Isolation and biodiversity in Cytisus villosus Pourret (Fabaceae,Genisteae): enzyme polymorphism in disjunct populations

ABSTRACT

The genetic diversity of isolated populations of Cytisus villosus has been studied by means of enzyme polymorphism analysis. Two types of isolated populations were studied: “terrestrial islands” in Sicily, and “true islands” in the Aeolian archipelago. In the populations of “true islands” the number of alleles and the heterozygosity are lower than in “terrestrial islands”. Isolation amongst Sicilian populations seems to be more recent than isolation of the Aeolian populations, and may be attributed to climatic changes which occurred during the Holocene and/or to human activities. The disjunction of the Aeolian populations seems much more recent than the origin of the isles themselves; the colonization of the archipelago is attributed to a single, recent dispersal event not followed by local evolution. In view of the biological structure of the Aeolian populations, C. villosus must be regarded as a locally endangered species.     

Phylogenetic relationships among Boleosoma darter species (Percidae: Etheostoma)

Darters represent a species rich group of North American freshwater fishes studied in the context of their diverse morphology, behavior, and geographic distribution. We report the first molecular phylogenetic analyses of the Boleosoma darter clade that includes complete species sampling. We estimated the relationship among the species of Boleosoma using DNA sequence data from a mitochondrial (cytochrome b) and a nuclear gene (S7 ribosomal protein intron 1). Our analyses discovered that the two Boleosoma species with large geographic distributions (E. nigrum and E. olmstedi) do not form reciprocally monophyletic groups in either gene trees. Etheostoma susanae and E. perlongum were phylogenetically nested in E. nigrum and E. olmstedi, respectively. While analysis of the nuclear gene resulted in a phylogeny where E. longimanum and E. podostemone were sister species, the mitochondrial gene tree did not support this relationship. Etheostoma vitreum was phylogenetically nested within Boleosoma in the mitochondrial DNA and nuclear gene trees. Our analyses suggest that current concepts of species diversity underestimate phylogenetic diversity in Boleosoma and that Boleosoma species likely provide another example of the growing number of discovered instances of mitochondrial genome transfer between darter species.     

Multiple intercontinental dispersals shaped the distribution area of Hordeum (Poaceae)

The grass genus Hordeum (Poaceae, Triticeae), comprising 31 species distributed in temperate and dry regions of the world, was analysed to determine the relative contributions of vicariance and long-distance dispersal to the extant distribution pattern of the genus. Sequences from three nuclear regions (DMC1, EF-G and ITS) were combined and analysed phylogenetically for all diploid (20 species) and two tetraploid Hordeum species and the outgroup Psathyrostachys. Ages of clades within Hordeum were estimated using a penalized likelihood analysis of sequence divergence. The sequence data resulted in an almost fully resolved phylogenetic tree that allowed the reconstruction of intrageneric migration routes. Hordeum evolved c. 12 million years ago in South-west Asia and spread into Europe and Central Asia. The colonization of the New World and South Africa involved at least six intercontinental exchanges during the last 4 million years (twice Eurasia-North America, North America-South America, twice South America-North America and Europe-South Africa). Repeated long-distance dispersal between the northern and southern hemisphere were important colonization mechanisms in Hordeum.     

Phylogenetic biogeography of the leafy liverwort Herbertus (Jungermanniales, Herbertaceae) based on nuclear and chloroplast DNA sequence data: correlation between genetic variation and geographical distribution

Aim The cosmopolitan genus Herbertus is notorious for having a difficult taxonomy and for the fact that there is limited knowledge of species ranges and relationships. Topologies generated from variable molecular markers are used to discuss biogeographical patterns in Herbertus and to compare them with the geological history of continents and outcomes reported for other land plants. Location Africa, Asia, Azores, Europe, southern South America, northern South America, North America, New Zealand. Methods Phylogenetic analyses of nuclear ribosomal internal transcribed spacer and chloroplast (cp) trnL–trnF sequences of 66 accessions of Herbertus and the outgroup species Triandrophyllum subtrifidum and Mastigophora diclados were used to investigate biogeographical patterns in Herbertus. Areas of putative endemism were defined based on the distribution of species included in the analyses. Maximum parsimony analyses were undertaken to reconstruct ancestral areas and intraspecies migration routes. Results The analyses reveal species‐level cladograms with a correlation between genetic variation and the geographical distribution of the related accessions. The southern South American Herbertus runcinatus is sister to the remainder of the genus, which is split into two main clades. One contains the Neotropical–African Herbertus juniperoideus and the New Zealand/Tasmanian Herbertus oldfieldianus. An African accession of H. juniperoideus is nested within Neotropical accessions. The second main clade includes species that inhabit Asia, the Holarctic, Africa, and northern South America. Maximum parsimony analyses indicate that this clade arose in Asia. Herbertus sendtneri originated in Asia and subsequently colonized the Holarctic and northern South America. An Asian origin and colonization into Africa is indicated for H. dicranus. Main conclusions The current distribution of Herbertus cannot be explained by Gondwanan vicariance. A more feasible explanation of the range is a combination of short‐distance dispersal, rare long‐distance dispersal events (especially into regions that faced floral displacements as a result of climatic changes) extinction, recolonization, and diversification. The African Herbertus flora is a mixture of Asian and Neotropical elements. Southern South America harbours an isolated species. The molecular data indicate partial decoupling of molecular and morphological variation in Herbertus. Biogeographical patterns in Herbertus are not dissimilar to those of other groups of bryophytes, but elucidation of the geographical ranges requires a molecular approach. Some patterns could be the result of maintenance of Herbertus in the inner Tropics during glacial maxima, and dispersal into temperate regions in warm phases.     

Molecular evidence for a Mediterranean origin of the Macaronesian endemic genus Argyranthemum (Asteraceae)

The internal transcribed spacers (ITS) of nuclear ribosomal DNA were sequenced for 52 species from 32 genera and eight subtribes of Anthemideae. Phylogenetic analyses of ITS data generated trees that are largely incongruent with the recent classification of Anthemideae; most of the subtribes examined are not resolved as monophyletic. However, ITS trees are congruent with morphological, isozyme, phytochemical, and chloroplast DNA (cpDNA) restriction site data in supporting a Mediterranean origin for Argyranthemum, the largest endemic genus of the Atlantic oceanic islands. A combined analysis of ITS sequences and cpDNA restriction sites indicates that Argyranthemum is sister to the other three genera of Chrysantheminae (i.e., Chrysanthemum, Heteranthemis, and Ismelia). Times of divergence of Argyranthemum inferred from the ITS sequences ranged between 0.26 and 2.1 million years ago (mya) and are lower than values previously reported from isozyme and cpDNA data (1.5-3.0 mya). It is likely that rate heterogeneity of the ITS sequences in the Anthemideae accounts for the low divergence-time estimates. Comparison of data for 20 species in Argyranthemum and Chrysantheminae indicates that the cpDNA restriction site approach provided much more phylogenetic information than ITS sequences. Thus, restriction site analyses of the entire chloroplast genome remain a valuable approach for studying recently derived island plants.     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

Phylogenetic relationships among four members of Stizostedion (Percidae) determined by mitochondrial DNA and allozyme analyses

Phylogenetic relationships among four Stizostedion species were examined using mitochondrial DNA (mtDNA) and allozyme analyses. Twenty-six allozyme loci were scored, and mtDNA variation was examined using 24 restriction endonucleases, yielding 48–57 restriction sites among the species. Genetic distance analyses show that the two North American species ( S. canadense and S. vitreum ) cluster in one group, while the two European species ( S. hciopercu and S. vogense ) form a second group. Nei's genetic distance between these two groups was 0.7 ± 0.2 for allozymes, while the corresponding mtDNA sequence divergence was 14.8 ± 2.0%, suggesting that these two groups diverged approximately 10 million years ago. Thus, these data are consistent with the hypothesis that Stizostedion colonized North America during the Pliocene.     

Taxonomic study of the genus Niwaella (Cypriniformes:Cobitidae) from East China,with description of four new species

Four loaches,Niwaella brevipinna Chen & Chen,sp.nov.,N.fimbriata Chen & Chen,sp.nov.,N.nigrolinea Chen & Chen,sp.nov.and N.qujiangensis Chen &Chen,sp.nov.,are described based on specimens collected from Zhejiang and Anhui Provinces,East China.The mitochondrial cytochrome b gene of 28 individuals of seven species from seven locations collected from Zhejiang,Anhui and Jiangxi Provinces were amplified and analyzed.Morphological and molecular data showed that N.fimbriata Chen & Chen,sp.nov.and N.nigrolinea Chen & Chen,sp.nov.,N.brevipinna Chen& Chen,sp.nov.and N.laterimaculata (Yan & Zheng),N.qujiangensis Chen & Chen,sp.nov.and N.longibarba Chen & Chen are closely related.The seven Chinese Niwaella species,N.brevipinna Chen & Chen,sp.nov.,N.fimbriata Chen & Chen,sp.nov.,N.laterimaculata,N.longibarba,N.nigrolinea Chen & Chen,sp.nov.,N.qujiangensis Chen & Chen,sp.nov.,and N.xinjiangensis are clearly distinguished by the combination of the color patter,mental lobes,suborbital spine,caudal peduncle,body shape,and subdorsal scales.     

Phylogenetic Study of Complete Cytochrome b Genes in Musk Deer (Genus Moschus) Using Museum Samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezovskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present). Interestingly, the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae.     

Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in Dianella (flax lilies; Asphodelaceae,Hemerocallidoideae)

A phylogeny of Dianella is presented based on Bayesian and maximum parsimony analyses of a combined molecular data set using three chloroplast markers (trnQ^UUG–5'rps16, 3'rps16–5'trnK^(UUU) and rpl14–rps8–infA–rpl36) and two nuclear markers (ITS and ETS). Accessions included most Dianella species, including all species from Australia, the centre of diversity for the genus, and related outgroup genera Eccremis, Stypandra, Thelionema and Herpolirion. The phylogeny showed Stypandra sister to Herpolirion + Thelionema, and confirmed the monophyly of Dianella. Within Dianella, a number of clades were resolved that revealed biogeographic relationships. Accessions from south-western Australia (extending into South Australia) formed the earliest diverging clade, followed by D. serrulata from New Guinea, sister to all other clades of Dianella from Australia and other regions. Tropical North Queensland species, including the D. pavopennacea complex, were related to a clade of accessions from New Caledonia and the Hawaiian Islands in the Pacific, and a clade that included samples of D. carolinensis (Caroline Islands) and the widespread D. ensifolia from South-East Asia and across the Indian Ocean to Mauritius and Madagascar. However, D. ensifolia is not monophyletic, with accessions from Japan and Taiwan related to a clade of Queensland samples that are part of the D. revoluta complex. Three New Zealand species (diploid, 2n?=?16) were found to be related to Norfolk Island D. intermedia (type locality; octoploid, 2n?=?64). In contrast ‘D. intermedia’ from Lord Howe Island was resolved as sister to the eastern Australian D. caerulea complex. The phylogenetic results indicate the need for taxonomic revision, particularly revision of the species ‘complexes’ D. longifolia and D. caerulea in Australia, and recognition of more than one species within D. ensifolia and within D. sandwicensis on the Hawaiian Islands.     

On the genetic diversity in the mitochondrial 12S rRNA gene of Platymantis frogs from Western New Guinea (Anura: Ceratobatrachidae)

Platymantis is a group of neobatrachian frogs that occurs from the Philippines to New Guinea – an area situated at the interface between the Australian and Asian biogeographical region that is highly fragmented by stretches of open sea. Partial sequences of the mitochondrial 12S rRNA gene are herein used to infer the relationships of species from the Indonesian part of New Guinea (Papua and West Papua Province). The phylogenetic trees reveal a deep bifurcation between the Asian and Western New Guinean clades being consistent with phylogeographic patterns observed in various other faunal groups. While most species are well differentiated in the examined locus, low interspecific genetic distances between one and three percent were observed in the New Guinean species Platymantis papuensis and P. cryptotis as well as P. pelewensis from Palau. Platymantis papuensis and P. pelewensis are geographically separated from each other by a 1100 km stretch of open sea. The minor degree of genetic differentiation between both species points to a recent event of transmarine dispersal as causation for the occurrence of P. pelewensis on Palau. The low genetic differentiation between P. cryptotis and the sympatric P. papuensis, two species that are bioacoustically and morphologically distinct, may indicate its possibly recent evolutionary origin or, alternatively, yet undetected hybridization between the two species. The same may also hold true for frogs from Yapen that exhibit calls different from the sympatric P. papuensis. Tentatively referred to as Platymantis spec., these frogs are also genetically not well differentiated. It is furthermore concluded that the partly low genetic differentiation of the New Guinean Platymantis species render this group one of the cases in which DNA barcoding would likely fail to produce reliable results.     

Phylogenetic relationships of Ceratitis fruit flies inferred from nuclear CAD and tango/ARNT gene fragments: Testing monophyly of the subgenera Ceratitis (Ceratitis) and C. (Pterandrus)

Systematic studies of Ceratitis (Tephritidae) fruit flies using molecular (i.e., COI, ND6, and period genes) and morphological (plus host-use characters) data have recently challenged the monophyly of the subgenera Ceratitis (Ceratitis) and Ceratitis (Pterandrus). In this paper, we report on the phylogenetic utility of three single-copy nuclear gene regions (two non-overlapping fragments of the carbamoylphosphate synthetase, CPS, locus of CAD, and a fragment of tango) within these taxa and investigate evolutionary relationships based on a concatenated ca. 3.4 kb data set that includes the six protein encoding gene regions. Results indicate that the CAD and tango genes provide useful phylogenetic signal within the taxa and are compatible with the previously studied genes. The two subgenera, as currently classified, are not monophyletic. Our molecular phylogenetic analyses support a revised classification in which (1) the subgenus C. (Pterandrus) comprises two lineages called A and B, (2) the C. (Pterandrus) B species should be included in C. (Ceratitis), and (3) the newly defined subgenera C. (Pterandrus) (=Pterandrus section A) and C. (Ceratitis) [=C. (Ceratitis) + C. (Pterandrus) section B] are reciprocally monophyletic.     

Out of Africa? Phylogenetic relationships between Falco biarmicus and the other hierofalcons (Aves: Falconidae)

The phylogeographic history of the lanner falcon ( Falco biarmicus ) and the phylogenetic relationships among hierofalcons ( F. biarmicus , Falco cherrug , Falco jugger and Falco rusticolus ) were investigated using mitochondrial (mt) DNA sequences. Of the two non-coding mt sections tested, the control region (CR) appeared more suitable as phylogenetic marker sequence compared with the pseudo control region (ΨCR). For the comprehensive analysis samples from a broad geographic range representing all four hierofalcon species and their currently recognized subspecies were included. Moreover, samples of Falco mexicanus were analysed to elucidate its phylogenetic relationships to the hierofalcons. The sequence data indicate that this species is more closely related to Falco peregrinus than to the hierofalcons. In the DNA-based trees and in the maximum parsimony network all hierofalcons appear closely related and none of the species represents a monophyletic group. The close relationships among haplotypes suggest that the hierofalcon complex is an assemblage of morphospecies not yet differentiated in the genetic markers used in the present study and that the radiation of the four hierofalcon species took place rather recently. Based on the high intraspecific diversity found within F. biarmicus we assume an African origin of the hierofalcon complex. The observed pattern of haplotype distribution in the extant species may be due to incomplete lineage sorting of ancestral polymorphisms, and interspecific gene flow through hybridization.     

Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia,Muridae) inferred from molecular data,with description of a new species

Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscus chiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscus chiropus (the type species of Chiromyscus), Chiromyscus langbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscus thomasi sp. n.