A phylogeny for the Old World newts, genus Triturus: biochemical and behavioural data

A reconstruction is presented of the phylogenetic relationships withing Triturus . Two different data sets are used. Protein electrophoretic data were scored for 19 presumptive gene loci in nine species (Rafinski & Arntzen, 1987) and a set of 16 behaviour characters from the courtship of Triturus was scored for the same nine species. When these are analysed in concernt, a single, fully resolved and robust solution is found. Consequently, two subgenera are recognized: Triturus and Palaeotriton , the former including all te medium- and large-bodied species: T. alpestris, T. vittatus, T. marmoratus, T. cristatus and its three former subspecies ( T. carnifex, T. dobrogicus and T. Karelini ); the latter comprising the small-bodied species: T. bascai, T. italicus, T. helveticus, T. vulgaris and T. montandoni . Within the subgenus Triturus, T. alpestris and T. vittatus are sister taxa to the remaining members of the subgenus. Similarly, T. boscai and T. italicus are a monophyletic group, sister to T. vulgaris, T. helveticus and T. montandoni . Alternative solutions may be found on the basis of a quantitative analysis of the behavioural characters employed in this study. An alternative phylogenetic tree is included as an example.     

Resolving phylogeny at the family level by mitochondrial cytochrome oxidase sequences: phylogeny of carrion beetles (Coleoptera, Silphidae)

We investigated the phylogenetic relationships of carrion beetles (Coleoptera, Silphidae) using 2094 bp of their mitochondrial cytochrome oxidase subunit I and II and tRNA leucine gene sequences. Shorter fragments of this gene region previously have been used to establish generic relationships in insects. In this study, they provided more than sufficient resolution, although the third positions of the protein-coding sequences reached saturation for the deeper divergences. This first published phylogeny for the Silphidae comprises 23 species from 13 genera sampled across the geographic range of the family. In addition, we included species from three related families as outgroups. One of these families, the Agyrtidae, was, until recently, included in the Silphidae, but its resolution here justifies its current position as a separate family. The silphid subfamilies Nicrophorinae and Silphinae are monophyletic in all analyses. All genera for which several species were sampled are supported as monophyletic groups, with the exception of the genus Silpha. European and North American representatives of two Nicrophorus species described from both continents are supported as each others' closest relatives. The lineage that colonized Gondwanaland and that most likely originated in the Palearctic is the most basal within the Silphinae.     

Mitochondrial DNA rates and biogeography in European newts (genus Euproctus)

Sequence divergence for segments of three mitochondrial DNA (mtDNA) genes encoding the 12S and 16S ribosomal RNA and cytochrome b was examined in newts belonging to the genus Euproctus (E. asper, E. montanus, E. platycephalus) and in three other species belonging to the same family (Salamandridae), Triturus carnifex, T. vulgaris, and Pleurodeles waltl. The three Euproctus species occur (one species each) in Corsica, Sardinia, and the Pyrenees. This vicariant distribution is believed to have been determined by the disjunction and rotation of the Sardinia-Corsica microplate from the Pyreneean region. Because time estimates are available for the tectonic events that led to the separation of the three landmasses, we used sequence data to estimate rates of evolution for the three gene fragments and investigated whether they conform to the rate-constancy hypothesis. By the Tajima (1993, Genetics 135:599-607) test, we could not detect rate heterogeneities for the ribosomal genes and for transversions in the cytochrome b gene. Assuming that these sites are evolving linearly over time and that cessation of gene flow occurred simultaneously with vicariant events, we compared the time of divergence estimated by molecular distances with the divergence times based on the geological estimates. Because we have two estimates of divergence time from the geological record, the split of Corsica/Sardinia from the Pyrenees and the split of Corsica from Sardinia, we could compare ratios of molecular divergence with the ratio of geological time divergence. The ratios are very similar, indicating that the molecular clock hypothesis cannot be rejected. These geological events also allowed us to calculate absolute rates of evolution for ribosomal and cytochrome b genes and compare them to rates for the same regions in other salamandrids and other vertebrates. Ribosomal mtDNA rates are comparable to those reported for other vertebrates, but cytochrome b rates are 3-7 times lower in salamanders than in other ectotherms. From a phylogenetic perspective, our data suggest that the cladogenic events leading to species formation in Euproctus and Triturus occurred very closely in time, indicating that the two genera may not be monophyletic. A duplication of the cytochrome b gene in T. carnifex was found, and the implications of this finding for mtDNA phylogenetic studies are discussed.     

Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny

Wu, Y., Wang, Y., Jiang, K., Chen, X. & Hanken, J. (2009). Homoplastic evolution of external colouration in Asian stout newts (Pachytriton) inferred from molecular phylogeny.—Zoologica Scripta, 39, 9–22. The Asian stout newts of the genus Pachytriton (Salamandridae) inhabit montane streams in south-eastern China. Despite their abundance in the pet trade, the phylogeny and systematics of this genus are poorly understood. Colouration is often used to delimit species under the assumption that consistent chromatic differences characterize independent evolutionary lineages. We present the first phylogenetic study of Pachytriton that incorporates 2.35 kb of mitochondrial DNA (ND2, cytb) and 1.2 kb of nuclear sequence data (RAG-1) along with morphometric characters to infer evolutionary relationships and patterns of colour evolution among the three described species: Pachytriton brevipes, Pachytriton labiatus and Pachytriton archospotus. Our results support the monophyly of Pachytriton and recover P. archospotus as the sister taxon to P. brevipes. Monophyly of P. labiatus is significantly rejected: south-western populations are sister to the group of P. brevipes plus P. archospotus, whereas north-eastern populations nest with P. brevipes. The two geographic units are further separated by multivariate morphological analyses. South-western P. labiatus is the type species; misidentification of north-eastern populations as P. labiatus results from their similar colouration. An unspotted, dark brown dorsum is the likely ancestral state for the genus, whereas black-spotted colouration characterized the common ancestor of P. brevipes, P. archospotus, and north-eastern P. labiatus and was secondarily lost in the latter group. Homoplastic evolution and intraspecific variation render colour pattern in Pachytriton an unreliable character for delimiting species boundaries. North-eastern populations of P. labiatus are declining as the result of human collection and habitat destruction and are in urgent need of conservation protection.     

Sexual size dimorphism in the evolutionary context of facultative paedomorphosis: insights from European newts

Background  

Sexual size dimorphism (SSD) is a key evolutionary feature that has been studied in many organisms. In a wide range of species, this pattern is more complex because of polymorphism within each sex. However, it is not known whether the magnitude and direction of SSD could be affected by alternative developmental trajectories within sexes. Our aim was to test whether an intrasexual polymorphism, facultative paedomorphosis (a process in which the development of somatic and gonadal tissues differs in alternative morphs), could affect SSD variation patterns in European newts.     

Resolving insect phylogeny: The significance of cephalic structures of the Nannomecoptera in understanding endopterygote relationships

The Nannomecoptera are among the most enigmatic and controversial taxa of endopterygote insects, the phylogenetic resolution of which is crucial to understanding the evolution of neopteran insects. Once considered a subordinate lineage within the Mecoptera, renewed interest in nannochoristids has been prompted by evidence that the Nannomecoptera are not admissible to the clade of extant scorpion flies but are more likely to belong to the clade Siphonaptera + Nannomecoptera + Diptera. The overarching purpose of the present account is to provide novel and extensive morphological character traits in addition to those already existing for adult structures. The aim is to determine if these traits support molecular data sets that have been suggested elsewhere to clarify the phyletic position of Nannochoristidae. This account focuses on nannomecopteran larvae, which unlike those of other mecopterans have received little attention. Thus, the thrust of this investigation is to provide detailed anatomical data on nannochoristid larvae for a targeted inquiry into their phylogenetic affinities. The described characters are discussed and presented in a data matrix comprising representatives of all endopterygote orders. While the study is based primarily on the New Zealand species Nannochorista philpotti, it is proposed that all nannomecopteran larvae will prove to be similar to this taxon in most if not all structural features of significance to a higher-level phylogenetic context.     

Resolving and dating the phylogeny of Cornales--Effects of taxon sampling, data partitions, and fossil calibrations

The order Cornales descends from the earliest split in the Asterid clade of flowering plants. Despite a few phylogenetic studies, relationships among families within Cornales remain unclear. In the present study, we increased taxon and character sampling to further resolve the relationships and to date the early diversification events of the order. We conducted phylogenetic analyses of sequence data from 26S rDNA and six chloroplast DNA (cpDNA) regions using parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI) methods with different partition models and different data sets. We employed relaxed, uncorrelated molecular clocks on BEAST to date the phylogeny and examined the effects of different taxon sampling, fossil calibration, and data partitions. Our results from ML and BI analyses of the combined cpDNA sequences and combined cpDNA and 26S rDNA data suggested the monophyly of each family and the following familial relationships ((Cornaceae-Alangiaceae)-(Curtisiaceae-Grubbiaceae))-(((Nyssaceae-Davidiaceae)-Mastixiaceae)-((Hydrostachyaceae-(Hydrangeaceae-Loasaceae))). These relationships were strongly supported by posterior probability and bootstrap values, except for the sister relationship between the N-D-M and H-H-L clades. The 26S rDNA data and some MP trees from cpDNA and total evidence suggested some alternative alignments for Hydrostachyaceae within Cornales, but results of SH tests indicated that these trees were significantly worse explanations of the total data. Phylogenetic dating with simultaneous calibration of multiple nodes suggested that the crown group of Cornales originated around the middle Cretaceous and rapidly radiated into several major clades. The origins of most families dated back to the late Cretaceous except for Curtisiaceae and Grubbiaceae which may have diverged in the very early Tertiary. We found that reducing sampling density within families and analyzing partitioned data sets from coding and noncoding cpDNA, 26S rDNA, and combined data sets produced congruent estimation of divergence times, but reducing the number and changing positions of calibration points resulted in very different estimations.     

Marker-derived phylogeny of European cattle supports demic expansion of agriculture

Using frequencies of 86 genes from 23 loci of blood group systems, blood and milk proteins, the genetic relationships among 14 cattle breeds including four native Balkan and four synthetic Balkan-Alp breeds were studied. The dendrogram and nonlinear map construction shows a consensus ‘Balkan breed cluster’, an ‘Alp breed cluster’, an unstable position of synthetic breeds and well-separated American breeds. Positive partial correlations between genetic distance and time elapsed since introduction of farming while keeping geographical distances constant, and regular patterns over thousands of kilometres indicate that large-scale cattle population movements together with human migration (in the Neolithic age) from the Near East into Europe across the Balkans are the most likely explanation for the genetic distances observed in our data. More recent breed differentiation and selection do not yet blur this initial pattern of European cattle populations.     

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.     

Multigene phylogeny of the Mustelidae: Resolving relationships,tempo and biogeographic history of a mammalian adaptive radiation

Background  

Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve.     

Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region

Previous molecular phylogenies of European cyprinids led to some solid facts and some uncertainties. This study is based on a stretch of more than 1 kb in the mitochondrial control region newly sequenced for 35 European cyprinids and on previous cytochrome b and 16S rDNA data. The trees based on the control region are more accurate and robust than those obtained from the two other genes. Character incongruence among the three genes was tested using the incongruence length difference (ILD) test. Iterative removals of individual sequences followed by new ILD tests identified two sequences responsible for statistically significant incongruence. A partial combination was conducted, that is, a combination of the three data sets, removing the two sequences previously identified. The phylogenetic analysis of this partial combination gives a more robust and resolved picture of subfamilial interrelationships. The Rasborinae are the sister group of all other cyprinids. The monophyletic Cyprininae emerges next. Tinca tinca first and then Rhodeus are the sister groups of all the remaining nonrasborine and noncyprinine species. Gobio is the sister group of the Leuciscinae, in which the Phoxinini are the sister group of the Leuciscini. Within the Leuciscini, the genus Leuciscus and the subfamily Alburninae are both paraphyletic. The Rasborinae are the most basal cyprinid subfamily and the Tincinae are not the sister group of the Cyprininae. These two results challenge only two anatomical characters, which need to be reinterpreted or considered as homoplastic in cyprinid evolution: the modification of the first pleural rib and its parapophysis and the bony composition of the interorbital septum.     

Peptide pheromones in newts

This article reviews the current state of understanding of reproductive pheromones in amphibians, focusing mainly on the purification and characterization of peptide pheromones in newts of the genus Cynops, molecular cloning of cDNAs encoding the pheromone molecules, and hormonal control of secretion of these pheromones. Pheromones that attract sexually developed female Cynops pyrrhogaster and C. ensicauda newts were isolated from the male abdominal glands. The C. pyrrhogaster and C. ensicauda pheromones are peptides, designated sodefrin and silefrin, with the amino acid sequences SIPSKDALLK and SILSKDAQLK, respectively. Each pheromone attracts only conspecific females. Molecular cloning of cDNAs encoding sodefrin and silefrin revealed the presence of precursor proteins that are considered to generate these pheromone peptides. Pheromone precursor mRNA levels and radioimmunoassayable pheromone concentrations in the abdominal glands were elevated by prolactin and androgen. Sexual dimorphism and hormone dependency of the responsiveness of vomeronasal epithelium to sodefrin were noted. Significance of pheromones in the form of peptide for those performing reproductive behavior in an aquatic environment was also discussed.     

Sexual size and shape evolution in European newts (Amphibia: Caudata: Salamandridae) on the Balkan Peninsula

We used a phylogenetic perspective in an examination of the direction and extent of sexual dimorphism in body size and body shape in European newts from the Balkan Peninsula (alpine newts, Mesotriton alpestris; crested newts, Triturus cristatus superspecies; smooth newts, Lissotriton vulgaris). We found a strong, female‐biased sexual size dimorphism (SSD) in the analysed clades of alpine newt, whereas within crested newts we found a less stringent female‐biased SSD in Triturus carnifex, Triturus macedonicus and Triturus karelinii, and no significant SSD in T. cristatus or Triturus dobrogicus. Among the smooth newts, we found male‐biased SSD in Lissotriton vulgaris vularis and Lissotriton vulgaris greacus and no SSD in Lissotriton vulgaris meridionalis. Most of these newts also exhibit a significant sexual dimorphism in body shape, which varied more randomly than body size, regardless of SSD level. Female and male body size as well as the degree of SSD displayed statistically significant phylogenetic signal, while sexual dimorphism in body shape was phylogenetically independent. The relationship between independent contrast data for female size and male size indicated that SSD in European newts could be driven by a disproportionate increase in female size as increase in female size was not accompanied by a proportional increase in male size.     

Molecular phylogeny of European muroid rodents based on complete cytochrome b sequences

Phylogenetic relationships among 18 species of mainly European muroid rodents that belong to three subfamilies were estimated using complete sequences of the mitochondrial cytochrome b gene. The inferred monophyly of the subfamilies Murinae (mice and rats) and Arvicolinae (voles, lemmings, and muskrats) is in agreement with previous studies. Within the Murinae, the morphology-based division of the genus Apodemus into three subgenera is supported by these DNA sequence data. The relationships among the different genera of the Murinae were generally poorly resolved, and the relationships of Micromys and Acomys to the other murine genera remained unresolved. Within the subfamily Arvicolinae, the relations of the genera Arvicola, Clethrionomys, and Microtus remained tentative with our data. However, within the Microtus group, there is a good molecular support for the phylogenetic relationships. These findings suggest that the origin of the different murine and arvicoline lineages was rapid, indicating an adaptive radiation with fast speciation.     

Intermittent erythropoiesis in anemic newts

A group of 88 newts, Triturus cristatus carnifex (Laurenti), was rendered totally anemic by administering acetylphenylhydrazine (APH) in the breeding water for 48 h at a concentration of 25 mg/liter. The course of erythron restoration was followed for 5 months, sacrificing four specimens per week and analyzing the blood and spleen hemopoietic tissue. The return to the normal values of the red blood cell count occurred through marked increases in concentration at fairly regular intervals, which is best explained by a discontinuous, rhythmic erythropoiesis. This fact is strictly correlated with the intermittent mitotic activity observed in the spleen and with the periodic appearance of large quantities of immature elements in the blood smears. The APH-induced synchronization of newt erythropoietic activity revealed the approximate length of each erythropoietic cycle to be 4 to 5 weeks and the erythropoietic life span to be 50 to 60 days.     

Taxonomy and phylogeny of European Monochamus species: first molecular and karyological data

The worldwide distributed genus Monochamus Megerle, 1821 (Coleoptera Cerambicydae) comprises beetles that may become pests of economic importance in conifer stands in the Nearctic and Palearctic Regions. Besides direct damage due to the larval tunnelling habits, they have also been recognized as main vectors of the phytoparasitic nematode Bursaphelenchus xylophilus (Steiner & Buhrer, 1934) (Nematoda Aphelenchoididae). We analysed the complete mitochondrial cytochrome oxidase I gene and a fragment of the small subunit RNA gene sequences (1536 base pairs) in the five European species. These are: Monochamus galloprovincialis (Olivier, 1795), morphologically distinguished in two subspecies M. galloprovincialis galloprovincialis (Olivier, 1795) and M. galloprovincialis pistor (Germar, 1818); Monochamus sutor (Linneus 1758); Monochamus saltuarius (Gebler 1830); Monochamus sartor (Fabricius, 1787) and Monochamus urussovi (Fischer, 1806). For appropriate comparisons, also the Asiatic Monochamus alternatus Hope, 1842 and a Japanese M. saltuarius sample have been analysed. Both genes show an absolute identity between the two subspecies of M. galloprovincialis and a strong affinity between M. sartor and M. urussovi: the morphological subdivisions of the former taxon in two subspecies and of the latter in two entities of specific level are therefore not supported genetically. On the other hand, the Italian and the Japanese samples of M. saltuarius always cluster together in all trees, and for the remaining taxa, no doubt about their rank of specific differentiation emerges from present analyses. From a phyletic point of view, tree topology indicates the Japanese M. alternatus as the most differentiated taxon and the Euroasiatic M. saltuarius as basal to all other strictly European entities. Chromosome analyses show that the diploid autosomal complement ranges from 18 in M. saltuarius to 20 in M. galloprovincialis, and 22 in M. sartor, but a XX–Xy_p sex determining system is shared by all analysed taxa. The M. saltuarius karyotype appears as the most primitive from which the others may be derived through Robertsonian fissions. Karyological data therefore agree with molecular analyses in indicating a basal position of Euroasiatic M. saltuarius with respect to the group of European Monochamus taxa; among these, M. galloprovincialis and M. sartor represent two clearly diverging evolutionary units. Furthermore, karyotype analyses substantiate molecular conclusions about the identity between M. galloprovincialis galloprovincialis and M. galloprovincialis pistor.