Intrageneric Phylogeny ofAcomys(Rodentia, Muridae) Using Mitochondrial Gene Cytochromeb

This paper investigates interspecies relationships within the genusAcomys(spiny mice) by analyzing entire mitochondrial cytochromebgene (1141 bp). This gene provides strong phylogenetic signal, as shown by high support of the topology obtained (bootstrap value and RNA support number). The phylogeny is congruent with inferences from allozymes for the species considered. Controversial taxonomy ofAcomys cahirinus, dimidiatus, airensis,andignitusis clarified, with their specific ranks confirmed on the basis of tree topology and nucleotide distances. Phylogenetic relationship between the undescribed speciesAcomyssp. from west Africa andA. airensisargue in favor of two distinct colonization events in this zone.     

Evolution of the Gibbon Subgenera Inferred from CytochromebDNA Sequence Data

DNA sequences for the mitochondrial cytochromebgene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochromebgene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

Phylogenetic Relationships within GenusLeuciscus(Pisces, Cyprinidae) in Portuguese Fresh Waters, Based on Mitochondrial DNA CytochromebSequences

To investigate phylogenetic relationships amongLeuciscusspecies occurring in Portuguese inland waters, the cytochromebgene was sequenced from representatives of the main rivers. This study supports the recognition of the species level forL. pyrenaicus,including populations from the southern Portuguese drainages (Tejo, Sado, and Guadiana drainages), and forL. carolitertii,including populations from the northern Portuguese drainages. The existence of two new species occurring in the extreme southwestern drainages of Mira and Arade is also suggested. The present results support the monophyly of the Mira and the Arade populations, as well as an early divergence of these two lineages. The present-day distribution ofLeuciscusspecies is seen as a consequence of Pliocene and Pleistocene events, such as river disjunctions and posterior confluence in epicontinental seas and river captures. A mixture of haplotypes was observed in the Mondego and the Tejo drainages, which could be a consequence of ancient river captures, with a possible mitochondrial DNA introgression in the Tejo drainage and a recent introduction by man in the Mondego drainage. The pattern of differentiation among mtDNA haplotypes and their geographic distribution is discussed in terms of evolutionary aspects.     

The First Complete Mitochondrial Genome Sequence in the Genus Aphanius (Teleostei)

Journal of Ichthyology - In the present study, for the first time we isolated and characterized the complete mitochondrial genome sequence of the endangered Farsi killifish Aphanius farsicus by...     

Evolution of a mitochondrial cytochrome b gene sequence in the species-rich genus sebastes (Teleostei, Scorpaenidae) and its utility in testing the monophyly of the subgenus Sebastomus

The ecologically diverse and species-rich rockfishes (Sebastes) are a useful group for the study of marine speciation. The monophyly of the genus is generally accepted, as is the validity of most of the numerous species found along the West Coast of North America. However, the subgeneric groupings that would help in the proposal and interpretation of various speciation schemes are poorly supported based on widely overlapping morphological characters. The use of genetic characters provides an alternative approach. In this study, we present the first quantitative analysis supporting the monophyly of all 14 species of the subgenus Sebastomus among 54 congeners. The structural features and evolution of the 750 bp of the cytochrome b gene used to test the monophyly were similar to those of other vertebrates. Low levels of intrageneric sequence divergence (<10%) and incipient levels of saturation at third-codon positions were found in the gene. The monophyly of Sebastomus was supported in extensive phylogenetic analyses using distance, cladistic, and likelihood methods. Further corroboration was obtained from permutation- and simulation-based statistical tests.     

Annual cycle of stored spermatozoa within the ovaries of Helicolenus dactylopterus dactylopterus (Teleostei, Scorpaenidae)

The aim of this work was to analyse the ultrastructure of storage crypts and stored spermatozoa, and to describe changes during the annual reproductive cycle of the bluemouth Helicolenus dactylopterus dactylopterus , which has internal fertilization and a zygoparous mode of reproduction. Spermatozoa had elongated heads and long midpieces, two characteristics which are thought to be fairly advanced and correlated with internal fertilization, as is the case of the bluemouth. A remarkable spermatozoon feature was the retention of a significant quantity of cytoplasm around the head, a condition that appeared to be related to nourishment during the long storage period, up to 10 months in the intraovarian crystal structures of the female. Male sex cells' protection against the female immune system was ensured by junctional complexes between the crypt cells composed of tight junctions and desmosomes.     

Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences

Recent mitogenomic studies suggest a new position for the deep-sea fishes of the order Alepocephaliformes, placing them within the Otocephala in contrast to their traditional placement within the Euteleostei. However, these studies included only two alepocephaliform taxa and left several questions unsolved about their systematics. Here we use whole mitogenome sequences to reconstruct phylogenetic relationships for 11 alepocephaliform taxa, sampled from all five nominal families, and a large selection of non-alepocephaliform teleosts, to address the following three questions: (1) is the Alepocephaliformes monophyletic, (2) what is its phylogenetic position within the Teleostei and (3) what are the relationships among the alepocephaliform families? Our character sets, including unambiguously aligned, concatenated mitogenome sequences that we have divided into four (first and second codon positions, tRNA genes, and rRNA genes) or five partitions (same as before plus the transversions at third codon positions, using "RY" coding), were analyzed by the partitioned maximum likelihood and Bayesian methods. Our result strongly supported the monophyly of the Alepocephaliformes and its close relationship to the Clupeiformes and Ostariophysi. Altogether, these three groups comprise the Otocephala. Statistical comparison using likelihood-based SH test confidently rejected the monophyly of the Euteleostei when including the Alepocephaliformes. However, increasing the taxonomic sampling within the Alepocephaliformes did not resolve its position relative to the Clupeiformes and Ostariophysi. Within the Alepocephaliformes, our results strongly supported the monophyly of the platytroctid genera but not that of the remaining taxa. From one analysis to other, platytroctids were either the sister group of the remaining taxa or nested within the alepocephalids. Inferred relationships among alepocephaliform taxa were not congruent with any of the previously published phylogenetic hypotheses based on morphological characters.     

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.     

Ultrastructure of spermiogenesis in Plagioscion squamosissimus (Teleostei, Perciformes, Sciaenidae)

Spermiogenesis in Plagioscion squamosissimus occurs in cysts. It involves a gradual differentiation process of spermatids that is characterized mainly by chromatin compaction in the nucleus and formation of the flagellum, resulting in the spermatozoa, the smallest germ cells. At the end of spermiogenesis, the cysts open and release the newly formed spermatozoa into the lumen of the seminiferous tubules. The spermatozoa do not have an acrosome and are divided into head, midpiece, and tail or flagellum. The spermatozoa of P. squamosissimus are of perciform type with the flagellum parallel to the nucleus and the centrioles located outside the nuclear notch.     

Monophyly of the Citharidae (Pleuronectoidei: Pleuronectiformes: Teleostei) with considerations of pleuronectoid phylogeny

The monophyly of Citharidae, the pleuronectoid family thought to be a transitional group between the Psettodoidei and other typical pleuronectoids, has been in question mainly because of the lack of recognized synapomorphies for the family. In this study, the citharid skeleton is described, and the monophyly of the family and its phylogenetic position within the Pleuronectoidei are reassessed following a phylogenetic analysis based on 45 osteological, myological, and external characters. The Citharidae was found to represent a monophyletic group, supported by six synapomorphies (e.g., first dorsal proximal radials firmly wedged into notch of blind side lateral ethmoid; anterior dorsal proximal radials tightly mutually attached; blind side posterior nostril considerably enlarged). Two previously recognized subfamilies, sinistral Citharinae and dextral Brachypleurinae, are invalid because of their nonmonophylies. Interrelationships of the pleuronectoids shown herein are discussed. Received: February 19, 2001 / Revised: July 10, 2001 / Accepted: July 23, 2001     

Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard Lacerta dugesii (Lacertidae, Sauria)

Abstract We sequenced the complete control region (CR) and adjacent tRNAs, partial 12S rRNA, and cytochrome b (over 3100 bp) from eight individuals of Madeiran wall lizards, Lacerta dugesii, from four distinct island populations. The tRNAs exhibit a high degree of intraspecific polymorphisms compared to other vertebrates. All CR sequences include a minisatellite that varies in length between populations but is apparently fixed within them. Variation in minisatellite length appears between populations separated by apparently very short evolutionary time spans. Many motifs identified in the CR of other vertebrates are not highly conserved, although conserved blocks are identifiable between the few published reptile CR sequences. Overall there are extensive differences in the internal organization of the reptile CR compared to the more widely studied mammals and birds. Variability in the CR is lower than in cytochrome b, but higher than in 12S rRNA. Phylogenetic analysis of these sequences produces a well-resolved estimate of relationships between populations.     

A Human Homologue (BICD1) of theDrosophila Bicaudal-DGene

We previously isolated a cDNA fragment homologous to theDrosophila Bicaudal-Dgene (Bic-D) using a hybridization selection procedure with cosmids derived from the short arm of human chromosome 12. A PCR-mediated cDNA cloning strategy was applied to obtain the coding sequence of the human homologue (BICD1) and to generate a partial mouse (Bicdh1) cDNA. TheDrosophila Bicaudal-Dgene encodes a coiled coil protein, characterized by five α-helix domains and a leucine zipper motif, that forms part of the cytoskeleton and mediates the correct sorting of mRNAs for oocyte- and axis-determining factors during oogenesis. Analysis of the predicted amino acid sequence of theBICD1cDNA clones indicates that the sequence similarity is essentially limited to the amphipatic helices and the leucine zipper, but the conserved order of these domains suggests a similar function of the protein in mammalians. A database search further indicates the existence of a second human homologue on chromosome arm 9q and aCaenorhabditis eleganshomologue. Northern blot analysis indicates that both the human and the murine homologues produce an mRNA species of 9.5 kb expressed in brain, heart, and skeletal muscle and during mouse embryonic development. The conserved structural characteristics of theBICD1protein and its expression in muscle and especially brain suggest thatBICD1is a component of a cytoskeleton-based mRNA sorting mechanism conserved during evolution.     

Morphometric Relationship,Phylogenetic Correlation,and Character Evolution in the Species-Rich Genus Aphis (Hemiptera: Aphididae)

Background

The species-rich genus Aphis consists of more than 500 species, many of them host-specific on a wide range of plants, yet very similar in general appearance due to convergence toward particular morphological types. Most species have been historically clustered into four main phenotypic groups (gossypii, craccivora, fabae, and spiraecola groups). To confirm the morphological hypotheses between these groups and to examine the characteristics that determine them, multivariate morphometric analyses were performed using 28 characters measured/counted from 40 species. To infer whether the morphological relationships are correlated with the genetic relationships, we compared the morphometric dataset with a phylogeny reconstructed from the combined dataset of three mtDNA and one nuclear DNA regions.

Principal Findings

Based on a comparison of morphological and molecular datasets, we confirmed morphological reduction or regression in the gossypii group unlike in related groups. Most morphological characteristics of the gossypii group were less variable than for the other groups. Due to these, the gossypii group could be morphologically well separated from the craccivora, fabae, and spiraecola groups. In addition, the correlation of the rates of evolution between morphological and DNA datasets was highly significant in their diversification.

Conclusions

The morphological separation between the gossypii group and the other species-groups are congruent with their phylogenetic relationships. Analysis of trait evolution revealed that the morphological traits found to be significant based on the morphometric analyses were confidently correlated with the phylogeny. The dominant patterns of trait evolution resulting in increased rates of short branches and temporally later evolution are likely suitable for the modality of Aphis speciation because they have adapted species-specifically, rapidly, and more recently on many different host plants.     

Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochromeb

Distinguishing noise from signal presents a problem when DNA sequences are used for phylogeny reconstruction. Multiple substitutions at sites are a primary cause of noise and this is compounded by variation in substitution rates among sites. For protein-coding genes, one method used to determine if data are noisy is to assess levels of saturation of substitutions by codon position. However, this procedure may not be a fine enough filter for assessing noise. Variation in substitution rates may also be caused by constraints on change imposed by the function of the protein product. Using a structural model of the cytochromebprotein as a template, I divided cytbsequence data for species within the avian family Falconidae (falcons and caracaras) into three functional domains. Saturation of substitutions of sequences within these regions was assessed graphically. This qualitative determination of saturation was then used to differentially weight phylogenetic analysis, resulting in an hypothesis congruent with existing cladistic analyses and traditional morphology. These results demonstrate that saturation of substitutions is correlated with functional regions of cytochromeband that using this information improves phylogenetic inference.     

Gene Rearrangements and Evolution of tRNA Pseudogenes in the Mitochondrial Genome of the Parrotfish (Teleostei: Perciformes: Scaridae)

Genomic size of animal mitochondrial DNA is usually minimized over time. Thus, when regional duplications occur, they are followed by a rapid elimination of redundant material. In contrast to this general view, we report here long-sustained tRNA pseudogenes in the mitochondrial genome (mitogenome) of teleost fishes of the family Scaridae (parrotfishes). During the course of a molecular phylogenetic study of the suborder Labroidei, we determined the complete nucleotide sequence of the mitogenome for a parrotfish, Chlorurus sordidus, and found a gene rearrangement accompanied by a tRNA pseudogene. In the typical gene order of vertebrates, a tRNA-gene cluster between ND1 and ND2 genes includes tRNA^Ile (I), tRNA^Gln (Q), and tRNA^Met (M) genes in this order (IQM). However, in the mitogenome of the parrotfish, the tRNA^Met gene was inserted between the tRNA^Ile and the tRNA^Gln genes, and the tRNA^Gln gene was followed by a putative tRNA^Met pseudogene (_M). Such a tRNA gene rearrangement including a pseudogene (IMQ_M) was found in all of the 10 examined species, representing 7 of the 10 currently recognized scarid genera. All sister groups examined (20 species of Labridae and a single species of Odacidae) had the typical gene order of vertebrate mitogenomes. Phylogenetic analysis of the tRNA^Met genes and the resulting pseudogenes demonstrated that the ancestral tRNA^Met gene was duplicated in a common ancestor of the parrotfish. Based on the fossil record, these results indicate that the pseudogenes have survived at least 14 million years. Most of the vertebrate mitochondrial gene rearrangements involving the IQM region have held the tRNA^Met gene just upstream of the ND2 gene, and even in a few exceptional cases, including the present ones, the tRNA pseudogenes have been found in that position. In addition, most of these tRNA^Met pseudogenes maintained clover-leaf secondary structures, with the remainder sustaining the clover-leaf structure in the top half (TC and acceptor arms). Considering their potential secondary structures (holding top halves of the clover-leaf structures), locations within mitogenomes (flanking the 5 ends of the ND2 genes) and stabilities over time (survived at least 14 Myr), it is likely that the tRNA pseudogenes retain function as punctuation marks for mitochondrial ND2 mRNA processing.This article contains online supplementary material.Reviewing Editor: Dr. Axel Meyer     

Mitochondrial cytochrome b Sequence Variation and Phylogenetics of the Highly Specialized Schizothoracine Fishes (Teleostei: Cyprinidae) in the Qinghai-Tibet Plateau

The complete 1140 bp mitochondrial cytochrome b sequences were obtained from 39 individuals representing five species of all four genera of highly specialized schizothoracine fishes distributed in the Qinghai-Tibet plateau. Sequence variation of the cytochrome b gene was surveyed among the 39 individuals as well as three primitive schizothoracines and one outgroup. Phylogenetic analysis suggested that the group assignment based on 1140 bp of the cytochrome b sequence is obviously different from previous assignments, and the highly specialized schizothoracine fishes (Schizopygopsis pylzovi, Gymnocypris przewalskii, G. eckloni, Chuanchia labiosa, and Platypharodon extremus) form a monophyletic group that is sister to the clade formed by the primitive schizothoracine fishes (Schizothorax prenanti, S. pseudaksaiensis, and S. argentatus). The haplotypes of Schizopygopsis pylzovi and G. przewalskii were paraphyletic based on cytochrome b data, which most likely reflected incomplete sorting of mitochondrial DNA lineages. The diploid chromosome numbers of Schizothoracinae were considered in phylogenetic analysis and provided a clear pattern of relationships. Molecular dating estimated for highly specialized schizothoracine fishes suggested that the highly specialized schizothoracine fishes diverged in the late Miocene Pliocene to Pleistocene (4.5 × 10⁴–4.05 × 10⁶ years BP). The relationship between the cladogenesis of highly specialized schizothoracine fishes and geographical events of the Qinghai-Tibet plateau is discussed.     

Mitochondrial DNA Phylogeny of the Family Cichlidae: Monophyly and Fast Molecular Evolution of the Neotropical Assemblage

A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts. Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these high evolutionary rates were significantly higher among geophagine cichlids. Received: 18 September 1998 / Accepted: 16 December 1998     

Partial Deletion of both the Spermine Synthase Gene and thePexGene in the X-linked Hypophosphatemic, Gyro (Gy) Mouse

Gy, along withHyp, is a dominant mutation of the normal genePexcausing X-linked hypophosphatemia in the mouse. HemizygousGymale mice, however, have greater defects in survival, bodily growth, skeletal mineralization, and neurological function than those found in heterozygousGyfemales or inHypmice. Since the gene for spermine synthase is immediately upstream of the homologous human genePEX, we compared the effects of theGyandHypmutations on both the spermine synthase gene and thePexgene. Barely detectable levels of spermine (<5 % of normal) with elevated levels of its precursor, spermidine, were found in organs ofGymale mice compared to normal male littermates. NeitherGyfemales norHypmale mice were significantly affected. Four missing introns of the spermine synthase gene were identified inGymale mice, suggesting extensive gene disruption. A pseudogene for spermine synthase was also identified in the mouse genome.PexmRNA was found in several but not all tissues studied in adult normal mice.PexmRNA was altered in bothGyandHypmice. All maleHypmice were lacking the 3′ end of thePexmessage, whereas all maleGymice were deficient at the 5′ end. In summary, theGymutation is associated with a recessively expressed mutation of the spermine synthase gene, leading to spermine deficiency, and a dominantly expressed mutation of thePexgene, leading to hypophosphatemia. Alterations in two contiguous genes inGymay explain the additional phenotypic abnormalities present in theGymale mouse.     

暗纹东方鲀线粒体基因组核苷酸全序列测定与分析

以暗纹东方鲀(Takifugu fasciatus)肝的线粒体DNA为模板,参照红鳍东方鲀(T.rubripes)等近源鱼类的线粒体基因组DNA序列,设计合成14对特异引物,进行PCR扩增并测序,首次获得了暗纹东方鲀线粒体基因组全序列。结果表明,暗纹东方鲀线粒体基因组序列全长16 444 bp(GenBank登录号为GQ409967),A+T含量为55.8%,其mtDNA结构与其他脊椎动物相似,由22个tRNA基因、2个rRNA基因、13个蛋白质编码基因和1段819 bp非编码的控制区(D-loop)所组成。蛋白质基因除COⅠ和ND6的起始密码子为GTG、CCT以外,均为典型的起始密码子ATG。ND1、ATPase8、COⅢ、ND4L、ND5、Cyt b使用典型的终止密码子TAA,其他的使用不完全终止密码子。除ND6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测定的鲀类一致,这显示了鲀类线粒体基因排列顺序上的保守性。tRNA基因核苷酸长度为64～73nt,预测了22个tRNA基因的二级结构,均呈较为典型的三叶草状。基于19种鲀类mtDNA全序列构建的进化树表明,暗纹东方鲀与红鳍东方鲀、中华东方鲀(T.chinensis)聚成一个姊妹群。结果还支持东方鲀属鱼类为一单系类群。     

Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages

We describe the phylogeographic structure of 28 Chinese populations of the cyprinid Opsariichthys bidens across three main Chinese river drainages. Our study is based on the phylogenetic analysis of the complete mitochondrial cytochrome b gene (1140 bp). We combined this analysis with population processes inferred from nested clade analysis (NCA) and mismatch distributions. Both analyses showed that Chinese O. bidens consists of five mtDNA lineages (Opsariichthys 1-5) with high genetic divergence among them. Molecular divergences (TrN+G) higher than 20% among the Opsariichthys 1-5 mtDNA lineages suggest a taxonomic underestimation at the species level. About 92% of the genetic variance among samples was explained by differences among Opsariichthys mtDNA lineages. Drainage-restricted haplotypes with high frequencies and moderate nucleotide diversity show that Opsariichthys populations have evolved independently. NCA results were congruent with the phylogeny, and unimodal mismatch distributions with negative Tajima's D values suggest population expansions in some Opsariichthys lineages. The phylogeographic structure of the Opsariichthys 1-5 mtDNA lineages appears to be related to their long-term interruption of gene flow (theta(ST)>0.97). Our results suggested that fragmentation of ancestral ranges might have caused Opsariichthys diversification in Chinese waters. However, current distribution of common haplotypes across the Yangtze and Pearl drainages suggests a recent river connection that could have favoured gene flow across drainages. Overall, the results indicated that the richness of current Asian widespread species might have been underestimated, and that the cyprinid populations of O. bidens in the Yangtze, Pearl and Hai He drainages may correspond to five species.