A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences

Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.     

Phylogenetic position of the genus Tetraophasis (Aves, Galliformes, Phasianidae) as inferred from mitochondrial and nuclear sequences

The genus Tetraophasis is endemic to China and the systematic relationships of the genus in Phasianidae based solely on their morphology are not clear. The phylogenetic position of this genus and other genera in Phasianidae was investigated in this study using the mitochondrial genes cytochrome b (CYT B), NADH dehydrogenase subunit 2 (ND2) and nuclear ovomucoid intron G (OVO-G). Maximum parsimony, Bayesian and maximum likelihood analyses were employed. Comparison between the mitochondrial and nuclear findings suggested that our final combined data had higher resolving power than the separate data. Both separate data and combined data yielded a sister relationship between Tetraophasis and Lophophorus with strong support, which provided new evidence that pheasants and partridges were not monophyletic. In addition, our results indicated a basal position of Ithaginis, but the position of Perdix and Pucrasia were still unresolved. The result of this study provided a phylogenetic background for a revised classification of Galliformes.     

Novel features of metazoan mtDNA revealed from sequence analysis of three mitochondrial DNA segments of the land snail Albinaria turrita (Gastropoda: Clausiliidae)

The mitochondrial DNA (mtDNA) size of the terrestrial gastropod Albinaria turrita was determined by restriction enzyme mapping and found to be approximately 14.5 kb. Its partial gene content and organization were examined by sequencing three cloned segments representing about one-fourth of the mtDNA molecule. Complete sequences of cytochrome c oxidase subunit II (COII), and ATPase subunit 8 (ATPase8), as well as partial sequences of cytochrome c oxidase subunit I (COI), NADH dehydrogenase subunit 6 (ND6), and the large ribosomal RNA (IrRNA) genes were determined. Nine putative tRNA genes were also identified by their ability to conform to typical mitochondrial tRNA secondary structures. An 82-nt sequence resembles a noncoding region of the bivalve Mytilus edulis, even though it might contain a tenth tRNA gene with an unusual 5-nt overlap with another tRNA gene. The genetic code of Albinaria turrita appears to be the same as that of Drosophila and Mytilus edulis. The structures of COI and COII are conservative, but those of ATPase8 and ND6 are diversified. The sequenced portion of thelrRNA gene (1,079 nt) is characterized by conspicuous deletions in the 5 and 3 ends; this gene represents the smallest coelomate IrRNA gene so far known. Sequence comparisons of the identified genes indicate that there is greater difference between Albinaria and Mytilus than between Albinaria and Drosophila. An evolutionary analysis, based on COII sequences, suggests a possible nonmonophyletic origin of molluskan mtDNA. This is supported also by the absence of the ATPase8 gene in the mtDNA of Mytilus and nematodes, while this gene is present in the mtDNA of Albinaria and Cepaea nemoralis and in all other known coelomate metazoan mtDNAs.     

Phytogeny of Brassica and allied genera based on variation in chloroplast and mitochondrial DNA patterns: molecular and taxonomic classifications are incongruous

Summary Chloroplast DNA (cpDNA) variability of 60 taxa of the genus Brassica and allied genera comprising 50 species was studied. RFLPs for seven enzymes were generated and F values were estimated from five frequently cutting enzymes. Phenetic clusterings indicated a clear division of Brassica coenospecies into two distinct lineages referred to as the Brassica and Sinapis lineages. Two unexplored genera, Diplotaxis and Erucastrum, also exhibited two lineages in addition to the genera Brassica and Sinapis. This finding is inconsistent with the existing taxonomic classification based on morphology. Mitochondrial DNA (mtDNA) variability studied from EcoRI RFLP patterns, by hybridizing total DNA with four cosmid clones containing non-overlapping mtDNA fragments, did not show any congruence with cpDNA variation patterns. However, at the cytodeme level, the patterns of genetic divergence suggested by the cpDNA data could be correlated with mtDNA variation. In the Brassica lineage, Diplotaxis viminea was identified as the female parent of the allotetraploid D. muralis. The chloroplast DNAs of Erucastrum strigosum and Er. abyssinicum were found to be very closely related. In the Sinapis lineage, Brassica maurorum was found to be the diploid progenitor of autotetraploid B. cossoneana. B. amplexicaulis showed a very different cpDNA pattern from other members of the subtribe. Brassica adpressa was closest to Erucastrum laevigatum and could be the diploid progenitor of autotetraploid Er. laevigatum. Based on the close similarity of the cpDNA pattern of Diplotaxis siifolia with that of D. assurgens, we have proposed the retention of this species in the genus Diplotaxis. The taxonomic positions of some other species have also been discussed.     

Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report

We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates. Correspondence to: S. Horai     

Evidence from DNA nucleotide sequences and ISSR profiles indicates paraphyly in subspecies of the Southern Grey Shrike (Lanius meridionalis)

We obtained DNA sequence data from mitochondrial (cytochrome b) and nuclear genes (myoglobin and ornithine decarboxylase) to reconstruct the phylogenetic relationships among eight species of shrikes (Lanius). Phylogenetic analyses based on maximum parsimony, maximum likelihood and Bayesian inference all converged into a congruent topology and defined several well-supported clades. Our multi-gene approach based on nucleotide sequences from fast-evolving and conserved genes strongly supported the paraphyly of Southern Grey Shrikes (Lanius meridionalis). The Canary Islands subspecies (L. m. koenigi) differed significantly from its European counterpart (L. m. meridionalis). Furthermore, the genetic distinctiveness of L. m. koenigi was confirmed by ISSR genomic fingerprinting. By contrast, we did not find evidence to distinguish the Canarian Southern Grey Shrike from L. m. algeriensis on the African mainland (Tunisia), and therefore these two taxa may be considered as synonymous. Together, they correspond to a separate species. The origin of the taxa investigated in this study might have originated about 6 Mya at the Miocene/Pliocene boundary when a remarkable worldwide faunal turnover and global vegetation change occurred. The Lanius genus represents a complex and taxonomically challenging group that requires additional research.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Phylogeography of the blue tit ( Parus teneriffae -group) on the Canary Islands based on mitochondrial DNA sequence data and morphometrics

An analysis of the sequences of the mitochondrial cytochrome b gene (1005 bp) of the Parus teneriffae-group from the Canary Islands and North Africa revealed new insights into the phylogeography of this taxon. The origin of the radiation on the Canarian Archipelago was apparently one of the central islands—Tenerife or Gran Canaria. The populations on El Hierro (P. t. ombriosus) and La Palma (P. t. palmensis) represent distinct monophyletic lineages. Blue tits from Gran Canaria are genetically distinct from those of La Gomera and Tenerife (P. t. teneriffae), which supports the results of other studies and suggests the existence of an—until now—undescribed taxon there. In contrast, the populations on the eastern islands of Fuerteventura and Lanzarote (P. t. degener) could not be distinguished from North African blue tits (P. t. ultramarinus), and these populations should be subsumed under the subspecies ultramarinus. Taxonomic recommendations based on these results include the distinction of the northern European P. caeruleus from P. teneriffae, including blue tits from North Africa and the Canary Islands, the treatment of degener and ultramarinus as synonymous (P. teneriffae ultramarinus) and a new blue tit taxon on the island of Gran Canaria (P. t. hedwigii nov. ssp.), which is formally described. The genetic results are in parts supported by bioacoustic and morphological data.     

The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications

The population genetic structure of the loggerhead sea turtle (Caretta caretta) nesting in the eastern Mediterranean was assessed by sequencing a fragment of the control region of the mitochondrial DNA (n = 190) and seven microsatellites (n = 112). The two types of markers revealed genetic structuring (mtDNA: γ_st = 0.212, P < 0.001; nDNA F _st = 0.006, P < 0.001), thus indicating that both females and males are philopatric and that gene flow between populations is restricted. Mitochondrial DNA data indicate that the female populations nesting on the islands of Crete and Cyprus have suffered a recent bottleneck or colonization event. However, no bottleneck or founder effect was revealed by nuclear markers, thus indicating male-mediated gene flow from other populations that would increase nuclear genetic variability. Crete, and to a lower extent Cyprus, are thought to play a central role in such male-mediated gene flow that may reduce the negative effect of genetic drift or inbreeding on the small populations of Lebanon and Israel. This population structure indicates that assessing population relevance only on the basis of genetic variability and size would be misleading, as some populations not fulfilling those requirements may play a relevant role in genetic exchange and hence contribute to the overall genetic variability.     

The genus Setulipes (Marasmiaceae) in Madagascar and the Mascarenes, including a key to other African taxa

The authors report first records for the genus Setulipes in Madagascar, with the presence of Setulipes cf. hakgalensis and two new species, Setulipes funaliformis and S. moreaui, as well as a new species from Mauritius: S. mauritiensis. A key to these taxa, as well as to other African species, is supplied.     

Achlya mitochondrial DNA: gene localization and analysis of inverted repeats

Summary Mitochondrial DNA from four strains of the oomycete Achlya has been compared and nine gene loci mapped, including that of the ribosomal protein gene, var1. Examination of the restriction enzyme site maps showed the presence of four insertions relative to a map common to all four strains. All the insertions were found in close proximity to genic regions. The four strains also cotained the inverted repeat first observed in A. ambisexualis (Hudspeth et al. 1983), allowing an examination by analysis of retained restriction sites of the evolutionary stability of repeated DNA sequences relative to single copy sequences. Although the inverted repeat is significantly more stable than single copy sequences, more detailed analysis indicated that this stability is limited to the portion encoding the ribosomal RNA genes. Thus, the apparent evolutionary stability of the repeat does not appear to derive from the inverted repeat structure per se.Abbreviations ATPase 6, 9 genes for ATPase subunits 6 and 9 - COI, II, III genes for cytochrome oxidase subunits 1, 2, and 3 - COB gene for apocytochrome b - L-, S-RNA genes for the mitochondrial large and small ribosomal RNAs - mtDNA mitochondrial DNA - var1 gene for the S. cerevisiae mitochondrially, encoded ribosomal protein - m.u. map units - bp base pairs - kb kilobase pairs     

On the phylogenetic position of the Okinawa woodpecker (Sapheopipo noguchii)

The Okinawa woodpecker Sapheopipo noguchii is the rarest extant woodpecker species. The monotypic genus Sapheopipo was considered to be a representative of an old lineage of woodpeckers that led to the Eurasian genera Picus and the Blythipicus–Gecinulus species. This view, based on similarities in color patterns, external morphology and foraging behavior, has been adopted in all major accounts of the family. The alternative view, that this woodpecker may be related to the widespread white-backed woodpecker Dendrocopos leucotos, which evolved distinctive subspecies on other East Asian islands, has not been generally accepted. We analyzed partial sequences of the mitochondrial cytochrome b (cyt b) gene to test these hypotheses. The data suggest that the Okinawa woodpecker is a member of the genus Dendrocopos, with white-backed woodpecker and great spotted woodpecker D. major as close relatives. Color patterns support the genetic results and indicate a closer relationship with the white-backed woodpecker. Consequently, the correct taxonomic designation of the Okinawa woodpecker would be Dendrocopos noguchii (Seebohm in Ibis 5(5):173–182, 1887) in the tribe Campetherini rather than Picini.This revised version was published online in February 2005 with corrections to tables 1 and 2.     

Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences

Wild common carp from two lakes and two rivers in Greece were genetically characterized with sequencing analysis of two mitochondrial DNA segments: cytochrome b (1119 bp) and D-loop (646 bp). A total of 9 variable singleton sites and 7 unique haplotypes were detected. A common haplotype was found in three out of the four populations examined, which seems to be the ancestral one and represents the European origin of common carp from Greece. This haplotype could be also justified by the introductions reported with individuals belonging to the Central European race, into many natural habitats in Greece. Limited genetic variation — in Evros and Aliakmonas populations — could be due to bottleneck effects and small effective population sizes, whereas the different haplotypes found in Lake Volvi could represent different common carp stocks. Values of sequence divergence among Greek haplotypes ranged from 0.0006 to 0.0023. The Neighbour-Joining (NJ) phylogenetic tree constructed based on the combined sequences, reveals that the populations of common carp from Greece belong to the European group of populations — which is highly divergent from the South East-Asia cluster — and to the subspecies Cyprinus carpio carpio.     

A vital function for mitochondrial DNA in the petite-negative yeastKluyveromyces lactis

Petite-negative yeasts do not form viable respiratory-deficient mutants on treatment with DNA-targeting drugs that readily eliminate the mitochondial DNA (mtDNA) from petite-positive yeasts. However, in the petite-negative yeastKluyveromyces lactis, specific mutations in the nuclear genesMGI2 andMGI5 encoding the- and-subunits of the mitochondrial F₁-ATPase, allow mtDNA to be lost. In this study we show that wild-typeK. lactis does not survive in the absence of its mitochondrial genome and that the function ofmgi mutations is to suppress lethality caused by loss of mtDNA. Firstly, we find that loss of a multicopy plasmid bearing amgi allele readily occurs from a wild-type strain with functional mtDNA but is not tolerated in the absence of mtDNA. Secondly, we cloned theK. lactis homologue of theSaccharomyces cerevisiae mitochondrial genome maintenance geneMGM101, and disrupted one of the two copies in a diploid. Following sporulation, we find that segregants containing the disrupted gene form minicolonies containing 6-8000 inviable cells. By contrast, disruption ofMGM101 is not lethal in a haploidmgi strain with a specific mutation in a subunit of the mitochondrial F₁-ATPase. These observations suggest that mtDNA inK. lactis encodes a vital function which may reside in one of the three mitochondrially encoded subunits of F₀.     

TheBrassica mitochondrial DNA plasmid and large RNAs are not exclusively associated with cytoplasmic male sterility

Summary More than 100 differentBrassica nucleo-cytoplasmic combinations were analysed for the presence or absence of the 11.3 kb mitochondrial plasmid. Contrary to some previous reports, no close association exists between the presence of the plasmid and cytoplasmic male sterility. Some novel abundant RNAs which copurified withBrassica mitochondria are described.     

Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences

This study investigates the molecular phylogeny of seven lionfishes of the genera Dendrochirus and Pterois. MP, ML, and NJ phylogenetic analysis based on 964 bp of partial mitochondrial DNA sequences (cytochrome b and 16S rDNA) revealed two main clades: (1) “Pterois” clade (Pterois miles and Pterois volitans), and (2) “Pteropterus–Dendrochirus” clade (remainder of the sampled species). The position of Dendrochirus brachypterus either basal to the main clades or in the “Pteropterus–Dendrochirus” clade cannot be resolved. However, the molecular phylogeny did not support the current separation of the genera Pterois and Dendrochirus. The siblings P. miles and P. volitans are clearly separated and our results support the proposed allopatric or parapatric distribution in the Indian and Pacific Ocean. However, the present analysis cannot reveal if P. miles and P. volitans are separate species or two populations of a single species, because the observed separation in different clades can be either explained by speciation or lineage sorting. Molecular clock estimates for the siblings P. miles and P. volitans suggest a divergence time of 2.4–8.3 mya, which coincide with geological events that created vicariance between populations of the Indian and Pacific Ocean.     

Involvement of two differenturf-s related mitochondrial sequences in the molecular evolution of the CMS-specificS-Pcf locus in petunia

In petunia, a mitochondrial (mt) locus,S-Pcf, has been found to be strongly associated with cytoplasmic male sterility (CMS). TheS-Pcf locus consists of three open reading frames (ORF) that are co-transcribed. The first ORF,Pcf, contains parts of theatp9 andcoxII genes and an unidentified reading frame,urf-s. The second and third ORFs contain NADH dehydrogenase subunit 3 (nad3) and ribosomal protein S12 (rps12) sequences, respectively. Thenad3 andrps12 sequences included in theS-Pcf locus are identical to the corresponding sequences on the mt genome of fertile petunia. In both CMS and fertile petunia, only a single copy ofnad3 andrps12 has been detected on the physical map of the main mt genome. The origin of theurf-s sequence and the molecular events leading to the formation of the chimericS-Pcf locus are not known. This paper presents evidence indicating that two different mt sequences, related tourf-s and found in fertile petunia lines (orf-h and Rf-1), might have been involved in the molecular evolution of theS-Pcf locus. Southern analysis of mtDNA derived from both fertile and sterile petunia plants suggests that one of theseurf-s related sequences (showing 100% homology tourf-s and termedorf-h) is located on a sublimon. An additional, low-homologyurf-s related sequence (Rf-1) is shown to be located on the main mt genome 5′ to thenad3 gene. It is, thus, suggested that the sequence of events leading to the generation of theS-Pcf locus might have involved introduction of theorf-h sequence, via homologous recombination, into the main mt genome 5′ tonad3 at the region where the Rf-1 sequence is located. Contribution [No. 1581-E (1995 series)] from the Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel 50 250     

comparison between the complete mitochondrial DNA sequences ofHomo and the common chimpanzee based on nonchimeric sequences

The complete mitochondrial DNA (mtDNA) molecules ofHomo and of the common chimpanzee were sequenced. Each sequence was established from tissue of one individual and thus nonchimeric. Both sequences were assembled in their entirety from natural (not PCR amplified) clones. Comparison with sequences in the literature identified the chimpanzee specimen asPan troglodytes verus, the West African variety of the species. The nucleotide difference between the complete human and chimpanzee sequences is 8.9%. The difference between the control regions of the two sequences is 13.9% and that between the remaining portions of the sequences 8.5%. The mean amino acid difference between the inferred products of the 13 peptide-coding genes is 4.4%. Sequences of the complete control regions, the complete 12S rRNA genes, the complete cytochromeb genes, and portions of the NADH4 and NADH5 genes of two other chimpanzee specimens showed that they were similar but strikingly different from the same regions of the completely sequenced molecule fromPan troglodytes verus. The two specimens were identified asPan troglodytes troglodytes, the Central African variety of the common chimpanzee.