Molecular-based Phylogeny Research Articles

New camaenid genus and species from Zhejiang, East China (Eupulmonata, Helicoidea).

We report a new land snail species representing a new genus from the mountainous area of Zhejiang, China. The snail has a depressed shell with granules all over the surface. The soft part of the new taxon is characterized by the presence of a mantle lobe whose form is reviewed herein across a wide range of helicoid snails, the presence of a developed epiphallic papilla, and the absence of a penial sheath, a dart sac apparatus and a flagellum. As indicated by a molecular-based phylogeny (16S + ITS2), the new taxon is deeply nested in the eastern Asian camaenid genera and shows a close relationship with the camaenids distributed in Central China.

Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes.

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.

Evidence using morphology, molecules, and biogeography clarifies the taxonomic status of mole crabs of the genus Emerita Scopoli, 1777 (Anomura, Hippidae) and reveals a new species from the western Atlantic.

Uncertainties regarding the taxonomic status and biogeographical distribution of some species of the genus Emerita from the western Atlantic led to thorough examination of the subtle morphological differences between two coexistent species (E.brasiliensis Schmitt, 1935 and E.portoricensis Schmitt, 1935) along the Brazilian coast and compare them using two genetic markers. The molecular phylogenetic analysis based on sequences of the 16S rRNA and COI genes showed that individuals identified as E.portoricensis were clustered into two clades: one containing representatives from the Brazilian coast and another containing specimens distributed in Central America. Our molecular-based phylogeny, combined with a detailed morphological analysis, revealed the Brazilian population as a new species, which is described here as Emeritaalmeidai Mantelatto & Balbino, sp. nov. The number of species in the genus Emerita is now raised to 12, with five of them occurring in the western Atlantic, five in the Indo-Pacific, and two in the eastern Pacific.

Molecular phylogeny and revision of species groups of Nearctic bombardier beetles (Carabidae, Brachininae, Brachinus ( Neobrachinus)).

Bombardier beetles of the genus Brachinus Weber are notorious for their explosive defensive chemistry. Despite ongoing research on their defense mechanism, life history, and ecology, the group lacks a robust molecular-based phylogeny. In this study, three loci from mitochondrial and nuclear genomes (COI, CAD, 28S) are used to reconstruct the phylogeny of the large subgenus Neobrachinus, and test species group boundaries hypothesized by Erwin (1970) based on morphological characters. Erwin's fumans species group is found to be polyphyletic, and is herein re-defined with eight new species groups erected to reflect clades based on molecular evidence: the cinctipennis, cyanipennis, galactoderus, gebhardis, mexicanus, phaeocerus, quadripennis, and tenuicollis species groups. Erwin's cordicollis group is also expanded to include Brachinus (Neobrachinus) medius and the americanus group.

New Molecular-Based Phylogeny of Mussel-Associated Mites Reveals a New Subgenus and Three New Species Representing an Example of a Host-Driven Radiation in Indochina and Confirms the Concept of Division of the Genus Unionicola Haldeman, 1842 (Acari: Unionicolidae) into Numerous Subgenera

Here we describe a new subgenus and three new species of parasitic water mites in the genus Unionicola (Acari: Hydrachnidia) from Myanmar: Myanmaratax subgen. nov., Unionicola (Myanmaratax) savadiensis subgen. and sp. nov. (hosts: Lamellidens savadiensis and L. generosus), U. (My.) generosa sp. nov. (the same hosts), and U. (My.) trapezidenssp. nov. (hosts: Trapezidens dolichorhynchus and T. angustior). These taxa were identified based on a two-gene phylogenetic analysis (COI + 28S), which also confirms the division of the genus Unionicola into numerous subgenera. The new species are cryptic species, which are morphologically indistinguishable but strongly resemble U. (Prasadatax) brandti Vidrine, 1985 described from Thailand (hosts: Lens spp. and Ensidens spp.). We also transfer the latter taxon from Prasadatax to Myanmaratax based on a set of morphological evidence and propose U. (My.) brandti comb. nov. The new subgenus contains a total of five species, one of which needs future sampling efforts and will be described elsewhere. Additionally, 56 valid subgenera, which were placed in the synonymy of the genus and in one case raised to the genus level, are restored here until robust phylogenetic evidence on their taxonomic status is available. Our results also confirm that Unionicola mites are narrow host specialists that are associated with either one or a few closely related freshwater mussel species belonging to one or two sister genera.

Phylogeny and revised classification of the saucer bugs (Hemiptera: Nepomorpha: Naucoridae)

Abstract The true bug infraorder Nepomorpha contains 11 families with classifications mostly using morphological features and not based on phylogenetic analyses. Presented here is the first molecular-based phylogeny for a family of Nepomorpha including more than half of the constituent taxa. Two nuclear (18S rRNA and 28S rRNA) and two mitochondrial (COI and COII) genes were used to reconstruct phylogenetic relationships with both Bayesian inference and maximum likelihood analyses. Ingroup taxa included all six subfamilies, 41 of the 43 genera, and 221 species and subspecies. Results of the analyses were mostly congruent and revealed Naucoridae to be monophyletic, but two of the subfamilies (Cheirochelinae and Naucorinae) and three genera (Heleocoris, Laccocoris and Naucoris) as polyphyletic. Two clades formerly in Naucorinae were recovered as distinct subfamily-level clades: Macrocorinae subfam. nov. contains the African Macrocoris and Neomacrocoris, and Ilyocorinae stat. nov. contains the Palaearctic Ilyocoris and Neotropical Placomerus. Laccocorinae is unchanged in its constituent membership, but its organization now includes four tribe-level groups. Limnocorinae and the recently revised Cryphocricinae and Ambrysinae are unchanged. An annotated list of all subfamily-, tribe- and genus-group taxa is presented, including new taxa descriptions, synonymies and new combinations.

Phylogeny of the Rhinocylapus complex (Heteroptera, Miridae, Cylapinae, Fulviini)

Cylapinae Kirkaldy, 1903 is a highly diverse lineage of the plant bug family Miridae Hahn, 1831, confined mainly to the tropics. Despite an increasing amount of recent studies on that group, many species remain undescribed and biological data are lacking for most of the taxa. To date, a molecular-based phylogeny has been published only for Rhinomirini Gorczyca, 2000, one out of five Cylapinae tribes. The tribe was rendered as non-monophyletic and the Rhinocylapus Poppius, 1909 complex was transferred to the Fulviini Uhler, 1886. However, phylogenetic relationships within the complex have remained unresolved. In the present study, morphological and molecular data are employed to generate a significantly improved phylogeny of the group compared with previous work. Topologies were constructed using methods of parsimony, maximum likelihood, and Bayesian inference, and were based on an expanded morphological matrix with 65 encoded characters for 38 species and molecular data for 23 species on four markers (COI, 16S rRNA, 18S rRNA and 28S rRNA). As a result, a more resolved phylogeny of the Rhinocylapus complex is presented. A generic synopsis for the representatives of the complex and key to the genera are provided. Taxonomically and phylogenetically important morphological characters for the Rhinocylapus complex and its subgroupings are discussed. Dorsal habitus images, scanning micrographs of selected morphological structures, and illustrations of male and female genitalia are provided for Proamblia Bergroth, 1910, Punctifulvius Schmitz, 1978, Rhinocylapidius Poppius, 1915, Rhinocylapus Poppius, 1909, Rhinomiridius Poppius, 1909, and Yamatofulvius Yasunaga, 2000.

Darwin’s Tree of Life is Numbered. Resolving the Origins of Species by Mass

A new view of the tree of life has been conceived and implemented to construct a molecular-based phylogeny for a wide range of animal species without the need for gene or protein sequences using mass map data in a so-called “phylonumerics” approach. Numerical mass map data generated following the proteolytic digestion of proteins expressed across an array of organisms are used to build phylogenetic-like mass trees using a purpose built MassTree algorithm. The algorithm inputs sets of numbers for each organism and builds the tree, by default, using a relaxed Neighbour-Joining Approach with mid-point rooting. Single point mutations are also uniquely identified from peptide mass differences and these mutations displayed on branches of the mass trees. Here a wide array of animal species comprising insects, fish, birds, land and aquatic reptiles, and large mammals are successfully resolved and correctly grouped according to their origins on such a number-based tree. The mass tree is found to be highly congruent with that generated using sequence data and can be used to study evolutionary pathways at the molecular protein level without sequence generation or alignment. Mass trees provide a useful complement and viable alternative to conventional gene sequence trees. The approach brings together previously disparate fields and provides a universally applicable means with which to represent life forms and their evolutionary history employing a new molecular-based phylogeny that should find widespread application among the evolutionary biology community.

Sponge symbiosis is facilitated by adaptive evolution of larval sensory and attachment structures in barnacles.

Symbiotic relations and range of host usage are prominent in coral reefs and crucial to the stability of such systems. In order to explain how symbiotic relations are established and evolve, we used sponge-associated barnacles to ask three questions. (1) Does larval settlement on sponge hosts require novel adaptations facilitating symbiosis? (2) How do larvae settle and start life on their hosts? (3) How has this remarkable symbiotic lifestyle involving many barnacle species evolved? We found that the larvae (cyprids) of sponge-associated barnacles show a remarkably high level of interspecific variation compared with other barnacles. We document that variation in larval attachment devices are specifically related to properties of the surface on which they attach and metamorphose. Mapping of the larval and sponge surface features onto a molecular-based phylogeny showed that sponge symbiosis evolved separately at least three times within barnacles, with the same adaptive features being found in all larvae irrespective of phylogenetic relatedness. Furthermore, the metamorphosis of two species proceeded very differently, with one species remaining superficially on the host and developing a set of white calcareous structures, the other embedding itself into the live host tissue almost immediately after settlement. We argue that such a high degree of evolutionary flexibility of barnacle larvae played an important role in the successful evolution of complex symbiotic relationships in both coral reefs and other marine systems.

Phylogeny of the genus Pinnixa White, 1846 (Crustacea, Brachyura, Pinnotheridae) and allies inferred from mitochondrial and nuclear molecular markers, with generic reassignment of twenty-one species

We used mitochondrial 16S-NADH1 complex, mitochondrial 12S, and nuclear histone 3 genes to infer a molecular-based phylogeny, which allowed us to study phylogenetic relationships between species of PinnixaWhite, 1846sensu lato and other closely related pinnotherids. Polyphyly of Pinnixa s.l. was confirmed by maximum likelihood analyses. By our restricted definition, the genus Pinnixa sensu stricto is represented in these analyses only by its type species, Pinnixa cylindrica (Say, 1818). As a result of these molecular analyses, in combination with morphological studies, twelve species are reassigned to existing genera: Pinnixa faba (Dana, 1851), Pinnixa franciscanaRathbun, 1918, Pinnixa littoralis Holmes, 1894, Pinnixa schmittiRathbun, 1918, and Pinnixa tubicola Holmes, 1894 are placed in the genus Scleroplax Rathbun, 1893, whereas Laminapinnixa miamiensisMcDermott, 2014, Laminapinnixa faxoni (Rathbun, 1918), Pinnixa abbotti Glassell, 1935, Pinnixa arenicola Rathbun, 1922, Pinnixa floridanaRathbun, 1918, Pinnixa leptosynaptae Wass, 1968 and Laminapinnixa vanderhorstiRathbun, 1924 are reassigned to GlassellaCampos & Wicksten, 1997, the last two strictly on morphological bases. In addition, three new genera are erected to receive nine species: Rathbunixa n. gen. includes members of the Pinnixa pearseiWass, 1955– Pinnixa sayana Stimpson, 1860 complex, Pinnixa affinisRathbun, 1918, and species in the Pinnixa californiensisRathbun, 1894 – Pinnixa occidentalis Rathbun, 1893 complex; Tubicolixa n. gen. includes Pinnixa chaetopterana Stimpson, 1860 and the Pinnixa brevipollexRathbun, 1898 – Pinnixa rapax Bouvier, 1917 complex; and Sayixa n. gen. is established for Pinnixa monodactyla (Say, 1818).

Ecological and Phylogenetic Relationships Shape the Peripheral Olfactory Systems of Highly Specialized Gall Midges (Cecidomiiydae).

Insects use sensitive olfactory systems to detect relevant host volatiles and avoid unsuitable hosts in a complex environmental odor landscape. Insects with short lifespans, such as gall midges (Diptera: Cecidomyiidae), are under strong selection pressure to detect and locate suitable hosts for their offspring in a short period of time. Ephemeral gall midges constitute excellent models for investigating the role of olfaction in host choice, host shift, and speciation. Midges mate near their site of emergence and females migrate in order to locate hosts for oviposition, thus females are expected to be more responsive to olfactory cues emitted by the host compared to males. In this study, we explored the correlation between host choice and the function of the peripheral olfactory system in 12 species of gall midges, including species with close phylogenetic relationships that use widely different host plants and more distantly related gall midge species that use similar hosts. We tested the antennal responses of males and females of the 12 species to a blend of 45 known insect attractants using coupled gas chromatographic-electroantennographic detection. When the species-specific response profiles of the gall midges were compared to a newly generated molecular-based phylogeny, we found they responded to the compounds in a sex- and species-specific manner. We found the physiological response profiles of species that use annual host plants, and thus have to locate their host every season, are similar for species with similar hosts despite large phylogenetic distances. In addition, we found closely related species with perennial hosts demonstrated odor response profiles that were consistent with their phylogenetic history. The ecology of the gall midges affects the tuning of the peripheral olfactory system, which in turn demonstrates a correlation between olfaction and speciation in the context of host use.

Molecular phylogeny of the Laboulbeniomycetes (Ascomycota)

A first molecular-based phylogeny is presented for the Laboulbeniomycetes, a group of ascomycete fungi that utilize arthropods for nutrition and/or dispersal. Morphological diversification and life-history evolution has made it difficult to resolve relationships within the group, and to identify close relatives. Here, we infer a preliminary phylogeny based on acquisition of 51 new SSU rDNA sequences, representing a total of 65 taxa. The results of this study demonstrate that Laboulbeniomycetes is monophyletic, and related to Sordariomycetes. The class could be divided into at least 4 or 5 orders, though we refrain from formally giving names to these at this stage. Further evidence for the occurrence of asexuality within the class is provided by the inclusion of the genera Chantransiopsis and Tetrameronycha, both known only as asexual taxa with thalli consisting of linearly superposed cells. The precise placement of the genus Herpomyces (Herpomycetaceae), on cockroaches, remains unresolved in our analysis, but lies outside of the main clade of sexually reproducing Laboulbeniales. There is good support for this latter grouping, comprising taxa that are found on both aquatic and terrestrial hosts. Within this large assemblage, we recognize 5 distinct clades (clades E, F, G, H, I). Relationships among the so-called “aquatic genera” (≡ Ceratomycetaceae + some Euceratomycetaceae and Zodiomyces) are poorly resolved in our analyses, accounting for 3 of these clades (E, F, G), with the remainder of the taxa (largely equivalent to Laboulbeniaceae) split into two major groupings (clades H, I). Across all taxa, antheridial characteristics, features on which the earliest classifications were based, are shown to be homoplastic. On the other hand, features of perithecial development show an overall trend towards reduction, and appear to be phylogenetically informative. Morphological characters are identified that support the dichotomy in the Laboulbeniaceae and subclades within the two major groupings are discussed further in light of information on thallus morphology, development, and host relationships.

The relationships within the Chaitophorinae and Drepanosiphinae (Hemiptera, Aphididae) inferred from molecular-based phylogeny and comprehensive morphological data.

The Chaitophorinae is a bionomically diverse Holarctic subfamily of Aphididae. The current classification includes two tribes: the Chaitophorini associated with deciduous trees and shrubs, and Siphini that feed on monocotyledonous plants. We present the first phylogenetic hypothesis for the subfamily, based on molecular and morphological datasets. Molecular analyses were based on the mitochondrial gene cytochrome oxidase subunit I (COI) and the nuclear gene elongation factor-1α (EF-1α). Phylogenetic inferences were obtained individually on each of genes and joined alignments using Bayesian inference (BI) and Maximum likelihood (ML). In phylogenetic trees reconstructed on the basis of nuclear and mitochondrial genes as well as a morphological dataset, the monophyly of Siphini and the genus Chaitophorus was supported. Periphyllus forms independent lineages from Chaitophorus and Siphini. Within this genus two clades comprising European and Asiatic species, respectively, were indicated. Concerning relationships within the subfamily, EF-1α and joined COI and EF-1α genes analysis strongly supports the hypothesis that Chaitophorini do not form a monophyletic clade. Periphyllus is a sister group to a clade containing Chaitophorus and Siphini. The Asiatic unit of Periphyllus also includes Trichaitophorus koyaensis. The analysis of morphological dataset under equally weighted parsimony also supports the view that Chaitophorini is an artificial taxon, as Lambersaphis pruinosae and Pseudopterocomma hughi, both traditionally included in the Chaitophorini, formed independent lineages. COI analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. These analyses were extended to include the species of closely related and phylogenetically unstudied subfamily Drepanosiphinae, which produced congruent results. Genera Drepanosiphum and Depanaphis are monophyletic and sister. The position of Yamatocallis tokyoensis differs in the molecular and morphological analyses, i.e. it is either an independent lineage (EF-1α, COI, joined COI and EF-1α genes) or is nested inside this unit (morphology). Our data also support separation of Chaitophorinae from Drepanosiphinae.

Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.

Phylogenetic relationships of eight new Dacrymycetes collected from New Zealand.

Dacrymycetes, sister to Agaricomycetes, is a noteworthy lineage for studying the evolution of wood-decaying basidiomycetes; however, its species diversity and phylogeny are largely unknown. Species of Dacrymycetes previously used in molecular phylogenetic analyses are mainly derived from the Northern Hemisphere, thus insufficient knowledge exists concerning the Southern Hemisphere lineages. In this study, we investigated the species diversity of Dacrymycetes in New Zealand. We found 11 previously described species, and eight new species which were described here: Calocera pedicellata, Dacrymyces longistipitatus, D. pachysporus, D. stenosporus, D.parastenosporus, D. cylindricus, D. citrinus, and D. cyrtosporus. These eight newly described species and seven of the known ones, namely, Calocera fusca, C. cf. guepinioides, C. lutea, Dacrymyces flabelliformis, D.intermedius, D. subantarcticensis, and Heterotextus miltinus, have rarely or never been recorded from the Northern Hemisphere. In a molecular-based phylogeny, these New Zealand strains were scattered throughout the Dacrymycetaceae clade. Sequences obtained from specimens morphologically matching C. guepinioides were separated into three distant clades. Because no obvious morphological differences could be discerned between the specimens in each clade and no sequence exists from the type specimen, a C. guepinioides s.str. clade could not be determined. This survey of dacrymycetous species in the Southern Hemisphere has increased taxon sampling for phylogenetic analyses that can serve as a basis for the construction of a stable classification of Dacrymycetes.

The complete mitochondrial genome of Euthrix laeta (Lepidoptera: Lasiocampidae)

The complete mitochondrial genome of Euthrix laeta (GenBank accession number KU870700) was sequenced by traditional PCR amplification and primer walking methods. The total length was 15,368 bp, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a A + T-rich region. The base composition of the genome was A (40.85%), T (39.34%), C (12.01%) and G (7.8%), respectively. The arrangement of all genes was identical to other lepidopteran insects. The phylogenetic relationships were established based on the nucleotide sequences of 13 protein-coding genes of mitochondrial genomes by the neighbor-joining method. The molecular-based phylogeny supported the traditional morphological classification on relationships within Lepidoptera species.

A new species of Ptychochromis from southeastern Madagascar (Teleostei: Cichlidae).

We describe a new species in the endemic Malagasy cichlid genus Ptychochromis. Ptychochromis mainty, new species, is known from four individuals, all collected in the Fort Dauphin region of southeastern Madagascar, and shares a palatine morphology (eastern-type palatine) with other eastern congeners. Ptychochromis mainty is distinguished from all congeners by a nearly uniform dark brown to black pigmentation pattern in preservation and by the presence of a relatively continuous and expansive black longitudinal midlateral blotch in life, extending from the posterior margin of the opercle to the caudal peduncle. The new species is further distinguished from other eastern Ptychochromis species by having minimal or no overlap of the first supraneural with the dorsoposterior region of the supraoccipital crest (vs. marked overlap). We present a molecular-based phylogeny for all available Ptychochromis species, which supports the hypothesis that P. mainty is a distinct taxon. The new species is recovered as the sister taxon to P. grandidieri within a clade comprising species with an eastern-type palatine morphology. We present a geometric morphometric analysis that provides additional evidence to distinguish P. mainty from congeners.

Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis.

Mitochondrial DNA (mtDNA) has been widely used in species identification and genetic diversification. Comparisons among mtDNAs of closely related species are valuable for phylogenetic studies. However, only the partial mtDNA Cytb gene and the D-loop sequences were used to analysis the phylogenetic relationship between donkey breeds due to lack of complete mitochondrial genome. Dezhou donkey, as a bigger somatotype ass, is one of Chinese domestic donkey breeds, and used by many places as breeding stock. To further investigate the phylogenetic relationship of Dezhou donkey with other breeds, the complete mtDNA was firstly sequenced and de novo assembled using next generation sequence data from total genomic DNA. The genome was 16,813bp in length (NCBI submission number: KT182635) and contained 13 protein coding genes, 2 ribosomal RNA genes, 25 transfer RNA genes, and 1 control region. Based on the novel complete mtDNA sequence, the sequences of 13 protein coding genes and 2 ribosomal RNA genes were amplifying in other 2 Dezhou donkeys and 3 Yunnan donkeys, respectively. The pattern of genetic variation in horse, wild ass and domestic donkeys among these 15 genes indicated the sequence polymorphisms. The more accurate phylogenetic relationships of donkey species (Dezhou donkey, Yunnan donkey and previously published donkeys) were first obtained using the combined sequences of 12S rRNA+16S rRNA+13 protein-coding genes. Molecular-based phylogeny supported the hypothesis that Chinese domestic donkey breeds may have originated from Somali wild ass, not from Asian wild ass by analyzing mitochondrial genomes.

The complete mitochondrial genome of Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae)

We determined the complete mitochondrial genome (mitogenome) sequence of Cryptolestes ferrugineus (GenBank accession number KT182067) by the long PCR and primer walking method. The mitochondrial genome is a typical circular DNA molecule of 15 511 bp in length, and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a A + T-rich region (D-loop). The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. The base composition of the genome is A (39.17%), T (37.24%), C (14.22%), and G (9.37%) with an A + T-rich hallmark as that of other invertebrate mitochondrial genomes. All protein-coding genes start with ATN codon and terminate with the stop codon T (AA) or TAG. The A + T-rich region is located between 12S rRNA and tRNAIle. In this study, the phylogenetic relationships of Coleoptera species were constructed based on the nucleotides sequences of 13 PCGs of mitogenomes. The molecular-based phylogeny supported the traditional morphological classification on relationships within Coleoptera species.

The mitochondrial genome of Cethosia biblis (Drury) (Lepidoptera: Nymphalidae)

We present the complete mitogenome of Cethosia biblis (Drury) (Lepidoptera: Nymphalidae) in this article. The mitogenome was a circle molecular consisting of 15,286 nucleotides, 37 genes, and an A + T-rich region. The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. The overall base composition of the genome is A (37.41%), T (42.80%), C (11.87%), and G (7.91%) with an A + T-rich hallmark as that of other invertebrate mitochondrial genomes. The start codon was mainly ATA in most of the mitochondrial protein-coding genes such as ND2, COI, ATP8, ND3, ND5, ND4, ND6, and ND1, but COII, ATP6, COIII, ND4L, and Cob genes employing ATG. The stop codon was TAA in all the protein-coding genes. The A + T region is located between 12S rRNA and tRNAMet. The phylogenetic relationships of Lepidoptera species were constructed based on the nucleotides sequences of 13 PCGs of mitogenomes using the neighbor-joining method. The molecular-based phylogeny supported the traditional morphological classification on relationships within Lepidoptera species.