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 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.     

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.     

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, 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.     

Systematics, biogeography, and evolution of the Neotropical peacock basses Cichla (Perciformes: Cichlidae)

To investigate forces influencing diversification in Neotropical fishes, the phylogenetic relationships among species and populations of the cichlid genus Cichla were examined. Mitochondrial DNA was sequenced for 454 individuals of the 5 nominal Cichla species and several putative undescribed species. Phylogenetic analyses support the distinction of two major clades of Cichla. Clade A includes C. temensis and two undescribed species from the lower Amazonas and Xingu Rivers. Clade B includes C. orinocensis, C. monoculus, C. ocellaris. C, intermedia, and an undescribed species from the upper Madeira River. Species boundaries were relatively well-circumscribed for clade B, while incomplete lineage sorting was inferred for clade A. Three probable instances of introgression were observed, including a regional population of C. orinocensis from the Negro River that shows a history of introgression. Biogeographic patterns from Cichla are partially congruent with those seen in several other Neotropical fish clades, and the diversification of Cichla species is inferred to result from both vicariance and sympatric divergence.     

Phylogeny and biogeography of the genus Illadopsis (Passeriformes: Timaliidae) reveal the complexity of diversification of some African taxa

African jungle babblers or illadopsises, genus Illadopsis Heine, 1859, are small shy babblers which occupy the undergrowth of African humid forest habitats. The taxonomy of Illadopsis as well as its biogeography are currently poorly known because the morphological differentiation is rather subtle and no phylogenetic analysis has been undertaken. To investigate these issues, we sequenced four loci (mitochondrial ND2 and ND3, and nuclear myoglobin intron 2 and β-fibrinogen intron 5) for the seven species of Illadopsis . Our analyses retrieve the monophyly of Illadopsis and suggest that I. albipectus and I. cleaveri , I. puveli and I. rufescens , some individuals of I. rufipennis and I. pyrrhoptera are sister taxa respectively. I. fulvescens appears to be an isolated taxon and our data reveal several cases of "incipient speciation" among its populations. Our dating analyses, using a Bayesian relaxed-clock method, reveal that most splits in Illadopsis occurred synchronously around the Plio-Pleistocene transition, suggesting that some diversification events in African forest taxa took place before the onset of the large-amplitude climatic cycles of the Pleistocene epoch. Thus, the diversification of African taxa in time and space to be more complex than the Pleistocene time frame traditionally associated with the diversification of African forest taxa. Instead we observe a process of differentiation which roughly corresponds to the broadly hypothesised lowland refugia of upper Guinea, eastern and western Guinea-Congolia, although the time frame of this divergence well predates the Pleistocene epoch. Our results also suggest that deep genetic divergences do exist among species complexes of African birds which differ only slightly in morphological characters. As such, molecular analyses are powerful and essential tools if we are to construct the evolutionary history of such lineages in a meaningful manner.     

Phylogeny,biogeography and ecological diversification of Sarcocornia (Salicornioideae,Amaranthaceae)

Background and Aims Sarcocornia comprises about 28 species of perennial succulent halophytes distributed worldwide, mainly in saline environments of warm-temperate and subtropical regions. The genus is characterized by strongly reduced leaves and flowers, which cause taxonomic difficulties; however, species in the genus show high diversity in growth form, with a mat-forming habit found in coastal salt marshes of all continents. Sarcocornia forms a monophyletic lineage with Salicornia whose species are all annual, yet the relationship between the two genera is poorly understood. This study is aimed at clarifying the phylogenetic relationship between Sarcocornia and Salicornia, interpreting biogeographical and ecological patterns in Sarcocornia, and gaining insights into putative parallel evolution of habit as an adaptation to environmental factors.Methods A comprehensively sampled and dated phylogeny of Sarcocornia is presented based on nuclear ribosomal DNA (external transcribed spacer) and chloroplast DNA (atpB-rbcL, rpl32-trnL) sequences; representative samples of Salicornia were also included in the analyses. To infer biogeographical patterns, an ancestral area reconstruction was conducted.Key Results The Sarcocornia/Salicornia lineage arose during the Mid-Miocene from Eurasian ancestors and diversified into four subclades: the Salicornia clade, the American Sarcocornia clade, the Eurasian Sarcocornia clade and the South African/Australian Sarcocornia clade. Sarcocornia is supported as paraphyletic, with Salicornia nested within Sarcocornia being sister to the American/Eurasian Sarcocornia clade. The American and the South African/Australian Sarcocornia clade as well as the Salicornia clade were reconstructed to be of Eurasian origin. The prostrate, mat-forming habit arose multiple times in Sarcocornia.Conclusions Sarcocornia diversified in salt-laden environments worldwide, repeatedly evolving superficially similar prostrate, mat-forming habits that seem advantageous in stressed environments with prolonged flooding, high tidal movement and frost. Some of these prostrate-habit types might be considered as ecotypes (e.g. S. pacifica or S. pillansii) while others represent good ecospecies (e.g. S. perennis, S. decumbens, S. capensis), hence representing different stages of speciation.     

The genus Dugesia in Australia, with its phylogenetic analysis and historical biogeography (Platyhelminthes, Tricladida, Dugesiidae)

The new species Dugesia notogaea Sluys & Kawakatsu, sp. n. is described from Queensland, Australia, representing the first record of the genus Dugesia for that continent. A phylogenetic analysis of the 68 species of Dugesia resulted in the discovery of a new apomorphy for the genus, and a cladogram showing two major phyletic groups. The distributional range of one group has a western accent, whereas that of the other group has an eastern emphasis; the ranges of these two groups overlap in Africa and the Mediterranean region. We attempt to determine the ancestral area for both the Dugesiidae and Dugesia. A scenario for the historical biogeography of the genus Dugesia is discussed. In this scenario it is presumed that the geological history of the Australasian region enabled Dugesia's from southeast Asia to colonize northern Australia. © 1998 The Norwegian Academy of Science and Letters     

Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri-Tyrrhenian area

The land snail genus Solatopupa consists of six species and has a peri-Tyrrhenian distribution; most of the species have a very narrow range and all of them except one (Solatopupa cianensis, which inhabits porphyritic rocks) are strictly bound to calcareous substrates. One species (Solatopupa guidoni) is limited to Sardinia, Corsica, and Elba Island. Because the potential for dispersal of these snails is low, the insular range of this species has been traditionally related to the Oligocenic detachment of the Sardinia-Corsica microplate from the Iberian plate and its subsequent rotation towards the Italian peninsula. In this study, we used sequences of three mitochondrial and one nuclear gene to reconstruct the evolutionary history of the genus. Our phylogenetic results are consistent with the genetic relationships found using allozymes, but contrast with the phylogenetic hypotheses based on karyology and morphology. Molecular clock estimates indicate that the main cladogenetic events in the genus occurred between the middle Miocene and the middle-late Pliocene. Patterns of phylogenetic relationships and geological considerations suggest that the cladogenesis of the genus can be explained by vicariant (tectonic) processes. Our datings do not support a causal relation between the split of S. guidoni from its continental sister taxon and the initial phases of the detachment of the Corsica-Sardinia microplate from the mainland. On the contrary, time estimates coincide with the very last phase of detachment of the microplate (from 5 to 3 Myrs ago). Overall, our molecular clock estimates are in good agreement with the latest geological views on the tectonic evolution of the peri-Tyrrhenian area.     

Morphological development of larval and juvenile Alectis indica (Perciformes: Carangidae) reared in captivity

Larvae and juveniles of Alectis indica reared in captivity are described based on 47 specimens (3.2–32.0 mm in body length: BL). Development was typical for the tribe Carangini except for the presence of elongated fin filaments. Elongated dorsal-fin filaments were present at preflexion (3.2 mm BL). During flexion, the anal- and pelvic-fin rays elongated and the body deepened. The full complement of fin spines and rays was present by 7.1 mm BL. The larvae of A. indica could be differentiated from those of Alectis ciliaris, which also inhabits in the Indo-Pacific waters, by the presence of a ventral series of melanophores on the tail, elongated pelvic fins, and the timing of anal-fin spine migration. The rounded body and elongated fin rays of A. indica cause it to resemble venomous Cubomedusae.     

Life History of Mediterranean Horse Mackerel Trachurus mediterraneus (Carangidae) from Crimea (Black Sea)

Journal of Ichthyology - The sex ratio, body length–age structure, growth rate, maturity dynamics, and mortality are studied in Mediterranean horse mackerel Trachurus mediterraneus from the...     

The red-fin Decapterus group (Perciformes: Carangidae) with the description of a new species, Decapterus smithvanizi

The carangid genus Decapterus can be defined by having a single finlet behind both the second dorsal and anal fins, and lacking scutes on the anterior curved part of the lateral line. We revised taxonomically the species of Decapterus with red-colored caudal fins (the red-fin Decapterus group) and established that the group consisted of the following four species: Decapterus akaadsi Abe 1958, distributed in the eastern Indian Ocean and West Pacific from the Andaman Sea to Indonesia, north to central Japan; Decapterus kurroides Bleeker 1855, distributed in the Indo-West Pacific from the Red Sea and eastern coast of Africa to eastern Australia, north to the Philippines; Decapterus smithvanizi sp. nov., occurring in the Andaman Sea, the South China Sea, and Indonesia; and Decapterus tabl Berry 1968, distributed circumglobally in tropical and subtropical seas. The diagnostic characters of these species are as follows: D. akaadsi—curved part of lateral line with 43–53 cycloid scales, straight part of lateral line with 26–29 scutes, head length 26.7–30.1 % SL, and body depth 24.0–27.9 % SL; D. kurroides—curved part of lateral line with 45–51 cycloid scales, straight part of lateral line with 30–32 scutes, head length 30.3–33.0 % SL, and body depth 23.4–26.4 % SL; D. smithvanizi—lower gill rakers 25–31, curved part of lateral line with 54–62 cycloid scales, body depth 19.4–22.5 % SL, pectoral-fin tip usually beyond the level of second dorsal-fin origin; D. tabl—tip of upper jaw usually hooked and opercular membrane partly serrated in larger specimens, lower gill rakers 28–33, curved part of lateral line with 61–72 cycloid scales, body depth 16.6–23.0 % SL, pectoral-fin tip not reaching to the level of second dorsal-fin origin.     

Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei)

Labyrinth fishes (Perciformes: Anabantoidei) are primary freshwater fishes with a disjunct African-Asian distribution that exhibit a wide variety of morphological and behavioral traits. These intrinsic features make them particularly well suited for studying patterns and processes of evolutionary diversification. We reconstructed the first molecular-based phylogenetic hypothesis of anabantoid intrarelationships using both mitochondrial and nuclear nucleotide sequence data to address anabantoid evolution. The mitochondrial data set included the complete cytochrome b, partial 12S rRNA, complete tRNA Val, and partial 16S rRNA genes (3332 bp) of 57 species representing all 19 anabantoid genera. The nuclear data set included the partial RAG1 gene (1494 bp) of 21 representative species. The phylogenetic analyses of a combined (mitochondrial+nuclear) data set recovered almost fully resolved trees at the intrafamily level with different methods of phylogenetic inference. Phylogenetic relationships at this taxonomic level were compared with previous morphology-based hypotheses. In particular, the enigmatic pike-head (Luciocephalus) was confidently placed within the "spiral egg" clade, thus resolving the long-standing controversy on its relative phylogenetic position. The molecular phylogeny was used to study the evolution of the different forms of parental care within the suborder. Our results suggest that the evolution of breeding behavior in anabantoids is highly correlated with phylogeny, and that brood care evolved three times independently from an ancestral free spawning condition without parental care. Ancestral character state reconstructions under maximum parsimony and maximum likelihood further indicated that both bubble nesting and mouthbrooding have evolved recurrently during anabantoid evolution. The new phylogenetic framework was also used to test alternative biogeographic hypotheses that account for the disjunct African-Asian distribution. Molecular divergence time estimates support either a drift vicariance linked to the breakup of Gondwana or Late Mesozoic Early Tertiary dispersal from Africa to Asia or vice versa.     

Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae)

The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.     

Molecular systematics,taxonomy and biogeography of the genus Cavia (Rodentia: Caviidae)

Phylogenetic analyses were conducted on cytochrome b sequence data of the most geographically and taxonomically broad sampling of Cavia taxa to date. Primary objectives included providing the first extensive molecular phylogenetic framework for the genus, testing the taxonomic and systematic hypotheses of previous authors and providing insight into the evolutionary and biogeographic history of the genus. Support was found for the morphologically defined species C. aperea, C. tschudii, C. magna and C. fulgida and the taxonomic placement of taxa previously subject to conflicting taxonomic opinions (e.g. C. nana, C. anolaimae and C. guianae) was further resolved. Additionally, we elevate the Ecuadorian C. a. patzelti to species status, restrict the distributional limits and suggest taxonomic affiliations of some C. tschudii subspecies, and provide strong evidence for the geographic origin of guinea pig domestication. Finally, we provide an estimated evolutionary timeline for the genus Cavia, which appears to extend well into the late Miocene.     

Tormopsolus attenuatus n. sp. (Digenea: Acanthocolpidae) from Seriola hippos (Perciformes: Carangidae), Western Australia,with some observations on the relationships in the genus

A new acanthocolpid, Tormopsolus attenuatus n. sp., is described from the carangid Seriola hippos from waters off the coast of SW Australia. A cladistic analysis of the genus using 31 morphological and metrical characters indicates that the closest species is T. asiatica Parukhin, 1976 status amend. (previously T. orientalis asiatica). T. attenuatus differs from T. asiatica in its smaller overall dimensions, more attenuated outline, relatively shorter post-testicular region, vitelline interruption at the level of the ovary, papillae on the oral sucker and, possibly, much longer genital atrium. Other similar species, T. orientalis Yamaguti, 1934 and T. medius Reimer, 1983, differ in having interruptions of the vitelline fields at the level of both testes and at the level of the ovary.     

Molecular phylogenetics of suborder Cactineae (Caryophyllales), including insights into photosynthetic diversification and historical biogeography

? Premise of the study: Phylogenetic relationships were investigated among the eight families (Anacampserotaceae, Basellaceae, Cactaceae, Didiereaceae, Halophytaceae, Montiaceae, Portulacaceae, Talinaceae) that form suborder Cactineae (= Portulacineae) of the Caryophyllales. In addition, photosynthesis diversification and historical biogeography were addressed. ? Methods: Chloroplast DNA sequences, mostly noncoding, were used to estimate the phylogeny. Divergence times were calibrated using two Hawaiian Portulaca species, due to the lack of an unequivocal fossil record for Cactineae. Photosynthetic pathways were determined from carbon isotope ratios (δ(13)C) and leaf anatomy. ? Key results: Maximum likelihood and Bayesian analyses were consistent with previous studies in that the suborder, almost all families, and the ACPT clade (Anacampserotaceae, Cactaceae, Portulacaceae, Talinaceae) were strongly supported as monophyletic; however, relationships among families remain uncertain. The age of Cactineae was estimated to be 18.8 Myr. Leaf anatomy and δ(13)C and were congruent in most cases, and inconsistencies between these pointed to photosynthetic intermediates. Reconstruction of photosynthesis diversification showed C(3) to be the ancestral pathway, a shift to C(4) in Portulacaceae, and five independent origins of Crassulacean acid metabolism (CAM). Cactineae were inferred to have originated in the New World. ? Conclusions: Although the C(3) pathway is inferred as the ancestral state in Cactineae, some CAM activity has been reported in the literature in almost every family of the suborder, leaving open the possibility that CAM may have one origin in the group. Incongruence among loci could be due to internal short branches, which possibly represent rapid radiations in response to increasing aridity in the Miocene.