Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analyses

Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North‐eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction‐direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour‐joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species‐specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter‐nucleotide and intra‐nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered.     

Phylogeny,diversification patterns and historical biogeography of euglossine orchid bees (Hymenoptera: Apidae)

The orchid bees constitute a clade of prominent insect pollinators distributed throughout the Neotropical region. Males of all species collect fragrances from natural sources, including flowers, decaying vegetation and fungi, and store them in specialized leg pockets to later expose during courtship display. In addition, orchid bees provide pollination services to a diverse array of Neotropical angiosperms when foraging for food and nesting materials. However, despite their ecological importance, little is known about the evolutionary history of orchid bees. Here, we present a comprehensive molecular phylogenetic analysis based on ～4.0 kb of DNA from four loci [cytochrome oxidase (CO1), elongation factor 1‐α (EF1‐α), arginine kinase (ArgK) and RNA polymerase II (Pol‐II)] across the entire tribe Euglossini, including all five genera, eight subgenera and 126 of the approximately 200 known species. We investigated lineage diversification using fossil‐calibrated molecular clocks and the evolution of morphological traits using disparity‐through‐time plots. In addition, we inferred past biogeographical events by implementing model‐based likelihood methods. Our dataset supports a new view on generic relationships and indicates that the cleptoparasitic genus Exaerete is sister to the remaining orchid bee genera. Our divergence time estimates indicate that extant orchid bee lineages shared a most recent common ancestor at 27–42 Mya. In addition, our analysis of morphology shows that tongue length and body size experienced rapid disparity bursts that coincide with the origin of diverse genera (Euglossa and Eufriesea). Finally, our analysis of historical biogeography indicates that early diversification episodes shared a history on both sides of Mesoamerica, where orchid bees dispersed across the Caribbean, and through a Panamanian connection, thus reinforcing the hypothesis that recent geological events (e.g. the formation of the isthmus of Panama) contributed to the diversification of the rich Neotropical biota. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 552–572.     

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae)

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short‐tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Chocó, Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.     

Phylogenetics,delimitation and historical biogeography of the pantropical tree genus Thespesia (Malvaceae,Gossypieae)

Thespesia consists of 16 species of trees and shrubs from Southeast Asia–Oceania, Africa and America, the most well known being T. populnea, a small tree of tropical coastal areas around the world. Phylogenetic relationships in the genus and among its allies in tribe Gossypieae were inferred using three plastid and two nuclear regions to ascertain its generic delimitation and explore its biogeographical history. Maximum‐likelihood and Bayesian analyses confirmed that Thespesia is not monophyletic and, based on these results, Azanza is reinstated to accommodate the two species previously placed in Thespesia section Lampas. Dating analyses and ancestral range estimation indicated that Thespesia s.s. most likely originated in Southeast Asia–Oceania c. 30 Mya, but extant species did not begin to differentiate until the late Miocene. Two dispersal events, one into Africa c. 11 Mya and another into America (Antilles) c. 9 Mya, gave rise to the African and the Greater Antillean endemics, respectively. The two most widespread hydrochorous species, T. populnea and T. populneoides, originated in Southeast Asia–Oceania from where they spread to other parts of the world. Our analysis also indicated a much earlier origin than previously reported for the eumalvoid clade and its tribes Gossypieae, Malveae and Hibisceae suggesting that vicariance might have had an important role early in the history of these groups.     

Molecular phylogeny and historical biogeography of the large carpenter bees, genus Xylocopa (Hymenoptera: Apidae)

The biogeographical history of major groups of bees with worldwide distributions have often been explained through hypotheses based on Gondwanan vicariance or long distance dispersal events, but until recently these hypotheses have been very difficult, if not impossible, to distinguish. New fossil data, comprehensive information on Mesozoic and Cenozoic coastline positions and the availability of phylogenetically informative DNA markers now makes it feasible to test these hypotheses for some groups of bees. This paper presents historical biogeographical analyses of the genus Xylocopa Latreille, based on phylogenetic analyses of species belonging to 22 subgenera using molecular data from two nuclear genes, elongation factor‐1α (EF‐1α) and phosphoenolpyruvate carboxykinase (PEPCK), combined with previously published morphological and mitochondrial data sets. Phylogenetic analyses based on parsimony and likelihood approaches resulted in several groups of subgenera supported by high bootstrap values (>85%): an American group with the Oriental/Palaearctic subgenera Nyctomelitta and Proxylocopa as sister taxa; a geographically diverse group (Xylocopa s.l); and a group consisting of African and Oriental subgenera. The relationships among these three clades and the subgenus Perixylocopa remained unresolved. The Oriental subgenus Biluna was found to be the sister group of all other carpenter bee subgenera included in this study. Using a relaxed molecular clock calibrated using fossil carpenter bees, we show that the major splits in the carpenter bee phylogeny occurred well after the final breakup of Gondwanaland (the separation of South America and Africa, 100 Mya), but before important Miocene fusion events. Ancestral area analysis showed that the genus Xylocopa most likely had an Oriental‐Palaearctic origin and that the present world distribution of Xylocopa subgenera resulted mainly from independent dispersal events. The influence of Pleistocene glaciations on carpenter bee distributions is also discussed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 77 , 249–266.     

Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses

Pines comprise one of the largest coniferous genera, are distributed throughout the Northern Hemisphere, and have an abundant fossil record. Distributions of fossils have been used to derive a three-step hypothesis of early pine evolution, which postulates a Mesozoic origin for the genus, east-west expansions across Laurasia, and retraction into Eocene refugia. Here, we present phylogenetic tests of this hypothesis using chloroplast sequence data from four loci for 83 pine species. We used the fossil-based hypothesis to derive null expectations concerning monophyly of taxonomic groups, dates of cladogenesis, and patterns of diversification. Phylogenetic analyses using several algorithms subsequently provided rigorous tests of these expectations. Our inferred phylogenies illustrated broad congruence with taxonomic groups, but highlighted consistent problems within subgenus Strobus. Estimated minimum dates of divergence derived from relaxed clock methods were largely consistent with the fossil record and yielded a date for the ingroup node of Pinus of 128+/-4 mya, depending upon the calibration used for subgenus Pinus. Ancestral area reconstructions showed Pinus to have most likely originated in Eurasia. Major clades differed in biogeographic patterns, but were consistent with the fossil-based hypothesis. We found weak support, however, for a change in diversification rate in the Eocene as interpretations of fossil distributions would have predicted.     

Origin and diversification of the clawed lobster genus Metanephrops (Crustacea: Decapoda: Nephropidae)

A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) but refutes monophyly of the other two groups (the arafurensis and thomsoni groups). The results in general support a recent morphology-based cladistic analysis of this genus except that this study suggests M. neptunus to be a basal rather than a derived species as indicated in the morphological analysis. This species is genetically diverse over its geographical range. Moreover, the two color forms of M. thomsoni are genetically distinct, most likely representing different species. The molecular phylogeny and current distribution pattern of the extant species, together with the fossil record, suggest that the genus originated in the Antarctica in the Cretaceous, followed by diversification and dispersal along the continental shelf of different continents as a result of the vicariant events associated with the breakup of the Southern Temperate Gondwana since Late Cretaceous.     

Molecular phylogeny and historical biogeography of the genus Platycerus (Coleoptera,Lucanidae) in East Asia

The genus Platycerus is a cool temperature zone taxon widely distributed in the Northern Hemisphere. In East Asia, 10, one and 28 species are known in Japan, Korea and China, respectively. Recent studies of Platycerus have revealed the divergence pattern in Japan and South Korea, but that of Chinese Platycerus is unknown. We conducted a phylogenetic and biogeographical study of Platycerus in East Asia, including China, using 68, 87 and 296 sequence data of the nuclear wingless gene, internal transcribed spacer (ITS) region and mitochondrial COI gene, respectively. Although the introgression of mitochondrial genes had been known in Japanese Platycerus, the essential contradiction was not recognized between the phylogenetic trees of nuclear genes and COI in Chinese Platycerus. In the COI tree, the Japanese clade and Asian continental clade diverged around 10.84 million years ago, and four major clades were recognized in the latter. For the shape of the posterolateral corner of the Platycerus pronotum, sharp (S)-type species are distributed in higher latitudinal and lower altitudinal areas than round (R)-type species in the Asian continent. S-type species have evolved from R-type species at least three times in more northerly areas, where the annual amplitude of temperature change is large. The genus Platycerus has been differentiated and speciated by a process unique to South Korea, Japan and China, according to regional topography. Thus, genetic differentiation and speciation in Platycerus are related to latitudinal and altitudinal gradients, as well as the site topographical profile and niche differentiation.     

Origin and diversification of the cryptic ant genus Stenamma Westwood (Hymenoptera: Formicidae), inferred from multilocus molecular data,biogeography and natural history

The genus Stenamma Westwood comprises a group of cryptic, cold tolerant ants that occur throughout the Holarctic and Middle American regions. Traditional approaches to taxonomy and phylogeny are confounded by multiple factors, including the conservative and often convergent morphology of workers and the rarity of reproductive castes in collections. Monophyly of Stenamma and relationships within the genus are uncertain as nearly all previous taxonomic work has been regional in scope. Furthermore, the sister group to Stenamma has not been well established. Here an extensive molecular dataset consisting of ten genes (～8 kb of data), 48 ingroup taxa (20 Nearctic, 6 Palaearctic and 22 Neotropical) and 8 outgroup taxa (6 closely related non‐Stenamma and 2 additional myrmicines) is used to investigate the broad‐scale phylogeny and evolutionary history of Stenamma. Phylogenetic analysis is performed under maximum likelihood and Bayesian frameworks on individual genes and several alternate concatenated datasets, which are used to investigate the effects of inclusion or exclusion of COI and intronic regions. The timing of Stenamma evolution is inferred in beast and ancestral areas are reconstructed using both the s‐diva and DEC methods, as implemented in the programs rasp and lagrange , respectively. Stenamma is revealed as monophyletic with high support and tentatively is sister to a group of New World species placed currently in Aphaenogaster Mayr and Messor Forel. Within Stenamma, two major clades are recovered: a ‘Holarctic clade’ (HOC) and a ‘Middle American clade’ (MAC). The HOC consists of the European S. striatulum Emery sister to two well‐supported groups, the informal ‘debile’ and ‘brevicorne’ clades. The ‘brevicorne’ clade is entirely Nearctic, whereas the ‘debile’ clade includes both Nearctic and Palaearctic representatives. The MAC occurs from the southern United States to northern South America and, with the exception of S. huachucanum Smith, is almost completely isolated geographically from the HOC. It includes a depauperate northern clade and the ‘MAC core’, which is a diverse assemblage of wet forest adapted species found throughout Central America. Divergence dating and biogeographic reconstruction show that Stenamma is most likely to have originated in the Nearctic at the Eocene–Oligocene boundary (～35 Ma) and diversified more rapidly at 16 and 8 Ma for the HOC and MAC, respectively. Potential environmental factors affecting the evolution of Stenamma include the intense global cooling of the late Eocene combined with aridification and mountain building. The phylogenetic results are discussed in relation to the current Stenamma species groups and several new morphological characters are presented to help in identification.     

Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae).

Phylogenetic relationships among the 12 recognized fish species in the New World genus Centropomus (Pisces, Centropomidae) were analyzed using allozyme electrophoresis and 618 bp of the mitochondrial DNA 16S ribosomal RNA (rRNA) gene. Molecular phylogenetic trees were generally consistent with previously published partial hypotheses based on morphological evidence. However, previously undefined sister group relationships between major species groups were resolved using molecular data, and phylogenetic hypotheses for Centropomus based on 16S rRNA sequences were better supported than were allozyme-based hypotheses. The high level of congruence among the trees inferred from the nuclear and mitochondrial characters provided a firm phylogenetic basis for analysis of ecological diversification and molecular evolution in the genus. Compared to basal Centropomus species, members of the most nested species group were significantly larger in body size and occupied a marine niche only peripherally utilized by their congeners. We also observed substitution rate heterogeneity among 16S rRNA lineages; in contrast to expectations based on "metabolic rate" and "generation interval" models, relative substitution rates were faster than expected for the group of large-bodied snooks. Using the Pliocene rise of the Central American isthmian marine barrier to calibrate rates of 16S ribosomal gene evolution in Centropomus, we found that the rates for the genus were similar to those reported for higher vertebrates. Analysis of the three sets of transisthmian geminate taxa in Centropomus indicated that two of the pairs were probably formed during the Pliocene rise of the isthmus while the third pair diverged several million years earlier.     

Molecular phylogeny and the historical biogeography of the warblers of the genus Sylvia (Aves)

A molecular phylogeny based on DNA/DNA hybridization revealed that the Sylvia-Parisoma complex is monophyletic and includes three main groups of species, the “mid-European” warblers, the genus Parisoma, and the “eu-Mediterranean” Sylvia species sensu stricto. The latter can be assigned to three main clusters, a “West-Mediterranean” group, a “Central-Mediterranean group”, and an “East-Mediterranean” group. The radiation of the whole complex is much more ancient than formerly believed. It started ca 12–13 Ma ago and the ancestors of the main extant groups differentiated during the Pliocene. Only speciation events within the “eu-Mediterranean” lineages occurred during the Pleistocene. The paleoclimatical and paleoecological history of the Mediterranean region is too complicated to provide any evidence for direct relationships between past events and evolutionary steps of these taxa which did not leave any reliable fossil record. However, some major speciation events may be related to well documented climatical crises as well as paleobotanical data. The largely man-induced extension of matorrals over several millenia presumably extended the range of several species that were formerly much more restricted, which complicates reconstruction of the spatio-temporal course of speciation.     

Redescription and molecular characterisation of Allogastrocotyle bivaginalis Nasir & Fuentes Zambrano, 1983 (Monogenea: Gastrocotylidae) from Trachurus picturatus (Bowdich) (Perciformes: Carangidae) off the Algerian coast,Mediterranean Sea

Systematic Parasitology - Allogastrocotyle bivaginalis Nasir & Fuentes Zambrano, 1983, the sole species of Allogastrocotyle Nasir & Fuentes Zambrano, 1983, was described from...     

Molecular phylogeny and historical biogeography of the genus Tuber, the 'true truffles'

Aim Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography. Location Europe, North Africa, China, Asia, North America. Methods Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal‐transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima’s relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S‐ITS2 rRNA and β‐tubulin sequences evolved in a clock‐like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees using mega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal–vicariance analysis (diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. Results The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups. diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Main conclusions Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra‐ and inter‐continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra‐continental dispersal events between Europe and Asia and inter‐continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary.     

Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae)

Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato) from 3.3-Kilobase (kb) sequences of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidases I and II and 1.0 kb of elongation factor 1 alpha). Congruent phylogenetic trees were recovered within Papilio from analyses of combined data using maximum likelihood, Bayesian analysis, and maximum parsimony bootstrap consensus. Several disagreements with the traditional classification of Papilio were found. Five major previously hypothesized subdivisions within Papilio were well supported: Heraclides, Pterourus, Chilasa, Papilio (sensu stricto), and Eleppone. Further studies are required to clarify relationships within traditional "Princeps," which was paraphyletic. Several biologically interesting characteristics of Papilio appear to have polyphyletic origins, including mimetic adults, larval host associations, and larval morphology. Early diversification within Papilio is estimated at 55-65 million years ago based on a combination of biogeographic time constraints rather than fossils. This divergence time suggests that Papilio has slower apparent substitution rates than do Drosophila and fig-pollinating wasps and/or divergences corrected using best-fit substitution models are still being consistently underestimated. The amount of sequence divergence between Papilio subdivisions is equivalent to divergences between genera in other tribes of the Papilionidae, and between genera of moths of the noctuid subfamily Heliothinae.