Higher-level Phylogenetic Analysis Research Articles

Taxonomic Revision of Scaly-toed Geckos (Reptilia: Gekkonidae: Lepidodactylus) in the Northern Philippines, with Descriptions of Four New Species

Recent higher level phylogenetic analyses of gekkonid lizards of the genus Lepidodactylus uncovered an array of unrecognized species diversity, particularly within the Philippine archipelago. Novel phylogenetic analyses of multilocus data sets suggest that as many as five, previously undescribed, species-level lineages of Scaly-toed Geckos occur in just the northern portions of the archipelago. Here, we evaluate Lepidodactylus species diversity in the Lepidodactylus yami–balioburius clade and describe four new forest species from Luzon Island and surrounding minor island groups. Interestingly, these species are the first endemic Lepidodactylus taxa described from Luzon proper and peripheral islands. In this first review of Philippine Scaly-toed Gecko diversity in nearly half a century, we use a suite of morphological characters along with molecular data to delimit evolutionary lineages. All species described in this paper can be distinguished from congeners by an array of discrete external traits; all are also monophyletic groups, separated in our phylogenetic analyses of the mitochondrial ND2 gene. This study increases significantly the number of known Scaly-toed Geckos in the Philippines from 7 to 11, which is likely still an underestimate of the species diversity in this understudied clade.

Evolution and homologies of primate and modern human hand and forearm muscles, with notes on thumb movements and tool use

In this paper, we explore how the results of a primate-wide higher-level phylogenetic analysis of muscle characters can improve our understanding of the evolution and homologies of the forearm and hand muscles of modern humans. Contrary to what is often suggested in the literature, none of the forearm and hand muscle structures usually present in modern humans are autapomorphic. All are found in one or more extant non-human primate taxa. What is unique is the particular combination of muscles. However, more muscles go to the thumb in modern humans than in almost all other primates, reinforcing the hypothesis that focal thumb movements probably played an important role in human evolution. What makes the modern human thumb myology special within the primate clade is not so much its intrinsic musculature but two extrinsic muscles, extensor pollicis brevis and flexor pollicis longus, that are otherwise only found in hylobatids. It is likely that these two forearm muscles play different functional roles in hylobatids and modern humans. In the former, the thumb is separated from elongated digits by a deep cleft and there is no pulp-to-pulp opposition, whereas modern humans exhibit powerful thumb flexion and greater manipulative abilities, such as those involved in the manufacture and use of tools. The functional and evolutionary significance of a third peculiar structure, the intrinsic hand structure that is often called the ‘interosseous volaris primus of Henle’ (and which we suggest is referred to as the musculus adductor pollicis accessorius) is still obscure. The presence of distinct contrahentes digitorum and intermetacarpales in adult chimpanzees is likely the result of prolonged or delayed development of the hand musculature of these apes. In relation to these structures, extant chimpanzees are more neotenic than modern humans.

Testing the phylogenetic utility of MCM7 in the Ascomycota

The Ascomycota are a group of filamentous fungi that occur as saprobes, pathogens and symbionts of immense industrial, medical, ecological, and economical importance. The search for new markers appropriate for molecular phylogenetic analysis of Ascomycota remains a challenging problem. In this study, we explore the phylogenetic utility of a single copy protein-coding gene, MCM7; newly recognized as useful for inferring phylogenetic relationships among the major classes of the Ascomycota. Our specific goals were to; 1) test the phylogenetic utility of MCM7 for estimating phylogenies at various taxonomic ranks (class and below) with an emphasis on non-lichenized ascomycetes; and, 2) compare the congruence, robustness and resolving power of MCM7-based phylogenies with that of nuclear large subunit 28S rDNA (LSU)-based phylogenies for the same taxon set. A dataset of sequence data for MCM7 as well as LSU was assembled for 80 species belonging to 63 genera of lichenized or non-lichenized ascomycetes in the classes Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, and Sordariomycetes. We obtained 99 new sequences of which 65 are MCM7 and 34 are LSU. Maximum-Likelihood and Bayesian analyses were performed using single as well as combined gene datasets and partitions. We also assessed substitution saturation for the MCM7 gene. Results indicate that MCM7 can be used successfully for determining phylogenetic relationships of non-lichenized ascomycetes and provided good resolution and support at half the cost compared to LSU. Phylogenetic informativeness profiles using PhyDesign tool shows MCM7 was a higher phylogenetic informative gene than LSU. The MCM7 gene is also a valuable phylogenetic marker for both lower as well as higher level phylogenetic analyses within the non-lichenized Ascomycota, especially when used in combination with the LSU gene. We found that although the third codon position of MCM7 is saturated, it was better to analyze the dataset with all codon positions included. Phylogenetic performance of MCM7 with and without the third codon position is discussed.

Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists

Abstract: As phylogenetic analyses become larger, one of the greatest methodological difficulties is representing speciose supraspecific clades in higher-level analyses (e.g. trilobites within studies of arthropod phylogeny). Several strategies have been proposed, including using representative single composite terminals or species-level exemplars, and various methods are currently used in the palaeontological literature. However, this is problematic, as simulation studies and empirical arguments in the systematics literature have clearly identified multiple exemplars as the optimal method. The continuing usage of suboptimal strategies in palaeontology may lessen the accuracy of phylogenies and hampers comparison between alternative studies. Here, I outline problems with suboptimal strategies, review arguments in support of multiple exemplars and provide guidelines for palaeontologists undertaking higher-level phylogenetic analyses.

An annotated checklist of the handsome fungus beetles of the world (Coleoptera: Cucujoidea: Endomychidae)

A worldwide checklist is provided for the family Endomychidae (Coleoptera: Cucujoidea). An updated subfamilial classification is presented, based on recent higher-level phylogenetic analyses and incorporating many recently described taxa. At present, Endomychidae contains 1782 valid species and subspecies in 130 genera organized into 12 subfamilies. Two new synonyms are recognized: Symbiotes latus Redtenbacher, 1849 = Symbiotes latus var. roberti Falcoz & Roman, 1930 syn. nov.; and Cholovocerida Belon, 1884 = Displotera Reitter, 1887b syn. nov. Two new combinations are proposed: Cholovocerida ecitonis (Wasmann, 1890) for Coluocera ecitonis Wasmann, 1890 comb. nov.; and Cholovocerida maderae (Wollaston, 1854) for Cholovocera maderae Wollaston, 1854 comb. nov. Loeblia ceylanica Dajoz, 1972a is here designated as the type species for Loeblia Dajoz, 1972a, and Rhymbus hemisphaericus Gerstaecker, 1858 is designated as the type species for Rhymbus Gerstaecker, 1858. Nomen nudum status is proposed for Mycetaea tafilaletica Smirnoff, 1957. Thirty-two species originally described under Corynomalus Chevrolat, 1836 and subsequently transferred to Amphix Laporte, 1840, have been returned to Corynomalus. Known fossil taxa are summarized.

Phylogeny of the cactus-feeding phycitines and their relatives (Lepidoptera, Pyralidae) based on adult morphology: Evaluation of adult character-systems in phycitine systematics and evidence for a single origin of Cactaceae-feeding larvae

AbstractThe cactus-feeding Phycitinae are a New World group of moth genera that has long been the focus of ecological and biological control related studies, but the group's evolutionary and phylogenetic relationships have remained largely unknown. Here phylogenetic relationships of 15 cactus-associated and 12 allegedly related but non cactus-associated genera of Phycitinae are established based on 64 characters from adult morphology. The resulting phylogeny is the first cladistic higher-level phylogenetic analysis for any group of Phycitinae genera. It is well resolved, albeit weakly supported, and supports the monophyly of a previously suggested group comprised by the true cactus-feeders and the genera Baphala, Zophodia and Rhagea. A clade comprising all cactus feeders with the non-cactus feeder genus Rhagea nested within is retrieved, indicating a single origin of cactus feeding within Phycitinae; however, this clade is poorly supported. Larvae that are predacious on scale insects appear to have evolved at least twice. Evaluations of the different character systems in adult skeletal morphology demonstrate that although some systems contribute little to overall partitioned Bremer support, they might provide critical support at individual nodes. This is supporting earlier workers who suggested that as many characters as possible are needed to establish phylogenetic relationships within Phycitinae. The hitherto scarcely explored region of the pregenitalic abdomen promises to be of considerable importance in phycitine phylogenetics.

ADVANCES IN APOCYNACEAE: THE ENLIGHTENMENT, AN INTRODUCTION1

Abstract This issue of the Annals of the Missouri Botanical Garden is devoted to advances in the Apocynaceae s.l. and is based on the symposium, “Recent Progress in the Systematics of Apocynaceae,” held at the XVII International Botanical Congress in Vienna in 2005. The collection of papers presented here spans the phylogenetic and geographic breadth of the family and includes at least one study focused on representatives from each of the five subfamilies: Rauvolfioideae, Apocynoideae, Periplocoideae, Secamonoideae, and Asclepiadoideae. The papers range from higher-level phylogenetic analyses to more narrowly defined case studies and include new results in phylogenetics, taxonomy, biogeography, pollination biology, and a pharmacophagous plant–butterfly interaction involving pyrrolizidine alkaloids, as well as a new hypothesis for the evolution of pollinia and loss of a compitum in some advanced taxa. An updated classification scheme of the Apocynaceae is presented, with one additional tribe recognized in ...

Phylogenetic analysis of Lumbrineridae Schmarda, 1861 (Annelida: Polychaeta)

This study represents the first phylogenetic reconstruction of lumbrinerid genera using parsimony analyses of 38 morphological characters. Following higher-level phylogenetic analysis, Oenone (Oenonidae) was selected as outgroup. The analysis was restricted to type species for each genus, yielded 24 equally parsimonious trees, which after successive weighting were reduced to one tree (CI= 0.7396). The topology of this tree revealed the separation of the family into four main clades: 1. Lysarete, 2. Arabellonereis, 3. Scoletoma, Lumbrineris, Hilbigneris gen. nov., Kuwaita, Lumbricalus, Sergioneris gen. nov. and Eranno, and 4. Abyssoninoe, Cenogenus, Lumbrinerides, Lumbrineriopsis, Augeneria, Loboneris gen. nov., Gallardoneris gen. nov., Helmutneris gen. nov., and Gesaneris gen. nov.; the position of Ninoe is unclear. A diagnosis of each genus is provided, including the description of six new genera and three new species. A key to lumbrinerid genera is included.

Intra- and interspecific variation in the early internal shell features of some Cretaceous ammonoids

Intra- and interspecific variation in the early internal shell features of ammonoids has been examined in 14 Late Cretaceous species representing four suborders on the basis of large samples from Hokkaido (Japan) and the U.S. Western Interior Province. Our observations indicate that quantitative characters such as the size of the initial chamber and ammonitella, the length of the prosiphon, and the ammonitella angle exhibit moderate variation within species. The ranges of variation partly overlap among species, indicating that these characters are not suitable for studies of the higher-level systematics of ammonoids, but may sometimes help diagnose species. In contrast, there is much less variation within species with respect to qualitative characters such as the shape of the prosiphon, the presence or absence of accessory threads of the prosiphon, the shape of the caecum, and the initial position of the siphuncle. Examination of these characters shows that they appear to be stable at the superfamily level for the Ammonitina, but variable among species in the Lytoceratina. Thus, these characters are potentially more useful for higher-level phylogenetic analysis.

INTRA- AND INTERSPECIFIC VARIATION IN THE EARLY INTERNAL SHELL FEATURES OF SOME CRETACEOUS AMMONOIDS

Intra- and interspecific variation in the early internal shell features of ammonoids has been examined in 14 Late Cretaceous species representing four suborders on the basis of large samples from Hokkaido (Japan) and the U.S. Western Interior Province. Our observations indicate that quantitative characters such as the size of the initial chamber and ammonitella, the length of the prosiphon, and the ammonitella angle exhibit moderate variation within species. The ranges of variation partly overlap among species, indicating that these characters are not suitable for studies of the higher-level systematics of ammonoids, but may sometimes help diagnose species. In contrast, there is much less variation within species with respect to qualitative characters such as the shape of the prosiphon, the presence or absence of accessory threads of the prosiphon, the shape of the caecum, and the initial position of the siphuncle. Examination of these characters shows that they appear to be stable at the superfamily level for the Ammonitina, but variable among species in the Lytoceratina. Thus, these characters are potentially more useful for higher-level phylogenetic analysis.

Using caddisfly (Trichoptera) case-building behaviour in higher level phylogeny reconstruction

Higher level phylogenetic analyses rarely include behavioural data, predominantly because such groups seldom have complex behaviours that are susceptible to analysis. Even when broad groups do share a complex behaviour, there is skepticism about the appropriateness of using behavioural traits in higher level phylogenetic analyses. The Integripalpia is a suborder of caddisflies and is an appropriate group to investigate the use of behaviour in higher level analyses because all larvae use a complex suite of behaviours to build portable cases. A thorough investigation of case-building in 10 families (19 exemplar genera) yielded 24 behavioural characters. A parsimony analysis produced 87 equally parsimonious trees (length = 56 steps, consistency index (CI) = 0.84, retention index (RI) = 0.88) that supported the monophyly of the integripalpian families, except for the Limnephilidae. Interfamilial relationships, although resolved, were not well supported with behaviour. Certain interfamilial relationships have also been difficult to establish reliably with morphological information, indicating a need for more characters (e.g., molecular) at this taxonomic level. This study indicates that if taxa share a complex behaviour (e.g., case building), then regardless of taxonomic level, one is likely to find shared derived behavioural characters that are useful for phylogeny reconstruction.

CHLOROPLAST DNA VARIATION IN GLIRICIDIA SEPIUM (LEGUMINOSAE): INTRASPECIFIC PHYLOGENY AND TOKOGENY

An analysis of chloroplast DNA restriction site variation in Gliricidia sepium reveals two geographically distinct chloroplast lineages, one in the Yucatan Peninsula and the other along the Pacific Coast in Mexico and Central America. Geographical, morphological, biochemical, and habitat distinctions suggest that these two chloroplast lineages reflect organismal lineages. Within the Pacific coastal chloroplast lineage, there exist sublineages that most likely reflect tokogenetic systems of relationship rather than organismal phytogeny, a hypothesis supported by the co‐occurrence of more than one of these chloroplast sublineages in a single population. The genetic distance between any two of these chloroplast lineages ranges from 0.0001 to 0.0024 nucleotide substitutions per site and reveals relatively high levels of intraspecific divergence. We suggest that assessing intraspecific chloroplast DNA variation is important generally in higher level phylogenetic analysis because it enables one to obtain truer estimates of homoplasy, detect potentially cryptic species, and distinguish among molecular markers that reflect phylogenetic vs. tokogenetic relationships. This is in addition to determining the extent of potential complicating factors such as introgression and lineage sorting from polymorphic ancestry.

Chloroplast DNA Variation in Gliricidia sepium (Leguminosae): Intraspecific Phylogeny and Tokogeny

An analysis of chloroplast DNA restriction site variation in Gliricidia sepium reveals two geographically distinct chloroplast lineages, one in the Yucatan Peninsula and the other along the Pacific Coast in Mexico and Central America. Geographical, morphological, biochemical, and habitat distinctions suggest that these two chloroplast lineages reflect organismal lineages. Within the Pacific coastal chloroplast lineage, there exist sublineages that most likely reflect tokogenetic systems of relationship rather than organismal phytogeny, a hypothesis supported by the co-occurrence of more than one of these chloroplast sublineages in a single population. The genetic distance between any two of these chloroplast lineages ranges from 0.0001 to 0.0024 nucleotide substitutions per site and reveals relatively high levels of intraspecific divergence. We suggest that assessing intraspecific chloroplast DNA variation is important generally in higher level phylogenetic analysis because it enables one to obtain truer estimates of homoplasy, detect potentially cryptic species, and distinguish among molecular markers that reflect phylogenetic vs. tokogenetic relationships. This is in addition to determining the extent of potential complicating factors such as introgression and lineage sorting from polymorphic ancestry.