Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes

Phylogenetic relationships among the salamander families have been difficult to resolve, largely because the window of time in which major lineages diverged was very short relative to the subsequently long evolutionary history of each family. We present seven new complete mitochondrial genomes representing five salamander families that have no or few mitogenome records in GenBank in order to assess the phylogenetic relationships of all salamander families from a mitogenomic perspective. Phylogenetic analyses of two data sets—one combining the entire mitogenome sequence except for the D-loop, and the other combining the deduced amino acid sequences of all 13 mitochondrial protein-coding genes—produce nearly identical well-resolved topologies. The monophyly of each family is supported, including the controversial Proteidae. The internally fertilizing salamanders are demonstrated to be a clade, concordant with recent results using nuclear genes. The internally fertilizing salamanders include two well-supported clades: one is composed of Ambystomatidae, Dicamptodontidae, and Salamandridae, the other Proteidae, Rhyacotritonidae, Amphiumidae, and Plethodontidae. In contrast to results from nuclear loci, our results support the conventional morphological hypothesis that Sirenidae is the sister-group to all other salamanders and they statistically reject the hypothesis from nuclear genes that the suborder Cryptobranchoidea (Cryptobranchidae + Hynobiidae) branched earlier than the Sirenidae. Using recently recommended fossil calibration points and a “soft bound” calibration strategy, we recalculated evolutionary timescales for tetrapods with an emphasis on living salamanders, under a Bayesian framework with and without a rate-autocorrelation assumption. Our dating results indicate: (i) the widely used rate-autocorrelation assumption in relaxed clock analyses is problematic and the accuracy of molecular dating for early lissamphibian evolution is questionable; (ii) the initial diversification of living amphibians occurred later than recent estimates would suggest, from the Late Carboniferous to the Early Permian (294 MYA); (iii) living salamanders originated during the Early Jurassic (183 MYA), and (iv) most salamander families had diverged from each other by Late Cretaceous. A likelihood-based ancestral area reconstruction analysis favors a distribution throughout Laurasia in the Early Jurassic for the common ancestor of all living salamanders.     

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

Background

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

Results

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as “duplicate tRNA^Glu–CR” and “duplicate tRNA^Thr–tRNA^Pro and CR”, were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication - random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

Conclusions

The duplicate tRNAThr–CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr–CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-573) contains supplementary material, which is available to authorized users.     

Chromosome studies of 8 species of parrots of the families Cacatuidae and Psittacidae (Aves: Psittaciformes)

The karyotypes of 7 species of Psittaciformes new to cytology are described: Cacatua galerita, Calyptorhynchus magnificus and Probosciger aterrimus of the Cacatuidae, and Ara macao, A. ararauna, Amazona viridigenalis and Psittrichas fulgidens of the Psittacidae. For reasons of comparison the karyotype of Melopsittacus undulatus is also described. These karyotypes are compared to 8 psittaciform karyotypes previously recorded. There is a remarkable heterogeneity of karyotypes in the Psittaciformes. Nevertheless, it seems possible to recognize Cacatua, Calyptorhynchus and probably also Probosciger (Cacatuidae) by their karyotypes as a clearly related group. The karyotypes of these cacatuids also bear some resemblance to that of Loriculus (Psittacidae). The psittacid genera Amazona, Ara, Nestor, Melopsittacus, Psittacula, Psittacus and Psittrichas are karyologically heterogeneous, but their karyotypes show certain relationships. The karyotype of Brotogeris is very different from those of other psittacids.     

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper.     

Complete mitochondrial genome of Saturnia jonasii (Lepidoptera: Saturniidae): Genomic comparisons and phylogenetic inference among Bombycoidea

The complete mitochondrial genome (mitogenome) of Saturnia jonasii (Lepidoptera: Saturniidae) was sequenced and compared to those of 19 other bombycoid species. Furthermore, the mitogenome sequences were used to infer phylogenetic relationships among bombycoid species. The 15,261-bp Saturnia jonasii mitogenome contained the typical sets of genes and gene arrangements found in majority of Lepidoptera. All Bombycoidea species, including Saturnia jonasii, have a 15–33-bp spacer sequence at the trnS₂-ND1 junction. The phylogenetic reconstruction of bombycoid species consistently and strongly supported monophylies of the families, Saturniidae, Bombycidae, and Sphingidae, based on Bayesian inference (BI) and maximum-likelihood (ML) methods. Among these families, the Bombycidae and Sphingidae species consistently showed a sister relationship, regardless of data partitions; the BI method strongly supported this relationship, whereas it was moderately supported using the ML method.     

Complete mitochondrial genome of Periplaneta brunnea (Blattodea: Blattidae) and phylogenetic analyses within Blattodea

The complete mitochondrial genome (mitogenome) of Periplaneta brunnea was sequenced in this study and used to reconstruct the phylogenetic relationship of Blattodea. The circular mitogenome was 15,604?bp long and exhibited typical gene organization and order, consistent with other sequenced Periplaneta mitogenomes. The initiation codon of the P. brunnea COX1 gene was unusual in that no typical ATN or TTG start codon was found. The two longest intergenic spacer sequences found in the P. brunnea mitogenome were 21 and 17?bp long. Twenty-one base spacer had a 4?bp motif (TATT) between tRNA-Glu and tRNA-Met that conservatively displayed in 9 sequenced blattarian mitogenomes. The second spacer was between tRNA-Ser (UCN) and NAD1 containing a 7?bp motif (WACTTAA) that was highly conserved in 14 blattarian mitogenomes. The control region showed a relatively fixed motif present in 6 Blattidae mitogenomes, with a big stem-loop structure. Phylogenetic analyses were conducted using site-homogeneous models based on 13 protein-coding genes (PCGs) and two RNA genes. The trees derived from Bayesian inference and maximum likelihood analyses and recovered a relatively stable relationship among major lineages except for the position of Polyphagidae and inter-family relationships of Blaberidae. Analyses supported the monophyly of Blattidae, Blaberidae, Blattellidae, Polyphagidae, Dictyoptera, and the paraphyly of Blattaria. We also found Mantodea was the sister clade to (Blattaria?+?Isoptera), being the basal position of Dictyoptera in all topologies. Meanwhile, our results also consistently supported that Isoptera should be clustered with Blattaria of Blattodea.     

Molecular evidence for the age, origin, and evolutionary history of the American desert plant genus Tiquilia (Boraginaceae)

Although the deserts of North America are of very recent origin, their characteristic arid-adapted endemic plant lineages have been suggested to be much older. Earlier researchers have hypothesized that the ancestors of many of these modern desert lineages first adapted to aridity in highly localized arid or semi-arid sites as early as the late Cretaceous or early Tertiary, and that these lineages subsequently spread and diversified as global climate became increasingly arid during the Cenozoic. No study has explicitly examined these hypotheses for any North American arid-adapted plant group. The current paper tests these hypotheses using the genus Tiquilia (Boraginaceae), a diverse North American desert plant group. A strongly supported phylogeny of the genus is estimated using combined sequence data from three chloroplast markers (matK, ndhF, and rps16) and two nuclear markers (ITS and waxy). Ages of divergence events within the genus are estimated using penalized likelihood and a molecular clock approach on the ndhF tree for Tiquilia and representative outgroups, including most of the major lineages of Boraginales. The dating analysis suggests that the stem lineage of Tiquilia split from its nearest extant relative in the Paleocene or Eocene ( approximately 59-48 Ma). This was followed by a relatively long period before the first divergence in the crown group near the Eocene/Oligocene boundary ( approximately 33-29 Ma), shortly after the greatest Cenozoic episode of rapid aridification. Divergence of seven major lineages of Tiquilia is dated to the early-to-mid Miocene ( approximately 23-13 Ma). Several major lineages show a marked increase in diversification concomitant with the onset of more widespread semi-arid and then arid conditions beginning in the late Miocene ( approximately 7 Ma). This sequence of divergence events in Tiquilia agrees well with earlier researchers' ideas concerning North American desert flora assembly.     

Biological invasion as a natural experiment of the evolutionary processes: introduction of the special feature

Although biological invasion has a devastating impact on biodiversity, it also provides a valuable opportunity for natural experiments on evolutionary responses. Alien populations are often subject to strong natural selection when they are exposed to new abiotic and biotic conditions. Native populations can also undergo strong selection when interacting with introduced enemies and competitors. This special feature aims to highlight how evolutionary studies take advantage of biological invasion and, at the same time, emphasizes how studying evolutionary processes deepens our understanding of biological invasions. We hope this special feature stimulates more invasion studies taking evolutionary processes into account. Those studies should provide fundamental information essential for formulating effective measures in conserving native biodiversity, as well as valuable empirical tests for evolutionary theories.     

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis(Aves,Passeridae) complete mitochondrial genome

In this study,both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome(KC836121).The results showed that the complete mitochondrial genome of P.ruficollis is 16909 bp in length with 55.0%A+T content,harboring the typical 37 genes.The mitogenome had the same gene order with that of Podoces hendersoni.All protein coding genes started with ATG codon,except ND3 with GTG.For the stop codon usage,most genes terminate with codons TAA or TAG,but ND5 terminated with AGA,while ND1 and COI genes with AGG,and both the genes COIII and ND4 have an incomplete termination codon(T).The secondary structures of 22 tRNA genes were also predicted,showing that all tRNAs can form typical clover-leaf secondary structures,except for the tRNASer(AGN)which loses the DHU arm,while tRNAPhe harbor an extra nucleotide inserted in the TψC arm.The predicted secondary structures of 12S rRNA and16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively.The control region of P.ruficollis with the length of 1 305 bp was located between tRNAGlu and tRNAPhe,and typical domains of which could be found as other bird groups.Using the data from 13 mitochondrial protein-coding genes,results of a final phylogenetic analysis strongly supports the traditional view that P.ruficollis is closely related with Passeridae and Fringillidae.     

Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs

We have examined and dated primate divergences by applying a newly established molecular/paleontological reference, the evolutionary separation between artiodactyls and cetaceans anchored at 60 million years before present (MYBP). Owing to the morphological transformations coinciding with the transition from terrestrial to aquatic (marine) life and the large body size of the animals (which makes their fossils easier to find), this reference can be defined, paleontologically, within much narrower time limits compared to any local primate calibration marker hitherto applied for dating hominoid divergences. Application of the artiodactyl/cetacean reference (A/C-60) suggests that hominoid divergences took place much earlier than has been concluded previously. According to a homogenous-rate model of sequence evolution, the primary hominoid divergence, i.e., that between the families Hylobatidae (gibbons) and Hominidae, was dated at 36 MYBP. The corresponding dating for the divergence betweenPongo (orangutan) andGorilla-Pan (chimpanzee)-Homo is 24.5 MYBP, that forGorilla vsHomo-Pan is 18 MYBP, and that forHomo vsPan 13.5 MYBP. The split between Sumatran and Bornean orangutans was dated at 10.5 MYBP and that between the common and pygmy chimpanzees at 7 MYBP. Analyses of a single gene (cytochromeb) suggest that the divergence within the Catarrhini, i.e., between Hominoidea and Old World monkeys (Cercopithecoidea), took place >40 MYBP; that within the Anthropoidea, i.e., between Catarrhini and Platyrrhini (New World monkeys), >60 MYBP; and that between Anthropoidea and Prosimii (lemur), 80 MYBP. These separation times are about two times more ancient than those applied previously as references for the dating of hominoid divergences. The present findings automatically imply a much slower evolution in hominoid DNA (both mitochondrial and nuclear) than commonly recognized.     

Metallothionein primary structure in amphibians: Insights from comparative evolutionary analysis in vertebrates

Metallothioneins are cysteine-rich, low-molecular weight metal-binding proteins ubiquitously expressed in living organisms. In the last past years, the increasing amount of vertebrate non-mammalian metallothionein sequences available have disclosed for these proteins differences in the primary structure that have not been supposed before. To provide a more up-to-date view of the metallothioneins in non-mammalian tetrapods, we decided to increase the still scarce knowledge concerning the primary structure and the evolution of metallothioneins in amphibians. Our data demonstrate an unexpected diversity of metallothionein sequences among amphibians, accompanied by remarkable features in their phylogeny. Phylogenetic analysis also reveals the complexity of vertebrate metallothionein evolution, made by both ancient and more recent events of gene duplication and loss.     

尼罗鳄线粒体基因组全序列分析及鳄类系统发生关系的探讨

大多数脊椎动物的线粒体基因组（约16—18kb）的组成是相对较稳定的,但在不同类群中,线粒体基因组在基因结构和基因排列方式等方面均显示了极大的多样性,这种多样性可能反映了真核细胞不同的进化路线（Saccone et al．,1999）。就目前的研究而言,线粒体基因组是惟一一个能够从基因组水平上来分析动物系统发生的分子标记,可以从线粒体基因组序列信息、基因组成及基因排列方式等进行多方位的分子进化研究,因而线粒体基因组全序列将成为动物分子系统发生最有力的证据（Saccone et al．,1999）。     

Phylogeny and biogeography of the parrot genus Prioniturus (Aves: Psittaciformes)

The parrot genus Prioniturus occurs in the oceanic Philippines, Palawan and Wallacea, a geologically dynamic region with a complex history of land and sea. The described taxa of Prioniturus have been variously placed in different assemblages, and different numbers of species have been recognized. However, a phylogenetic framework is so far lacking. This would be the prerequisite to reconstructing dispersal and colonization patterns of Prioniturus across and within Wallacea and the Philippines. Following our robustly supported phylogenetic hypothesis based on two mitochondrial genes, we propose to treat Prioniturus mindorensis comb. nov. as well as Prioniturus montanus and Prioniturus waterstradti as separate species. In Prioniturus discurus discurus and Prioniturus discurus whiteheadi, further studies using additional data and specimens are necessary to clarify their taxonomic status. This result is congruent with other studies demonstrating that alpha diversity of the Philippine avifauna is strongly underestimated. According to our biogeographic reconstruction, Prioniturus has diversified by a complex combination of colonization of islands and subsequent divergence in allopatry among and within island groups. Dispersal between Sulawesi/Wallacea and the Philippines occurred twice and documents a rare case of faunal exchange between these two regions.     

The evolutionary demography of duplicate genes

Although gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, the rates of origin, loss, and preservation of gene duplicates are not well understood. Applying steady-state demographic techniques to the age distributions of duplicate genes censused in seven completely sequenced genomes, we estimate the average rate of duplication of a eukaryotic gene to be on the order of 0.01/gene/million years, which is of the same order of magnitude as the mutation rate per nucleotide site. However, the average half-life of duplicate genes is relatively small, on the order of 4.0 million years. Significant interspecific variation in these rates appears to be responsible for differences in species-specific genome sizes that arise as a consequence of a quasi-equilibrium birth-death process. Most duplicated genes experience a brief period of relaxed selection early in their history and a minority exhibit the signature of directional selection, but those that survive more than a few million years eventually experience strong purifying selection. Thus, although most theoretical work on the gene-duplication process has focused on issues related to adaptive evolution, the origin of a new function appears to be a very rare fate for a duplicate gene. A more significant role of the duplication process may be the generation of microchromosomal rearrangements through reciprocal silencing of alternative copies, which can lead to the passive origin of post-zygotic reproductive barriers in descendant lineages of incipient species.     

Hierarchal gene trees and molecular phylogeny of the Rotifera: use of the Polymerase Chain Reaction (PCR) to dissect ecological and evolutionary patterns

The study of rotifer phylogenies and the analysis of population-level processes historically have been disjunct. This is despite a growing recognition that there are many ways in which rotifer population biologists and ecologists might profit from the availability of a comprehensive phylogeny of the group. New molecular methods which can be applied to a wide range of genetic systems and systematic grades will shortly eliminate the methodological (and perhaps conceptual) distinction between these fields. Of particular importance is the development of the Polymerase Chain Reaction (PCR), a technique of synthetic DNA amplification which produces concentrated preparations of selected genes from complex mixtures of nuclear and mitochondrial genomes. Analysis of PCR products can provide hierarchal genetic comparisons from the level of local rotifer populations through broad evolutionary (at least molecular) phylogenies.     

The evolutionary relationships of two families of cottoid fishes of Lake Baikal (East Siberia) as suggested by analysis of mitochondrial DNA

Fragments of mtDNA genes Cyt B, ATPase 6, and ATPase 8 of six cottoid fishes species of Lake Baikal (East Siberia) were amplified and sequenced. In addition mtDNAs of the same fish were subjected to restriction analysis. The data obtained were used to construct phylogenetic trees. The topology of the ATPase tree differs from those of the Res (restriction) and Cyt B trees. Clustering of species within the trees confirms the viewpoint of Taliev (1955, Baicalian Sculpins (Cottoidei)) according to which Baikalian cottoids originate from two ancestral forms. The times of branching obtained do not confirm the existing viewpoint according to which the two golomyankas (Comephorus baicalensis and Comephorus dybowskii) are pre-Baikal (Myocene) relicts: these two species may have originated 1.2–1.8 million years ago in Baikal, and they seem to represent an example of rapid morphological evolution which resulted in the formation of a new family. Correspondence to: S. Ja. Slobodyanuk     

The parrots (Aves: Psittaciformes) from the Middle Miocene of Sansan (Gers,Southern France)

The occurrence of Archaeopsittacus sp. (Psittaciformes) in the fossil deposits of Sansan (France) is reported, testifying to a survival of this genus in the Middle Miocene, as Archaeopsittacus verreauxi was described from the Early Miocene of Saint-Gérand-le-Puy (France) and was recorded only from its type locality. The data discussed here indicate the presence of two parrot species from Sansan, as it is the type locality of another parrot species, Pararallus dispar, only known from this locality. The differences between the humeri of these two taxa are described in detail, together with the differences from the other European fossil parrot species. The presence of more than one species of parrot in the same locality is not rare, but in Europe it is recorded in Sansan for the second time. Evidence for parrots also confirms the paleoenvironmental reconstruction of Sansan, as parrots are primarily arboreal species. Archaeopsittacus also represents one of the few common elements between the Early and Middle Miocene European bird assemblages.     

Mitochondrial DNA phylogenetic structuring suggests similarity between two morphologically plastic genera of Australian freshwater mussels (Unionoida: Hyriidae)

In the Lake Eyre Basin, the Australian hyriid genus Velesunio is represented by three undescribed species, each of which are highly divergent genetically, but morphologically similar to Velesunio wilsonii (Lea 1859). A fourth species, Velesunio ambiguus (Philippi 1847), occurs not only in the Lake Eyre Basin but throughout much of eastern Australia, including the Murray-Darling Basin. In this study, we show that another hyriid, Alathyria jacksoni (Iredale 1934), which is sympatric with V. ambiguus, is genetically deeply nested within the Velesunio species complex, such that the genus Velesunio is paraphyletic with respect to A. jacksoni. Moreover, our mitochondrial phylogenetic reconstructions indicate that A. jacksoni is closely allied to one of the cryptic Velesunio species occurring in the Lake Eyre Basin, but distinct from V. ambiguus and the two other Velesunio species. These data suggest that the genera Alathyria and Velesunio are in need of revision. The shells of A. jacksoni and Velesunio spp. vary with local conditions and sometimes are difficult to distinguish. Our analyses also show that shell characters of these taxa do not closely match the phylogenetic data, and it appears that the traditional taxonomic emphasis on these plastic characters has obscured evolutionary relationships between these, and possibly other, Hyriidae.     

The Quiet Revolution: A New Synthesis of Biological Knowledge

A method is described for preparing thin-layer chromatography plates for use in the classroom. Glass plates are coated with adsorbent using a technique which is cheap, rapid and reliable and which avoids the need for expensive, commercially-available apparatus. It can be adapted to preparative use. The main adsorbent described is silicic acid H and G but other adsorbents such as cellulose can be spread by the same method. Points to watch for in setting up plates for thin-layer chromatography and applying solute samples are discussed.     

The evolutionary mechanism maintaining shell shape and molecular differentiation between two ecotypes of the dogwhelk Nucella lapillus

Two ecotypes of Nucella lapillus can occur allopatrically or sympatrically, according to different degrees of wave exposure and microhabitats, on rocky shores of NW Spain. We studied differences in shell size and shape in adults and families of shelled embryos captured in the wild, and molecular variation at 9 microsatellite loci and 4 mtDNA regions. Both adults and shelled embryos of the two ecotypes showed significant differences in size and shell-shape components (the most important being size of the shell aperture). Strong among-family variation suggests that shell-shape variation has an important genetic component, and the pattern of genetic differentiation was in agreement with traits being affected by divergent natural selection. No significant overall molecular differentiation was observed between the two ecotypes for mtDNA, although we found significant genetic structure at two microsatellite loci. Microsatellite differentiation between ecotypes at these two loci was larger in sympatry than in allopatry. These results and the comparison of tenacity suggest that the two forms are distinctly adapted to differences in shore level and degree of exposure to wave action.