The influence of riverine barriers on phylogeographic patterns of Malagasy reed frogs (Heterixalus)

We analyzed the influence of large rivers on the phylogeography of endemic widespread amphibians along Madagascar's east coast, using as models various species and species complexes of Malagasy reed frogs (Heterixalus spp.) that are specialized to either highland or lowland habitats. We assembled a dense sampling across the full species ranges and used mitochondrial (cob) as well as nuclear (Rag-1) DNA sequences to assess their phylogeographies. A multigene mtDNA phylogeny of each species was constructed to establish the relationships among the main phylogroups, in order to understand the geographical regions of clade origins and possible directions of historical range expansions. Distinct intraspecific lineages as diagnosed by mitochondrial haplotype clades were found in highlands and lowlands. Most geographical boundaries among these phylogroups did not coincide with rivers, indicating that the influence of rivers on the primary divergence of phylogroups is probably minor in these frogs. Nevertheless, we found evidence for the influence of one riverine barrier in the lowland species complex, where the most important genetic discontinuity (the border between Heterixalus madagascariensis and H. alboguttatus) coincides with the geographical position of the Mangoro River on Madagascar's central east coast. Analyses of the highland species H. betsileo revealed the existence of six deep haplotype lineages, separated in two major subpopulations which differ largely in altitudinal distribution and do not overlap with the geographical settings of rivers in the highlands. Furthermore, our analyses indicated that most of the major intraspecific lineages of reed frogs show signs of a rather recent population expansion.     

Molecular phylogeny and biogeography of Malagasy frogs of the genus Gephyromantis

The genus Gephyromantis is a clade within the Malagasy-Comoroan family Mantellidae composed of rainforest frogs that live and breed to varying degrees independently from water. Based on DNA sequences of five mitochondrial and five nuclear genes we inferred the phylogeny of these frogs with full taxon coverage at the species level. Our preferred consensus tree from a partitioned Bayesian analysis of 5843 base pairs of 51 nominal and candidate species supports various major clades within the genus although the basal relationships among these remain unresolved. The data provide strong evidence for the monophyly of the subgenera Gephyromantis (after exclusion of Gephyromantis klemmeri), Laurentomantis, Vatomantis, and Phylacomantis. Species assigned to the subgenus Duboimantis belong to two strongly supported clades of uncertain relationships. G. klemmeri, previously in the subgenus Gephyromantis, was placed with high support sister to the Laurentomantis clade, and the Laurentomantis + G. klemmeri clade was sister to Vatomantis. A reconstruction of ancestral distribution areas indicates a diversification of several subgenera in the northern biogeographic regions of Madagascar and the dispersal out of northern Madagascar for several clades.     

Karyological evolution and systematics of Malagasy microhylid frogs

Microhylid frogs are a group of largely unresolved phylogeny, and diverse data sets are needed to improve the evolutionary understanding of these amphibians. We here report karyological data for 22 species of this family, belonging to the Malagasy genera Anodonthyla, Cophyla, Platypelis, Plethodontohyla, Rhombophryne, and Stumpffia (Cophylinae); Scaphiophryne and Paradoxophyla (Scaphiophryninae); and Dyscophus (Dyscophinae); and the Asian genera Calluella and Ramanella (Microhylinae). All species studied have 2n=26 chromosomes, most of which are metacentric or submetacentric. Chromosome morphology, banding pattern, and position of the nucleolar organizer regions (NORs) provide relevant characters for the understanding of the phylogeny and systematics of these frogs. The species of the Cophylinae are characterized by a subtelocentric or telocentric fourth chromosome pair (submetacentric only in Anodonthyla), which can be seen as a synapomorphy for this subfamily. Shifts in NOR position within the Cophylinae are frequent and agree with recent mitochondrial DNA data, corroborating the non-monophyly of the genus Plethodontohyla. Changes of NOR position and chromosome morphology (i.e., occurrence of subtelocentric and telocentric elements) were also common in this subfamily, possibly being related to their faster mitochondrial substitution rate and high species diversity. The ninth chromosome pair of the examined specimens of Dyscophus guineti, all juveniles, is heteromorphic. In this pair, one of the two chromosomes is longer due to the addition of two heterochromatic segments, raising the possibility that one chromosome of this pair may be a sex chromosome.     

Molecular systematics of mantelline frogs from Madagascar and the evolution of their femoral glands

Several genera of frogs from Madagascar, classified in the family Mantellidae, subfamily Mantellinae, possess structures commonly called 'femoral glands' on the ventral side of their shanks. The question arises as to the origin and phylogenetic significance of these glands. A molecular phylogeny based on 3601 nucleotide DNA sequences of three mitochondrial and two nuclear genes of 30 mantellid species provided strong support for monophyly of the included mantellines, all characterized by enlarged femoral gland clusters, as well as for those with gland clusters of coordinated central arrangement of secretion ducts. However, the phylogeny also strongly supported the hypothesis of convergent evolution of structurally similar glands in unrelated frogs ( Indirana , Petropedetes ), and several trends of convergent evolution of gland structure within mantellines. We studied the light microscopic structure of the femoral glands in a representative array of 18 mantellid species. Males of all species of the subfamily Mantellinae were characterized by clusters of distinct single glands. Each was structurally similar to an enlarged granular gland and secreted independently, probably through a single duct. By contrast, the largely semi-aquatic frogs in the genus Mantidactylus had a specialized cluster of glands, in which the secretion ducts led into a macroscopically recognizable central depression. In Boophis opisthodon , a mantellid species of the subfamily Boophinae without externally recognizable femoral glands, we observed a large number of enlarged granular glands of various sizes in the ventral skin of the shank. This observation is consistent with the hypothesis that the large and more uniform organs of mantellines are derived granular glands.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 529–539.     

Molecular systematics and biogeography of the fanged frogs of Southeast Asia

Our analysis of parts of the mitochondrial ribosomal 12S and 16S genes from 39 populations of Southeast Asian ranid frogs confirms that the fanged frogs are a monophyletic clade. This group, properly called Limnonectes, appears to have arisen in the early Tertiary at a time when free faunal exchange was possible among Southeast Asia, Borneo, Sumatra, Java, and, probably, Sulawesi. Four species groups are tentatively identified within the clade. Part of group 1 includes species related to L. kuhlii that occur in Borneo. Another part of group 1 includes species from Malay Peninsula and Thailand that are related to L. pileata. Species group 2, L. leporina, occurs only in Borneo. Species group 3 is restricted to species distributed in Sulawesi and the Philippines. Species group 4 includes L. blythii and relatives. There is a lack of compatibility between phylogenetic hypotheses generated from molecular and morphological data sets. These differences are related, in large part, to whether some species of Limnonectes have secondarily lost fangs or whether lack of fangs represents the primitive condition.     

Molecular phylogeny and systematics of drosophila retrotransposons and retroviruses

Full classification of Drosophila melanogaster retrotransposons with long terminal repeats (LTR-retrotransposons) has been recomposed, and their evolutional analysis in sequenced genomes of different species of drosophila and other arthropods has been carried out. D. melanogaster LTR-retrotransposons are divided into three groups: gypsy (one, two, or three open reading frames (ORFs)), copia (one ORF), and BEL (one ORF). The gypsy group is divided into three subgroups. Subgroup I is underrepresented by retrotransposons-retroviruses with three ORFs and their derivatives, which have lost the env gene (ORF3). Subgroup II is underrepresented by retrotransposons with two ORFs, and subgroup III is underrepresented by retrotransposons with one ORF. A comparative analysis of homologs of gypsy group LTR-retrotransposons evidences that subgroups I and II are represented only in the genomes of Lepidoptera and Diptera. The gypsy group of LTR-retrotransposons with one and two ORFs is found in almost all genomes of arthropods. Most of the families of D. melanogaster gypsy group LTR-retrotransposons have close homologs in the genomes of other species of drosophila. A degree of identity of retrotransposons sequences is correlated with a degree of relation between species of drosophila, indicating vertical transmission of retrotransposons. Obvious cases of horizontal transfer of some mobile elements have been detected including retrotransposons without the env gene. Homologs of distinct ORFs of retrotransposons—genes gag and env—have been found. Gene-homolog of the gag gene—Grp (CG5680)—is under purifying selection, so it has an important function in drosophila genome.     

Molecular phylogeny of Malagasy poison frogs,genus Mantella (Anura: Mantellidae): homoplastic evolution of colour pattern in aposematic amphibians

We studied the evolution of colour pattern in Malagasy poison frogs, genus Mantella, a group of diurnal and toxic frogs endemic to Madagascar. Based on a phylogeny reconstructed using 1130 bp of the mitochondrial 16S rRNA gene, the genus can be divided into five species groups. Within some of these groups, interspecific genetic divergences were very low (1.2–2.8% sequence divergence) while colour patterns were markedly different. In contrast, Mantella madagascariensis and M. baroni, two species which show extremely similar dorsal coloration patterns, were not included in the same clade. This conclusion was supported by high bootstrap values and by significant rejection of alternative topologies using KH-tests. Analysis of colour patterns and tentative reconstruction of ancestral states yielded five character states shared by these two species but not by their respective sister species, M. aurantiaca and M. nigricans. Considering these detailed similarities as symplesiomorphic therefore requires the assumption of multiple reversals in other species, whereas a homoplastic colour evolution in the sympatric M. madagascariensis andM. baroni appears as most parsimonious. This parallelism may have been triggered by MÜllerian mimicry. However, additional data is necessary to support this hypothesis.     

Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates

The study of Amazonian biodiversity requires detailed knowledge of the phylogenetic relationships of closely related taxa distributed across Amazonia. The Amazonian poison frogs of the genus Dendrobates have undergone many taxonomic revisions, but the phylogenetic relationships within this group remain poorly understood. Most previous classifications were based on morphology and skin toxin analyses, with limited use of DNA sequence data. Using mtDNA sequence data from four gene regions (cytochrome b, cytochrome oxidase I, 16S rRNA, and 12S rRNA), we present a molecular phylogenetic analysis of the evolutionary relationships within a representative group of Amazonian Dendrobates. We use the resulting phylogenetic hypothesis to investigate different biogeographic hypotheses concerning genetic divergence and species diversity in Amazonia. The results of the analysis support the presence of ancient paleogeographic barriers to gene flow between eastern and western Amazonia, and indicate substantial genetic divergence between species found in the northern and southern regions of western Amazonia.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Molecular phylogeny and systematics of oligochaeta: Pro et contra

The systematics of oligochaete worms was discussed by experts for the entire 20th century. The development of computing and molecular techniques hold promise for the construction of a phylogenetically reasonable system. However, the eliminating of some paraphyletic lineages did not result in unanimous approval among a wide range of biologists (mainly morphologists and ecologists). Molecular systematics has helped clear up the position of many controversial species and genera, while causing doubts about the classification of higher rank taxa, which seemed to be logical and stable until recently.     

Molecular phylogeny and systematics of flowering plants of the family Crassulaceae DC

Crassulaceae (orpine or stonecrop family) is the most species-rich (ca. 1400 spp) family in the order Saxifragales. Most members of the family are succulent plants. Phenotypic diversity and large number of species complicates systematics of the family and obscures reconstruction of relationship within it. Phylogenetic analyzes based on morphological and molecular markers placed Crassulaceae as one of the crown clades of Saxifragales. In this contribution a review of phylogenetic studies on the family Crassulaceae, based on DNA nucleotide sequence comparisons is presented; major clades established in the family are characterised; their structure and polyphylesis of some genera are discussed. It is shown that the traditional taxonomic structure of Crassulaceae contradicts pattern of phylogenetic relationships between its members. We critically analyzed recent taxonomic systems of the family and stress that homoplasy of morphological characters does not allow to use them to reconstruct relationships between crassulacean taxa even at the low taxonomic levels.     

Molecular systematics, phylogeny and biogeography of roaches (Rutilus, Teleostei, Cyprinidae)

In this study we used sequence data from the entire mtDNA cytochrome b gene to reconstruct patterns and times of diversification in the roach genus Rutilus. The genus is present with numerous endemic species in the Eastern peri-Mediterranean area and with a few widespread species in Central Europe. Our phylogenetic results do not support the subdivision into two subgenera proposed on morphological grounds. Within R. pigus and R. rutilus we identify highly divergent and allopatric mitochondrial lineages. The deeper splits in the genus phylogeny date back to the middle Miocene; the main diversification took place at the Miocene-Pliocene boundary.     

Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves,Ramphastidae)

Bonaccorso, E., Guayasamin, J. M., Peterson, A. T. & Navarro‐Sigüenza, A. G. (2011). Molecular phylogeny and systematics of Neotropical toucanets in the genus Aulacorhynchus (Aves, Ramphastidae). —Zoologica Scripta, 40, 336–349. We studied the phylogenetic relationships in the genus Aulacorhynchus, an assemblage of Neotropical toucanets distributed from Mexico south to Bolivia. Based on mitochondrial and nuclear DNA characters, we obtained a robust hypothesis of relationships for all recognized species, including good representation of distinct geographic populations. Our results support the monophyly of the genus Aulacorhynchus, but contradict previous taxonomic arrangements. The genus is made up of three major clades: the Aulacorhynchus prasinus complex, Aulacorhynchus huallagae + Aulacorhynchus coeruleicinctis, and Aulacorhynchus haematopygus + Aulacorhynchus sulcatus + Aulacorhynchus derbianus. Andean populations of A. derbianus are more closely related to A. sulcatus than to Pantepuian populations of A. derbianus, rendering A. derbianus paraphyletic. Based on the molecular phylogeny, and information on geographic distributions and morphological and behavioural characters, we review the specific status of these taxa and propose a new taxonomic arrangement within Aulacorhynchus.     

Molecular phylogeny of French Guiana Hylinae: implications for the systematic and biodiversity of the Neotropical frogs

In this study we used nucleotide sequences from a segment of mitochondrial 16S ribosomal DNA gene to investigate the evolutionary relationships of some French Guiana Hylinae. New sequences, representing the members of different French Guiana frogs-five specimens of the Scinax genus, two Hyla, one Osteocephalus, one Hyalinobatrachium and two Rana as out-group-were examined. In addition, 26 sequences available from GenBank database representing the other subfamilies of the Hylidae were added to our study. This work allowed us to clarify relationships within the four hylids subfamilies (Pelodryadinae, Phyllomedusinae, Hemiphractinae and Hylinae) and the phylogenetic placement of the enigmatic Scinax genus within the Hylidae. We found that: (1) the Scinax genus displays a high level of differentiation in comparison to two other genera (Litoria and Hyla) belonging to 'Hylidae' family; (2) the Hylinae are paraphyletic given the position of the Litoria, which was the sister-group of the Hyla and the Osteocephalus genera; (3) the anterior works and our results (based on two different data sets) showed the paraphyly of the Hylidae questioning the validity of this family; (4) the reassessment of these different taxonomic groups will induce a huge implication on the estimation (past, present and future) of the biodiversity (in Neotropical frogs).     

Molecular phylogeny and biogeography of West Indian frogs of the genus Leptodactylus (Anura, Leptodactylidae)

Three endemic species of the aquatic-breeding frog genus Leptodactylus are recognized from the West Indies: Leptodactylus albilabris (Puerto Rico and the Virgin Islands), Leptodactylus dominicensis (Hispaniola), and Leptodactylus fallax (Lesser Antilles). DNA sequences were obtained from several mitochondrial genes to resolve taxonomic questions involving these species and to provide insights into their origin and distribution in the islands. We found low levels of sequence divergence between L. dominicensis and L. albilabris, supporting morphological evidence that the former species is a junior synonym of the latter species. Phylogenetic analysis supported previous species-group allocations, finding that L. albilabris is a member of the fuscus group and L. fallax is a member of the pentadactylus group. Molecular time estimates for the divergence of L. albilabris from its closest relative in South America (24-58 million years ago, Ma) and for L. fallax from its closest relative in South America (23-34Ma) indicate that they colonized the West Indies independently by over-water dispersal in the mid-Cenozoic. The absence of detectable sequence divergence between the two extant populations of L. fallax (Dominica and Montserrat), a species used for human food and now critically endangered, suggests that one or both arose by human introduction from an island or islands where that species originated. The relatively minor genetic differentiation of populations of L. albilabris can be explained by vicariance and dispersal in the Pleistocene and Holocene, although human introduction of some populations cannot be ruled out.     

Molecular systematics of aphids and their primary endosymbionts

Aphids constitute a monophyletic group within the order Homoptera (i.e., superfamily Aphidoidea). The Aphidoidea originated in the Jurassic about 150 my ago from some aphidiform ancestor whose origin can be traced back to about 250 my ago. They exhibit a mutualistic association with intracellular bacteria (Buchnera sp.) related to Escherichia coli. Buchnera is usually considered the aphids' primary endosymbiont. The association is obligate for both partners. The 16S rDNA-based phylogeny of Buchnera from four aphid families showed complete concordance with the morphology-based phylogeny of their aphid hosts, which pointed to a single original infection in a common ancestor of aphids some 100-250 my ago followed by cospeciation of aphids and Buchnera. This study concentrated on the molecular phylogeny of both the aphids and their primary endosymbionts of five aphid families including for the first time representatives of the family Lachnidae. We discuss results based on two Buchnera genes (16S rDNA and the beta subunit of the F-ATPase complex) and on one host mitochondrial gene (the subunit 6 of the F-ATPase complex). Although our data do not allow definitive evolutionary relationships to be established among the different aphid families, some traditionally accepted groupings are put into question from both bacterial and insect data. In particular, the Lachnidae and the Aphididae, which from morphological data are considered recently evolved sister groups, do not seem to be as closely related as is usually accepted. Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts.     

Molecular phylogeny and systematics of the highly polymorphic Rumex bucephalophorus complex (Polygonaceae)

Rumex bucephalophorus is a very polymorphic species that has been subjected to various taxonomic studies in which diverse infraspecific taxa have been recognised on the basis of diaspore traits. In this study we used molecular markers (ITS and AFLP) to explore this remarkable diversity, to test previous hypotheses of classification, and attempt to explain biogeographic patterns. Results show that R. bucephalophorus forms a monophyletic group in which diversification began around 4.2 Mya, at the end of Messinian Salinity Crisis. The two molecular markers clearly show a deep divergence separating subsp. bucephalophorus from all other subspecific taxa, among which subsp. canariensis also constitutes a separate and well distinguishable unit. In contrast, subspecies hispanicus and subsp. gallicus constitute a monophyletic group in which three subgroups can be recognised: subsp. hispanicus, subsp. gallicus var. gallicus and subsp. gallicus var. subaegeus. However, these three subgroups are not clearly distinguished genetically or morphologically, so that in formal classification it would be preferable to treat them at the varietal level.     

Molecular systematics of Salmonidae: combined nuclear data yields a robust phylogeny

The phylogeny of salmonid fishes has been the focus of intensive study for many years, but some of the most important relationships within this group remain unclear. We used 269 Genbank sequences of mitochondrial DNA (from 16 genes) and nuclear DNA (from nine genes) to infer phylogenies for 30 species of salmonids. We used maximum parsimony and maximum likelihood to analyze each gene separately, the mtDNA data combined, the nuclear data combined, and all of the data together. The phylogeny with the best overall resolution and support from bootstrapping and Bayesian analyses was inferred from the combined nuclear DNA data set, for which the different genes reinforced and complemented one another to a considerable degree. Addition of the mitochondrial DNA degraded the phylogenetic signal, apparently as a result of saturation, hybridization, selection, or some combination of these processes. By the nuclear-DNA phylogeny: (1) (Hucho hucho, Brachymystax lenok) form the sister group to (Salmo, Salvelinus, Oncorhynchus, H. perryi); (2) Salmo is the sister-group to (Oncorhynchus, Salvelinus); (3) Salvelinus is the sister-group to Oncorhynchus; and (4) Oncorhynchus masou forms a monophyletic group with O. mykiss and O. clarki, with these three taxa constituting the sister-group to the five other Oncorhynchus species. Species-level relationships within Oncorhynchus and Salvelinus were well supported by bootstrap levels and Bayesian analyses. These findings have important implications for understanding the evolution of behavior, ecology and life-history in Salmonidae.     

Molecular phylogeny and biogeography of the Malagasy and South Asian cichlids (Teleostei: Perciformes: Cichlidae)

Phylogenetic relationships of the Malagasy and South Asian cichlids are investigated using nucleotide characters from two mitochondrial genes, a 544 bp region of the large ribosomal subunit (16S) and a 649 bp region of cytochrome c oxidase subunit I (COI). This is the first molecular analysis to include a thorough taxonomic sampling of all Malagasy-South Asian genera, and a near complete taxonomic inventory of all valid species. Parsimony analysis of the combined data set (1193 aligned nucleotide positions) results in a single, completely resolved phylogenetic hypothesis. Results of this analysis, and that based on more comprehensive taxonomic sampling across Cichlidae for 16S alone (554 bp for 73 taxa), indicate that the Malagasy cichlids are paraphyletic, whereas the Malagasy and South Asian cichlids comprise a monophyletic group. In both analyses, the African and Neotropical assemblages are monophyletic. The Malagasy-South Asian cichlids are not recovered as plesiomorphic members of the family in either analysis. Two major clades are recovered within the Malagasy-South Asian assemblage and given subfamilial rank, Etroplinae, comprising Paretroplus (Madagascar) and Etroplus (southern India and Sri Lanka), and Ptychochrominae, comprising Ptychochromis, Ptychochromoides, and Oxylapia, all endemic Malagasy genera. Placement of the endemic Malagasy genus Paratilapia is equivocal depending on the gene fragment(s) analyzed. Inter- and intrageneric relationships within Ptychochrominae and Etroplinae are presented and discussed. The hypothesis of relationships for Cichlidae based on nucleotide characters from 16S alone, arguably the most comprehensive and broadly sampled data set across all major geographic assemblages to date, is congruent with prevailing hypotheses regarding the sequence of Gondwanan fragmentation and a vicariance scenario to explain the current distribution of cichlid fishes.