Molecular phylogeny of Elephantidae. Extreme divergence of the extant forest African elephant.

A phylogenetic study of the Elephantidae (Proboscidea, Mammalia) is based on the cytochrome b mitochondrial gene: 31 terminals, that is, all known sequences, one non-elephantid proboscidean, the extinct American mastodon, and four outgroups. The data set includes 11 new sequences with the first published sequence of the forest African elephant, L. a. cyclotis. The analyses of extant taxa only and of both extant and extinct taxa show that L. a. cyclotis is highly divergent from L. a. africana. It is as divergent from L. a. africana as Loxodonta is divergent from Elephas. Southern L. a. africana form a clade. The continental subspecies E. m. indicus is paraphyletic with individuals from India and Thailand closer to E. m. maximus (Sri-Lanka). Members of Mammuthus primigenius are more closely related to Loxodonta although they do not form a clade; two specimens of M. primigenius are closer to L. a. africana making the genus Loxodonta paraphyletic. The latter conclusion may be partly due to unequal length of the various polymorphic mammoth sequences.     

Molecular phylogeny and morphological change in the Psittacula parakeets

We reconstruct a phylogeny of the African and Asian Psittacula parakeets using approximately 800bp of mitochondrial cytochrome b sequence to examine their evolutionary relationships in reference to their head plumage and major morphological tail innovations. Our phylogeny identifies three groups, whose distinctiveness is also apparent from their possession of three different head plumage characters: a neck ring, a distinctive colouration of the head, and a 'moustache'-shaped pattern that extends from the chin to the cheek. We examine the extent of sexual dimorphism in tail length across the phylogeny and reveal large differences between closely related forms. We apply a range of published avian cytochrome b substitution rates to our data, as an alternative to internal calibration of a molecular clock arising from incomplete paleontological information. An ancestral Psittacula form appears to have evolved during the late Miocene-early Pliocene (3.4-9.7MYA), a time when regional geological processes on the Asian continent may have promoted subsequent diversity at the species level, and many forms diverged relatively early on in the evolutionary history of Psittacula (between 2.5 and 7.7MYA). However, others, such as the derbyan and moustached parakeets, diverged as recently as 0.2MYA. Our phylogeny also suggests that the echo parakeet from Mauritius diverged from the Indian ringneck parakeet as opposed to the African ringneck, and may have done so relatively recently. The molecular results indicate support for a southwards radiation from India across the Indian Ocean to Mauritius, where the arrival-date of the echo parakeet appears consistent with the island's volcanic formation.     

Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.     

Combined molecular and morphological evidence on the phylogeny of the earliest lepidopteran lineages

Agreement among recent morphological and molecular phylogenetic analyses has strengthened estimates of the relationships among the earliest lineages of the holometabolan order Lepidoptera. For a few major groups, evidence for monophyly and basal relationships remains relatively weak or contradictory — chiefly within the clades of basal Glossata and Heteroneura. Here we assess the support for these controversial areas of lepidopteran classification through molecular systematic investigation of 18S rDNA sequence variation. Parsimony and maximum likelihood analyses are presented for 1379 alignable sites of 18S. These data are then combined with 61 morphological features scored for major lineages of basal Glossata and Heteroneura. Our 18S rDNA data support recent hypotheses for the placement of Micropterigidae and Agathiphagidae as the basal-most lineages of Lepidoptera, and support the monophyly of the groups Neolepidoptera and Exoporia. 18S data alone are shown to be insufficient for resolving the monophyly and relationships of the Glossata, and for specifying relationships above the Neolepidoptera. Combination of the 18S data with published morphological ground-plan scorings improves overall support for the morphology-based hypothesis for basal glossatans, but phylogenetic resolution among published alternatives for the basal Heteroneura remains a major question for lepidopteran systematics.     

Molecular and morphological phylogeny of Menispermaceae (Ranunculales)

The phylogeny of Menispermaceae (Ranunculales) is reconstructed here using both morphological and molecular data from a broad sample of species. Morphological data include characters of leaves, wood, flowers, fruits, seeds, pollen and phytochemistry from 73 species representing the different subgroups recognized within the family. This dataset allowed us to study the morphological evolutionary trends in Menispermaceae. The molecular data focused on cpDNA sequences: rbcL and atpB. Maximum parsimony (MP) and Bayesian methods were used to reconstruct the phylogeny of Menispermaceae. The results obtained from the three datasets are partly incongruent. The morphology indicates that Menispermaceae can be divided into two major groups, one including the tribes Fibraureae and Tinosporeae, the other one including the tribes Anomospermeae, Pachygoneae and Menispermeae. Only Burasaia Thouars was not included in any of these groups. The characters of fruits and seeds appeared to be most useful to differentiate these groups whereas convergences were found for the androecium.     

Molecular evidence on Primate phylogeny from DNA sequences

Evidence from DNA sequences on the phylogenetic systematics of primates is congruent with the evidence from morphology in grouping Cercopithecoidea (Old World monkeys) and Hominoidea (apes and humans) into Catarrhini, Catarrhini and Platyrrhini (ceboids or New World monkeys) into Anthropoidea, Lemuriformes and Lorisiformes into Strepsirhini, and Anthropoidea, Tarsioidea, and Strepsirhini into Primates. With regard to the problematic relationships of Tarsioidea, DNA sequences group it with Anthropoidea into Haplorhini. In addition, the DNA evidence favors retaining Cheirogaleidae within Lemuriformes in contrast to some morphological studies that favor placing Cheirogaleids in Lorisiformes. While parsimony analysis of the present DNA sequence data provides only modest support for Haplorhini as a monophyletic taxon, it provides very strong support for Hominoidea, Catarrhini, Anthropoidea, and Strepsirhini as monophyletic taxa. The parsimony DNA evidence also rejects the hypothesis that megabats are the sister group of either Primates or Dermoptera (flying lemur) or a Primate-Dermoptera clade and instead strongly supports the monophyly of Chiroptera, with megabats grouping with microbats at considerable distance from Primates. In contrast to the confused morphological picture of sister group relationships within Hominoidea, orthologous noncoding DNA sequences (spanning alignments involving as many as 20,000 base positions) now provide by the parsimony criterion highly significant evidence for the sister group relationships defined by a cladistic classification that groups the lineages to all extant hominoids into family Hominidae, divides this ape family into subfamilies Hylobatinae (gibbons) and Homininae, divides Homininae into tribes Pongini (orangutans) and Hominini, and divides Hominini into subtribes Gorillina (gorillas) and Hominina (humans and chimpanzees). A likelihood analysis of the largest body of these noncoding orthologues and counts of putative synapomorphies using the full range of sequence data from mitochondrial and nuclear genomes also find that humans and chimpanzees share the longest common ancestry. © 1994 Wiley-Liss, Inc.     

Molecular phylogeny and morphological evolution of the Acantharia (Radiolaria)

Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia.     

Molecular phylogeny of cetaceans prompts revision of morphological transformations

The echolocating toothed whales and the filter-feeding baleen whales are traditionally considered as two monophyletic lineages that originated from the extinct cetacean suborder Archaeoceti. While current interpretation of the morphological and behavioural data sets supports toothed-whale monophyly, molecular phylogenies contradict this long-accepted taxonomic subdivision. The molecular data indicate that one group of toothed whales, the sperm whales, Is more closely related to the morphologically highly divergent baleen whales than to other odontocetes. Furthermore, these molecular analyses tentatively suggest a more recent origin of baleen whales than has been generally accepted. Although a thorough cladistic analysis of all relevant morphological data is still needed, reevaluation of some of the most important of these characters helps to reconcile the morphological and the molecular approaches.     

Molecular evidence for the phylogeny of Australian gekkonoid lizards

Partial sequences of the mitochondrial 12S rRNA and nuclear c-mos genes were determined for 12 species of gekkonoid lizards representing the four major taxa of the Australian region, the Diplodactyhni and Carphodactylini (forming the subfamily Diplodactylinae), the Pygopodidae and the Gekkoninae. One further species represented a non-Australian gekkonoid lineage, the Eublepharinae. The combined sequence data were used to reconstruct the underlying molecular phylogeny. We used the molecular phylogeny to test the monophyly of the diplodactyline tribes and conflicting hypotheses of relationships of die pygopods and of the genus Oedura. Monophyly of the Diplodactylinae is supported, while pygopods form a monophyletic sister lineage to all Diplodactylinae. The molecular data support the monophyly of the Diplodactyhni, with Oedura firmly placed as a diplodactylin. Monophyly of the Carphodactylini is not supported. The four carphodactylin genera form a paraphyletic cluster at the base of the Diplodactyhni. Pygopods are nested within the traditional Gekkonidae and pygopods plus diplodactylines form a well-supported monophyletic group with respect to the remaining gekkonoids, the gekkonines and eublepharines.     

Molecular and morphological phylogeny of Diplazontinae (Hymenoptera,Ichneumonidae)

Klopfstein, S., Quicke, D. L. J., Kropf, C. & Frick, H. (2011) Molecular and morphological phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae). —Zoologica Scripta, 40, 379–402. Parasitoid wasps are among the most species rich and at the same time most understudied of all metazoan taxa. To understand their diversification and test hypotheses about their evolution, we need robust phylogenetic hypotheses. Here, we reconstruct the phylogeny of the subfamily Diplazontinae using four genes and 66 morphological characters both in separate analyses and in a total evidence approach. The resulting phylogeny is highly resolved, with most clades supported by multiple independent data partitions. It contains three highly supported genus groups, for which we suggest morphological and behavioural synapomorphies. The placement of some of the genera, especially Xestopelta Dasch, is unexpected, but also supported by morphology. Most of the genera are retrieved as monophyletic, with the exception of the morphologically diverse genus Syrphoctonus Förster. We split this genus into three genera, including Fossatyloides gen. n., to restore the phylogeny–classification link. Conflict between the morphological and the molecular topology was mostly resolved in favour of the molecular partition in the total evidence approach. We discuss reasons for this finding, and suggest strategies for future taxon and character sampling in Diplazontinae.     

Total evidence phylogeny of Gasterosteidae: combining molecular, morphological and behavioral data

Genealogical relationships among Gasterosteidae (Teleostei: Gasterosteiformes) were tested with 84 morphological, 48 behavioral, and 2879 molecular characters. Phylogenetic analysis of the combined data set identified a single (CI = 0.735) best‐supported hypothesis (Spinachia (Apeltes ((Pungitius + Culaea)(Gasterosteus aculeatus + G. wheatlandi)))). This hypothesis is identical to previous phylogenetic propositions proposed on the basis of behavioral, and behavioral plus morphological data. Our hypothesis, however, differed from a molecular‐based phylogeny in the placement of Apeltes. This analysis highlights the importance of combining all available evidence in order to produce the best‐supported proposition of genealogical relationships.     

Molecular phylogeny of the moonseed family (Menispermaceae): implications for morphological diversification

We used the chloroplast gene ndhF to reconstruct the phylogeny of the moonseed family (Menispermaceae), a morphologically diverse and poorly known cosmopolitan family of dioecious, primarily climbing plants. This study includes a worldwide sample of DNA sequences for 88 species representing 49 of the 70 genera of all eight traditionally recognized tribes. Phylogenetic relationships were estimated, and the Shimodaira-Hasegawa test was used to compare the likelihood of alternative phylogenetic hypotheses and to evaluate the monophyly of tribes currently in use. The monospecific Indo-Malesian Tinomiscium is sister to the remaining members of the family, within which are two major clades. Within these two clades, well-supported clades correspond to four of the eight traditionally recognized tribes, while others, such as Menispermeae, are polyphyletic. Mapping of major morphological characters on the phylogeny indicates that the crescent-shaped seed is derived from a straight seed, the tree habit has arisen multiple times, endosperm has been lost many times, but unicarpellate flowers evolved only once. Morphological synapomorphies for Menispermaceae include the presence of a condyle, a large embryo, and druplets. The phylogeny provides for the first time a detailed molecular-based assessment of relationships in Menispermaceae and clarifies our understanding of morphological diversification within the family.     

Molecular phylogeny of flat‐footed flies (Diptera: Platypezidae): main clades supported by new morphological evidence

The molecular phylogeny of flat‐footed flies is inferred from analysis of DNA sequence data from the five mitochondrial genes 12S, 16S, COI, COII and CytB, and the nuclear gene 28S and discussed with the recent systematics based on morphological features. The Bayesian inference, maximum likelihood and maximum parsimony analyses included 42 species of 18 genera, representing all four extant subfamilies (Microsaniinae, Melanderomyiinae, Callomyiinae and Platypezinae) and all known genera except one (Metaclythia). Representatives of the brachycerous taxa Lonchopteridae, Phoridae, Sciadocerinae (Phoridae) and Opetiidae are used as outgroups, and Lonchoptera was used to root the trees. Our results show Platypezidae consisting of two well‐supported clades, the first with the subfamilies Melanderomyiinae + Callomyiinae and the second formed by subfamily Platypezinae. Genus Microsania was resolved as a separate lineage distant from Platypezidae which clustered with Opetiidae as its sister group, both together forming a sister group to Platypezidae. At the generic level, the genus Agathomyia proved not to be monophyletic in any of the analyses. The species Chydaeopeza tibialis is sister to Agathomyia sexmaculata, and consequently, the genus Chydaeopeza Shatalkin, 1992 is a new junior synonym of Agathomyia Verrall, 1901. Bifurcated setae on legs of adult Platypezidae are documented as a new synapomorphy of the family, exclusive of Microsania. Outstretched wings and only a small overlap of their surfaces at resting position are considered a new synapomorphy for the subfamily Platypezinae. Other phylogenetically important characters defining main clades are documented, and their relevance/validity in phylogenetic studies is discussed. The current systematic concept of Platypezidae is discussed, and new phylogenetic hypotheses are proposed.     

Molecular phylogeny

The avalanche of molecular sequence data from a wide variety of organisms and genes makes the construction and testing of evolutionary trees a widespread and demanding activity. We present the most recent advances in the interpretation of molecular data, as well as recent phylogenetic results affecting both molecular evolutionary biology and other areas of biological research.     

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae)

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution.     

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.