Phylogeny of Orthotrichum s.l. and Ulota s.l. (Orthotrichaceae,Bryophyta): Insights into stomatal evolution

Orthotrichum Hedw. s.l. and Ulota Mohr s.l. are two of the most speciose genera of the xerophytic moss family Orthotrichaceae. We reconstructed the phylogeny of these two genera using three data matrices: (i) organellar genomes and 33 taxa; (ii) six loci from three genomes and 144 taxa; and (iii) two plastid loci and 163 taxa. The present phylogeny, based on the maximum sampling of genes or taxa to date, generally confirms the new classification of Orthotrichum and Ulota, and indicated that all Ulota species, except Ulota phyllantha Brid., form a clade and three lineages comprise the cryptoporous Orthotrichum clade. We provided new morphological characters that support the present division of the two genera. Ancestral state reconstruction of stoma indicates that superficial stomata in Orthotrichum represent a plesiomorphic character and semi-immersed stomata were derived from immersed stomata. The results also suggest that immersed stomata independently arose once in Orthotrichum, whereas semi-immersed stomata probably arose more than once. Molecular dating analysis reveals that the occurrence of immersed stomata is probably related to arid environments during the early Oligocene to late Miocene, whereas the appearance of semi-immersed stomata might be associated with the mesic–xeric or semiarid environments during the middle Miocene to Pliocene. Ancestral state reconstruction of habitat indicates that the saxicolous habitat is apomorphic and independently evolved multiple times in Orthotrichum and Ulota, which supports the former hypothesis. Considering morphological statistics, the development of the cryptopore in Orthotrichum could provide increased resilience to dry habitats, and might promote their habitat shift during evolution.     

Patterns of evolution in western North American Mimulus (Phrymaceae)

A well-supported phylogeny is presented from both chloroplast DNA (the trnL/F region) and two regions of nuclear rDNA (ITS [internal transcribed spacer] and ETS [external transcribed spacer]) with nearly complete sampling for Mimulus (Phrymaceae) in western North America. Three separate genera are derived from within the clade that contains all the Mimulus species in western North America. The taxonomic status of the proposed sections of Mimulus and the relationships of many taxonomically difficult species are considered with observations on morphological evolution. Discordance between data sources provides support for the hypothesis that M. evanescens is a hybrid between M. latidens and M. breviflorus. In two major clades (Eunanus and Diplacus), patterns of genetic variation do not match the current taxonomy. The clustering of taxa in Eunanus is strongly associated with geographic distributions. Mimulus aurantiacus sensu Thompson, M. nanus, and M. floribundus are found to be progenitor species to other species that appear to be derived from within them. Polyploidy and aneuploidy events are clustered near the tips of the phylogeny. Thus, these two mechanisms are concluded to have played a relatively small role in the evolution of persistent lineages in Mimulus. The phylogenetic distribution of rare taxa is also examined.     

Studies in cave life evolution: a rationale for future theoretical developments using phylogenetic inference

As in every field of comparative biology, phylogeny provides an independent reference system in studies on cave life evolution to test current theoretical proposals. Using phylogeny, sound hypotheses on the ancestral states of characters and their subsequent changes can be made by polarizing the characters between related taxa. Hypotheses on evolutionary processes can also be tested by comparing the patterns they imply with independently inferred phylogenetic patterns. The power of the tests relies upon the independence of phylogenetic patterns (built with cladistics using Wagner parsimony) and the theoretical proposals under study. Classical assumptions on the evolution of troglobitic life are analysed with this methodology. The following points are discussed: what is a troglobitic taxon? Are there features characteristic of troglobitic taxa? Is troglobitic life an evolutionary dead end? What circumstances favour troglobitic evolution? Using phylogenetic analysis, the presence or absence of so-called troglomorphic features were inferred in troglobitic taxa. In fact these taxa can be characterized only by their behavioural ecology. Pre-adaptations (exaptations) can also be precisely defined. Cave living does not appear to be an evolutionary dead end. Two patterns subsequent to cave life appearance have been documented: speciation of troglobitic taxa in the subterranean environment, and reversal to an epigean habitat. Troglobitic life thus turns out to be one step in the diversification of clades. Troglobitic life is usually explained as an evolution under the pressure of unfavourable environmental conditions, or the conquest of a new resource, or the result of biological interactions (competition, predation). Phylogenetic analyses show that none of these hypotheses propose clear alternatives on cave life evolution. Moreover most of their a priori statements cannot easily be falsified. As such they have only limited explanatory power.     

The evolution of the Proteocephalidea (Platyhelminthes,Eucestoda) based on an enlarged molecular phylogeny,with comments on their uterine development

We present a molecular phylogeny of the Proteocephalidea based on 28S rDNA sequence data that is a follow-up to the paper by Zehnder & Mariaux (1999). Twenty-three new sequences, including three outgroups are added in our new data-set. The Gangesiinae Mola, 1929 and the Acanthotaeniinae Freze, 1963 appear to be the most primitive clades. They are followed by a robust clade comprising the Palaearctic Proteocephalinae Mola, 1929 from freshwater fishes. The structure of the more derived clades, comprising most Neotropical and Nearctic species, is less resolved. At the nomenclatural level, we erect a new genus, Glanitaenia n. g. for G. osculata (Goeze, 1782) n. comb., previously Proteocephalus osculatus, and define an aggregate for the Palaearctic Proteocephalus Weinland, 1858. After a re-examination of all of the studied taxa, we identify two types of uterine development and show the importance of this character for the systematics of the order. Our phylogeny does not support the classical view of a Neotropical origin for the Proteocephalidea but rather favours an Old World origin of the group either in saurians or Palaearctic Siluriformes.     

Character evolution in Hydrozoa (phylum Cnidaria)

The diversity of hydrozoan life cycles, as manifested in the wide range of polyp, colony, and medusa morphologies, has been appreciated for centuries. Unraveling the complex history of characters involved in this diversity is critical for understanding the processes driving hydrozoan evolution. In this study, we use a phylogenetic approach to investigate the evolution of morphological characters in Hydrozoa. A molecular phylogeny is reconstructed using ribosomal DNA sequence data. Several characters involving polyp, colony, and medusa morphology are coded in the terminal taxa. These characters are mapped onto the phylogeny and then the ancestral character states are reconstructed. This study confirms the complex evolutionary history of hydrozoan morphological characters. Many of the characters involving polyp, colony, and medusa morphology appear as synapomorphies for major hydrozoan clades, yet homoplasy is commonplace.     

Towards a phylogenetic framework for the evolution of shakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae)

A phylogeny of 19 of the 22 currently recognized species of Myiarchus tyrant-flycatchers is presented. It is based on 842bp of mitochondrial DNA (mtDNA) sequences from the ATPase subunit 8 and ATPase subunit 6 genes. Except for the morphologically distinct M. semirufus, mtDNAs of the remaining 18 species fall into either of two clades. One comprises predominantly Caribbean and Central and North American taxa (Clade I), and the other is of predominantly South American taxa (Clade II). The phylogeny is only very broadly concordant with some vocal characters and also with the limited morphological diversity for which the group is well known. Paraphyly in several species (M. swainsoni, M. tuberculifer, M. ferox, M. phaeocephalus, M. sagrae, M. stolidus) suggests that morphological evolution, albeit resulting in limited morphological diversity, has been more rapid than that of mtDNA, or that current taxonomy is faulty, or both. A South American origin for Myiarchus is likely. Dispersal and vicariance both appear to have been involved in generating the present-day distribution of some species. Relatively recent dispersal events out of South America are inferred to have brought species of Clades I and II into broad sympatry. Jamaica has been colonized independently at least twice by members of Clades I and II. The phylogeny brings a historical perspective that in turn suggests that ecological study of closely related species from within each major clade where they are sympatric will be especially rewarding.     

A total-evidence phylogeny of ticks provides insights into the evolution of life cycles and biogeography.

We inferred the phylogeny of 33 species of ticks from the subfamilies Rhipicephalinae and Hyalomminae from analyses of nuclear and mitochondrial DNA and morphology. We used nucleotide sequences from 12S rRNA, cytochrome c oxidase I, internal transcribed spacer 2 of the nuclear rRNA, and 18S rRNA. Nucleotide sequences and morphology were analyzed separately and together in a total-evidence analysis. Analyses of the five partitions together (3303 characters) gave the best-resolved and the best-supported hypothesis so far for the phylogeny of ticks in the Rhipicephalinae and Hyalomminae, despite the fact that some partitions did not have data for some taxa. However, most of the hidden conflict (lower support in the total-evidence analyses compared to that in the individual analyses) was found in those partitions that had taxa without data. The partitions with complete taxonomic sampling had more hidden support (higher support in the total-evidence analyses compared to that in the separate-partition analyses) than hidden conflict. Mapping of geographic origins of ticks onto our phylogeny indicates an African origin for the Rhipicephalinae sensu lato (i.e., including Hyalomma spp.), the Rhipicephalus-Boophilus lineage, the Dermacentor-Anocentor lineage, and the Rhipicephalus-Booophilus-Nosomma-Hyalomma-Rhipicentor lineage. The Nosomma-Hyalomma lineage appears to have evolved in Asia. Our total-evidence phylogeny indicates that (i) the genus Rhipicephalus is paraphyletic with respect to the genus Boophilus, (ii) the genus Dermacentor is paraphyletic with respect to the genus Anocentor, and (iii) some subgenera of the genera Hyalomma and Rhipicephalus are paraphyletic with respect to other subgenera in these genera. Study of the Rhipicephalinae and Hyalomminae over the last 7 years has shown that analyses of individual datasets (e.g., one gene or morphology) seldom resolve many phylogenetic relationships, but analyses of more than one dataset can generate well-resolved phylogenies for these ticks.     

Developmental genetics and early hominid craniodental evolution

Although features of the dentition figure prominently in discussions of early hominid phylogeny, remarkably little is known of the developmental basis of the variations in occlusal morphology and dental proportions that are observed among taxa. Recent experiments on tooth development in mice have identified some of the genes involved in dental patterning and the control of tooth specification. These findings provide valuable new insight into dental evolution and underscore the strong developmental links that exist among the teeth and the jaws and cranium. The latter has important implications for cladistic studies that traditionally consider features of the skull independently from the dentition.     

The evolution of soldier reproduction in social thrips

We estimated the degree of reproductive differentiation betweenfoundresses and soldiers in multiple populations of five speciesof haplodiploid Australian gall-forming thrips using microsatellitedata, ovarian dissections, and census data. Microsatellite-basedspecies estimates of average per capita reproductive outputof soldiers relative to the foundresses ranged from 0.005 to0.64, and dissection and census-based estimates ranged from0.17 to 1.1. Mapping of these estimates onto a phylogeny showedthat levels of soldier reproduction were apparently higherin three basal lineages than in two more derived lineages.We infer from this phylogenetic pattern that soldier morphologyand behavior of thrips evolved in the presence of substantial levels of soldier reproduction. This pattern of evolutionarychange is similar to that proposed for the origin of soldiersin aphids and termites, but it differs from the scenario proposedfor the origin of workers in Hymenoptera, within which helpingand strong reproductive division of labor apparently evolvedbefore morphological differentiation. We suggest that this difference in evolutionary routes to eusociality between taxa with soldiersand taxa with foraging workers was driven by a weaker trade-offbetween helping and reproducing, and a greater ability of thehelpers to withstand reproductive domination, in taxa withsoldiers. This is the first study to analyze the social-evolutionarytrajectories of reproductive, behavioral, and morphologicaldifferentiation in the context of a species-level phylogeny.     

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.     

A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (chiroptera)

Bats (Order Chiroptera), the only mammals capable of powered flight and sophisticated laryngeal echolocation, represent one of the most species-rich and ubiquitous orders of mammals. However, phylogenetic relationships within this group are poorly resolved. A robust evolutionary tree of Chiroptera is essential for evaluating the phylogeny of echolocation within Chiroptera, as well as for understanding their biogeographical history. We generated 4 kb of sequence data from portions of four novel nuclear intron markers for multiple representatives of 17 of the 18 recognized extant bat families, as well as the putative bat family Miniopteridae. Three echolocation-call characters were examined by mapping them onto the combined topology: (1) high-duty cycle versus low-duty cycle, (2) high-intensity versus low-intensity call emission, and (3) oral versus nasal emission. Echolocation seems to be highly convergent, and the mapping of echolocation-call design onto our phylogeny does not appear to resolve the question of whether echolocation had a single or two origins. Fossil taxa may also provide insight into the evolution of bats; we therefore evaluate 195 morphological characters in light of our nuclear DNA phylogeny. All but 24 of the morphological characters were found to be homoplasious when mapped onto the supermatrix topology, while the remaining characters provided insufficient information to reconstruct the placement of the fossil bat taxa with respect to extant families. However, a morphological synapomorphy characterizing the Rhinolophoidea was identified and is suggestive of a separate origin of echolocation in this clade. Dispersal-Vicariance analysis together with a relaxed Bayesian clock were used to evaluate possible biogeographic scenarios that could account for the current distribution pattern of extant bat families. Africa was reconstructed as the center of origin of modern-day bat families.     

Fossils and seed plant phylogeny reanalyzed

In a cladistic analysis of Recent seed plants, Loconte and Stevenson (1990) obtained results that conflict with our 1986 analysis of both extant and fossil groups and argued that fossil data had led us to incorrect conclusions. To explore this result and the general influence of fossils on phylogeny reconstruction, we assembled new “Recent” and “Complete” (extant plus fossil) data sets incorporating new data, advances in treatment of characters, and those changes of Loconte and Stevenson that we consider valid. Our Recent analysis yields only one most parsimonious tree, that of Loconte and Stevenson, in which conifers are linked with Gnetales and angiosperms (anthophytes), rather than with Ginkgo, as in our earlier Recent and Complete analyses. However, the shortest trees derived from our Complete analysis show five arrangements of extant groups, including that of Loconte and Stevenson and our previous arrangements, suggesting that the result obtained from extant taxa alone may be misleading. This increased ambiguity occurs because features that appear to unite extant conifers and anthophytes are seen as convergences when fossil taxa are interpolated between them. All trees found in the Complete analysis lead to inferences on character evolution that conflict with those that would be drawn from Recent taxa alone (e.g., origin of anthophytes from plants with a “seed fern” morphology). These results imply that conclusions on many aspects of seed plant phylogeny are premature; new evidence, which is most likely to come from the fossil record, is needed to resolve the uncertainties.     

The comparative evolution of lizard claw and toe morphology and clinging performance

In this study, I utilize the expected functional relationships between claw and toe morphology and clinging performance as a basis for examining evolutionary trends across 85 lizard taxa from 13 families. After controlling for body size and phylogeny, multivariate comparisons indicate that several aspects of claw and toe morphology are correlated with clinging performance. Specifically, evolutionary increases in claw curvature, toe width and adhesive lamella number are correlated with increases in clinging performance on smooth substrates. Furthermore, evolutionary increases in claw height and decreases in toe length are correlated with increases in clinging performance on rough substrates. Sensitivity analyses revealed that changes in both branch lengths and procedural order of correction for body size and phylogeny do not generally have an effect on phylogenetic comparisons. These results demonstrate that the evolution of claw and toe morphology is correlated with the evolution of clinging performance across a wide range lizard taxa.     

A second varanopseid skull from the Upper Permian of South Africa: implications for Late Permian 'pelycosaur' evolution

Late Permian terrestrial faunas of South Africa and Russia are dominated taxonomically and ecologically by therapsid synapsids. On the basis of a single specimen from the Upper Permian of South Africa, the varanopseid Elliotsmithia longiceps is the sole basal synapsid ('pelycosaur') known from Gondwana. Recent fieldwork in the Upper Permian of South Africa has produced a second varanopseid specimen that is referrable to Elliotsmithia . Data from both this specimen and the holotype suggest that Elliotsmithia forms a clade with Mycterosaurus from the Lower Permian of North America and Mesenosaurus from the Upper Permian of Eastern Europe. That postulate is supported by the three most parsimonious trees discovered in a new analysis of varanopseid phylogeny. However, the available data cannot resolve the interrelationships of these three genera. The new phylogenetic results contrast with earlier work identifying Elliotsmithia as the basal member of a clade that includes the North American taxa Aerosaurus , Varanops , and Varanodon . The new trees reduce the stratigraphic debt required by the latter scenario, and the one with the least stratigraphic debt identifies Elliotsmithia and Mesenosaurus as sister taxa. Two new taxa are erected, Mycterosaurinae and Varanodontinae, for the two varanopseid subclades.     

Deciphering the early evolution of echinoderms with Cambrian fossils

Echinoderms are a major group of invertebrate deuterostomes that have been an important component of marine ecosystems throughout the Phanerozoic. Their fossil record extends back to the Cambrian, when several disparate groups appear in different palaeocontinents at about the same time. Many of these early forms exhibit character combinations that differ radically from extant taxa, and thus their anatomy and phylogeny have long been controversial. Deciphering the earliest evolution of echinoderms therefore requires a detailed understanding of the morphology of Cambrian fossils, as well as the selection of an appropriate root and the identification of homologies for use in phylogenetic analysis. Based on the sister‐group relationships and ontogeny of modern species and new fossil discoveries, we now know that the first echinoderms were bilaterally symmetrical, represented in the fossil record by Ctenoimbricata and some early ctenocystoids. The next branch in echinoderm phylogeny is represented by the asymmetrical cinctans and solutes, with an echinoderm‐type ambulacral system originating in the more crownward of these groups (solutes). The first radial echinoderms are the helicoplacoids, which possess a triradial body plan with three ambulacra radiating from a lateral mouth. Helicocystoids represent the first pentaradial echinoderms and have the mouth facing upwards with five radiating recumbent ambulacra. Pentaradial echinoderms diversified rapidly from the beginning of their history, and the most significant differences between groups are recorded in the construction of the oral area and ambulacra, as well as the nature of their feeding appendages. Taken together, this provides a clear narrative of the early evolution of the echinoderm body plan.     

Phylogenetic analysis of Alloglossidium (Digenea: Macroderoididae) and related genera: life-cycle evolution and taxonomic revision

A phylogenetic analysis was performed on 13 species of digenetic trematodes in the Macroderoididae, including 10 species of Alloglossidium, 2 species of Alloglossoides, and Hirudicolotrema richardsoni. The evolution of the unusual life-cycle patterns in the group was assessed in light of the proposed phylogeny. The results support previous hypotheses that taxa with a 3-host life cycle involving catfish as definitive hosts are basal to taxa with a 2-host life cycle involving invertebrates such as crustaceans and leeches as definitive hosts. Our results also strongly suggest that species maturing in leeches evolved from an ancestor that matured in crustaceans. Our phylogeny places Alloglossoides and Hirudicolotrema within Alloglossidium, showing Alloglossidium to be paraphyletic. To achieve a natural classification, Alloglossoides and Hirudicolotrema are synonymized with Alloglossidium, and a revised generic diagnosis for Alloglossidium is given.     

The morphology,taxonomy and evolution ofRhodocoma (Restionaceae)

The vegetative and reproductive morphology, culm and rhizome anatomy and seed surface micromorphology ofRhodocoma are described. It is shown that this variation is best contained by recognizing three new species in the genus. These new taxa are described, and the phylogeny of the genus is investigated by cladistic analysis. The environmental parameters and distributions of the species are related to the cladogram. This suggests that the species are at present ecologically separated, and indicates that the speciation may have been sympatric. This is the first support for the hypothesis that sympatric speciation may have been important in the speciose Cape flora.     

Reconstructing the evolution of complex bird song in the oropendolas

The elaborate songs of songbirds are frequent models for investigating the evolution of animal signals. However, few previous studies have attempted to reconstruct historical changes in song evolution using a phylogenetic comparative approach. In particular, no comparative studies of bird song have used a large number of vocal characters and a well-supported, independently derived phylogeny. We identified 32 features in the complex vocal displays of male oropendolas (genera Psarocolius, Gymnostinops, and Ocyalus) that are relatively invariant within taxa and mapped these characters onto a robust molecular phylogeny of the group. Our analysis revealed that many aspects of oropendola song are surprisingly evolutionarily conservative and thus are potentially useful characters for reconstructing historical patterns. Of the characters that varied among taxa, nearly two thirds (19 of 29) showed no evidence of evolutionary convergence or reversal when mapped onto the tree, which was reflected in a high overall consistency index (CI = 0.78) and retention index (RI = 0.88). Some reconstructed patterns provided evidence of selection on these signals. For example, rapid divergence of the songs of the Montezuma oropendola, Gymnostinops montezuma, from those of closely related taxa suggests the recent influence of strong sexual selection. In general, our results provide insights into the mode of vocal evolution in songbirds and suggest that complex vocalizations can provide information about phylogeny. Based on this evidence, we use song characters to estimate the phylogenetic affinities of three oropendola taxa for which molecular data are not yet available.