Turtle carotid circulation: a character analysis case study

The bony canals permeating the turtle skull associated with the cranial circulation have long been considered integral to an understanding of extinct and extant turtle systematics. Recent phylogenetic analyses, employing a variety of data sets, suggest alternatives to the traditional arrangement of crown turtles. Of particular note is the recent failure of investigations employing molecular techniques to retrieve a monophyletic Trionychoidea, a clade supported largely by shared circulatory features. These alternative phylogenies may also have implications for extinct forms. The turtle cranial arterial circulation therefore represents an ideal system upon which to conduct a detailed, multipronged analysis of a systematically influential character. In the present study, the theoretical underpinnings of character analysis are critically evaluated, and a new interpretation of circulatory variation in turtles is offered, including a revised phylogenetic character suite. This assessment indicates an autapomorphic circulatory pattern in Trionychia, whereas Trionychoidea is not supported.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 239–256.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

Phylogenetic relationships of the suckermouth armoured catfishes (Loricariidae) with emphasis on the Hypostominae and the Ancistrinae

A phylogenetic analysis of nearly all genera of the Hypostominae and the Ancistrinae is provided based on osteology, external anatomy, and digestive tract anatomy. The results suggest that the Hypostominae is a paraphyletic assemblage. Delturus and Upsilodus form a monophyletic group sister to all other loricariids. Hemipsilichthys , Isbrueckerichthys , Kronichthys , and Pareiorhina form a monophyletic group with Neoplecostomus and the Hypoptopomatinae and are transferred to the Neoplecostominae. The remainder of the Hypostominae is made paraphyletic by the continuing recognition of the Ancistrinae. Ancistrinae is returned to the Hypostominae and recognized as a tribe, Ancistrini. In addition, four new tribes (Corymbophanini, Hypostomini, Pterygoplichthini, and Rhinelepini) are described. Hypostomus is also paraphyletic, the bulk of it forming a monophyletic clade with Aphanotorulus , Cochliodon , and Isorineloricaria . All of the potential monophyletic groups within Hypostomus grade into one another; therefore, Aphanotorulus , Cochliodon , and Isorineloricaria are placed in the synonymy of Hypostomus . Pterygoplichthys and Glyptoperichthys are also polyphyletic, and Liposarcus and Glyptoperichthys are recognized as synonyms of Pterygoplichthys . Sister to Pterygoplichthys is the Hemiancistrus annectens group (including Hypostomus panamensis ) which represents an undescribed genus. The phylogeny presented is compared with previous hypotheses.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 141 , 1−80.     

Molecular phylogeny of New World sheath-tailed bats (Emballonuridae: Diclidurini) based on loci from the four genetic transmission systems in mammals

Multiple unlinked loci are surveyed in a methodological approach for mammalian systematics that uses genes from the four pathways of genetic transmission: mitochondrial, autosomal, and X and Y sex chromosomes. Each of these components has different properties, such as effective population size, mutation rate, and recombination, that result in a robust hypothesis of evolutionary history. The utility of this experimental design is tested with bats in the family Emballonuridae and the hypothesis that the New World taxa are monophyletic. Parsimony and Bayesian analyses of the individual data sets give generally congruent topologies with high bootstrap proportions and posterior probabilities for monophyletic clades representing species and genera. The mitochondrial gene has significantly faster rates of substitution, higher levels of homoplasy, and a greater degree of saturation than the nuclear genes that contributed to the loss of phylogenetic signal at deeper branches of the tree. However, there is better resolution and support for the more slowly evolving nuclear introns including a New World clade, indicating a single origin of emballonurid bats in the Neotropics (tribe Diclidurini). One novel subtribe has a hard basal polytomy that is unresolved for all of the nuclear partitions, suggesting a rapid burst of evolution during the diversification of genera.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 189–209.     

Convergent evolution of chemical defence in Galerucine larvae

Selection pressure by natural enemies on phytophagous insect larvae is intense and has frequently triggered the evolution of chemical defence as an effective counterstrategy. In the chrysomelid subfamily Galerucinae, glandular structures and defensive fluids have been described for the tribe Sermylini Wilcox, 1965. Previous morphological and ultrastructural studies raised doubts that these defensive devices in Sermylini can be traced back to a common origin. The taxonomy of the Galerucinae cannot clear these doubts because the phylogeny of this taxon is a matter of current debate. We therefore investigated the phylogeny of the Galerucinae based on approximately 1740 bp of the mitochondrial 12S and 16S rRNA and the nuclear elongation factor 1 alpha genes. Our data support the hypothesized close relationship between the subfamilies Galerucinae and Alticinae, yet, by contrast to other recent analyses, the two groups are mostly resolved as monophyletic sister groups or, in some analyses, with the Galerucinae nested paraphyletically within the Alticinae. Within the subfamily Galerucinae, only the tribe Galerucini formed a monophyletic taxon, except for one species, Cerochroa brachialis Stal, 1858. In none of our analyses were the Sermylini recovered as a monophyletic tribe. However, our data support monophyly of each of the three groups within the Sermylini that have morphologically distinguishable larval defensive openings. We conclude that the defensive structures in larvae of Sermylini have no common origin, but evolved independently. Our data suggest that the tremendous selection pressure by natural enemies led to the recurrent evolution of similar chemical defensive devices in Sermylini larvae.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 165–175.     

Multiple levels of allopatric divergence in the endemic Philippine fruit bat Haplonycteris fischeri (Pteropodidae)

As part of a larger comparative phylogeographical study of Philippine fruit bats, I used fragments of the mitochondrial genes cytochrome  b and ND2 to investigate phylogeography and diversification in Haplonycteris fischeri , a pteropodid bat endemic to the Philippines but widespread within the archipelago. Genetic diversity in H. fischeri was extremely high in these commonly studied genes, with 101 unique haplotypes in 123 sequenced individuals, although small, continuously isolated islands had less diversity than had large island complexes. Seven monophyletic groups and one paraphyletic group were restricted to individual islands, groups of islands, or parts of islands. Each Pleistocene island complex had a single resident monophyletic lineage; these five groups were separated by approximately 6–8% sequence divergence and apparently have been diverging for 4–6 Myr. Within island groups, monophyletic lineages on some individual islands suggest that current ocean channels have also been barriers to gene flow; in some cases, multiple allopatric clades were present on single islands. Basal divergence dates were estimated to be in the early Pliocene, and most diversification was apparently connected to the ongoing geological evolution of the Philippines. Geological history and current geography interact with ecology to cause substantial genetic differentiation within this primary forest-specialist species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 329–349.     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

A phylogenetic analysis of the genus Eunice (Eunicidae, polychaete, Annelida)

Species of Eunice are distributed worldwide, inhabiting soft and hard marine bottoms. Some of these species play significant roles in coral reef communities and others are commercially important. Eunice is the largest and most poorly defined genus in Eunicidae. It has traditionally been subdivided in taxonomically informal groups based on the colour and dentition of subacicular hooks, and branchial distribution. The monophyly of Eunice and of its informal subgroups is tested here using cladistic analyses of 24 ingroup species based on morphological data. In the phylogenetic hypothesis resulting from the present analyses Eunice and its subgroups are paraphyletic; the genus may be divided in at least two monophyletic groups, Eunice s.s. and Leodice , but several species do not fall inside these two groups. Most of the traditional characters used in the taxonomy of Eunice are homoplasies; however, characters used for the first time in this study, such as certain jaw characters and characters derived from a close examination of chaetal variation along the body, are promising sources of phylogenetic signal.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 413–434.     

Revision of the New Caledonian endemic genus Gracilipsodes (Trichoptera: Leptoceridae: Grumichellini)

The taxonomy and systematics of the New Caledonian endemic caddisfly genus Gracilipsodes Sykora, 1967 (Trichoptera: Leptoceridae: Grumichellini) are reviewed. Seven new species represented by males are described and illustrated: Gracilipsodes aoupiniensis sp. nov. , Gracilipsodes aureus sp. nov. , Gracilipsodes aurorus sp. nov. , Gracilipsodes grandis sp. nov. , Gracilipsodes koghiensis sp. nov. , Gracilipsodes lanceolatus sp. nov. , and Gracilipsodes robustus sp. nov. Molecular phylogenetic analyses are applied to discern the relationships among the species of the genus and their closest relatives, based on sequence characters from the nuclear gene translation elongation factor-1α (EF-1α) and the three mitochondrial genes cytochrome oxidase I (COI), COII, and ribosomal large subunit (16S). The data are analyzed using parsimony and Bayesian inference, revealing a monophyletic Gracilipsodes with the eastern Australian monotypic genus Triplexa as its closest relative. Gracilipsodes is in turn divided into two major lineages.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 425–452.     

Phylogeny of Australasian agamid lizards based on nuclear and mitochondrial genes: implications for morphological evolution and biogeography

Recent mtDNA phylogenies of Australasian agamid lizards are highly incongruent with existing morphological views. To resolve this discrepancy we sequenced two nuclear gene regions, c- mos and brain-derived neurotrophic factor (BDNF). These were highly concordant with each other and the mtDNA phylogeny, but not the morphology. A combined molecular analysis reveals substantial hidden support (additional phylogenetic signal that emerges only when the data sets interact in a combined analysis). Bayesian posteriors, and a partitioned bootstrap procedure introduced here, indicate strong support for most nodes. The resultant tree implies extensive morphological homoplasy, with many genera emerging as non-monophyletic ( Amphibolurus , Rankinia , Ctenophorus , Physignathus , Diporiphora ). The water and forest dragons ( Physignathus and Hypsilurus ) form a paraphyletic basal assemblage to the more derived Australian forms such as Amphibolurus and Ctenophorus , which include almost all the xeric taxa. However, the thorny devil Moloch horridus is a basal lineage and not closely related to the other arid forms. Tree topology, inferred divergence dates, palaeogeographical and palaeoclimatic data are all consistent with Miocene immigration into Australia from the north by mesic forest ecomorphs, followed by initial diversification in mesic habitats before radiation into xeric habitats facilitated by increasing aridity.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 343–358.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

How to Read a Phylogenetic Tree

It has been over 50 years since Willi Hennig proposed a new method for determining genealogical relationships among species, which he called phylogenetic systematics. Many people, however, still approach the method warily, worried that they will have to grapple with an overwhelming number of new terms and concepts. In fact, reading and understanding phylogenetic trees is really not difficult at all. You only need to learn three new words, autapomorphy, synapomorphy, and plesiomorphy. All of the other concepts (e.g., ancestors, monophyletic groups, paraphyletic groups) are familiar ones that were already part of Darwinian evolution before Hennig arrived on the scene.     

Species: towards new, well-grounded practices

Velasco recently criticized our formal definition of the species concept, arguing for its inappropriateness both in fundamental and practical aspects [Velasco JD (2008) Biological Journal of the Linnean Society , 93 , 865–869]. Here, we clarify some misunderstandings that are at the basis of Velasco's paper. First, we show why and how the definition of the species concept can be grounded in the theory of evolution and what that implies. Then, we explain why Velasco's formal criticisms are unjustified. Finally, we point out the practical and methodological consequences of a rigorous conceptual framework for species study, and we show that today's development of species delimitation methods fully agrees with our proposal.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 217–222.     

Cymbonotus (Compositae: Arctotideae, Arctotidinae): an endemic Australian genus embedded in a southern African clade

The Compositae (Asteraceae) is the largest flowering plant family if described, accepted taxa are considered. Recent revisions in the taxonomy of the family have resulted in the recognition of ten subfamilies and 35 tribes. The tribe Arctotideae is one of the smallest, with around 200 species; it contains two subtribes and several hard-to-place taxa. Previous work has shown that the subtribe Arctotidinae is well defined and is restricted to southern Africa, except for the Australian genus Cymbonotus . Molecular data from internal transcribed spacer (ITS), ndh F, and trn L-F sequences were used (24 previously published sequences; 47 new sequences) to determine the patterns of relationships within the subtribe. Twenty-three samples from the ingroup, including members of all genera and all three species of Cymbonotus , were included in the analysis, together with two outgroup taxa. Cymbonotus is monophyletic and deeply embedded in the subtribe; Haplocarpha is paraphyletic and basal in position; all other genera are monophyletic; however, Arctotis has over 60 species and only eight were sampled for this study, so additional work may prove otherwise. Arctotis is nested high in the tree and has short branch lengths; this may reflect recent radiation. By contrast, the species of the paraphyletic and basal Haplocarpha have long branches, which may indicate an older radiation and a shared ancestry with the remainder of the subtribe. The presence of Cymbonotus in Australia is most probably the result of long-distance dispersal.  Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 1–8. No claim to original US government works