Extensive and evolutionarily persistent mitochondrial tRNA editing in Velvet Worms (phylum Onychophora)

Mitochondrial genomes of onychophorans (velvet worms) present an interesting problem: Some previous studies reported them lacking several transfer RNA (tRNA) genes, whereas others found that all their tRNA genes were present but severely reduced. To resolve this discrepancy, we determined complete mitochondrial DNA (mtDNA) sequences of the onychophorans Oroperipatus sp. and Peripatoides sympatrica as well as cDNA sequences from 14 and 10 of their tRNAs, respectively. We show that tRNA genes in these genomes are indeed highly reduced and encode truncated molecules, which are restored to more conventional structures by extensive tRNA editing. During this editing process, up to 34 nucleotides are added to the tRNA sequences encoded in Oroperipatus sp. mtDNA, rebuilding the aminoacyl acceptor stem, the TΨC arm, and in some extreme cases, the variable arm and even a part of the anticodon stem. The editing is less extreme in P. sympatrica in which at least a part of the TΨC arm is always encoded in mtDNA. When the entire TΨC arm is added de novo in Oroperipatus sp., the sequence of this arm is either identical or similar among different tRNA species, yet the sequences show substantial variation for each tRNA. These observations suggest that the arm is rebuilt, at least in part, by a template-independent mechanism and argue against the alternative possibility that tRNA genes or their parts are imported from the nucleus. By contrast, the 3' end of the aminoacyl acceptor stem is likely restored by a template-dependent mechanism. The extreme tRNA editing reported here has been preserved for >140 My as it was found in both extant families of onychophorans. Furthermore, a similar type of tRNA editing may be present in several other groups of arthropods, which show a high degree of tRNA gene reduction in their mtDNA.     

Support for vicariant origins of the New Zealand Onychophora

Aim The distribution of Onychophora across the southern continents has long been considered the result of vicariance events. However, it has recently been hypothesized that New Zealand was completely inundated during the late Oligocene (25–22 Ma) and therefore that the entire biota is the result of long-distance dispersal. We tested this assumption using phylogenetic and molecular dating of DNA sequence data from Onychophora. Location New Zealand, Australia, South Africa, Chile (South America). Methods We obtained DNA sequence data from the nuclear genes 28S and 18S rRNA to reconstruct relationships among species of Peripatopsidae (Onychophora). We performed molecular dating under a Bayesian relaxed clock model with a range of prior distributions using the rifting of South America and South Africa as a calibration. Results Our phylogenetic trees revealed that the New Zealand genera Ooperipatellus and Peripatoides, together with selected Australian genera (Euperipatoides, Phallocephale and an undescribed genus from Tasmania), form a monophyletic group that is the sister group to genera from Chile (Metaperipatus) and South Africa (Peripatopsis and Opisthopatus). The relaxed clock dating analyses yielded mean divergence times from 71.3 to 78.9 Ma for the split of the New Zealand Peripatoides from their Australian sister taxa. The 0.95 Bayesian posterior intervals were very broad and ranged from 24.5 to 137.6 Ma depending on the prior assumptions. The mean divergence of the New Zealand species of Ooperipatellus from the Australian species Ooperipatellus insignis was estimated at between 39.9 and 46.2 Ma, with posterior intervals ranging from 9.5 to 91.6 Ma. Main conclusions The age of Peripatoides is consistent with long-term survival in New Zealand and implies that New Zealand was not completely submerged during the Oligocene. Ooperipatellus is less informative on the question of continuous land in the New Zealand region because we cannot exclude a post-Oligocene divergence. The great age of Peripatoides is consistent with a vicariant origin of this genus resulting from the rifting of New Zealand from the eastern margin of Gondwana and supports the assumptions of previous authors who considered the Onychophora to be a relict component of the New Zealand biota.     

Unexplored Character Diversity in Onychophora (Velvet Worms): A Comparative Study of Three Peripatid Species

Low character variation among onychophoran species has been an obstacle for taxonomic and phylogenetic studies in the past, however we have identified a number of new and informative characters using morphological, molecular, and chromosomal techniques. Our analyses involved a detailed examination of Epiperipatus biolleyi from Costa Rica, Eoperipatus sp. from Thailand, and a new onychophoran species and genus from Costa Rica, Principapillatus hitoyensis gen. et sp. nov.. Scanning electron microscopy on embryos and specimens of varying age revealed novel morphological characters and character states, including the distribution of different receptor types along the antennae, the arrangement and form of papillae on the head, body and legs, the presence and shape of interpedal structures and fields of modified scales on the ventral body surface, the arrangement of lips around the mouth, the number, position and structure of crural tubercles and anal gland openings, and the presence and shape of embryonic foot projections. Karyotypic analyses revealed differences in the number and size of chromosomes among the species studied. The results of our phylogenetic analyses using mitochondrial COI and 12S rRNA gene sequences are in line with morphological and karyotype data. However, our data show a large number of unexplored, albeit informative, characters in the Peripatidae. We suggest that analysing these characters in additional species would help unravel species diversity and phylogeny in the Onychophora, and that inconsistencies among most diagnostic features used for the peripatid genera in the literature could be addressed by identifying a suite of characters common to all peripatids.     

Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora)

A combination of single-strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540-bp COI sequences from Peripatoides revealed mean among-clade genetic distances of up to 11. 4% using Kimura 2-parameter (K2P) analysis or 17.5% using general time-reversible (GTR + I + Gamma) analysis. Phylogenetic analysis revealed eight well-supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well-developed mate recognition despite minimal morphological variation and low overall genetic diversity.     

Geographical affinities of the Cape flora, South Africa

Aim The flora characteristic of the Cape Floristic Region (CFR) is dominated by a relatively small number of clades that have been proposed as ‘Cape clades’. These clades have variously been suggested to have African or Austral affinities. Here we evaluate the support for these conflicting hypotheses. In addition, we test the hypothesis that these clades share a common time of differentiation from their geographical neighbours. Location The Cape Floristic Region, South Africa Methods We use both published and unpublished phylogenetic information to investigate the geographical sister areas of the Cape clades as well as the timing and the direction of biogeographical disjunctions. Results Almost half of the Cape clades for which unambiguous sister areas could be established show a trans‐Indian Ocean disjunction. The earliest trans‐Indian Ocean disjunction dates from 80 Ma. Other disjunctions date from various times in the Cenozoic, and we suggest that the process of recruiting lineages into the Cape flora might be ongoing. Relatively few Cape clades show a sister relationship with South America and tropical Africa, despite their relative geographical proximity. Numerous Cape clades contain species also found on tropical African mountains; in all cases tested, these species are shown to be embedded within the Cape clades. While many Cape clades show a relationship with the Eurasian temperate flora, this is complicated by their presence in tropical Africa. The single case study addressing this to date suggests that the Cape clade is nested within a European grade. Main conclusions Although many Cape clades show Austral rather than African relationships, there are numerous other patterns suggestive of a cosmopolitan flora. This spatial variation is echoed in the temporal data, from which, although there is wide variance around the dates of disjunctions, it is clear the Cape flora has been assembled over a long time period. There is no simple hypothesis that can account for the geographical sources of the currently distinctive Cape flora. The phylogenetic positions of Afromontane members of Cape clades suggest a history of dispersal from the CFR, rather than the reverse.     

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth′s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the family allows for a reappraisal of the family′s origins, timing, and geographic spread and the factors that have promoted diversification. We reconstructed a time-calibrated grass phylogeny and inferred ancestral areas using chloroplast DNA sequences from nearly 90% of extant grass genera. With a few notable exceptions, the phylogeny is well resolved to the subtribal level. The family began to diversify in the Early–Late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Vicariance from the splitting of Gondwana may be responsible for the initial divergence in the family. However, Africa clearly served as the center of origin for much of the early diversification of the family. With this phylogenetic, temporal, and spatial framework, we review the evolution and biogeography of the family with the aim to facilitate the testing of biogeographical hypotheses about its origins, evolutionary tempo, and diversification. The current classification of the family is discussed with an extensive review of the extant diversity and distribution of species, molecular and morphological evidence supporting the current classification scheme, and the evidence informing our understanding of the biogeographical history of the family.     

Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago

We analysed the phylogenetic relationships of ten of the 13 known species of the genus Apomys using DNA sequences from cytochrome b . Apomys, endemic to oceanic portions of the Philippine archipelago, diversified during the Pliocene as these oceanic islands arose de novo . Several of the speciation events probably took place on Luzon or Mindanao, the two largest, oldest, and most topographically complex islands. Only one speciation event is associated with vicariance due to Pleistocene sea-level fluctuation, and a Pleistocene diversification model in which isolation is driven by sea-level changes is inconsistent with the data. Tectonic vicariance is nearly absent from the Philippines, in which tectonic coalescence plays a significant role. Most speciation events (about two-thirds) are associated with dispersal to newly developed oceanic islands. The data imply that the species have persisted for long periods, measured in millions of years after their origins; further implications therefore are that faunal turnover is very slow, and persistence over geological time spans is more prominent than repeated colonization and extinction. Neither the equilibrium nor the vicariance model of biogeography adequately encompasses these results; a model incorporating colonization, extinction, and speciation is necessary and must incorporate long-term persistence to accommodate our observations.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 699–715.     

Phylogenetic relationships and speciation patterns in an African savanna dwelling bird genus (Myrmecocichla)

Phylogenetic relationships among eight of nine Myrmecocichla chat species were inferred from DNA data. Bayesian posterior probabilities and maximum‐likelihood bootstrap percentages strongly supported most branches in the phylogeny. Based on these results, Myrmecocichla, as currently defined, is not monophyletic. The results indicated that Myrmecocichla albifrons is part of a Cercomela + Oenanthe clade, whereas Oenanthe monticola is shown to be a Myrmecocichla. In addition, Myrmecocichla arnotti is shown to be polyphyletic. Phylogenetic analyses support three Southern versus Eastern or Northern speciation events. The dating of these speciation events suggests that they correspond to periods when the Afrotropical forests were expanded to coastal Kenya, 3–5 Mya. This forest expansion thus served as a vicariant driver of speciation in the genus, a result consistent with speciation patterns in other arid‐adapted African bird genera. Our haplotype analysis within one of the most widespread and habitat diverse Myrmecocichla species (formicivora, a southern African endemic) showed little genetic variation. Along with speciation patterns shown for Myrmecocichla and other avian genera, this lack of standing variation would appear to support large, inter‐regional drivers of speciation as having the largest effect on the diversification of arid‐adapted Africa bird species, which is in stark contrast to other vertebrate lineages whose genetic structure often shows strong intra‐regional effects. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 180–190.     

Phylogeny and biogeography of the sharpshooters (Hemiptera: Cicadellidae: Cicadellinae)

Sharpshooters (Cicadellinae), a large subfamily of the Cicadellidae, exhibit a global distribution and a broad array of ecological preferences. To explore the phylogenetic relationships and roles of global historical, biotic and biogeographic processes in the diversification of sharpshooters, we analysed DNA sequence data from three mitochondrial and two nuclear genes for 243 taxa representing all Cicadellinae tribes, generic groups, regional faunas and data of geographic distributions of sharpshooter species compiled from online databases and available literature. The maximum likelihood (ML) and Bayesian inference (BI) analyses strongly support the monophyletic clade including Cicadellinae and Phereurininae. Divergence time estimates and biogeographic analyses suggest that sharpshooters originated in the Neotropical region or were more widespread in Gondwana during the Early Cretaceous and diversified through a combination of ancient vicariance and dispersal following the evolution of angiosperm-dominated habitats. The earliest divergence during the Cretaceous gave rise to Oriental and New World lineages, the latter of which subsequently dispersed into the Old World and gave rise to the diverse endemic fauna of Madagascar. The Oriental lineage shows high diversity and endemism in tropical Asia and the Pacific, with striking distributional discontinuities in Wallacea. These results suggest that a combination of environmental and evolutionary factors including continental-scale vicariance, long-distance dispersal and diversification of terrestrial microhabitats and host plants may explain the diversity of the modern sharpshooter fauna.     

Extreme long-distance dispersal of the lowland tropical rainforest tree Ceiba pentandra L. (Malvaceae) in Africa and the Neotropics

Many tropical tree species occupy continental expanses of rainforest and flank dispersal barriers such as oceans and mountains. The role of long-distance dispersal in establishing the range of such species is poorly understood. In this study, we test vicariance hypotheses for range disjunctions in the rainforest tree Ceiba pentandra, which is naturally widespread across equatorial Africa and the Neotropics. Approximate molecular clocks were applied to nuclear ribosomal [ITS (internal transcribed spacer)] and chloroplast (psbB-psbF) spacer DNA sampled from 12 Neotropical and five West African populations. The ITS (N=5) and psbB-psbF (N=2) haplotypes exhibited few nucleotide differences, and ITS and psbB-psbF haplotypes were shared by populations on both continents. The low levels of nucleotide divergence falsify vicariance explanations for transatlantic and cross-Andean range disjunctions. The study shows how extreme long-distance dispersal, via wind or marine currents, creates taxonomic similarities in the plant communities of Africa and the Neotropics.     

Minute moss beetles in the Southern Hemisphere: Molecular phylogeny,historical biogeography and habitat shifts (Coleoptera: Hydraenidae)

Minute moss beetles (Hydraenidae) are one of the most speciose and widespread families of aquatic Coleoptera, with an estimated 4000 extant species, found in the majority of aquatic habitats from coastal rock pools to mountain streams and from the Arctic Circle to the Antarctic islands. Molecular phylogenetic works have improved our understanding of the evolutionary history of the megadiverse Hydraena, Limnebius and Ochthebius in recent years, but most genera in the family have not yet been included in any phylogenetic analyses, particularly most of those which are restricted to the Southern Hemisphere. Using a multimarker molecular matrix, sampling over 40% of described species richness and 75% of currently recognized genera, we infer a comprehensive molecular phylogeny of these predominantly Gondwanan Hydraenidae. Whilst the genera we focus on are morphologically diverse, and currently classified across all four hydraenid subfamilies, our phylogenetic analyses suggest that these Gondwanan genera may instead constitute a single clade. As a result of our findings, the African genus Oomtelecopon Perkins syn.n. is shown to nest within Coelometopon Janssens, the New Zealand Homalaena Ordish syn.n. and Podaena Ordish syn.n. are synonymised with Orchymontia Broun, and the South African Pterosthetops Perkins syn.n. is synonymised with Prosthetops Waterhouse, resulting in Pterosthetopini Perkins syn.n. being synonymised with Prosthetopini Perkins. Mesoceratops Bilton & Jäch gen.n. is erected to accommodate six former members of Mesoceration Janssens, which is shown to be polyphyletic. We propose the replacement name Orchymontia ordishi Jäch & Bilton nom.n. for Homalaena dilatata Ordish, 1984 (now a junior homonym); altogether 39 new combinations are proposed. Our Bayesian divergence times infer an origin for this ‘Gondwana group’ of genera in Africa plus Madagascar in the mid-Cretaceous and suggest that both vicariant and dispersal processes, together with extinctions, have shaped the biogeographic history of these beetles in the Southern Hemisphere during the Cretaceous, resulting in geographically conserved extant lineages. Finally, we reconstruct ancestral habitat shifts across our phylogeny, revealing numerous changes in habitat occupancy in these genera, including multiple origins of fully terrestrial, humicolous taxa in different regions.     

A new species of Typhlatya (Crustacea: Decapoda: Atyidae) from anchialine caves on the French Mediterranean coast

A new species of the thermophylic Tethyan relict prawn Typhlatya is described from two anchialine caves near Perpignan (southern France). The new species is closely related to a congener known only from a freshwater cave at Castellón (eastern Spain), about 400 km to the south-west, differing apparently only in the size and shape of the rostrum and the armature of the dactylus of the fifth pereiopod. Based on palaeogeographical evidence and assuming a sister-group relationship between both species, we suggest that their common ancestor could not be older than early Pliocene in age, and that it was already a stygobiont taxon adapted to live in shallow-water marine crevicular habitats. This ancestor would have vanished from the western Mediterranean after the cooling associated with the onset of northern Hemisphere glaciation, about 3 Mya, as documented for other Mediterranean marine taxa. Indeed, the genus is completely stygobiont and does not occur in fluvial environments. The Pyrenees represent a watershed boundary that eliminates the possibility of the derivation of one species from the other by active dispersal after establishment in continental waters.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 387–414.     

The female genital system of Ooperipatellus decoratus (Onychophora, Peripatopsidae): an ultrastructural study

The female genital system of the oviparous peripatopsid Ooperipatellus decoratus consists of an ovary, oviducts equipped with receptacula seminis and additional pouches, uteri, and a vagina. It is examined using transmission and scanning electron microscopy. The ovary is made up of paired ovarian tubes united anteriorly and posteriorly and differentiated into a sterile dorsal part and a fertile ventral part with exogenous oocytes. Fertilization presumably occurs in the oviducts once the oocytes pass the receptaculum seminis. Although the receptacula seminis have been reported to occur in juvenile O. decoratus females only, the present study reveals that they are present in adult females as well. Their wall consists of a cuboidal epithelium covered with a thin collagen-muscle layer. The additional pouches are projections of the oviducts facing the receptacula seminis. They are distally closed to the haemocoel by a flattened epithelium and lack external muscle cells. A thin collagen layer is only found proximally. The uteri are characterized by a columnar epithelium with folded cell membranes allowing extension of the uteri, thus facilitating the passage of the large uterine eggs towards the vagina. Another dominating feature of the uteri is a distally increasing secretory production, which probably contributes to chorion development. Cilia occurring along the entire length of the uteri are considered to assist in the transport of eggs towards the vagina.     

Seminal receptacula in gravid and virgin female Peripatus (Macroperipatus) acacioi Marcus and Marcus (Onychophora,Peripatidae)

The ovoid seminal receptacula in Peripatus acacioi are located at the junctions of the short paired oviducts with the two horns of the uterus. Associated with each is a tubular funnel that opens into the haemocoel. In P. acacioi, spermatozoa may be stored in the seminal receptacula for several years (Campiglia and Walker '95, J. Morphol. 224:179–198). Observations of the structure of the seminal receptaculum using transmission electron microscopy (TEM) show that there are numerous tracheae within its wall indicating a good oxygen supply. The ultrastructure of the epithelium lining the seminal receptaculum indicates that these cells secrete the material that forms the luminal matrix that surrounds and provides nutrition for the stored spermatozoa. The ducts that interconnect the ovary, seminal receptaculum, funnel, and uterus are all packed with cilia. The structure of the seminal receptaculum and associated parts in the mature virgin female is identical to that of the gravid female, but the luminal matrix does not contain any spermatozoa. J. Morphol. 237:127–136, 1998. © 1998 Wiley-Liss, Inc.     

The application of scanning electron microscopy to the systematics of the neotropical Peripatidae (Onychophora)

The taxonomy of the New World Peripatidae is poorly known both because of their rarity and difficulty in the determination of specimens. The distribution of papillae on the dorsal integument is an important taxonomic; character but is difficult to interpret under the light microscope. In this study the integument of a range of New World onychophoran species was studied using scanning electron microscopy. Twenty-one species were examined. Three species of Peripatopsidae were also studied for comparison. This technique revealed (a) the pattern of distribution of papillae on the integument, and (b) the morphology of the papillae. A pattern of three smaller papillae between two large was common to many species. Differences observed in some species were probably modifications of this basic pattern. There was interspecific variation in the number of scales in the apical and basal pieces of the papillae. The specimens examined fell into two main groups: (1) species with more than three scale ranks in the apical piece ( Oroperipatus and Peripatus ) and (2) species with three or fewer scale ranks ( Epiperipatus, Macroperipatus and others). The results thus support a distinction between Epiperipatus and Peripatus . However Macroperipatus is shown not to be a natural group. The relationships of some species which did not fit into this pattern are discussed. This paper shows scanning electron microscopy to be a potentially useful technique in a revision of the New World Peripatidae.     

Ultrastructure of the eggshell and its formation in Planipapillus mundus (Onychophora: Peripatopsidae)

Although the majority of onychophorans are viviparous or ovoviviparous, oviparity has been described in a number of species found exclusively in Australia and New Zealand. Light microscopy and scanning and transmission electron microscopy were used to examine developing eggs and the reproductive tract of the oviparous Planipapillus mundus. Deposited eggs and fully developed eggs dissected from the terminal end of the uteri have an outer thick, slightly opaque chorion, and an inner thin, transparent vitelline membrane. The chorion comprises an outermost extrachorion, sculptured with domes equally spaced over the surface; a middle exochorion, with pores occurring in a pattern of distribution equivalent to that of the domes of the extrachorion above; and an innermost, thick endochorion consisting of a spongelike reticulum of cavities comparable to the respiratory network found in insect eggs. The vitelline membrane lies beneath the chorion, from which it is separated by a fluid‐filled space. The vitelline membrane tightly invests the developing egg. Examination of oocytes in the ovary and developing eggs at various stages of passage through the uterus indicate that the majority of chorion deposition occurs in the midregion of the uterus, where vast networks of endoplasmic reticulum are present in the columnar epithelium. The vitelline membrane, however, is believed to begin its development as a primary egg membrane, surrounding the developing oocytes in the ovary. The vitelline membrane is transformed after fertilization, presumably by secretions from the anterior region of the uterus; hence, it should be more accurately referred to as a fertilization membrane. Aspects of the reproductive biology of P. mundus are also included. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.