DNA sequence data reveal a subfamily-level divergence within Thamnophilidae (Aves: Passeriformes)

The Thamnophilidae is a diverse radiation of insectivorous passerine birds that comprises nearly 220 species and is mostly restricted to the lowlands and lower montane forests of the Neotropics. Current classification within Thamnophilidae relies primarily on morphological variation, but recent incorporation of molecular and vocal data has promoted changes at various taxonomic levels. Here we demonstrate that the genus Terenura is polyphyletic because Terenura callinota, T. humeralis, T. spodioptila, and T. sharpei are phylogenetically distant from the type species of the genus, Terenura maculata. More importantly, the former four species are not particularly closely related to any other thamnophilids and represent a clade that is sister to all other members of the family. Because no genus name is available for this previously undetected lineage in the Thamnophilidae, we describe the genus Euchrepomis for callinota, humeralis, spodioptila, and sharpei, and erect the subfamily Euchrepomidinae. We discuss the taxonomic and evolutionary significance of this divergent lineage. This study highlights the importance of taxonomic coverage and the inclusion of type taxa to redefine classifications to reflect accurately evolutionary relationships.     

Molecular phylogeny of the Canary Island lacertids (Gallotia): mitochondrial DNA restriction fragment divergence in relation to sequence divergence and geological time

Restriction fragment length polymorphisms of 6 base pair recognising endonucleases are used to reconstruct the phylogeny of the endemic Canary Island lacertid, Gallotia. The division into conventional species is upheld by this molecular analysis and the western Canary Island lizard (G. galloti) and eastern Canary Island lizard (G. atlantica) are hypothesized to be sister species. A more comprehensive study of the intraspecific relationships of G. galloti, based on nineteen restriction enzymes, indicates that there are distinct southern and northern lineages within this species. The phylogenetic analysis does not uphold the conventional subspecies, but suggests an alternative arrangement with one northern (La Palma, Tenerife) and one southern (Gomera, Hierro) subspecies. The inferred timing of molecular divergence of populations of G. galloti, based on RFLP analysis, is compatible with the geological timing for island origin and fossil data. Mantel tests show that mitochondrial RFLP divergence is correlated with mitrochondrial 12s rRNA and cytochrome oxidase I sequence divergence and highly correlated with mitochondrial cytochrome b sequence divergence.     

Evolutionary and biogeographic patterns of the Badidae (Teleostei: Perciformes) inferred from mitochondrial and nuclear DNA sequence data

We reconstructed phylogenetic relationships of the family Badidae using both mitochondrial and nuclear nucleotide sequence data to address badid systematics and to evaluate the role of vicariant speciation on their evolution and current distribution. Phy-logenetic hypotheses were derived from complete cytochrome b (1,140 base pairs) sequences of 33 individuals representing 13 badid species, and using three species of Nandidae as outgroups. Additionally, we sequenced the nuclear RAG1 (1,473 base pairs) and Tmo-4C4 (511 base pairs) genes from each of the badid species and one representative of the outgroup. Our molecular data provide the first phylogenetic hypothesis of badid intrarelationships. Analysis of the mitochondrial and nuclear nucleotide sequence data sets resulted in well-supported trees, indicating a basal split between the genera Dario and Badis, and further supporting the division of the genus Badis into five species groups as suggested by a previous taxonomic revision of the Badidae. Within the genus Badis, mitochondrial and nuclear phylogenies differed in the relative position of B. kyar. We also used our molecular phylogeny to test a vicariant speciation hypothesis derived from geological evidence of large-scale changes in drainage patterns in the Miocene affecting the Irrawaddy- and Tsangpo-Brahmaputra drainages, in the southeastern Himalaya. Within both genera, Badis and Dario, we observed a divergence into Irrawaddy- and Tsangpo-Brahmaputra clades. Using a cytb substitution rate of 8.2 x 10(-9) (substitutions x base pair(-1) x year(-1), we tentatively date this vicariant event at the Oligocene-Miocene boundary (19-24Myr). It is concordant with a hypothesized paleo connection of the Tsangpo river with the Irrawaddy drainage that was most likely interrupted during Miocene orogenic events through tectonic uplifts in eastern Tibet. Our data, therefore, indicate a substantial role of vicariant-based speciation shaping the current distribution patterns of badids.     

Morphological variation of hypaxial musculature in salamanders (Lissamphibia: Caudata)

Despite the acknowledged importance of the locomotory and respiratory functions associated with hypaxial musculature in salamanders, variation in gross morphology of this musculature has not been documented or evaluated within a phylogenetic or ecological context. In this study, we characterize and quantify the morphological variation of lateral hypaxial muscles using phylogenetically and ecologically diverse salamander species from eight families: Ambystomatidae (Ambystoma tigrinum), Amphiumidae (Amphiuma tridactylum), Cryptobranchidae (Cryptobranchus alleganiensis), Dicamptodontidae (Dicamptodon sp.), Plethodontidae (Gyrinophilus porphyriticus), Proteidae (Necturus maculosus), Salamandridae (Pachytriton sp.), and Sirenidae (Siren lacertina). For the lateral hypaxial musculature, we document 1) the presence or absence of muscle layers, 2) the muscle fiber angles of layers at mid‐trunk, and 3) the relative dorsoventral positions and cross‐sectional areas of muscle layers. Combinations of two, three, or four layers are observed. However, all species retain at least two layers with opposing fiber angles. The number of layers and the presence or absence of layers vary within species (Necturus maculosus and Siren lacertina), within genera (e.g., Triturus), and within families. No phylogenetic pattern in the number of layers can be detected with a family‐level phylogeny. Fiber angle variation of hypaxial muscles is considerable: fiber angles of the M. obliquus externus range from 20–80°; M. obliquus internus, 14–34°; M. transversus abdominis, 58–80° (acute angles measured relative to the horizontal septum). Hypaxial musculature comprises 17–37% of total trunk cross‐sectional area. Aquatic salamanders show relatively larger total cross‐sectional hypaxial area than salamanders that are primarily terrestrial. J. Morphol. 241:153–164, 1999. © 1999 Wiley‐Liss, Inc.     

Episodes of adaptive evolution of mitochondrial genome in asiatic salamanders (Amphibia,Caudata, Hynobiidae)

To elucidate the effect of natural selection on the evolution of mitochondrial DNA (mtDNA) in Asiatic salamanders of the family Hynobiidae, nucleotide sequences of 12 protein-coding genes were analyzed. Using a mixed effects model of evolution, it was found that, in spite of the pronounced effect of negative selection on the mtDNA evolution in Hynobiidae (which is typical for the animals in general), two phylogenetic clusters, the West Asian one, represented by the genera Ranodon and Paradactylodon, and North Eurasian one, represented by the genus Salamandrella, were formed under the influence of episodic positive selection. Analysis of protein sequences encoded by the mitochondrial genome also supported the influence of positive selection on the evolution of Hynobiidae at some stages of their cladogenesis. It is suggested that the signatures of adaptive evolution detected in the mtDNA of Hynobiidae were determined by the complex and long-lasting history of their formation, accompanied by adaptation to the changing environment.     

Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings

We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian mt genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians.     

The complete mitochondrial genome sequence of the Kori salamander Hynobius yangi (Caudata: Hynobiidae)

The complete mitochondrial genome (JN415127) was sequenced and annotated newly from an individual of Hynobius yangi populations which were collected in Ulju-gun, Korea. The total length of the H. yangi genome is 16,403 bp, with a total base composition of 33.5% A, 32.3% T, 20.5% C, and 13.6% G.     

Molecular phylogeny and evolution of Sorex shrews (Soricidae: insectivora) inferred from mitochondrial DNA sequence data

Shrews of the genus Sorex are characterized by a Holarctic distribution, and relationships among extant taxa have never been fully resolved. Phylogenies have been proposed based on morphological, karyological, and biochemical comparisons, but these analyses often produced controversial and contradictory results. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences (1011 bp) were used to examine the relationships among 27 Sorex species. The molecular data suggest that Sorex comprises two major monophyletic lineages, one restricted mostly to the New World and one with a primarily Palearctic distribution. Furthermore, several sister-species relationships are revealed by the analysis. Based on the split between the Soricinae and Crocidurinae subfamilies, we used a 95% confidence interval for both the calibration of a molecular clock and the subsequent calculation of major diversification events within the genus Sorex. Our analysis does not support an unambiguous acceleration of the molecular clock in shrews, the estimated rate being similar to other estimates of mammalian mitochondrial clocks. In addition, the data presented here indicate that estimates from the fossil record greatly underestimate divergence dates among Sorex taxa.     

Recent divergence between two morphologically differentiated subspecies of bluethroat (Aves: Muscicapidae: Luscinia svecica) inferred from mitochondrial DNA sequence variation

We assessed the mitochondrial DNA sequence divergence of a 718 bp fragment of the control region and 1007 bp of the cytochrome b gene between two allopatric morphologically different subspecies of bluethroat ( Luscinia svecica ). None of the 17 total haplotypes was shared between L. s. namnetum and L. s. svecica . However, the mean distances between subspecies were very low for both fragments (0.00168 ± 0.00001 (mean ± SE) for the control region; 0.00306 ± 0.00016 for the cytochrome b gene). Only one substitution made the two subspecies genetically differentiated, highlighting their recent divergence. Interestingly, the control region was not more variable than the cytochrome b gene.     

Radiation and divergence in the Rhagoletis pomonella species complex: inferences from DNA sequence data

Here, we investigate the evolutionary history and pattern of genetic divergence in the Rhagoletis pomonella (Diptera: Tephritidae) sibling species complex, a model for sympatric speciation via host plant shifting, using 11 anonymous nuclear genes and mtDNA. We report that DNA sequence results largely coincide with those of previous allozyme studies. Rhagoletis cornivora was basal in the complex, distinguished by fixed substitutions at all loci. Gene trees did not provide reciprocally monophyletic relationships among US populations of R. pomonella, R. mendax, R. zephyria and the undescribed flowering dogwood fly. However, private alleles were found for these taxa for certain loci. We discuss the implications of the results with respect to identifiable genetic signposts (stages) of speciation, the mosaic nature of genomic differentiation distinguishing formative species and a concept of speciation mode plurality involving a biogeographic contribution to sympatric speciation in the R. pomonella complex.     

VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data

SUMMARY: VeriScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; (3) facilitates the visualization of the results in the most commonly used genome browsers.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.     

Phylogenetic relationships of honey bees (Hymenoptera:Apinae:Apini) inferred from nuclear and mitochondrial DNA sequence data

Two different genomic regions (ND2 mitochondrial gene and EF1-alpha intron) were PCR amplified, cloned and sequenced for the ten known honey bee species collected within their natural range distribution. DNA sequences were analyzed using parsimony, distance and maximum likelihood methods to investigate phylogenetic relationships within Apis. The phylogenetic analyses strongly supported the basic topology recoverable from morphometric analysis, grouping the honey bees into three major clusters: giant bees (A. dorsata, A. binghami, and A. laboriosa), dwarf bees (A. andreniformis and A. florea), and cavity-nesting bees (A. mellifera, A. cerana, A. koschevnikovi, A. nuluensis, and A. nigrocincta). However, the clade of Asian cavity-nesting bees included paraphyletic taxa. Exemplars of Apis cerana collected from divergent portions of its range were less related to each other than were sympatric A. cerana, A. nuluensis, and A. nigrocincta taxa. Nucleotide sequence divergence between allopatrically distributed western (A. mellifera) and eastern (A. cerana, A. koschevnikovi, A. nigrocincta, and A. nuluensis) cavity-nesting species, around 18% for the mitochondrial gene and 10-15% for the nuclear intron, suggested an earlier divergence for these groups than previously estimated from morphometric and behavioral studies. This latter finding neccessitates reevaluation of the hypothesized origin of extant European, African, and west Asian Apis mellifera. Sequence divergence between A. laboriosa and A. dorsata was consistent with behavioral data and supports the species status of A. laboriosa.     

Detecting a genetic bottleneck in Gilbert's Potoroo (Potorous gilbertii) (Marsupialia: Potoroidae), inferred from microsatellite and mitochondrial DNA sequence data

Gilbert's Potoroo isAustralia's most critically endangeredmarsupial, known from a single population inthe Two Peoples Bay National Park in WesternAustralia. We present results from a study ofgenetic variation in microsatellite andmitochondrial DNA. Mean heterozygosity at fivemicrosatellite loci was 49.3%, and the amountof mtDNA variation was extremely low ( =0.0004). There was evidence for a bottleneckin both sets of markers, and this wasconsistent with a demographic decline. Effective population size was estimated usingtwo different models of mutation formicrosatellites (N _e = 243 and 362). The results from this study highlight theconcern for the long-term survival of thisspecies.     

Status of Japanese Dytiscus species (Coleoptera: Dytiscidae) based on mitochondrial DNA sequence data

We sequenced 628 base pairs of the mitochondrial cytochrome‐c oxidase subunit 1 (cox1) gene to investigate the genetic differentiation among Japanese Dytiscus diving beetles (Coleoptera: Dytiscidae). Dytiscus beetles are a charismatic part of the fauna of lakes, ponds and swamps. Three species are known from Japan: D. dauricus Gebler, 1832; D. marginalis czerskii Zeitzev * , 1953; and D. sharpi Wehncke, 1875. Adults of D. sharpi collected in Chiba and Ishikawa Prefectures were morphologically highly similar, but here we found that they differed by 20 cox1 base pairs (3.18%). Our results imply that conservation strategies especially for Japanese D. sharpi sharpi and D. sharpi validus Régimbart, 1899 might need to be adjusted to address the presence of two evolutionarily significant units.     

Phylogenetics of barbets (Aves: Piciformes) based on nuclear and mitochondrial DNA sequence data

A combination of nuclear (beta-fibrinogen intron 7; 938 bp) and mitochondrial (cytochrome b; 1045 bp) DNA sequence data analyzed with model-based phylogenetic methods yields a hypothesis of barbet and toucan relationships supported by high Bayesian posterior probabilities and several synapomorphic indels in the nuclear intron data. The basal topology differs from previous morphology and mitochondrial DNA sequence based hypotheses, but is consistent with DNA-DNA hybridization results. The mitochondrial DNA sequence data provide resolution at the tips of the tree, but when analyzed alone, yield a different basal topology than the combined data. However, the basal nodes in the mitochondrial-based tree have little statistical support. Combined data analysis produced strong statistical support at basal nodes and a relatively simple geographic structure. Barbets from each of the three tropical regions are monophyletic, but the Old World barbets are paraphyletic. The African and New World clades are sister taxa, and the Asian clade is basal. This geographic structure indicates that similarities in plumage, voice, and behavior between Gymnobucco and Calorhamphus are convergent. The data are not conclusive, but suggest paraphyly of the New World barbets. Only 4% of the Bayesian posterior distribution unites Semnornis with the other New World barbets.     

Multiple cryptic genetic units in Hypothenemus hampei (Coleoptera: Scolytinae): evidence from microsatellite and mitochondrial DNA sequence data

Hypothenemus hampei is the most important insect pest of coffee and has spread to most coffee‐growing countries worldwide. There have been very few studies and none have addressed the population genetics of the beetle using microsatellite markers. In the present study, 683 individuals collected from 37 locations in 18 countries worldwide were screened at nine polymorphic microsatellite loci. Sixty‐five out the 683 and six additional individuals were analyzed on a 400‐bp fragment of the mitochondrial cytochrome oxidase I gene. Bayesian clustering analysis and phylogenetic approaches were used to infer the genetic structure of H. hampei over the sampling that encompassed almost all its range. Microsatellite markers made it possible to achieve sufficiently significant power for the delineation of five morphocryptic evolutionary units. Supported by 27 new COI haplotypes, an unexpected considerably high level of genetic differentiation and genetic divergence was revealed between five geographically delineated clusters. Both markers and approaches showed that the clusters included specimens from (1) Ethiopia, (2) Kenya and Uganda, (3) Brazil, (4) Central America excluding Jamaica, and (5) all samples from Asia, West Africa, and Jamaica. These findings clearly suggest the existence of a ‘species complex in H. hampei’. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 113–129.     

Measuring genome divergence in bacteria: a case study using chlamydian data

We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estimated to 59 +/- 6 events, including 13% inversions, 38% short inversions, and 49% transpositions. In contrast to previous findings, no examples of horizontal gene transfer subsequent to species divergence were identified, nor any evidence for an excessive number of tandem gene duplications. A statistical model was used to compare nucleotide frequencies for a set of genes uniquely present in one species to a set of orthologous genes present in both species. The two data sets were not significantly different, which is indicative of a low frequency of horizontal gene transfer events. This is based on the assumption that a foreign gene of different nucleotide content will not have become completely ameliorated, as verified by simulations of the amelioration rate at twofold and fourfold degenerate codon sites. The frequencies of nucleotide substitutions at twofold and fourfold degenerate sites, deletions, inversions, and translocations were estimated to 1.42, 0.62, 0.18, 0.01, and 0.01 per site, respectively.     

Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae: Draco) as inferred from mitochondrial DNA sequence data

Phylogenetic analysis of mitochondrial DNA sequence data using maximum parsimony, minimum evolution (of log-determinant distances), and maximum-likelihood optimality criteria provided a robust estimate of Draco phylogenetic relationships. Although the analyses based on alternative optimality criteria were not entirely congruent, non-parametric bootstrap analyses identified many well-supported clades that were common to the analyses under the three altrenative criteria. Relationships within the major clades are generally well resolved and strongly supported, although this is not the case for the Philippine volans subclade. The hypothesis that a clade composed primarily of Philippine species represents a rapid radiation could not be rejected. A revised taxonomy for Draco is provided.