman traps from 19 localities around the country. We detected six taxa: Crocidura olivieri lineages II, III and IV, C. hildegardeae, C. jouvenetae, and C. foxi. Among these, C. hildegardeae and C. jouvenetae are reported in Nigeria for the first time. Phylogenetic comparison of our genetic sequences to those generated from other parts of Africa demonstrate that all species in our study, as currently defined, are in need of taxonomic revision. Geographically, Nigeria seems to represent the easternmost boundary for C. olivieri lineage II and C. jouvenetae, and the western distribution limit of C. olivieri lineage IV and C. hildegardeae. The Niger River appears to be the most significant topographical barrier restricting these taxa. This information is vital to preserving the diversity but also managing the epidemiological potential of these small mammals.     

Evolutionary history of the genus Sorex (Soricidae,Eulipotyphla) as inferred from multigene data

The genus Sorex is one of the most diverse and ecologically successful lineages of the family Soricidae. We present the first multilocus nuclear phylogeny focusing on the nominal subgenus Sorex s.str., which is distributed mainly in the northern Palearctic. The nuclear tree (six exons) provides more resolution than the mitochondrial data (cytb) and supports subdivision into eight species groups within Sorex s.str., most of which correspond to those recognized from chromosome data. The European species S. alpinus is consistently placed as the basal lineage in the Palearctic clade, while the next split separates the east‐Tibetan group of striped shrews (S. aff. cylindricauda, S. bedfordiae, S. excelsus). Within the remaining species, the following well‐supported clades are identified at the supra‐group level: “araneus” species group+S. samniticus; the “caecutiens” group+the “minutus” group, the latter also including S. minutissimus, S. gracillimus and S. thibetanus. S. raddei and S. roboratus represent separate lineages with no close relatives. The fossil‐calibrated molecular clock placed the divergence between Sorex s.str. and Otisorex at the Early/Middle Miocene boundary. Basal radiation of the crown Sorex s.str. was estimated to have occurred in the middle of the Late Miocene. A more than threefold increase in the diversification rate is inferred for the Early Pliocene. Taxonomic implications including potential genus ranks for Sorex s.str. and Otisorex are discussed. S. alpinus is placed in the monotypic subgenus Homalurus. The full species status of S. buchariensis and S. thibetanus and close relationships between S. cf. cansulus and S. caecutiens are confirmed.     

Molecular Phylogeny of the Genus Paramesotriton (Caudata: Salamandridae)

To elucidate the phylogeny of the genus Paramesotriton (Caudata: Salamandridae), we investigated three mitochondrial DNA gene fragments (1207 bp in total) of cytochrome b, ND2, and ND4 for its six recognized species. The phylogenetic relationships within Paramesotriton were reconstructed by maximum parsimony (MP) and maximum likelihood (ML) methods. Phylogenetic trees (MP and ML trees) that were constructed from the combined data set of the three gene fragments indicated that all six species of Paramesotriton formed a monophyletic group, with P. caudopunctatus as basal to the other five species. This result suggests that P. fuzhongensis is a valid species in Paramesotriton.     

The colonization of Scottish islands by the common shrew, Sorex araneus (Eulipotyphla: Soricidae)

In this paper we apply molecular methods to study the colonization of islands off the west coast of Scotland by the common shrew ( Sorex araneus L.), and current gene flow. We collected 497 individuals from 13 islands of the Inner Hebrides and Clyde Island groups and six mainland regions. Individuals were genotyped at eight microsatellite loci, and the mitochondrial cytochrome b sequence (1140 base pairs) was obtained for five individuals from each island/mainland region. Based on these molecular data, island colonization apparently proceeded directly from the mainland, except for Islay, for which Jura was the most likely source population. Raasay may also have been colonized by island hopping. Most island populations are genetically very distinct from the mainland populations, suggesting long periods of isolation. Two exceptions to this are the islands of Skye and Seil, which are geographically and genetically close to the mainland, suggesting in each case that there has been long-term gene flow between these islands and the mainland. We consider possible methods of island colonization, including human-mediated movement, swimming, and land and ice bridges.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 797–808.     

中国浙江麝鼩属(劳亚食虫目:鼩鼱科)一新种描记

2017年8月,在浙江省拟建淳安磨心尖省级自然保护区和拟建东阳市东江源省级自然保护区捕获麝鼩属（Crocidura）共5号标本。基于线粒体细胞色素b基因构建的系统发育树显示采集于浙江的麝鼩属样本与大麝鼩（Crocidura lasiura）和日本麝鼩（Crocidura dsinezumi）构成姊妹群,遗传距离最近,而与中国西南部分布的小体型印支小麝鼩（Crocidura indochinensis）、五指山小麝鼩（Crocidura wuchihensis）及东北部分布的山东小麝鼩（Crocidua shantungensis）、北小麝鼩（Crocidua suaveolens）亲缘关系较远,其遗传距离分别为0.114、0.124、0.139和0.144。这些样本与麝鼩属其他物种之间的遗传距离在0.101~0.155之间,最小遗传距离出现在来自浙江的样本和大麝鼩之间,最大遗传距离在浙江样本与中麝鼩之间。形态上,采集于浙江的麝鼩属标本个体小,体长48~61mm（平均：55.60mm）,尾长35~49mm（平均：43.14mm）;尾长与体长之比72.92%~80.36%;尾近乎裸露,尾基1/3~1/2着生稀疏长毛;尾上下双色,背部黑褐色,腹部较淡;颅较短,颅全长15.60~17.16mm（平均：16.46mm）,与中国东北部分布的山东小麝鼩和北小麝鼩相近又有区别,与已知其它麝鼩属物种形态差异较大;综合形态和系统发育关系证实采集于浙江的麝鼩属物种为一新物种,命名为东阳江麝鼩（Crocidura dongyangjiangensis Liu Y, Chen SD, and Liu SY sp. nov.）。本文对其形态、栖息环境和与近缘种的区别进行了详细记述。     

Molecular Phylogeny of the Butterfly Genus Polytremis (Hesperiidae,Hesperiinae, Baorini) in China

Background

The genus Polytremis, restricted to the continental part of the southeastern Palaearctic and northern Oriental regions, is one of the largest and most diverse lineages of the tribe Baorini. Previous studies on the genus were focused mainly on morphological classification and identification of new species. Due to the lack of effective and homologous traits of morphology, there were many challenges in the traditional classification. In this report, we reconstruct the phylogeny to provide a solid framework for these studies and to test the traditional limits and relationships of taxa.

Methodology and Principal Findings

We sequenced a mitochondrial and three nuclear gene fragments, coupled with an evaluation of traditional morphological characters, to determine the phylogenetic relationships for a total of 15 species representing all major species groups of the Polytremis genus in China, and to elucidate their taxonomic status.

Conclusions and Significance

Analysis of mitochrondial and nuclear DNA showed considerable congruent phylogenetic signal in topology at the inter-species level. We found strong support for the monophyly of Polytremis and some clades were recognized with morphological data. Thus, the COI sequence in our study could be used as a DNA barcode to identify almost all members of the genus. However, incongruences of phylogenetic analyses occurred: in contrast to the phylogenetic trees of mitochondrial COI, it was not possible for nuclear rDNA to discriminate P. gotama from P. caerulescens, suggesting a possible recent separation of these two species. Additionally, P. theca was the only species with a greater intra-specific genetic distance compared to some inter-specific genetic distances in this study and some problems associated with the cryptic diversity of the species are discussed. The results of this study will helpful to reveal the causes of the high degree of diversity of butterflies, and possibly other groups of insects in China.     

Molecular Phylogeny and Biogeography of the Genus Ilex L. (Aquifoliaceae)

The chloroplast atpB-rbcL spacer was sequenced for 115 speciesof Ilex and forNemopanthus mucronatus (Aquifoliaceae). In addition,rbcL sequences were obtained for 47 selected species. Takentogether with fossil records in the literature, the data indicatethat: (1) the lineage Ilex was already cosmopolitan long beforethe end of the Cretaceous. A relative test of the rate of nucleotidesubstitution indicates that extant species do not representthe entire lineage because of the extinction of its basal branches.The common ancestor of the extant species probably appearedat the upper Tertiary. (2) Several Asian/North American disjunctionsare observed, as well as North American/South American relationships.The directions of these relationships are yet to be determined.The African species Ilex mitis is closely related to Asian species.Ilex anomala (Hawaii and Tahiti) is related to American species.Ilex perado and Ilex canariensis (both in Macaronesia) havetotally different relationships, the former being related toEurasian species, while relationships of the latter remain obscure.(3) Gene trees substantially contradict the systematics of Loesener.Nemopanthus,closely related to Ilex amelanchier, is nested in the genusIlex. The family Aquifoliaceae is organized in four groups,each of them having a geographic or ecological peculiarity.Copyright 2000 Annals of Botany Company Aquifoliaceae, chloroplast DNA, fossil record, historical biogeography, Ilex (holly tree), molecular phylogeny.     

A new genus of Asiatic short-tailed shrew(Soricidae,Eulipotyphla) based on molecular and morphological comparisons

Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist(mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies.However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages,one a close relative to B. quadraticauda, whereas the other—comprised of topotype specimens from southern Gansu—diverged from other Blarinella in the middle Miocene(ca. 18.2 million years ago(Ma),95% confidence interval=13.4–23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P~4. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly,some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella.Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.     

Molecular Phylogeny and Species Identification of Pufferfish of the Genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosomal RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within each species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus. Received September 29, 2000; accepted February 26, 2001.     

Tiny teeth of consequence: Vestigial antemolars provide key to Early Miocene soricid taxonomy (Eulipotyphla: Soricidae)

In the soricid fauna of the Early Miocene Petersbuch 28 fissure fill from Bavaria, Germany, specimens of Miosorex desnoyersianus (Lartet, 1851) and Paenelimnoecus micromorphus (Doben-Florin, 1964) retain a tiny penultimate antemolar. This antemolar was previously unknown for P. micromorphus, because the tiny antemolar has not been preserved until now. Miosorex desnoyersianus retains the rudimentary tooth; its possible function was to keep the p4 in upright position. The younger species of Paenelimnoecus have lost this vestigial tooth. Based on the alveoli, Miosorex pusilliformis is interpreted as a junior synonym of M. desnoyersianus, and the diagnoses of Miosorex desnoyersianus and Paenelimnoecus micromorphus are emended.     

Molecular Phylogeny of Polychaos annulatum (Amoebozoa,Tubulinea, Euamoebida) Shows that Genus Polychaos Belongs to the Family Hartmannellidae

We have obtained a sequence of the 18S rRNA gene of the species Polychaos annulatum (Penard 1902) Smirnov et Goodkov 1998 using the isolation of a single nucleus from an amoeba cell. Attempts to amplify the 18S rRNA gene from the DNA of this species by conventional PCR were not successful, so we applied the whole genome amplification of the nuclear DNA followed by NGS sequencing. The 18S rRNA gene was found among the resulting contigs. The analysis unexpectedly shows that P. annulatum robustly groups within the family Hartmannellidae, but not Amoebidae. This finding warrants revision of the basic morphological criteria used to classify Euamoebida families and show that “proteus‐type” amoebae may belong to other families rather than Amoebidae. This makes taxonomic assignments of such species more complex and the borders between Euamoebida families more nuanced. It is getting evident that molecular data are necessary to clarify the position of species even in this most “classical” order of naked lobose amoebae.     

Molecular Phylogeny of the Small Ermine Moth Genus Yponomeuta (Lepidoptera,Yponomeutidae) in the Palaearctic

Background

The small ermine moth genus Yponomeuta (Lepidoptera, Yponomeutidae) contains 76 species that are specialist feeders on hosts from Celastraceae, Rosaceae, Salicaceae, and several other plant families. The genus is a model for studies in the evolution of phytophagous insects and their host-plant associations. Here, we reconstruct the phylogeny to provide a solid framework for these studies, and to obtain insight into the history of host-plant use and the biogeography of the genus.

Methodology/Principal Findings

DNA sequences from an internal transcribed spacer region (ITS-1) and from the 16S rDNA (16S) and cytochrome oxidase (COII) mitochondrial genes were collected from 20–23 (depending on gene) species and two outgroup taxa to reconstruct the phylogeny of the Palaearctic members of this genus. Sequences were analysed using three different phylogenetic methods (parsimony, likelihood, and Bayesian inference).

Conclusions/Significance

Roughly the same patterns are retrieved irrespective of the method used, and they are similar among the three genes. Monophyly is well supported for a clade consisting of the Japanese (but not the Dutch) population of Yponomeuta sedellus and Y. yanagawanus, a Y. kanaiellus–polystictus clade, and a Rosaceae-feeding, western Palaearctic clade (Y. cagnagellus–irrorellus clade). Within these clades, relationships are less well supported, and the patterns between the different gene trees are not so similar. The position of the remaining taxa is also variable among the gene trees and rather weakly supported. The phylogenetic information was used to elucidate patterns of biogeography and resource use. In the Palaearctic, the genus most likely originated in the Far East, feeding on Celastraceae, dispersing to the West concomitant with a shift to Rosaceae and further to Salicaceae. The association of Y. cagnagellus with Euonymus europaeus (Celastraceae), however, is a reversal. The only oligophagous species, Y. padellus, belongs to the derived western Palaearctic clade, evidence that specialisation is reversible.     

Patterns of morphological and ecological similarities of small-eared shrews (Soricidae,Cryptotis) in tropical montane cloud forests from Mesoamerica

It has been proposed that high morphological similarity between closely related species of small-eared shrews resulted from a recent divergence and intermittent population connectivity, presumably due to Pleistocene climatic fluctuations and associated changes in forest habitat distribution. Here we examined the morphological variation of two sister species of small-eared shrews inhabiting cloud forests from Mexico, Cryptotis obscurus and C. mexicanus. We then used ecological niche modelling to provide compelling evidence for current environmental barriers for population connectivity, and for detecting divergent ecological niches between candidate species. Our results indicated that the species boundaries in this clade should be subject to change. High morphological similarity suggested that populations of C. obscurus and C. mexicanus located west of the Isthmus of Tehuantepec, a major geographic barrier for montane species, are conspecific. Niche divergence between these two putative species was not supported indicating niche conservatism across the evolutionary history of these small-eared shrews. In addition, several barriers seem to play a main role for current lineage divergence between populations within this clade. The population located east of the Isthmus, previously referred to C. mexicanus, might prove to represent a new species based on morphological distinction and current geographic isolation. We have highlighted that estimating species’ potential distributions provides insights to evaluating the effect of geographic barriers on lineage divergence and making stronger inferences when delimiting species.     

Exceptional biting capacities of the Early Pleistocene fossil shrew Beremendia fissidens (Soricidae,Eulipotyphla, Mammalia): new taphonomic evidence

The discovery of small, very well-defined and perfectly preserved toothmarks on a humerus of a mole Talpa cf. europaea from level TE9 of Sima del Elefante (Sierra de Atapuerca, Burgos) with a chronology of the Early Pleistocene is extraordinary. In a previous paper, this bite was compared with current small carnivores such as Mustela nivalis molars and with fossil remains of Mustela palerminea and the soricid (Eulipotyphla and Mammalia) Beremendia fissidens with the purpose of identifying the predator. It was hypothesised that Beremendia fissidens could be the bite maker. However, it was not possible to rule out other predators due to the shortage of Beremendia fissidens remains. Recently, new fossil remains of this insectivore have been found in Sima del Elefante levels, allowing the upper dentition to be measured. These new data suggest that effectively Beremendia fissidens may have had the capacity to bite prey larger than itself, even though it did not possess morphological characteristics specialised for the consumption of small mammals. The addition of small vertebrates (like talpids) to complement a diet based on insects could have been a way of responding to the needs of the high metabolic rate characteristic of Beremendia fissidens.     

Skeletal morphology of the forefoot in shrews (Mammalia: Soricidae) of the genus Cryptotis, as revealed by digital X-rays

Variation in the forefoot skeleton of small-eared shrews (family Soricidae, genus Cryptotis) has been previously documented, but the paucity of available skeletons for most taxa makes assessment of the degrees of intraspecific and interspecific variation difficult. We used a digital X-ray system to extract images of the forefoot skeleton from 101 dried skins of eight taxa (seven species, including two subspecies of one species) of these shrews. Lengths and widths of each of the four bones of digit III were measured directly from the digital images, and we used these data to quantify variation within and among taxa. Analysis of the images and measurements showed that interspecific variation exceeds intraspecific variation. In fact, most taxa could be distinguished in multivariate and some bivariate plots. Our quantitative data helped us define a number of specific forefoot characters that we subsequently used to hypothesize evolutionary relationships among the taxa using the exhaustive search option in PAUP, a computer program for phylogenetic analysis. The resulting trees generally concur with previously published evolutionary hypotheses for small-eared shrews. Cryptotis meridensis, a taxon not previously examined in recent phylogenies, is rooted at the base of the branch leading to the C. mexicana group of species. The position of this species suggests that the mostly South American C. thomasi group shares an early ancestor with the C. mexicana group.