Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.     

The complete mitochondrial genome of the nudibranch Roboastra europaea (Mollusca: Gastropoda) supports the monophyly of opisthobranchs

The complete nucleotide sequence (14,472 bp) of the mitochondrial genome of the nudibranch Roboastra europaea (Gastropoda: Opisthobranchia) was determined. This highly compact mitochondrial genome is nearly identical in gene organization to that found in opisthobranchs and pulmonates (Euthyneura) but not to that in prosobranchs (a paraphyletic group including the most basal lineages of gastropods). The newly determined mitochondrial genome differs only in the relative position of the trnC gene when compared with the mitochondrial genome of Pupa strigosa, the only opisthobranch mitochondrial genome sequenced so far. Pupa and Roboastra represent the most basal and derived lineages of opisthobranchs, respectively, and their mitochondrial genomes are more similar in sequence when compared with those of pulmonates. All phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, and Bayesian) based on the deduced amino acid sequences of all mitochondrial protein-coding genes supported the monophyly of opisthobranchs. These results are in agreement with the classical view that recognizes Opisthobranchia as a natural group and contradict recent phylogenetic studies of the group based on shorter sequence data sets. The monophyly of opisthobranchs was further confirmed when a fragment of 2,500 nucleotides including the mitochondrial cox1, rrnL, nad6, and nad5 genes was analyzed in several species representing five different orders of opisthobranchs with all common methods of phylogenetic inference. Within opisthobranchs, the polyphyly of cephalaspideans and the monophyly of nudibranchs were recovered. The evolution of mitochondrial tRNA rearrangements was analyzed using the cox1+rrnL+nad6+nad5 gene phylogeny. The relative position of the trnP gene between the trnA and nad6 genes was found to be a synapomorphy of opisthobranchs that supports their monophyly.     

Molecular phylogeny of euthyneura (mollusca: gastropoda)

A new phylogenetic hypothesis for Euthyneura is proposed based on the analysis of primary sequence data (mitochondrial cox1, trnV, rrnL, trnL(cun), trnA, trnP, nad6, and nad5 genes) and the phylogenetic utility of two rare genomic changes (the relative position of the mitochondrial trnP gene, and an insertion/deletion event in a conserved region of the mitochondrial Cox1 protein) is addressed. Both sources of phylogenetic information clearly rejected the monophyly of pulmonates, a group of gastropods well supported so far by morphological evidence. The marine basommatophoran pulmonate Siphonaria was placed within opisthobranchs and shared with them the insertion of a Glycine in the Cox 1 protein. The marine systellommatophoran pulmonate Onchidella was recovered at the base of the opisthobranch + Siphonaria clade. Opisthobranchs, Siphonaria, and Onchidella shared the relative position of the mitochondrial trnP gene between the mitochondrial trnA and nad6 genes. The land snails and slugs (stylommatophoran pulmonates) were recovered as an early split in the phylogeny of advanced gastropods. The monophyly of the Euthyneura (Opisthobranchia + Pulmonata) was rejected by the inclusion of the heterostrophan Pyramidella.     

Parallel rate heterogeneity in chloroplast and mitochondrial genomes of Brazil nut trees (Lecythidaceae) is consistent with lineage effects

We investigated whether relative rates of divergence were correlated between the mitochondrial and chloroplast genomes as expected under lineage effects or were genome specific as expected with locus-specific effects. Five mitochondrial noncoding regions (nad1B_C, nad4exon1_2, nad7exon2_3, nad7exon3_4, and rps14-cob) for 21 samples from Lecythidaceae were sequenced. Three chloroplast regions (rpl20-5'rps12, trnS-trnG, and psbA-trnH) were sequenced to expand the taxa in an existing data set. Absolute rates of nucleotide and insertion and deletion (indel) changes were 13 times faster in the chloroplast genome than in the mitochondrial genome. Similar indel length frequency distributions for both organelles suggested that common mechanisms were responsible for generating indels. Molecular clock tests applied to phylogenetic trees estimated from mitochondrial and chloroplast sequences revealed global rate heterogeneity of nucleotide substitution. Maximum likelihood and Tajima's 1D relative rate tests show that Lecythis zabucajo exhibited a rate acceleration for both the mitochondrial and chloroplast sequences. Whereas Eschweilera romeu-cardosoi showed a significant rate slowdown for chloroplast sequences, the mitochondrial sequences for 3 Eschweilera taxa showed evidence for a rate slowdown only when compared with L. zabucajo. Significant rate heterogeneity was also observed for indel changes in the mitochondrial genome but not for the chloroplast. The lack of mitochondrial nucleotide changes for some taxa as well as chloroplast indel homoplasy may have limited the power of relative rate tests to detect rate variation. Relative ratio tests consistently indicated rate proportionality among branch lengths between the mitochondrial and chloroplast phylogenetic trees. The relative ratio tests showed that taxa possessing rate heterogeneity had parallel relative divergence rates in both mitochondrial and chloroplast sequences as expected under lineage effects. A neutral replication-dependent model of rate heterogeneity for both nucleotide and indel changes provides a simple explanation for common patterns of rate heterogeneity across the 2 organelle genomes in Lecythidaceae. The lineage effects observed here were uncoupled from annual/perennial habit because all the species from this study are perennial.     

The complete mitochondrial genome of the relict frog Leiopelma archeyi: insights into the root of the frog Tree of Life

Determining the root of the anuran Tree of Life is still a contentious and open question in frog systematics. Two genera with disjunct distributions have been traditionally considered the most basal among extant frogs: Leiopelma, which is endemic to New Zealand, and Ascaphus, which lives in North America. However, their specific phylogenetic position is rather elusive because each genus shows many autapomorphies, and together they retain many symplesiomorphic characters. Therefore, several alternative hypotheses have been proposed regarding the relative phylogenetic position of both Leiopelma and Ascaphus. In order to distinguish among these competing phylogenetic hypotheses, we sequenced the complete mitochondrial (mt) genome of Leiopelma archeyi and used it along with previously reported frog mt genomes (including that of Ascaphus truei) to infer a robust phylogeny of major anuran lineages. The reconstructed maximum likelihood and Bayesian inference phylogenies recovered identical topology, which supports the sister group relationship of Ascaphus and Leiopelma, and the placement of this clade at the base of the anuran tree. Interestingly, the mt genome of L. archeyi displays a novel gene arrangement in frog mt genomes affecting the relative position of cytochrome b, trnT, NADH dehydrogenase subunit 6, trnE, and trnP genes. The tandem duplication-random loss model of gene order change explains the origin of this novel frog mt genome arrangement, which is convergent with others reported in some fishes and salamanders. These results, together with comparative data for other available vertebrate mt genomes, provide evidence that the 5' end of the control region is a hot spot for gene order rearrangement.     

The mitochondrial genome of Priapulus caudatus Lamarck (Priapulida: Priapulidae)

We sequenced and annotated the complete mitochondrial (mt) genome of the priapulid Priapulus caudatus in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The genome was 14,919 bp in its entirety with few, short non-coding regions. A number of protein-coding and tRNA genes overlapped, making the genome relatively compact. The gene order was: cox1, cox2, trnK, trnD, atp8, atp6, cox3, trnG, nad3, trnA, trnR, trnN, rrnS, trnV, rrnL, trnL(yaa), trnL(nag), nad1, -trnS(nga), -cob, -nad6, trnP, -trnT, nad4L, nad4, trnH, nad5, trnF, -trnE, -trnS(nct), trnI, -trnQ, trnM, nad2, trnW, -trnC, -trnY; where '-' indicates genes transcribed on the opposite strand. The gene order, although unique amongst Metazoa, shared the greatest number of gene boundaries and the longest contiguous fragments with the chelicerate Limulus polyphemus. The mt genomes of these taxa differed only by a single inversion of 18 contiguous genes bounded by rrnS and trnS(nct). Other arthropods and nematodes shared fewer gene boundaries but considerably more than the most similar non-ecdysozoan.     

Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones

The evolutionary relationships of the burrowing amphisbaenians ('worm lizards') have long been controversial for several reasons: the rarity of museum specimens available for study, highly derived morphological conditions that can confound comparative studies and difficulty in obtaining tissues for molecular phylogenetic studies because of their secretive habits in the wild. We present a phylogenetic analysis of two nuclear genes obtained from both fresh tissues and museum specimens of worm lizards. We achieved sufficient taxonomic sampling for analysis by extracting DNA from museum specimens using a modified forensics protocol. Results show the limbless Rhineuridae to be the most basal lineage, whereas the limbed Bipedidae occupy a more derived position as the sister-taxon to a Trogonophidae-Amphisbaenidae clade. This pattern of relationships indicates widespread morphological convergence within the group, including three independent incidences of limb loss. Convergence in skull shape and scalation is also prevalent. Mosaic evolution in the skull versus postcranial skeleton parallels that seen in snake evolution.     

The mitochondrial nad2 gene as a novel marker locus for phylogenetic analysis of early land plants: a comparative analysis in mosses

The mitochondrial nad2 gene is established as a novel marker locus for phylogenetic analyses among early land plants. The potential of this gene for phylogenetic resolution was checked with a broad taxon sampling of 42 mosses (Bryopsida, including the enigmatic genus Takakia) to allow both a comparative analysis with the recently explored nad5 gene and the fusion of independent data sets. The mitochondrial gene sequences provide valuable phylogenetic information on the relationships of classically defined orders and their respective monophylies. The more rapidly diverging sequences of a group I intron in nad5 and of a group II intron in nad2 add information for fine resolution. Although both genes provide phylogenetic information in the same taxonomic range (above family level), the combined sequence alignment results in an approximate doubling in the number of nodes with significant bootstrap support (>90). According to our data, Buxbaumiales are a paraphyletic taxon in a key position between the earliest branching taxa (Sphagnales, Takakiales, Andreaeales, Polytrichales, and Tetraphidales) and all other orders, possibly to be placed in the subclass Bryidae. A dichotomy in the latter recalls two previously suggested superorders Hypnanae and Dicrananae. Both genes independently question the monophyly of the orders Dicranales and Neckerales and reject the inclusion of the genera Schistostega, Timmia, and Encalypta among Eubryales.     

Evolution of the nad3-rps12 Gene Cluster in Angiosperm Mitochondria: Comparison of Edited and Unedited Sequences

We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic reconstruction. The two coding regions, containing from 25 to 35 editing sites in the various plants, have been concatenated in order to increase the significance of the analysis. Differing from the corresponding chloroplast sequences, unedited mitochondrial DNA sequences seem to evolve under a quasi-neutral substitution process which undifferentiates the nucleotide substitution rates for the three codon positions. By using complete gene sequences (all codon positions) we found that genomic sequences provide a classical angiosperm phylogenetic tree with a clear-cut grouping of monocotyledons and dicotyledons with Magnoliidae at the basal branch of the tree. Conversely, owing to their low nucleotide substitution rates, edited mRNA sequences were found not to be suitable for studying phylogenetic relationships among angiosperms. Received: 24 January 1996 / Accepted: 5 June 1996     

Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards

DNA sequences from 195 squamate reptiles indicate that mitochondrial gene order is the most reliable phylogenetic character establishing monophyly of acrodont lizards and of the snake families Boidae, Colubridae, and Viperidae. Gene order shows no evidence of evolutionary parallelisms or reversals in these taxa. Derived secondary structures of mitochondrial tRNAs also prove to be useful phylogenetic characters showing no reversals. Parallelisms for secondary structures of tRNAs are restricted to deep lineages that are separated by at least 200 million years of independent evolution. Presence of a stem-and-loop structure between the genes encoding tRNA(Asn) and tRNA(Cys), where the replication origin for light-strand synthesis is typically located in vertebrate mitochondrial genomes, is found to undergo at least three and possibly as many as seven evolutionary shifts, most likely parallel losses. This character is therefore a less desirable phylogenetic marker than the other structural changes examined. Sequencing regions that contain multiple genes, including tRNA genes, may be preferable to the common practice of obtaining single-gene fragments for phylogenetic inference because it permits observation of major structural changes in the mitochondrial genome. Such characters may occasionally provide phylogenetic information on relatively short internal branches for which base substitutional changes are expected to be relatively uninformative.     

Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes

A phylogenetic analysis of the Poales was conducted to assess relationships among Poaceae and allied families. The analysis included 40 taxa, representing all families of the Poales as circumscribed by the Angiosperm Phylogeny Group (APG), plus five of the six unplaced Commelinid families in the APG system. The data matrix included 98 informative characters representing variation in morphology and chloroplast genome structure (including three inversions in the chloroplast genome), and 563 informative characters derived from rbcL and atpA nucleotide sequences. Ecdeiocolea has the 6-kilobase (kb) chloroplast genome inversion previously reported in Joinvillea and Poaceae, and like Joinvillea it lacks the trnT inversion that occurs in grasses. Analysis of the morphological data places Poaceae in an unresolved relationship relative to several other taxa, including Joinvillea and Ecdeiocolea, while analysis of the molecular and combined data resolves Ecdeiocolea as sister of Poaceae, with Joinvillea the sister of this group. Although the 6-kb and trnT inversions are non-homoplasious in the phylogenies obtained in this study, the 28-kb inversion is optimized as having originated twice (once in Restionaceae and another time in the most recent common ancestor of Ecdeiocolea, Joinvillea, and the grasses); an alternative interpretation is that it arose once and was later lost in Anarthria. Ecdeiocolea shares with Poaceae the presence of operculate, annulate pollen that lacks scrobiculi, and a dry, indehiscent fruit.     

Making the most of mitochondrial genomes--markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea)

An increasing number of complete sequences of mitochondrial (mt) genomes provides the opportunity to optimise the choice of molecular markers for phylogenetic and ecological studies. This is particularly the case where mt genomes from closely related taxa have been sequenced; e.g., within Schistosoma. These blood flukes include species that are the causative agents of schistosomiasis, where there has been a need to optimise markers for species and strain recognition. For many phylogenetic and population genetic studies, the choice of nucleotide sequences depends primarily on suitable PCR primers. Complete mt genomes allow individual gene or other mt markers to be assessed relative to one another for potential information content, prior to broad-scale sampling. We assess the phylogenetic utility of individual genes and identify regions that contain the greatest interspecific variation for molecular ecological and diagnostic markers. We show that variable characters are not randomly distributed along the genome and there is a positive correlation between polymorphism and divergence. The mt genomes of African and Asian schistosomes were compared with the available intraspecific dataset of Schistosoma mansoni through sliding window analyses, in order to assess whether the observed polymorphism was at a level predicted from interspecific comparisons. We found a positive correlation except for the two genes (cox1 and nad1) adjoining the putative control region in S. mansoni. The genes nad1, nad4, nad5, cox1 and cox3 resolved phylogenies that were consistent with a benchmark phylogeny and in general, longer genes performed better in phylogenetic reconstruction. Considering the information content of entire mt genome sequences, partial cox1 would not be the ideal marker for either species identification (barcoding) or population studies with Schistosoma species. Instead, we suggest the use of cox3 and nad5 for both phylogenetic and population studies. Five primer pairs designed against Schistosoma mekongi and Schistosoma malayensis were tested successfully against Schistosoma japonicum. In combination, these fragments encompass 20-27% of the variation amongst the genomes (average total length approximately 14,000bp), thus providing an efficient means of encapsulating the greatest amount of variation within the shortest sequence. Comparative mitogenomics provides the basis of a rational approach to molecular marker selection and optimisation.     

The mitochondrial genome of Gyrodactylus derjavinoides (Platyhelminthes: Monogenea)--a mitogenomic approach for Gyrodactylus species and strain identification

Systematists and evolutionary biologists are constantly on the lookout for new sources of characters to discriminate amongst taxa and estimate interrelationships within and between taxa. Entire mitochondrial genomes provide a wealth of data, both at the nucleotide and amino acid level. Molecular markers are of particular utility when applied to small, morphologically conserved taxa, as is the case for many monogenean ectoparasites of fish. Gyrodactylus species display a considerable degree of anatomical conservatism, complicating diagnostics based solely on morphology, and some are significant pests of wild and cultured fish. Here we sequenced the complete mitochondrial genome of Gyrodactylus derjavinoides Malmberg, Collins, Cunningham & Behiar 2007, one of the most frequently found gyrodactylid species on salmonids in Scandinavia, and compared it with the recently published genomes of Gyrodactylus salaris Malmberg, 1957 and Gyrodactylus thymalli Zitnan 1960. Through comparative sliding window analysis we identified regions of high sequence variability and designed new primer sequences. In total, 6 new primer pairs have been developed, amplifying fragments of cox1, cox3, nad1, nad2, nad4, nad5 and atp6. Together, they amplify regions capturing almost half the nucleotide variability present in the complete mitochondrial genome. These degenerate primers should also work for other Gyrodactylus species parasitizing salmonids. In addition, we developed a multiplex assay that simultaneously amplifies four fragments in a single PCR reaction. Besides the diagnostic value, these fragments can be used for studying the transmission dynamics of Gyrodactylus, providing crucial information for an improved understanding of the spread and epidemiology of these important fish pathogens.     

Mitochondrial genomic investigation of flatfish monophyly

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.     

The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny.

The second intron in the mitochondrial gene nad1 was surveyed using PCR, DNA sequencing, or Southern hybridization in 323 species (313 genera, 212 families) of seed plants. The intron was absent in all 22 species (22 genera, 8 families) of non-Pinaceae conifers studied, in Welwitschia mirabilis, and in seven angiosperms. Whereas absence of the intron in seven angiosperms and Welwitschia is likely due to seven independent losses when evaluated against the recently published multigene phylogenies, the lack of the intron in all non-Pinaceae conifers can be best explained by a single loss. These data suggest that the non-Pinaceae conifers represent a monophyletic group. We also conducted a phylogenetic analysis of seed plants using a combined data set of the partial exon and intron sequences of nad1 generated from this study and published sequences of mitochondrial cox1 and small subunit (SSU) rDNA, chloroplast rbcL, and nuclear 18S rDNA. The results supported the split of conifers into two groups: Pinaceae and non-Pinaceae conifers. The Gnetales were sister to Pinaceae, in agreement with the conclusion from other recent molecular phylogenetic studies that refute the anthophyte hypothesis.     

A repeat complex in the mitochondrial control region of Adélie penguins from Antarctica.

We have determined the nucleotide sequence of the entire mitochondrial control region (CR) of the Adélie penguin (Pygoscelis adeliae) from Antarctica. Like in most other birds, this CR region is flanked by the gene nad6 and transfer (t)RNA trnE(uuc) at the 5' end and the gene rns and trnF(gaa) at the 3' end. Sequence analysis shows that the Adelie penguin CR contains many elements in common with other CRs including the termination associated sequences (TAS), conserved F, E, D, and C boxes, the conserved sequence block (CSB)-1, as well as the putative light and heavy strand promoters sites (LSP-HSP). We report an extraordinarily long avian control region (1758 bp) which can be attributed to the presence, at the 3' peripheral domain, of five 81-bp repeat sequences, each containing a putative LSP-HSP, followed by 30 tetranucleotide microsatellite repeat sequences consisting of (dC-dA-dA-dA)30. The microsatellite and the 81-bp repeat reside in an area known to be transcribed in other species.     

Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications

In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.     

Exclusive conservation of mitochondrial group II intron nad4i548 among liverworts and its use for phylogenetic studies in this ancient plant clade

Liverworts occupy a pivotal position in land plant (embryophyte) phylogeny as the presumed earliest-branching major clade, sister to all other land plants, including the mosses, hornworts, lycophytes, monilophytes and seed plants. Molecular support for this earliest dichotomy in land plant phylogeny comes from strikingly different occurrences of introns in mitochondrial genes distinguishing liverworts from all other embryophytes. Exceptionally, however, the nad5 gene--the mitochondrial locus hitherto used most widely to elucidate early land plant phylogeny--carries a group I type intron that is shared between liverworts and mosses. We here explored whether a group II intron, the other major type of organellar intron, would similarly be conserved in position across the entire diversity of extant liverworts and could be of use for phylogenetic analyses in this supposedly most ancient embryophyte clade. To this end, we investigated the nad4 gene as a candidate locus possibly featuring different introns in liverworts as opposed to the non-liverwort embryophyte (NLE) lineage. We indeed found group II intron nad4i548 universally conserved in a wide phylogenetic sampling of 55 liverwort taxa, confirming clade specificity and surprising evolutionary stability of plant mitochondrial introns. As expected, intron nad4i548g2 carries phylogenetic information in its variable sequences, which confirms and extends previous cladistic insights on liverwort evolution. We integrate the new nad4 data with those of the previously established mitochondrial nad5 and the chloroplast rbcL and rps4 genes and present a phylogeny based on the fused datasets. Notably, the phylogenetic analyses suggest a reconsideration of previous phylogenetic and taxonomic assignments for the genera Calycularia and Mylia and resolve a sister group relationship of Ptilidiales and Porellales.     

Phylogeny and evolution of Cervidae based on complete mitochondrial genomes

Mitochondrial DNA sequences can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes. We made phylogenetic analyses of 19 species of Cervidae, with Bos taurus as the outgroup. We used neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods on whole mitochondrial genome sequences. The consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Plesiometacarpalia and Telemetacarpalia, and four tribes, Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. The divergence times in these families were estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock method; the results were consistent with those of previous studies. We concluded that the evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; this method could be used broadly in phylogenetic evolutionary analysis of animal taxa.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.