The phylogenetic position of an undescribed paedomorphic clupeiform taxon: mitogenomic evidence

Molecular characters may offer a useful alternative to confidently estimate the phylogenetic position of paedomorphic taxa otherwise difficult to place based on morphology because of the reduction or absence of characters in their larvae-like adult stage. Here, we sequenced the complete mitogenome of a remarkable undescribed marine paedomorphic clupeiform fish to gain insight into its phylogenetic position. Of a length of 17,507 bp, this mitogenome exhibits a unique gene order within the Teleostei because of the inversion of the contiguous tRNA^Gln and tRNA^Ile within the IQM region and the presence of a putative second control region inserted between these tRNAs. Mitogenomic data from 27 clupeiform species and 22 non-clupeiform species were subjected to partitioned maximum likelihood and Bayesian analyses. All resultant phylogenetic trees strongly supported the placement of this undescribed taxon within the order Clupeiformes, suborder Clupeoidei, and the family Clupeidae, as the sister group of the tribe Spratelloidini (Jenkinsia + Spratelloides) of the subfamily Dussumieriinae. Together, they form a monophyletic group with Chirocentrus and, possibly, Etrumeus. Despite its overall resemblance to Sundasalanx, this undescribed taxa (Clupeidae gen. et sp. indet.) is not closely related to that genus and represents an independent paedomorphic lineage within the Clupeoidei. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Chirocentrids as engrauloids: evidence from suspensorium,branchial arches,and infraorbital bones (Clupeomorpha,Teleostei)

The Chirocentridae is a family of highly specialized large predatory clupeomorphs composed of two species from coastal waters of the Indian and western Pacific Oceans. Peculiarities of the anatomy of these fishes have puzzled ichthyologists who attempted to resolve their phylogenetic relationships. Despite controversy, it is currently accepted that the Chirocentridae is a family of Clupeiformes, included with the Clupeidae in the superfamily Clupeoidea. New data support an alternative hypothesis. Seven previously unreported derived character states from the suspensorium, branchial arches, and infraorbitals strongly indicate a hitherto unsuspected sister group relationship between the Chirocentridae and Engrauloidea, which comprises approximately 140 species of the commercially important fishes known as anchovies. These are character states: (1) the anterior margin of metapterygoid located anterior to the quadrate; (2) the ventral limb of hyomandibula and quadrate not separated by the metapterygoid; (3) the posterodorsal margin of metapterygoid in line with the condyle of articulation of the hyomandibula with the opercle; (4) the presence of a laminar outgrowth of the anterior margin of the quadrate; (5) the endochondral portion of the quadrate in the shape of an isosceles triangle; (6) the presence and arrangement of autogenous tooth plates on ceratobranchials 1 to 3; and (7) posterior region of infraorbital 1 well developed and extending along the ventral margin of infraorbital 2. Three of those character states are further modified and hypothesized as synapomorphies of the Engrauloidea: (1′) a substantial portion of the metapterygoid situated anterodorsal to the quadrate, (2′) articulation between the ventral limb of the hyomandibula and the quadrate, and (7′) infraorbitals 1 and 3 articulating by means of a well‐developed laminar process of the posterior region of infraorbital 1. The separation of the dorsal, paired elements of the branchial arches of the Chirocentridae and representative Engrauloidea is apomorphic within the Clupeoidei, and constitutes circumstantial evidence for the sister group relationship between those clades. Microphagy within the Engrauloidea is secondary, homoplastic to the same condition present in other clades of the Clupeiformes. The decomposition of character complexes into discrete morphological characters and its use in phylogenetic inference is discussed. The sister group relationship between the Chirocentridae and Engrauloidea renders the Clupeoidea paraphyletic. A new classification of the Clupeoidei, with the inclusion of the Chirocentridae in the Engrauloidea, is proposed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 363–383.     

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 Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.     

Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala

Although the order Gonorynchiformes includes only 31 species assigned to seven genera and four families, it exhibits a large variety of anatomical structures, making difficult the reconstruction of phylogenetic relationships among its representatives. Within the basal teleosts, the Gonorynchiformes belong to the Otocephala where they have been alternatively placed as the sister group of the Otophysi and of the Clupeiformes. In this context, we investigated the phylogeny of the Gonorynchiformes using whole mitogenome sequences from 40 species (six being newly determined for this study). Our taxonomic sampling included at least one species of each gonorynchiform genus and of each other major otocephalan lineage. Unambiguously aligned, concatenated mitogenomic sequences (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd, and 3rd codon positions, tRNA genes, and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenetic trees were fully resolved, with most of the nodes well supported by the high posterior probabilities. As expected, the Otocephala were recovered as monophyletic. Within this group, the mitogenome data supported the monophyly of Alepocephaloidei, Gonorynchiformes, Otophysi, and Clupeiformes. The Gonorynchiformes and the Otophysi formed a sister group, rending the Ostariophysi monophyletic. This result conflicts with previous mitogenomic phylogenetic studies, in which a sister relationship was found between Clupeiformes and Gonorynchiformes. We discussed the possible causes of this incongruence. Within the Gonorynchiformes, the following original topology was found: (Gonorynchus (Chanos (Phractolaemus (Cromeria (Grasseichthys (Kneria, Parakneria)))))). We confirmed that the paedomorphic species Cromeria nilotica and Grasseichthys gabonensis belong to the family Kneriidae; however, the two species together did not form a monophyletic group. This result challenges the value of reductive or absent characters as synapomorphies in this group.     

Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences

The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA(Leu (UUR))). Both are members of the same family, although their external morphologies differed so greatly (e.g., round vs. pointed head) that they have been placed in different subfamilies Macrouroidinae and Trachyrincinae, respectively. Additionally, we determined the whole mitogenome sequences of two other species, Bathygadus antrodes and Ventrifossa garmani, representing a total of four subfamilies currently recognized within Macrouridae. The latter two species also exhibited gene rearrangements, resulting in a total of three different patterns of unique gene order being observed in the four subfamilies. Partitioned Bayesian analysis was conducted using available whole mitogenome sequences from five macrourids plus five outgroups. The resultant trees clearly indicated that S. modificatus and T. murrayi formed a monophyletic group, having a sister relationship to other macrourids. Thus, monophyly of the two species with disparate head morphologies was corroborated by two different lines of evidence (nucleotide sequences and gene order). The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses.     

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

Background  

The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084).     

Deep genetic differentiation between two morphologically similar species of wolf herrings (Teleostei,Clupeoidei, Chirocentridae)

Wolf herrings (Chirocentridae; Clupeoidei) are commonly found in local fish markets throughout the Indo‐West Pacific region where they constitute an auxiliary source of food and income for local communities. The validity of the two species of wolf herrings, Chirocentrus dorab Forsskål, 1775 and C. nudus Swainon, 1839, is only supported by slight morphological differences. The identification of either species is challenging, especially for juveniles, and precludes accurate assessments of these natural resources at a species level. As a step towards gaining better knowledge of the genetic structure of these fishes, we examined genetic differentiation between these two species by reconstructing their entire mitogenomic sequences using high‐throughput sequencing technology. We found that the mitogenome of each species shared the same gene content and order that were the same for those found in most other teleost fishes. Despite their high morphological similarity, these two species of Chirocentrus were genetically well differentiated (p‐distance = 16.3% at their cytochrome oxidase I). A mitogenomic time‐calibrated phylogenetic analysis showed that wolf herrings originated about 35 million years ago, and they represent a case of morphological stasis. Furthermore, comparison of published and newly determined mitochondrial COI barcode region sequences from 22 individuals revealed species‐level cryptic genetic diversity within C. dorab. Altogether, these mitochondrial data are effective in discriminating species within this genus and informing population genetic relationships within species of wolf herrings.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Homology between the recessus lateralis and cephalic sensory canals, with the proposition of additional synapomorphies for the Clupeiformes and the Clupeoidei

The recessus lateralis , a complex structure in the otic region of the skull that is probably associated with detection and analysis of small vibrational pressures and displacements, is widely recognized as a synapomorphy of the Clupeiformes. The Clupeiformes includes the Denticipitoidei, with one living species, Denticeps clupeoides , and the Clupeoidei, with about 360 living species commonly known as herrings and anchovies. Comparisons between details of the recessus lateralis of the Clupeoidei and Denticipitoidei, and the sensory cephalic canals of other teleosts, lead to hypotheses of a series of transformations of the cephalic sensory canals . Treating that complex as a single binary 'presence vs. absence' character as was traditional practice obscures important phylogenetically informative variation. Specific synapomorphies in that system exist for the Clupeiformes and the Clupeoidei. Hypothesized synapomorphies in the recessus lateralis for the Clupeiformes are the presence of a dilated internal temporal sensory canal in the pterotic, a postorbital branch of the supraorbital sensory canal located in a bony groove in the lateral wing of the frontal, and the terminal portions of preopercular and infraorbital sensory canals closely positioned. Hypothesized synapomorphies for the Clupeoidei are the presence of a postorbital branch of the supraorbital sensory canal located deep within the body of the lateral wing of the frontal, with the distal portion of that branch totally internal on the cranium, and the expanded distal portion of the postorbital branch of the supraorbital sensory canal. The homology of the sinus temporalis of Clupeoidei, and of the dermosphenotic of both Denticeps and the Clupeoidei, with those of other teleosts is also considered.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 141 , 257–270.     

基于COⅡ基因序列的斑腿蝗科部分亚科的分子系统学研究

采用PCR产物直接测序法测定了斑腿蝗科10个亚科16属22种的COⅡ基因585 bp的片段, 对序列的碱基组成进行了分析,并评估了数据集的系统发育信号;最后,以癞蝗科的肃南 短鼻蝗作为外群,采用NJ法、MP法、ML法以及贝叶斯推论法构建了系统树,以解决这些物种所代表的亚科之间的系统发育关系。结果表明：22种斑腿蝗科昆虫的COⅡ基因序列碱基组成表现强烈的A+T含量偏向性。对COⅡ基因585 bp序列片段构成的全数据组和根据密码子不同位点划分的密码子第一、第二和第三位点数据组的系统发育信号分析显示,所有数据组都具有一定的系统发育信息。在4种方法得到的合一树中发现： （1）星翅蝗亚科、刺胸蝗亚科、黑背蝗亚科、斑腿蝗亚科的亲缘关系较近;（2）卵翅蝗亚科与稻蝗亚科亲缘关系较近,建议卵翅蝗亚科似乎应归入稻蝗亚科中,板胸蝗亚科与这两个亚科的关系较近;（3）黑蝗亚科和秃蝗亚科似乎应合并为一个亚科;（4）切翅蝗亚科的4个属未聚在一起,表明这些属的区别较大,不是一个单系群;（5）黑蝗亚科和秃蝗亚科关系较近,且与本研究中其他几个亚科的亲缘关系相对较远。研究结果表明COⅡ基因在解决斑腿蝗科的亚科以下属种间的系统发育关系时是一个有效的分子标记。     

虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

虾虎鱼类体态变异大、体型小、种类多, 形态鉴定及谱系分类较为困难。为深入开展虾虎鱼类的鉴定、分类及遗传进化等研究, 文章对已获得的26种虾虎鱼线粒体全基因组进行分析。结果发现, 虾虎鱼类线粒体基因组的基因组成及排列模式与大多数脊椎动物线粒体基因组特征基本一致; 由于不同物种的控制区存在不同数量的重复序列而导致基因组序列长度存在明显的差异; 26种虾虎鱼线粒体全基因组序列及不同基因中A+T的含量均超过50%, 并存在碱基G偏倚现象。基于37个编码基因序列, 利用Kimura双参数法计算遗传距离, 发现矛尾刺虾虎鱼与斑尾刺虾虎鱼、斑纹舌虾虎鱼与钝吻舌虾虎鱼分别为同种异名。通过对26种虾虎鱼线粒体基因组控制区序列的比较, 识别了终止结合序列区、中央保守区及保守序列区。利用26种虾虎鱼线粒体基因组的36个编码基因序列构建系统发育树, 发现部分聚类结果不同于传统的形态学分类方式, 虾虎鱼科中的5个亚科出现了明显的分化, 近盲虾虎鱼亚科、背眼虾虎鱼亚科、瓢虾虎鱼亚科亲缘关系较近而聚成一大支, 然后与拟虾虎鱼亚科种类形成姐妹类群, 虾虎鱼亚科与其它的4个亚科亲缘关系较远, 单独成为一个类群。根据分子钟估算结果推测虾虎鱼科物种可能起源于始新世晚期至渐新世时段, 在中新世进一步分化为具有现代表征的虾虎鱼种类。     

Swimbladder form in clupeoid fishes

The general form of the swimbladder is described and illustrated for representatives of 50 out of the 82 genera of clupeoid fishes (families Chirocentridae, Clupeidae, Pristigasteridae and Engraulididae of the suborder Clupeoidei), based mainly on preserved specimens. There is a remarkable diversity of shape, volume and silvering, as well as many curious specializations. The point of origin of the pneumatic duct from the gut, the presence or absence of an anal duct, and the length and diameter of the pre-coelomic ducts are noted, with attempts to explain their functional significance in terms of feeding and vertical migration. Specializations such as dorsal or lateral pockets, post-coelomic diverticula and internal muscular processes may be connected with sound production. The taxonomic implications of this diversity of swimbladder form are explored but, while some intra-and intergeneric relationships arc either confirmed or challenged, the swimbladder gives little help at suprageneric levels.     

Swimbladder form in clupeoid fishes

The general form of the swimbladder is described and illustrated for representatives of 50 out of the 82 genera of clupeoid fishes (families Chirocentridae, Clupeidae, Pristigasteridae and Engraulididae of the suborder Clupeoidei), based mainly on preserved specimens. There is a remarkable diversity of shape, volume and silvering, as well as many curious specializations. The point of origin of the pneumatic duct from the gut, the presence or absence of an anal duct, and the length and diameter of the pre-coelomic ducts are noted, with attempts to explain their functional significance in terms of feeding and vertical migration. Specializations such as dorsal or lateral pockets, post-coelomic diverticula and internal muscular processes may be connected with sound production. The taxonomic implications of this diversity of swimbladder form are explored but, while some intra-and intergeneric relationships arc either confirmed or challenged, the swimbladder gives little help at suprageneric levels.     

The mitochondrial genome of the quiet-calling katydids, <Emphasis Type="Italic">Xizicus fascipes</Emphasis> (Orthoptera: Tettigoniidae: Meconematinae)

To help determine whether the typical arthropod arrangement was a synapomorphy for the whole Tettigoniidae, we sequenced the mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae). The 16,166-bp nucleotide sequences of X. fascipes mitogenome contains the typical gene content, gene order, base composition, and codon usage found in arthropod mitogenomes. As a whole, the X. fascipes mitogenome contains a lower A+T content (70.2%) found in the complete orthopteran mitogenomes determined to date. All protein-coding genes started with a typical ATN codon. Ten of the 13 protein-coding genes have a complete termination codon, but the remaining three genes (COIII, ND5 and ND4) terminate with incomplete T. All tRNAs have the typical clover-leaf structure of mitogenome tRNA, except for tRNA(Ser(AGN)), in which lengthened anticodon stem (9 bp) with a bulged nuleotide in the middle, an unusual T-stem (6 bp in constrast to the normal 5 bp), a mini DHU arm (2 bp) and no connector nucleotides. In the A+T-rich region, two (TA)n conserved blocks that were previously described in Ensifera and two 150-bp tandem repeats plus a partial copy of the composed at 61 bp of the beginning were present. Phylogenetic analysis found: i) the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and ii) Meconematinae was the most basal group among these five subfamilies.     

The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae)

The complete 16,434-bp nucleotide sequence of the mitogenome of the bumble bee, Bombus ignitus (Hymenoptera: Apidae), was determined. The genome contains the base composition and codon usage typical of metazoan mitogenomes. An unusual feature of the B. ignitus mitogenome is the presence of five tRNA-like structures: two each of the tRNALeu(UUR)-like and tRNASer(AGN)-like sequences and one tRNAPhe-like sequence. These tRNA-like sequences have proper folding structures and anticodon sequences, but their functionality in their respective amino acid transfers remained uncertain. Among these sequences, the tRNALeu(UUR)-like sequence and the tRNASer(AGN)-like sequence are seemingly located within the A+T-rich region. This tRNASer(AGN)-like sequence is highly unusual in that its sequence homology is very high compared to the tRNAMet of other insects, including Apis mellifera, but it contains the anticodon ACT, which designates it as tRNASer(AGN). All PCG and rRNAs are conserved in positions observed most frequently in insect mitogenome structures, but the positions of the tRNAs are highly variable, presenting a new arrangement for an insect mitogenome. As a whole, the B. ignitus mitogenome contains the highest A+T content (86.9%) found in any of the complete insects mt sequences determined to date. All protein-coding sequences started with a typical ATN codon. Nine of the 13 PCGs have a complete termination codon (all TAA), but the remaining four genes terminate with the incomplete TA or T. All tRNAs have the typical clover-leaf structures of mt tRNAs, except for tRNASer(AGN), in which the DHU arm forms a simple loop. All anticodons of B. ignitus tRNAs are identical to those of A. mellifera. In the A+T-rich region, a highly conserved sequence block that was previously described in Orthoptera and Diptera was also present. The stem-and-loop structures that may play a role in the initiation of mtDNA replication were also found in this region. Phylogenetic analysis among three corbiculate tribes, represented by Melipona bicolor (Meliponini), A. mellifera (Apini), and B. ignitus (Bombini), showed the closest relationship between M. bicolor and B. ignitus.     

The First Mitochondrial Genome for the Superfamily Hagloidea and Implications for Its Systematic Status in Ensifera

Hagloidea Handlirsch, 1906 was an ancient group of Ensifera, that was much more diverse in the past extending at least into the Triassic, apparently diminishing in diversity through the Cretaceous, and now only represented by a few extant species. In this paper, we report the complete mitochondrial genome (mitogenome) of Tarragoilus diuturnus Gorochov, 2001, representing the first mitogenome of the superfamily Hagloidea. The size of the entire mitogenome of T. diuturnus is 16144 bp, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The order and orientation of the gene arrangement pattern is identical to that of D. yakuba and most ensiferans species. A phylogenomic analysis was carried out based on the concatenated dataset of 13 PCGs and 2 rRNA genes from mitogenome sequences of 15 ensiferan species, comprising four superfamilies Grylloidea, Tettigonioidae, Rhaphidophoroidea and Hagloidea. Both maximum likelihood and Bayesian inference analyses strongly support Hagloidea T. diuturnus and Rhaphidophoroidea Troglophilus neglectus as forming a monophyletic group, sister to the Tettigonioidea. The relationships among four superfamilies of Ensifera were (Grylloidea, (Tettigonioidea, (Hagloidea, Rhaphidophoroidea))).     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Two mitogenomes in Gruiformes (<Emphasis Type="Italic">Amaurornis akool</Emphasis>/<Emphasis Type="Italic">A. phoenicurus</Emphasis>) and the phylogenetic placement of Rallidae

Rallidae, with 34 genera including 142 species, is the largest family in the Gruiformes, the phylogenetic placement of this family was still in debate. The complete mitochondrial genomes (mitogenomes), with many advantageous characters, have become popular markers in phylogenetic analyses. We sequenced the mitogenomes of brown crake (Amaurornis akool) and white-breasted waterhen (Amaurornis phoenicurus), analyzed the genomic characters of mitogenomes in Rallidae, and explored the phylogenetic relationships between Rallidae and other four families in Gruiformes based on mitogenome sequences of 32 species with Bayesian method. The mitogenome of A. akool/A. phoenicurus was 16,950/17,213 bp in length, and contained 37 genes typical to avian mitogenomes and one control region, respectively. The genomic characters of mitogenomes in Rallidae were similar. The phylogenetic results indicated that, among five families, Rallidae had closest relationship with Heliornithidae, which formed a sister taxa to Gruidae, while Rhynochetidae located in the basal lineage. Within Rallidae, Rallina was ancestral clade. Gallirallus & Rallus and Aramides were closely related, Gallicrex & Amaurornis and Fulica & Gallinula had close relationships, and these two taxa formed a sister clade to Porphyrio & Coturnicops. Our phylogenetic analyses provided solid evidence for the phylogenetic placement of Rallidae and the evolutionary relationships among different genus within this family. In addition, the mitogenome data presented here provide useful information for further molecular systematic investigations on Gruiformes as well as conservation biology research of these species.     

Cytochrome b phylogeny of the family bovidae: resolution within the alcelaphini, antilopini, neotragini, and tragelaphini

The family Bovidae is characterized by an incomplete fossil record for the period during which most bovid subfamilies emerged. This, coupled to extensive morphological convergence among species, has given rise to inconsistencies in taxonomic treatments, especially at the tribal and subfamilial levels. In an attempt to clarify some of these issues we analyzed the complete mtDNA cytochrome b gene (1140 bp) from 38 species/subspecies representing at least nine tribes and six subfamilies. Specific emphasis was placed on the evolution of the Alcelaphini (hartebeest and wildebeest), the Tragelaphini (kudu, eland, and close allies), the Antilopini (gazelles), and the Neotragini (dwarf antelope). Saturation plots for the codon positions revealed differences between bovid tribes and this allowed for the exclusion of transitional substitutions that were characterized by multiple hits. There was no significant rate heterogeneity between taxa. By calibrating genetic distance against the fossil record, a transversion-based sequence divergence of 0.22% (+/-0.015%) per million years is proposed for cytochrome b clock calibrations in the Bovidae. All evidence suggests that the Alcelaphini form a monophyletic group; there was no support for the recognition of the Lichtenstein's hartebeest in a separate genus (Sigmoceros), and the acceptance of the previously suggested Alcelaphus is recommended for this species. High bootstrap support was found for a sister taxon relationship between Alcelaphus and Damaliscus, a finding which is in good agreement with allozyme and morphological studies. In the case of the Tragelaphini, the molecular data suggest the inclusion of Taurotragus in the genus Tragelaphus, and no genetic support was found for the generic status of Boocercus. Although associations within the Antilopinae (comprising the tribes Neotragini and Antilopini) could not be unequivocally resolved, there was nonetheless convincing evidence of non-monophyly for the tribe Neotragini, with the Suni antelope (Neotragus moschatus) grouping as a sister taxon to the Impala (Aepyceros melampus, tribe indeterminate, sensu Gentry, 1992) and the Klipspringer (Oreotragus oreotragus) falling within the duiker antelope tribe (Cephalophini).