A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima

The complete mitochondrial genome of deep-sea ophiuroid Ophioleila elegans (Echinodermata: Ophiuroidea) from the Shkolnik Guyot, a northwest Pacific seamount

Ophiuroids are a diversified benthic taxon in the deep sea. Given their various dispersal strategies, they are considered an adequate group to assess genetic connectivity, especially in the seamounts that function as islands. Ophioleila elegans A.H. Clark, 1949, in the family Ophiothamnidae, was previously reported from the Caiwei Guyot, a seamount in the northwest Pacific Ocean. Here, we described the mitochondrial genome of O. elegans collected from another seamount in the northwest Pacific. The whole mitogenome is 16,376 bp in length and encodes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis based on the mitogenome sequences showed that O. elegans was clustered with Histampica sp., the only species for which mitogenome sequence has been reported within the family Ophiothamnidae. The complete mitogenome of O. elegans first reported in the present study provides useful information for population genetics and evolutionary relationship of this taxon, especially in the northwest Pacific seamounts.

Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics

Background

Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs”. Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia.

Results

To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs”. Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades.

Conclusions

Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.

Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers

Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.

Complete mitochondrial genome of the crinoid echinoderm, Florometra species (Echinodermata, Crinoidea)

In this study, we report the sequence of the mitochondrial genome (mitogenome) of the crinoid echinoderm, Florometra species (Echinodermata, Crinoidea). The complete mitogenome of Florometra sp. was 15,792 base pairs long and was composed of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and three regions of unassigned sequence (UAS) including one putative control region. Unique nucleotide composition, a clear positive bias for T with an apparent loss of C in PCGs as observed in the Crinoidea mitogenomes, was also seen in the Florometra sp. mitogenome (45% T, 12% C). Phylogenetic analysis with the concatenated nucleotide sequences of entire PCGs of echinoderms confirmed that Florometra sp. is highly related to F. serratissima within the family Crinoidea.

Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber

Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Most of these genes are coded on the positive strand except for one protein-coding gene (nad6) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the B. marianensis mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in B. marianensis. Phylogenetic analysis revealed that B. marianensis clustered with Peniagone sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in nad2; 108 S, 114 S, 322 C, 400 T and 427 S in nad4) were positively selected sites with high posterior probabilities. We predict that nad2 and nad4 may be the important candidate genes for the further investigation of the adaptation of B. marianensis to the deep-sea environment.

Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea)

Brittle stars are conspicuous members of benthic ecosystems, fill many ecological niches and are the most speciose of all classes of echinoderms. With high levels of biodiversity, elucidating the evolutionary history of this group is important. Understanding of higher-level relationships within Ophiuroidea has been aided by multilocus nuclear data and DNA barcoding. However, the degree of consistency between mitochondrial and nuclear data within ophiuroids remains unclear and deserves further assessment. In this study, 17 mitochondrial genomes spanning the taxonomic breadth of Ophiuroidea were utilized to explore evolutionary relationships through maximum likelihood analyses, Bayesian inference and comparative assessment of gene order. Our phylogenetic analyses, based on both nucleotide and amino acid residues, support recent findings based on multilocus nuclear data and morphology, in that the brittle star clades Ophintegrida and Euryophiurida were recovered as monophyletic with the latter comprising Euyalida, Ophiuridae and Ophiopyrgidae. Only three different arrangements of the 13 protein coding and 2 ribosomal RNA genes were observed. As expected, tRNA genes were more likely to have undergone rearrangement but the order of all 37 genes was found to be conserved in all sampled Euryalida and Ophiuridae. Both Euryalida and the clade comprised of Ophiuridae and Ophiopyrgidae, each had their own conserved rearrangement of protein coding genes and ribosomal genes, after divergence from their last common ancestor. Euryalida has a rearrangement of the two ribosomal RNA genes, rrnS and rrnL, in contrast to Ophiuridae and Ophiopyrgidae, which had an inversion of the genes nad1, nad2, and cob relative to Ophintegrida. Further, our data support the gene order found in all sampled Euryalida as the most likely ancestral order for all Ophiuroidea.

A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians

Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades.

Complete sequence and characterization of the mitochondrial genome of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium (Cestoda: Diphyllobothriidae), using next generation sequencing

We first constructed and characterized the complete mitochondrial genome (mitogenome) sequence of Diphyllobothrium stemmacephalum, the type species of genus Diphyllobothrium, using next generation sequencing (NGS). The mitogenome of D. stemmacephalum was 13,716bp, including 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 longer intergenic non-coding regions, and has features common to mitogenomes of other cestodes. Although it has been accepted that tRNA for serine (trnS2_(UCN)) in Platyhelminthes lacks a D arm, the trnS2_(UCN) of D. stemmacephalum was predicted to have a paired D arm as in Diplogonoporus balaenopterae. The non-coding region 2 contained eight tandem repeat units (34nucleotides/unit). This study also corroborated that D. stemmacephalum is phylogenetically more closely related to Dip. balaenopterae than to Diphyllobothrium latum and Diphyllobothrium nihonkaiense. As demonstrated here, mitogenome sequence data obtained using NGS is useful for gaining a better understanding of the systematics, phylogeny and taxonomic revisions involving valuable specimens preserved in museums, universities or research institutes for which sequence data are not yet available, and also for making diagnoses based on clinical samples.

Fixed, free, and fixed: the fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin

Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian-Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231-252mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian-Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group.

Structure and evolution of the mitochondrial genome of Exorista sorbillans: the Tachinidae (Diptera: Calyptratae) perspective

The first complete mitochondrial genome (mitogenome) of Tachinidae Exorista sorbillans (Diptera) is sequenced by PCR-based approach. The circular mitogenome is 14,960 bp long and has the representative mitochondrial gene (mt gene) organization and order of Diptera. All protein-coding sequences are initiated with ATN codon; however, the only exception is Cox I gene, which has a 4-bp ATCG putative start codon. Ten of the thirteen protein-coding genes have a complete termination codon (TAA), but the rest are seated on the H strand with incomplete codons. The mitogenome of E. sorbillans is biased toward A+T content at 78.4 %, and the strand-specific bias is in reflection of the third codon positions of mt genes, and their T/C ratios as strand indictor are higher on the H strand more than those on the L strand pointing at any strain of seven Diptera flies. The length of the A+T-rich region of E. sorbillans is 106 bp, including a tandem triple copies of a13-bp fragment. Compared to Haematobia irritans, E. sorbillans holds distant relationship with Drosophila. Phylogenetic topologies based on the amino acid sequences, supporting that E. sorbillans (Tachinidae) is clustered with strains of Calliphoridae and Oestridae, and superfamily Oestroidea are polyphyletic groups with Muscidae in a clade.

Current Status of Echinoderm Genome Analysis - What do we Know?

Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.

The complete mitochondrial genome sequence of Oncicola luehei (Acanthocephala: Archiacanthocephala) and its phylogenetic position within Syndermata

In the present study, we determined the complete mitochondrial genome sequence of Oncicola luehei (14,281bp), the first archiacanthocephalan representative and the second complete sequence from the phylum Acanthocephala. The complete genome contains 36 genes including 12 protein coding genes, 22 transfer RNA (tRNA) genes and 2 ribosomal RNA genes (rrnL and rrnS) as reported for other syndermatan species. All genes are encoded on the same strand. The overall nucleotide composition of O. luehei mtDNA is 37.7% T, 29.6% G, 22.5% A, and 10.2% C. The overall A+T content (60.2%) is much lower, compared to other syndermatan species reported so far, due to the high frequency (18.3%) of valine encoded by GTN in its protein-coding genes. Results from phylogenetic analyses of amino acid sequences for 10 protein-coding genes from 41 representatives of major metazoan groups including O. luehei supported monophyly of the phylum Acanthocephala and of the clade Syndermata (Acanthocephala+Rotifera), and the paraphyly of the clade Eurotatoria (classes Bdelloidea+Monogononta from phylum Rotifera). Considering the position of the acanthocephalan species within Syndermata, it is inferred that obligatory parasitism characteristic of acanthocephalans was acquired after the common ancestor of acanthocephalans diverged from its sister group, Bdelloidea. Additional comparison of complete mtDNA sequences from unsampled acanthocephalan lineages, especially classes Polyacanthocephala and Eoacanthocephala, is required to test if mtDNA provides reliable information for the evolutionary relationships and pattern of life history diversification found in the syndermatan groups.

Complete mitochondrial genomes of Baylisascaris schroederi, Baylisascaris ailuri and Baylisascaris transfuga from giant panda, red panda and polar bear

Roundworms of the genus Baylisascaris are the most common parasitic nematodes of the intestinal tracts of wild mammals, and most of them have significant impacts in veterinary and public health. Mitochondrial (mt) genomes provide a foundation for studying epidemiology and ecology of these parasites and therefore may be used to assist in the control of Baylisascariasis. Here, we determined the complete sequences of mtDNAs for Baylisascaris schroederi, Baylisascaris ailuri and Baylisascaris transfuga, with 14,778 bp, 14,657 bp and 14,898 bp in size, respectively. Each mtDNA encodes 12 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs, typical for other chromadorean nematodes. The gene arrangements for the three Baylisascaris species are the same as those of the Ascaridata species, but radically different from those of the Spirurida species. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes from nine nematode species indicated that the three Baylisascaris species are more closely related to Ascaris suum than to the three Toxocara species (Toxocara canis, Toxocara cati and Toxocara malaysiensis) and Anisakis simplex, and that B. ailuri is more closely related to B. transfuga than to B. schroeder. The determination of the complete mt genome sequences for these three Baylisascaris species (the first members of the genus Baylisascaris ever sequenced) is of importance in refining the phylogenetic relationships within the order Ascaridida, and provides new molecular data for population genetic, systematic, epidemiological and ecological studies of parasitic nematodes of socio-economic importance in wildlife.

Characterization of mitochondrial genome of sea cucumber Stichopus horrens: a novel gene arrangement in Holothuroidea

The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens (Holothuroidea: Stichopodidae: Stichopus) is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene (nad6) and five tRNA genes (tRNA ( Ser(UCN) ), tRNA ( Gln ), tRNA ( Ala ), tRNA ( Val ), tRNA ( Asp )) which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases (AT skew=0.025; GC skew=-0.188). A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes except nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu (16.29%), Ser (10.34%) and Phe (8.37%). All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.

The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses

The nearly complete mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) was sequenced for its nucleotide sequence of 13,964 bp. The genome has a typical gene order identical to other lepidopteran species. All tRNAs showed same stable canonical clover-leaf structure as those of other insects, except for tRNA(Ser) (AGN), in which the dihydrouracil arm (DHU arm) could not form stable stem-loop structure. Anomalous initiation codons have been observed for the cox1 gene, where the ATTACG hexa-nucleotide was believed to be involved in the initiation signaling. Twelve mitochondrial protein-coding gene sequence data were used to infer the phylogenetic relationships among the insect orders. Even though the number of insect orders represented by complete mitochondrial genomes is still limited, several well-established relationships are evident in the phylogenetic analysis of the complete sequences. Monophyly of the Homometabola was not supported in this paper. Phylogenetic analyses of the available species of Bombycoidea, Pyraloidea, Papilionoidea and Tortricidea bolstered the current morphology-based hypothesis that Bombycoidea, Pyraloidea and Papilionoidea are monophyletic (Obtectomera). Bombycoidea (Bombyx mandarina and Antheraea pernyi) and Papilionoidea (P. xuthus and Coreana raphaelis) formed a sister group.

Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata)

BACKGROUND

The Syndermata (Rotifera+Acanthocephala) is one of the best model systems for studying the evolutionary origins and persistence of different life styles because it contains a series of lineage-specific life histories: Monogononta (cyclic parthenogenetic and free-living), Bdelloidea (entirely parthenogenetic and mostly benthic dweller), Seisonidea (exclusively bisexual and epizoic or ectoparasitic), and Acanthocephala (sexual and obligatory endoparasitic). Providing phylogenetic resolution to the question of Eurotatoria (Monogononta and Bdelloidea) monophyly versus paraphyly is a key factor for better understanding the evolution of different life styles, yet this matter is not clearly resolved. In this study, we revisited this issue based on comparative analysis of complete mitochondrial genome information for major groups of the Syndermata.

RESULTS

We determined the first complete mitochondrial genome sequences (15,319 bp) of a bdelloid rotifer, Rotaria rotatoria. In order to examine the validity of Eurotatoria (Monogononta and Bdelloidea) monophyly/paraphyly, we performed phylogenetic analysis of amino acid sequences for eleven protein-coding genes sampled from a wide variety of bilaterian representatives. The resulting mitochondrial genome trees, inferred using different algorithms, consistently failed to recover Monogononta and Bdelloidea as monophyletic, but instead identified them as a paraphyletic assemblage. Bdelloidea (as represented by R. rotatoria) shares most common ancestry with Acanthocephala (as represented by L. thecatus) rather than with monogonont B. plicatilis, the other representative of Eurotatoria.

CONCLUSION

Comparisons of inferred amino acid sequence and gene arrangement patterns with those of other metazoan mtDNAs (including those of acanthocephalan L. thecatus and monogonont B. plicatilis) support the hypothesis that Bdelloidea shares most common ancestry with Acanthocephala rather than with Monogononta. From this finding, we suggest that the obligatory asexuality of bdelloideans may have secondarily derived from some other preexisting condition in earlier lineage of rotifers. Providing a more complete assessment of phylogenetic relationships and inferring patterns of evolution of different types of life styles among Syndermata awaits comparisons requiring mitochondrial genome sequencing of Seisonidea.

Evolution of mitochondrial gene orders in echinoderms

A comprehensive analysis of the mitochondrial gene orders of all previously published and two novel Antedon mediterranea (Crinoidea) and Ophiura albida (Ophiuroidea) complete echinoderm mitochondrial genomes shows that all major types of rearrangement operations are necessary to explain the evolution of mitochondrial genomes. In addition to protein coding genes we include all tRNA genes as well as the control region in our analysis. Surprisingly, 7 of the 16 genomes published in the GenBank database contain misannotations, mostly unannotated tRNAs and/or mistakes in the orientation of tRNAs, which we have corrected here. Although the gene orders of mt genomes appear very different, only 8 events are necessary to explain the evolutionary history of echinoderms with the exception of the ophiuroids. Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions.

Characterization of the mitochondrial genome ofDiphyllobothrium latum(Cestoda: Pseudophyllidea) – implications for the phylogeny of eucestodes

The complete nucleotide sequence of the mitochondrial genome was determined for the fish tapewormDiphyllobothrium latum. This genome is 13 608 bp in length and encodes 12 protein-coding genes (but lacks theatp8), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes, corresponding to the gene complement found thus far in other flatworm mitochondrial (mt) DNAs. The gene arrangement of this pseudophyllidean cestode is the same as the 6 cyclophyllidean cestodes characterized to date, with only minor variation in structure among these other genomes; the relative position oftrnS2andtrnL1is switched inHymenolepis diminuta. Phylogenetic analyses of the concatenated amino acid sequences for 12 protein-coding genes of all complete cestode mtDNAs confirmed taxonomic and previous phylogenetic assessments, withD. latumbeing a sister taxon to the cyclophyllideans. High nodal support and phylogenetic congruence between different methods suggest that mt genomes may be of utility in resolving ordinal relationships within the cestodes. All species ofDiphyllobothriuminfect fish-eating vertebrates, andD. latumcommonly infects humans through the ingestion of raw, poorly cooked or pickled fish. The complete mitochondrial genome provides a wealth of genetic markers which could be useful for identifying different life-cycle stages and for investigating their population genetics, ecology and epidemiology.

The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes

Evolution of mitochondrial genes is far from clock-like. The substitution rate varies considerably between species, and there are many species that have a significantly increased rate with respect to their close relatives. There is also considerable variation among species in the rate of gene order rearrangement. Using a set of 55 complete arthropod mitochondrial genomes, we estimate the evolutionary distance from the common ancestor to each species using protein sequences, tRNA sequences, and breakpoint distances (a measure of the degree of genome rearrangement). All these distance measures are correlated. We use relative rate tests to compare pairs of related species in several animal phyla. In the majority of cases, the species with the more highly rearranged genome also has a significantly higher rate of sequence evolution. Species with higher amino acid substitution rates in mitochondria also have more variable amino acid composition in response to mutation pressure. We discuss the possible causes of variation in rates of sequence evolution and gene rearrangement among species and the possible reasons for the observed correlation between the two rates.

The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: Signature nucleotide bias and unique nad4L gene rearrangement within crinoids

Complete DNA sequences have been determined for the mitochondrial genomes of the crinoids Phanogenia gracilis (15892 bp) and Gymnocrinus richeri (15966 bp). The mitochondrial genetic map of the stalkless feather star P. gracilis is identical to that of the comatulid feather star Florometra serratissima (Scouras, A., Smith, M.J., 2001. Mol. Biol. Evol. 18, 61-73). The mitochondrial gene order of the stalked crinoid G. richeri differs from that of F. serratissima and P. gracilis by the transposition of the nad4L protein gene. The G. richeri nad4L mitochondrial map position is unique among metazoa and is likely a derived feature in this stalked crinoid. Nucleotide compositional analyses of protein genes encoded on the major sense strand confirm earlier conclusions regarding a crinoid-distinctive T over C bias. All three crinoids exhibit high T levels in third codon positions, whereas other echinoderm classes favor A or C in the third codon position. The nucleotide bias is reflected in the relative synonymous codon usage patterns of crinoids versus other echinoderms. We suggest that the nucleotide bias of crinoids, in comparison to other echinoderms, indicates that a physical inversion of the origin of replication has occurred in the crinoid lineage. Evolutionary rate tests support the use of the cytochrome b (cob) gene in molecular phylogenetic analyses of echinoderms. A consensus echinoderm tree was generated based on cytochrome b nucleotide alignments that placed the asteroids as a sister group to a clade containing the ophiuroids and the (echinoids+holothuroids) with the crinoids basal to the rest of the echinoderm classes: [Crinoid,(Asteroid,(Ophiuroid,(Echinoid,Holothuroid)))].

Species delimitation and distribution in Aporometra (Crinoidea:Echinodermata): endemic Australian featherstars

Aporometra Clark, 1938, which belongs to the monotypic Aporometridae, is a crinoid genus endemic to temperate Australian waters. It has been described as being ‘viviparous’ and is among the smallest of comatulids. The small size of specimens, and poor morphological justifications for specific diagnoses have created uncertainty over the number of species in the genus and their distributions. This study identified a suite of characters using data from scanning electron microscopy and mtDNA sequencing (CO1 and ND2) to assess the number of species of Aporometra. Specimens were obtained from museums and collected from Western Australia, South Australia, Victoria and New South Wales. Type material was also examined when possible. Phylogenetic hypotheses were generated using maximum parsimony-based analyses of the separate and combined datasets. The results support the monophyly of Aporometra and the presence of two species, Aporometra wilsoni (Bell, 1888) and Aporometra occidentalis A. H. Clark, 1938, along the southern Australian coast. The status of the third nominal species, Aporometra paedophora (H. L. Clark, 1909), remains to be resolved, but it may be a junior synonym of A. wilsoni. Morphological diagnoses are reviewed. Aporometra occidentalis was only found in Western Australia, while A. wilsoni was found from Western Australia to Victoria. Phylogeographic differentiation between the western and southern populations of A. wilsoni is briefly discussed.

The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences

One of the most important issues in asteroid phylogeny is the phylogenetic status of Paxillosida. This group lacks an anus and suckers on the tube feet in adults and does not develop the brachiolaria stage in early development. Two controversial hypotheses have been proposed for the phylogenetic status of Paxillosida, i.e., Paxillosida is primitive or rather specialized in asteroids. In this study, we determined the complete mitochondrial DNA nucleotide sequences from two paxillosidans (Astropecten polyacanthus and Luidia quinaria) and one forcipulatidan (Asterias amurensis). The mitochondrial genomes of the three asteroids were identical with respect to gene order and transcription direction, and were identical to the previously reported mitochondrial genomes of Asterina pectinifera (Valvatida) and Pisaster ochraceus (Forcipulatida) in this respect. Therefore, the comparison of genome structures was uninformative for the purposes of asteroid phylogeny. However, molecular phylogenetic analyses based on the amino acid sequences and the nucleotide sequences from the five asteroids supported the monophyly of the clade that included the two paxillosidans and Asterina. This suggests that the paxillosidan characters are secondarily derived ones.

New Complete Mitochondrial DNA Sequence of the Lancelet Branchiostoma lanceolatum (Cephalochordata) and the Identity of this Species' Sequences

Three mitochondrial (mt) genes were sequenced for two Atlantic lancelet species, Branchiostoma lanceolatum and B. floridae, to examine a serious discrepancy among previously published results of molecular studies: substantial sequence difference in a nuclear gene vs. virtual identity in the mt genome sequence. The results revealed that three mt genes of B. lanceolatum, collected from Helgoland in the North Sea and Naples in the Mediterranean, were quite diverged from those of B. floridae, collected from Tampa Bay, Florida. Therefore, the previously recognized identity in the mt genome between the two species is attributable to misidentification of materials used. To correct this misleading information, the complete mtDNA sequence of B. lanceolatum was determined for an individual from Helgoland.

Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species

Complete mitochondrial (mt) DNA sequences of two lancelets, Epigonichthys maldivensis and E. lucayanus, were compared with those of two Branchiostoma lancelets and several deuterostomes previously surveyed. The mt-gene order of E. lucayanus was quite different from that of E. maldivensis, the latter being identical to the two Branchiostoma species. A remarkable genomic change in E. lucayanus mtDNA was an inversion, indicating the possibility of recombination of the mt-genome. Gene rearrangements, probably attributable to tandem genome duplications and subsequent random deletions, were observed in two parts. Short major unassignable sequences of the examined lancelets were regarded as a part of putative regulative elements, judging from some sequence similarity to the conserved sequence block (CSB) in mammalian mtDNA. The considerable mt-genome reorganization in E. lucayanus seemed to have affected the nucleotide substitution pattern, suggested by base composition analyses. The present analysis also suggested that AGR codons in lancelet mtDNA were likely to correspond to serine residue, rather than glycine. Furthermore, the AGG codon, so far reputed to be unassignable in lancelet mtDNA, was found twice in E. maldivensis, indicating the availability of all four AGN codons in some lancelets. This finding lends support to an alternative hypothesis regarding the evolutionary history of AGR-codon assignment in extant chordates, rather than that previously proposed. A molecular phylogenetic tree of the Epigonichthys and Branchiostoma species based on DNA sequences of the 13 mt-protein genes doubted the monophyly of the former genus, unlike the prevailing classification based on their different gonadal arrangements.

Sequencing and comparing whole mitochondrial genomes of animals

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, which can be especially powerful. We describe here the protocols commonly used for physically isolating mitochondrial DNA (mtDNA), for amplifying these by polymerase chain reaction (PCR) or rolling circle amplification (RCA), for cloning, sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences with determining and comparing complete mitochondrial DNA sequences.

Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny

The complete mitochondrial genome sequences have been determined for the holothuroid Cucumaria miniata and two ophiuroid species Ophiopholis aculeata and Ophiura lütkeni. In addition, the nucleotide sequence of the mitochondrial protein-coding genes for the asteroid Pisaster ochraceus has been completed. Maximum-likelihood and LogDet distance analyses of concatenated protein-coding sequences produced a series of trees that did not conclusively support generally accepted models of echinoderm phylogeny. The ophiuroid data consistently demonstrated accelerated nucleotide divergence rates and lack of stationarity. This confounds the phylogenetic analyses. Molecular investigations using individual protein-coding gene alignments demonstrated that the cytochrome b gene exhibits the least deviation in rate and stationarity and generated some trees consistent with proposed echinoderm phylogenies. Phylogenies based on echinoderm mitochondrial gene rearrangements also proved problematic because of extensive variation in gene order between and within classes. A comparison of the two distinctive ophiuroid mitochondrial gene orders supports the hypothesis that O. lütkeni has a more derived mitochondrial gene order versus O. aculeata. The variation in the echinoderm mitochondrial gene maps reinforces the limitations of the application of mitochondrial gene rearrangements as a global phylogenetic tool.

Egg fucose sulfate polymer, sialoglycan, and speract all trigger the sea urchin sperm acrosome reaction

Macromolecules surrounding eggs induce the acrosome reaction (AR) of spermatozoa. In sea urchins, three egg jelly (EJ) molecules: a fucose sulfate polymer (FSP), a sialoglycan (SG), and speract mediate ionic fluxes triggering the AR. SG and speract are noninductive without FSP. Speract's role in AR induction is controversial. Here we show that speract potentiates the FSP-induced AR at pH 7.0, approximately 1 pH unit lower than natural seawater. At pH 7.0, a mixture of FSP, SG, and speract produces the intracellular pH increase necessary for maximum AR induction. Each EJ component may mediate a distinct intracellular pH control mechanism, and all three may function synergistically to increase the intracellular pH permitting AR induction. Speract peptides are an ancient family. Although important for activating cyclic nucleotide-mediated pathways in today's seawater of pH approximately 8, speract may have been more important in AR induction in the paleo-ocean of pH approximately 7.

The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: evidence for heteroplasmy and tRNA translocations

We present the complete 15,455-nt mitochondrial DNA sequence of the springtail Tetrodontophora bielanensis (Arthropoda, Hexapoda, Collembola). The gene content is typical of most metazoans, with 13 protein-coding genes (PCGs), 2 genes encoding for ribosomal RNA subunits, and 22 tRNA genes. The nucleotide sequence shows the well-known A+T bias typical of insect mtDNA; its A+T content is lower (72.7%) than that observed in other insect species, but still higher than that in other arthropodan taxa. The bias appears to be uniform across the whole molecule, unlike other insect taxa, which show increased A+T content in the so-called A+T-rich region. However, the bias is slightly higher in the third codon positions of the PCGs (81.4%). Anomalous initiation codons have been observed in the nad2 and the cox1 genes. In the latter, the ATTTAA hexanucleotide is suggested to be involved in the initiation signaling. All tRNAs could be folded into the typical cloverleaf secondary structure, but the tRNA for cysteine appears to be missing the DHU arm. Long tandemly repeated regions (193 nt) were found in the A+T-rich region, which in turn was shown to have the possibility of forming a complex array of secondary structures. One of these structures encompassed the junction between the repeats. The A+T-rich region was also interesting in that it showed heteroplasmy in the number of repeats. Three haplotypes were found, possessing 2, 3, and 4 identical repeats, respectively. The order of protein coding and rRNA genes in the molecule was determined and was identical to that of all insects studied so far. However, two tRNA translocations were found which were unprecedented among Arthropoda. These involved the trnQ, which was found between the rrnS and the A+T-rich region, and the trnS(ucn), which was located between trnM and trnI. A preliminary phylogenetic analysis based on the amino acid sequence of the PCGs failed to find support for the monophyly of Hexapoda.

Phylogenetic relationships of extant echinoderm classes

A well-supported phylogeny of echinoderm classes has eluded morphological, embryological, molecular, and combined analyses. From this body of work it is apparent that (i) echinoids (sea urchins) and holothuroids (sea cucumbers) are related, and (ii) crinoids (sea lilies) are the sister taxon to extant eleutherozoan classes (asteroids, ophiuroids, echinoids, and holothuroids). However, the relationships of asteroids and ophiuroids to other echinoderm classes have been difficult to recover. To address relationships between the asteroids and ophiuroids and other echinoderms, I have sequenced additional nuclear loci and taxa and used novel computational approaches for co-optimizing morphological with molecular evidence at the level of sequence alignment. Support for the monophyly of each class is strong. Support for a monophyletic Asteroidea + Xyloplax is as strong as for Asteroidea. Support for Asterozoa (Asteroidea + Ophiuroidea) is apparent, albeit not as strong as for other clades (e.g., Echinozoa, Eleutherozoa, and Echinodermata). I also present detailed sensitivity analyses to provide (i) a test of the monophyly of groups under a variety of evolutionary models and (ii) a statement of the evidential value of various character systems.