Bayesian inference of cetacean phylogeny based on mitochondrial genomes

The phylogeny of Cetacea (whales, dolphins, porpoises) has long attracted the interests of biologists and has been investigated by many researchers based on different datasets. However, some phylogenetic relationships within Cetacea still remain controversial. In this study, Bayesian analyses were performed to infer the phylogeny of 25 representative species within Cetacea based on their mitochondrial genomes for the first time. The analyses recovered the clades resolved by the previous studies and strongly supported most of the current cetacean classifications, such as the monophyly of Odontoceti (toothed whales) and Mysticeti (baleen whales). The analyses provided a reliable and comprehensive phylogeny of Cetacea which can provide a foundation for further exploration of cetacean ecology, conservation and biology. The results also showed that: (i) the mitochondrial genomes were very informative for inferring phylogeny of Cetacea; and (ii) the Bayesian analyses outperformed other phylogenetic methods on inferring mitochondrial genome-based phylogeny of Cetacea.     

A time-calibrated multi-gene phylogeny of the diatom genus Pinnularia

Pinnularia is an ecologically important and species-rich genus of freshwater diatoms (Bacillariophyceae) showing considerable variation in frustule morphology. Interspecific evolutionary relationships were inferred for 36 Pinnularia taxa using a five-locus dataset. A range of fossil taxa, including newly discovered Middle Eocene forms of Pinnularia, was used to calibrate a relaxed molecular clock analysis and investigate temporal aspects of the genus' diversification. The multi-gene approach resulted in a well-resolved phylogeny of three major clades and several subclades that were frequently, but not universally, delimited by valve morphology. The genus Caloneis was not recovered as monophyletic, confirming that, as currently delimited, this genus is not evolutionarily meaningful and should be merged with Pinnularia. The Pinnularia-Caloneis complex is estimated to have diverged between the Upper Cretaceous and the early Eocene, implying a ghost range of at least 10 million year (Ma) in the fossil record.     

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

Background  

Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3^rd codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs.     

A multi-locus time-calibrated phylogeny of the siphonous green algae

The siphonous green algae are an assemblage of seaweeds that consist of a single giant cell. They comprise two sister orders, the Bryopsidales and Dasycladales. We infer the phylogenetic relationships among the siphonous green algae based on a five-locus data matrix and analyze temporal aspects of their diversification using relaxed molecular clock methods calibrated with the fossil record. The multi-locus approach resolves much of the previous phylogenetic uncertainty, but the radiation of families belonging to the core Halimedineae remains unresolved. In the Bryopsidales, three main clades were inferred, two of which correspond to previously described suborders (Bryopsidineae and Halimedineae) and a third lineage that contains only the limestone-boring genus Ostreobium. Relaxed molecular clock models indicate a Neoproterozoic origin of the siphonous green algae and a Paleozoic diversification of the orders into their families. The inferred node ages are used to resolve conflicting hypotheses about species ages in the tropical marine alga Halimeda.     

Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes

The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.     

Molecular characterization of a cloned dolphin mitochondrial genome

Summary DNA clones have been isolated that span the complete mitochondrial (mt) genome of the dolphin,Cephalorhynchus commersonii. Hybridization experiments with purified primate mtDNA probes have established that there is close resemblance in the general organization of the dolphin mt genome and the terrestrial mammalian mt genomes. Sequences covering 2381 bp of the dolphin mt genome from the major noncoding region, three tRNA genes, and parts of the genes encoding cytochrome b, NADH dehydrogenase subunit 3 (ND3), and 16S rRNA have been compared with corresponding regions from other mammalian genomes. There is a general tendency throughout the sequenced regions for greater similarity between dolphin and bovine mt genomes than between dolphin and rodent or human mt genomes.     

The evolutionary origins of diadromy inferred from a time-calibrated phylogeny for Clupeiformes (herring and allies)

One of the most remarkable types of migration found in animals is diadromy, a life-history behaviour in which individuals move between oceans and freshwater habitats for feeding and reproduction. Diadromous fishes include iconic species such as salmon, eels and shad, and have long fascinated biologists because they undergo extraordinary physiological and behavioural modifications to survive in very different habitats. However, the evolutionary origins of diadromy remain poorly understood. Here, we examine the widely accepted productivity hypothesis, which states that differences in productivity between marine and freshwater biomes determine the origins of the different modes of diadromy. Specifically, the productivity hypothesis predicts that anadromous lineages should evolve in temperate areas from freshwater ancestors and catadromous lineages should evolve in tropical areas from marine ancestors. To test this, we generated a time-calibrated phylogeny for Clupeiformes (herrings, anchovies, sardines and allies), an ecologically and economically important group that includes high diversity of diadromous species. Our results do not support the productivity hypothesis. Instead we find that the different modes of diadromy do not have predictable ancestry based on latitude, and that predation, competition and geological history may be at least as important as productivity in determining the origins of diadromy.     

On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

Background  

Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems.     

Dental anomaly in a fossil squalodont dolphin from New Zealand,and the evolution of polydonty in whales

Abstract

A fragment of mandible of an indeterminate squalodontid dolphin (Upper Oligocene or lowermost Miocene, New Zealand) has 2 anomalous single-rooted teeth intercalated between typically squalodontid anterior cheek-teeth. The anomalous teeth are considered to be truly supernumerary, and not homologous with any erupted teeth in phylogenetically earlier Cetacea. This type of anomaly appears not to have been reported previously for any fossil cetacean. Polydonty, a characteristic of extant odontocetes, was probably attained initially in primitive odontocetes by intercalation of permanent and deciduous teeth, and later was elaborated by the addition of supernumerary teeth. The present specimen represents a morphological (but not phylogenetic) stage between odontocetes with limited and advanced polydonty. Some fossil mysticetes and embryonic extant mysticetes are also polydont, but mysticete polydonty and that of odontocetes have probably evolved convergently.     

Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes

The phylogeny and evolutionary history of the rice tribe (Oryzeae) were explored using sequences of five DNA fragments (matK, trnL, nad1, Adh2, and GPA1) from chloroplast, mitochondrial, and nuclear genomes. Results indicate that (1) Oryzeae is monophyletic and falls into two main clades corresponding to the traditionally recognized subtribes; (2) previous recognition of three monotypic genera (Hydrochloa, Porteresia, and Prosphytochloa) is not justified; and (3) close affinities of the monoecious genera are not supported, suggesting the possibility of multiple origins of unisexual florets. Based on the magnitude of matK and GPA1 sequence divergence, we suggest that Oryza and Leersia branched off from the remaining genera of Oryzeae ～20 million years ago (mya), and separated from each other ～14 mya. A divergence time of ～9 mya is obtained for the most basal split within Oryza. These estimates suggest that Oryzeae diverged during the Miocene, and thus imply that long-distance dispersal appears to be one of the important factors in the diversification of the tribe.     

Sequencing complete mitochondrial and plastid genomes

Organelle genomics has become an increasingly important research field, with applications in molecular modeling, phylogeny, taxonomy, population genetics and biodiversity. Typically, research projects involve the determination and comparative analysis of complete mitochondrial and plastid genome sequences, either from closely related species or from a taxonomically broad range of organisms. Here, we describe two alternative organelle genome sequencing protocols. The "random genome sequencing" protocol is suited for the large majority of organelle genomes irrespective of their size. It involves DNA fragmentation by shearing (nebulization) and blunt-end cloning of the resulting fragments into pUC or BlueScript-type vectors. This protocol excels in randomness of clone libraries as well as in time and cost-effectiveness. The "long-PCR-based genome sequencing" protocol is specifically adapted for DNAs of low purity and quantity, and is particularly effective for small organelle genomes. Library construction by either protocol can be completed within 1 week.     

Phylogeny of mysticete whales based on mitochondrial and nuclear data

Mysticetes or baleen whales are comprised of four groups: Eschrichtiidae, Neobalaenidae, Balaenidae, and Balaenopteridae. Various phylogenetic hypotheses among these four groups have been proposed. Previous studies have not satisfactorily determined relationships among the four groups with a high degree of confidence. The objective of this study is to determine the relationships among the mysticete whales. Mitochondrial and nuclear DNA were sequenced for phylogenetic analysis. Most species relationships determined using these data were well resolved and congruent. Balaenidae is the most basal group and Neobalaenidae is the second most basal and sister group to the balaenopterid-eschrichtiid clade. In this phylogenetic study, the resolution of Eschrichtiidae with two main lineages of Balaenopteridae was problematic. Some data partitions placed this group within the balaenopterids, and other partitions placed it as a sister taxon to the balaenopterids. An additive likelihood approach was used to determine the most optimal trees. Although it was not found in the combined phylogenetic analyses, the "best" tree found under the additive likelihood approach was one with a monophyletic Balaenopteridae.     

Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes

The complete sequenced genomes of chloroplast have provided much information on the origin and evolution of this organelle. In this paper we attempt to use these sequences to test a novel approach for phylogenetic analysis of complete genomes based on correlation analysis of compositional vectors. All protein sequences from 21 complete chloroplast genomes are analyzed in comparison with selected archaea, eubacteria, and eukaryotes. The distance-based analysis shows that the chloroplast genomes are most closely related to cyanobacteria, consistent with the endosymbiotic origin of chloroplasts. The chloroplast genomes are separated to two major clades corresponding to chlorophytes (green plants) s.l. and rhodophytes (red algae) s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution. For instance, the analysis places the chloroplasts of two chromophytes (Guillardia and Odontella) within the rhodophyte lineage, supporting secondary endosymbiosis as the source of these chloroplasts. The relationships among the green algae and land plants in our tree also agree with results from traditional phylogenetic analyses. Thus, this study establishes the value of our simple correlation analysis in elucidating the evolutionary relationships among genomes. It is hoped that this approach will provide insights on comparative genome analysis.     

Bird evolution: testing the Metaves clade with six new mitochondrial genomes

Background  

Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade.     

New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny

The aim of this work was to provide a set of mitochondrial markers to reveal polymorphism and to study the maternal phylogeny in citrus. We first used 44 universal markers previously described in the literature: nine of these markers produced amplification products but only one revealed polymorphism in citrus. We then designed six conserved pairs of primers using the complete mitochondrial DNA sequences of Arabidopsis thaliana and Beta vulgaris to amplify polymorphic intergenic and intronic regions. From these six pairs of primers, three from introns of genes coding for NADH dehydrogenase subunits 2, 5, and 7, revealed polymorphism in citrus. First, we confirmed that citrus have a maternal mitochondrial inheritance in two populations of 250 and 120 individuals. We then conducted a phylogenic study using four polymorphic primers on 77 genotypes representing the diversity of Citrus and two related genera. Seven mitotypes were identified. Six mitotypes (Poncirus, Fortunella, Citrus medica, Citrus micrantha, Citrus reticulata, and Citrus maxima) were congruent with previous taxonomic investigations. The seventh mitotype enabled us to distinguish an acidic mandarin group (‘Cleopatra’, ‘Sunki’ and ‘Shekwasha’) from other mandarins and revealed a maternal relationship with Citrus limonia (‘Rangpur’ lime, ‘Volkamer’ lemon) and Citrus jambhiri (‘Rough’ lemon). This mitotype contained only cultivated species used as rootstocks due to their good tolerances to abiotic stress. Our results also suggest that two species classified by Swingle and Reece, Citrus limon, and Citrus aurantifolia, have multiple maternal cytoplasmic origins.     

Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features

We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.     

Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny

The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.     

Intron phylogeny: a new hypothesis

The three major classes of intron are clearly of unequal antiquity. Structured (often self-splicing and sometimes mobile) introns are the most ancient, probably dating (at least for group I) from the ancestral (eubacterial) cell 3500 million years ago, and were originally restricted to tRNA. Protein-spliced introns (usually in tRNA) probably evolved from them by a radical change in splicing mechanism in the common ancestor of eukaryotes and archaebacteria, perhaps only about 1700 million years ago. Spliceosomal introns probably evolved from group-II-like self-splicing introns after the origin of the nucleus between 1700 and 1000 million years ago, and were probably mostly inserted into previously unsplit protein-coding genes after the origin of mitochondria 1000 million years ago.     

A phylogeny of the trimeresurus group of pit vipers: new evidence from a mitochondrial gene tree

The Trimeresurus group is an important radiation of over 40 Asian pit viper species. Once considered congeneric, four genera are generally currently recognized (Trimeresurus sensu stricto, Ovophis, Protobothrops, and Tropidolaemus) but relationships within and between these are still unclear. This study, based on mitochondrial cytochrome b sequences, is the first to include a large number of species (21) and demonstrates that the current taxonomy does not adequately represent either the relationships or the genetic diversity present in the complex. Although many deeper nodes are not strongly supported, the following novel conclusions are all well supported: (1) the paraphyly of Trimeresurus sensu stricto, (2) the presence of several divergent clades within Trimeresurus sensu stricto, (3) the paraphyly of some widespread, medically significant, species, (4) the nonmonophyly of Ovophis, and (5) the monophyly of Protobothrops. Mapping of morphological characters onto the mitochondrial tree further supports the four groups proposed for Trimeresurus sensu stricto.