Environmentally caused dwarfism or a valid species--is Testudo weissingeri Bour, 1996 a distinct evolutionary lineage? New evidence from mitochondrial and nuclear genomic markers

We examine the evolutionary relationships of the five traditionally recognized species of the western Palearctic tortoise genus Testudo (T. graeca, T. hermanni, T. horsfieldii, T. kleinmanni, and T. marginata) and the newly described dwarfed species T. weissingeri by using sequence data of the mitochondrial cytochrome b gene and nuclear genomic fingerprints with inter-simple sequence repeats (ISSR). Testudo weissingeri differs from T. marginata mainly by its smaller size and some color-pattern characteristics. T. weissingeri lives in the driest, poorest and hottest part of the distributional range of T. marginata. While both data sets demonstrated phylogenetic distinctness of the five traditionally recognized species of Testudo, some subspecies and even some local populations, we detected no differentiation between T. marginata and T. weissingeri. We conclude that T. weissingeri is not a distinct evolutionary unit. We suggest that its small size is the result of suboptimal environmental conditions with limited resources and synonymize it with T. marginata. T. marginata and T. kleinmanni form a clade that is supported both by our mtDNA and nuclear genomic data sets. According to mtDNA data, this clade is the sister taxon to the T. graeca complex. A sister group relationship of T. hermanni and ((T. marginata+T. kleinmanni)+T. graeca) is moderately to weakly supported by mtDNA data; T. horsfieldii is the sister taxon to a clade comprising all other Testudo species.     

Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences

To test phylogenetic relationships within the genus Testudo (Testudines: Testudinidae), we have sequenced a fragment of the mitochondrial (mt) 12S rRNA gene of 98 tortoise specimens belonging to the genera Testudo, Indotestudo, and Geochelone. Maximum likelihood and neighbor-joining methods identify two main clades of Mediterranean tortoises, one composed of the species Testudo graeca, Testudo marginata, and Testudo kleinmanni and a second of Testudo hermanni, Testudo horsfieldii, and Indotestudo elongata. The first clade, but not the second, was also supported by maximum parsimony analysis. Together with the genus Geochelone, a star-like radiation of these clades was suggested, as a sister-group relationship between the two Testudo clades could not be confirmed. The intraspecies genetic variation was examined by sequencing the mt 12S rRNA fragment from 28 specimens of T. graeca and 49 specimens of T. hermanni from various geographic locations. Haplotype diversity was found to be significantly larger in T. graeca compared with T. hermanni, suggestive of reduced genetic diversity in the latter species, perhaps due to Pleistocene glaciations affecting northern and middle Europe or other sources of lineage reduction. No ancient mt 12S rRNA gene haplotypes were identified in T. graeca and/or T. hermanni originating from islands in the Mediterranean Sea, suggesting that these islands harbor tortoise populations introduced from the European and African mainland.     

Molecular Systematics of Bats of the Genus Myotis (Vespertilionidae) Suggests Deterministic Ecomorphological Convergences

Based on extensive phenetic analyses, bats of the genus Myotis have been classically subdivided into four major subgenera each of which comprise many species with similar morphological and ecological adaptations. Each subgenus thus corresponds to a distinct “ecomorph” encompassing bat species exploiting their environment in a similar fashion. As three of these subgenera are cosmopolitan, regional species assemblages of Myotis usually include sympatric representatives of each ecomorph. If species within these ecomorphs are monophyletic, such assemblages would suggest extensive secondary dispersal across geographic areas. Conversely, these ecomorphological adaptations may have evolved independently through deterministic processes, such as adaptive radiation. In this case, phylogenetic reconstructions are not expected to sort species of the same ecomorph into monophyletic clades. To test these predictions, we reconstructed the phylogenetic history of 13 American, 11 Palaearctic, and 6 other Myotis species, using sequence data obtained from nearly 2 kb of mitochondrial genes (cytochrome b and nd1). Separate or combined analyses of these sequences clearly demonstrate the existence of several pairs of morphologically very similar species (i.e., sibling species) which are phylogenetically not closely related. None of the three tested subgenera constitute monophyletic units. For instance, Nearctic and Neotropical species currently classified into the three subgenera were clustered in a single, well-supported monophyletic clade. These species thus evolved independently of their ecological equivalents from the Palaearctic region. Independent adaptive radiations among species of the genus Myotis therefore produced strikingly similar evolutionary solutions in different parts of the world. Furthermore, all phylogenetic reconstructions based on mtDNA strongly supported the existence of an unsuspected monophyletic clade which included all assayed New World species plus M. brandtii (from the Palaearctic Region). This “American” clade thus radiated into a morphologically diverse species assemblage which evolved after the first Myotis species colonized the Americas. Molecular reconstructions support paleontological evidence that species of the genus Myotis had a burst of diversification during the late Miocene–early Pliocene epoch.     

Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae)

We investigated the phylogenetic relationships among 20 species of Oriental torrent frogs in the genus Amolops and its allies from China and Southeast Asia based on 1346-bp sequences of the mitochondrial 12S and 16S rRNA genes. Oriental species of the tribe Ranini form a monophyletic group containing 11 clades (Rana temporaria + Pseudoamolops, R. chalconota, four clades of Amolops, Meristogenys, three clades of Huia species, and Staurois) for which the phylogenetic relationships are unresolved. The genus Amolops consists of southern Chinese, southwestern Chinese, Thai, and Vietnamese-Malaysian lineages, but their relationships are also unresolved. The separation of southern and southwestern lineages within China conforms to previous morphological and karyological results. Species of Huia do not form a monophyletic group, whereas those of Meristogenys are monophyletic. Because P. sauteri is a sister species of R. temporaria, distinct generic status of Pseudoamolops is unwarranted.     

Celebrity with a neglected taxonomy: molecular systematics of the medicinal leech (genus Hirudo)

The medicinal leech is the most famous representative of the Hirudinea. It is one of few invertebrates widely used in medicine and as a scientific model object. It has recently been given considerable conservation effort. Despite all attention there is confusion regarding the taxonomic status of different morphological forms, with many different species described in the past, but only two generally accepted at present. The results of the phylogenetic analysis of a nuclear (ITS2+5.8S rRNA) and two mitochondrial gene sequences (12S rRNA, COI) suggest that the genus Hirudo is monophyletic. It consists, apart form the type Hirudo medicinalis and the East Asian Hirudo nipponia, of three other, neglected species. All of them have already been described either as species or morphological variety, and can readily be identified by their coloration pattern. The type species is in weakly supported sister relation with Hirudo sp. n. (described as variety orientalis) from Transcaucasia and Iran. Sister to them stands Hirudo verbana from southeastern Europe and Turkey, which is nowadays predominantly bred in leech farms and used as 'medicinal leech.' The North African Hirudo troctina is the sister taxon to this group of Western Eurasian species, whereas the basal split is between H. nipponia and the Western Palaearctic clade.     

Redescription of four species of Mehdiella from Testudinidae, with a key to the species and discussion on the relationships among the species of this genus

Four species of the genus Mehdiella Seurat, 1918 are redescribed: M. cristata Petter, 1966 and M. stylosa dollfusi Petter, 1966, parasite of Pyxix arachnoides Bell, 1827 from Madagascar, M. s. stylosa (Thapar, 1925) and M. uncinata (Drasche, 1884), parasite of Testudo graeca Linneaus, 1758, Testudo hermanni Gmelin, 1789 and Testudo horsfieldii (Gray, 1844) from Palaearctic region. Light microscopy and scanning electron microscopy (SEM) studies revealed new informations on the morphology of these species. On the basis of this morphological study, the sub-species Mehdiella stylosa dollfusi and M. s. stylosa are raised to level of species. The position of Mehdiella cristata among the species of the genus Mehdiella and the relationships among the species of the genus Mehdiella are discussed. A key to the eight valid species Mehdiella is given.     

A molecular phylogeny of four endangered Madagascar tortoises based on MtDNA sequences

Four of the five tortoise species in Madagascar, Pyxis arachnoides, P. planicauda, Geochelone radiata, and G. yniphora, are endemic and on the verge of extinction. Their phylogenetic relationships remain controversial and unresolved. Here we address the phylogeny of this group using DNA sequences for the 12S and 16S rDNA and cyt b genes in mitochondrial DNA. As outgroups we used two species of Geochelone, pardalis (mainland Africa) and nigra (Galápagos), as well as a more distant North American tortoise, Gopherus polyphemus. We conclude that the two Pyxis species are sister taxa and are imbedded in the genus Geochelone, rendering this latter genus paraphyletic. There is moderate support for the sister status of the two Madagascar Geochelone and for the monophyletic origin of all four endemics, suggesting a single colonization of the island. The separation of Madagascar from other land masses (90-165 mya) predates the origin of the endemic tortoises (estimated to be 14-22 mya). This suggests founding by rafting, a process known to have occurred with other tortoises. The derived morphological divergence of the Pyxis species in a relatively short period of time (13-20 my) stands in contrast to the notoriously slow rate of morphological evolution in most lineages of Chelonia.     

Phylogenetic relationships and taxonomy of subfamily Zygophylloideae (Zygophyllaceae) based on molecular and morphological data

Phylogenetic analysis of noncoding trnL plastid DNA sequences and morphological data for 43 species of Zygophylloideae, representing most of the morphological and geographical variation in the subfamily, indicates that the currently recognised genera Augea (monotypic, southern Africa), Tetraena (monotypic, China), and Fagonia (c. 30 species, widespread), are embedded in Zygophyllum (c. 150 species, widespread). A generic classification based on six monophyletic and morphologically distinctive entities is proposed: Roepera with c. 60 species in Australia and southern Africa, Zygophyllum with c. 50 species in Asia, Tetraena with c. 40 species in Africa and Asia, Augea with a single species in southern Africa, Melocarpum with two species in the Horn of Africa region, and Fagonia with c. 30 species in both the Old and the New World. Scanning electron microscopy studies of testa structure provided important characters for the delimitation of some genera. New combinations (61) are made in Roepera, a resurrected genus originally described from Australia, one new name is proposed in Zygophyllum, 35 new combinations are made in Tetraena, and two new combinations are made in Melocarpum (previously Zygophyllum sect. Melocarpum).     

Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes)

The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophenax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6-7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.     

Molecular systematics of the African snake family Lamprophiidae Fitzinger, 1843 (Serpentes: Elapoidea), with particular focus on the genera Lamprophis Fitzinger 1843 and Mehelya Csiki 1903

The snake family Lamprophiidae Fitzinger (Serpentes: Elapoidea) is a putatively Late Eocene radiation of nocturnal snakes endemic to the African continent. It incorporates many of the most characteristic and prolific of Africa's non-venomous snake species, including the widespread type genus Lamprophis Fitzinger, 1843 (house snakes). We used approximately 2500 bases of mitochondrial and nuclear DNA sequence data from 28 (41%) of the approximately 68 recognised lamprophiid species in nine of the eleven genera to investigate phylogenetic structure in the family and to inform taxonomy at the generic level. Cytochrome b, ND4 and tRNA gene sequences (mitochondrial) and c-mos sequences (nuclear) were analysed using Maximum Likelihood, Bayesian Inference and Maximum Parsimony methods. The genus Mehelya Csiki, 1903 was paraphyletic with respect to Gonionotophis Boulenger, 1893. To address this, the concept of Gonionotophis is expanded to include all current Mehelya species. The genus Lamprophis emerged polyphyletic: the enigmatic Lamprophis swazicus was sister to Hormonotus modestus from West Africa, and not closely related to its nominal congeners. It is moved to a new monotypic genus (Inyoka gen. nov.). The remaining Lamprophis species occur in three early-diverging lineages. (1) Lamprophis virgatus and the widely distributed Lamprophis fuliginosus species complex (which also includes Lamprophis lineatus and Lamprophis olivaceus) formed a clade for which the generic name Boaedon Duméril, Bibron & Duméril, 1854 is resurrected. (2) The water snakes (Lycodonomorphus) were nested within Lamprophis (sensu lato), sister to Lamprophis inornatus. We transfer this species to the genus Lycodonomorphus Fitzinger, 1843. (3) We restrict Lamprophis (sensu strictissimo) to a small clade of four species endemic to southern Africa: the type species of Lamprophis Fitzinger, 1843 (Lamprophis aurora) plus Lamprophis fiskii, Lamprophis fuscus and Lamprophis guttatus.     

Molecular phylogeny of the Cricetinae subfamily based on the mitochondrial cytochrome b and 12S rRNA genes and the nuclear vWF gene

Despite some popularity of hamsters as pets and laboratory animals there is no reliable phylogeny of the subfamily Cricetinae available so far. Contradicting views exist not only about the actual number of species but also concerning the validity of several genera. We used partial DNA sequences of two mitochondrial (cytochrome b, 12S rRNA) and one partial nuclear gene (von Willebrand Factor exon 28) to provide a first gene tree of the Cricetinae based on 15 taxa comprising six genera. According to our data, Palaearctic hamsters fall into three distinct phylogenetic groups: Phodopus, Mesocricetus, and Cricetus-related species which evolved during the late Miocene about 7-12MY ago. Surprisingly, the genus Phodopus, which was previously thought to have appeared during the Pleistocene, forms the oldest clade. The largest number of extant hamster genera is found in a group of Cricetus-related hamsters. The genus Cricetulus itself proved to be not truly monophyletic with Cricetulus migratorius appearing more closely related to Tscherskia, Cricetus, and Allocricetulus. We propose to place the species within a new monotypic genus. Molecular clock calculations are not always in line with the dating of fossil records. DNA based divergence time estimates as well as taxonomic relationships demand a reevaluation of morphological characters previously used to identify fossils and extant hamsters.     

Molecular data delineate four genera of "Thryothorus" wrens

Wrens of the genus Thryothorus comprise over a third of the species diversity in the family Troglodytidae. In addition to this species diversity, these wrens vary in a number of behavioral characteristics, in particular in the presence and structure of vocal duets, which makes them an interesting target for comparative evolutionary ecological and behavioral study. However, no phylogenetic hypothesis for this group-which would provide a sound basis for comparative analysis-is currently available. While previous molecular phylogenetic work established conclusively that the type of this genus, Thryothorus ludovicianus (Latham), was not part of a monophyletic group with other Thryothorus, the exact limits of the genus could not be established due to limited taxon sampling. Here, we present molecular data from all but four currently recognized species of Thryothorus. These data confirm that Thryothorus is paraphyletic, and that the type T. ludovicianus does not form a monophyletic group with any other member of the genus. Based on analyses of our data, we resurrect two previously recognized wren genera, Pheugopedius and Thryophilus, and erect a new genus-Cantorchilus-to house the remaining ex-Thryothorus species. Our hypothesis of relationships will provide a firm basis for future behavioral and morphological analyses of these species.     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.     

Marbleseeds are gromwells – Systematics and evolution of Lithospermum and allies (Boraginaceae tribe Lithospermeae) based on molecular and morphological data

Phylogenetic relationships are complex within the Lithospermeae, a large subgroup of the Boraginaceae s.str. The relationships of New World Lasiarrhenum, Macromeria, Nomosa, Onosmodium, Perittostoma, and Psilolaemus to subcosmopolitan and much larger Lithospermum have not been critically investigated in the recent past. No molecular data on the phylogeny of these genera and Lithospermum have so far been published. We investigated the relationships within Lithospermeae using three loci (nuclear ITS plus 5.8S rRNA, chloroplast trnL-F-spacer, and trnS-G-spacer) and micromorphological character traits (pollen, nutlets). Lithospermum s.l. constitutes the sistergroup of Asian Ulugbekia and is monophyletic only when its American segregates “Macromeria”, monotypic Nomosa, and Onosmodium are included. Both the African and the South American species groups of Lithospermum are monophyletic, but North American representatives are not resolved in a single clade. Morphological characters that have been considered as important for generic delimitation in the past (such as large, yellow corollas without faucal scales, particular pollen types, coarsely veined leaves, shrubby habit) have evolved in at least two only distantly related lineages within Lithospermum s.l. The reduction of American “Macromeria”, Nomosa, and Onosmodium as well as Asian Ulugbekia under Lithospermum is proposed to render the latter monophyletic. This redefined Lithospermum s.l. appears to have undergone a type of recent “island radiation” in the Americas, reflected in a morphological diversity far exceeding that found in the Old World.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

Differentiation and phylogeny of the olivaceous warbler Hippolais pallida species complex

The pattern of phenotypic and molecular variation within the polytypic olivaceous warbler H. pallida was examined. This species is distributed in the southern parts of the western Palaearctic, central Asia and in the arid parts of northern Africa, and also in parts of the sub-Saharan Sahel zone. Based on morphology, five subspecies, at times assigned to three groups, have been identified. By comparing morphological, behavioural, vocal and molecular variation, we investigated the phenotypic and phylogenetic relationships within the Hippolais pallida group. The morphological and genetic data of the present study support the view of splitting the olivaceous warbler into a western (former subspecies opaca) and an eastern form (former subspecies elaeica, pallida, reiseri and laeneni). Opaca is consistently and significantly larger than the other taxa in all size measurements, even if it does share morphological properties with elaeica in characters associated with migration. The song of the polytypic pallida differs clearly from that of opaca, and is remarkably consistent within its wide range which comprises four subspecies. The molecular analysis, and the resulting phylogenetic pattern, clearly separated opaca on a single branch distant from the other subspecies. The eastern form consists of two non-overlapping haplotype groups: elaeica with relatively diverse mtDNA variation, and the three African subspecies pallida, reiseri and laeneni, which all share the same or closely related mtDNA haplotypes. It remains open whether the African taxa should be regarded as three valid subspecies of the Eastern olivaceous warbler, or if they are better treated as a single African subspecies.     

Rove beetles of the subtribe Scopaeina Mulsant & Rey (Coleoptera: Staphylinidae) in the West Palaearctic: Phylogeny, biogeography and species catalogue

A cladistic analysis of the West Palaearctic Scopaeina Mulsant & Rey, 1878 (Coleoptera, Staphylinidae: Paederinae) is presented along with bionomic and biogeographic information. A total of 76 morphological characters were coded for the 88 currently known West Palaearctic species, except for S. bifossicapitata (Outerelo & Oromi, 1987). Results show that Scopaeina comprises two well-supported monophyletic groups in the West Palaearctic, Micranops Cameron, 1913 and Scopaeus Erichson, 1840, which are considered to represent distinct genera. Phylogenetic relationships to Orus Casey, 1884, distributed in North and South America, are briefly discussed. Whereas Micranops is only represented by M. pilicornis (Baudi, 1869) in the region under study, 87 species of Scopaeus are currently known from the West Palaearctic. Within Scopaeus, the cladistic analysis yielded many well-supported monophyletic species groups, most of which are restricted to the West Palaearctic. However, except for Hyperscopaeus Coiffait, 1984, they are not in agreement with the widely used subgeneric concept sensu Coiffait (1952–1984). The following polyphyletic subgenera are consequently synonymized: Alloscopaeus Coiffait, 1968, Anomoscopaeus Coiffait, 1968, Geoscopaeus Coiffait, 1960, and Hyposcopaeus Coiffait, 1960 synn. n. = Scopaeus Erichson, 1840. Nivorus Herman, 1965, and Microscopaeus Coiffait, 1981 synn. n. = Micranops Cameron, 1913. The monotypical genus Coecoscopaeus Coiffait, 1984, established for C. coecus (Peyerimhoff, 1906), is excluded from Scopaeina. Scopaeus mitratus perroti Ochs, 1953 is raised to species rank, and S. nigellus Wollaston, 1864, formerly a synonym of S. minimus Erichson, 1939, is revalidated. Finally, we present a catalogue of species and synonyms of West Palaearctic Scopaeina along with distributional data and five new synonymies of species group names: S. bordei Peyerimhoff, 1914 syn. n. = S. portai Luze, 1910; S. tassiliensis Jarrige, 1958, S. mauretanicus Coiffait, 1960 synn. n. = S. crassipes Wollaston, 1867; S. saoudiensis Coiffait, 1981 = S. sinaicus Coiffait, 1970; S. mateui Coiffait, 1953 syn. n. = S. didymus Erichson, 1840. A lectotype is designated for S. didymus Erichson, 1840.See also Electronic Supplement (Parts 13) at http://www.senckenberg.de/odes/02-02.htm