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

Ngāokeoke Aotearoa: The Peripatoides Onychophora of New Zealand

(1) Background: Originally described as a single taxon, Peripatoides novaezealandiae (Hutton, 1876) are distributed across both main islands of New Zealand; the existence of multiple distinct lineages of live-bearing Onychophora across this spatial range has gradually emerged. Morphological conservatism obscured the true endemic diversity, and the inclusion of molecular tools has been instrumental in revealing these cryptic taxa. (2) Methods: Here, we review the diversity of the ovoviviparous Onychophora of New Zealand through a re-analysis of allozyme genotype data, mitochondrial DNA cytochrome oxidase subunit I sequences, geographic information and morphology. (3) Results: New analysis of the multilocus biallelic nuclear data using methods that do not require a priori assumptions of population assignment support at least six lineages of ovoviviparous Peripatoides in northern New Zealand, and mtDNA sequence variation is consistent with these divisions. Expansion of mitochondrial DNA sequence data, including representation of all existing taxa and additional populations extends our knowledge of the scale of sympatry among taxa and shows that three other lineages from southern South Island can be added to the Peripatoides list, and names are proposed here. In total, 10 species of Peripatoides can be recognised with current data.

An updated world checklist of velvet worms (Onychophora) with notes on nomenclature and status of names

More than a decade has passed since the publication of the only world checklist available for Onychophora. During this period, numerous nomenclatural acts and taxonomic changes have been suggested within the group and a wealth of novel data has been published on many taxa. Herein, the up-to-date taxonomic scenario within Onychophora is presented, with appraisal of name status. This checklist covers both extant (Peripatidae and Peripatopsidae) and fossil taxa, and each species is accompanied by information on synonyms, type designation, holotype location, type locality, and language of original description. Additional remarks include nomenclatural inconsistencies, synonymizations, name misspellings, conflicting collecting event data, availability of taxonomically informative molecular data, etc. According to the data, 237 species are currently assigned to Onychophora: 140 of Peripatopsidae, 92 of Peripatidae, and five fossil species with unclear relationship to extant taxa. Since the previous checklist, 37 species have been added to Onychophora, representing an increase of 18.5% in the diversity described for the group. Yet, taxonomic descriptions seem slow-paced, with an average of 3.6 onychophoran species being described annually. From the taxonomic standpoint, 216 species are valid, although many of them require morphological revision and molecular characterization; 21 species exhibit major taxonomic ambiguities and have been regarded as nomina dubia. Recurrent taxonomic issues identified in the literature include inaccurate collecting event data, doubtful taxonomic assignment of molecular sequences, and non-observance of nomenclatural rules. These and other taxonomic aspects are addressed herein in the light of the directives established by the International Code of Zoological Nomenclature.

Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics

Onychophora ("velvet worms") are charismatic soil invertebrates known for their status as a "living fossil," their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group's evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.

Morphological and molecular phylogeny of Epiperipatus (Onychophora: Peripatidae): a combined approach

Onychophora, or velvet worms, are a key group for understanding ecdysozoan evolution. It comprises two families: Peripatopsidae, largely of Austral distribution, and Peripatidae, which is circumtropical. The interrelationships between the members of Peripatidae present many taxonomic issues exacerbated in the radiation of the Neotropical species or Neopatida. To understand the phylogeny of Neopatida, and to test the information of such morphological characters, we gathered novel molecular and morphological datasets focusing on Neotropical specimens. Our data were analysed using a combination of parsimony and maximum likelihood for the individual and combined molecular and morphological datasets. An analysis of morphology alone was inconclusive, supporting the notion that morphological characters used in peripatid taxonomy have little power to resolve phylogenetic relationships among higher taxa in Neopatida. However, the analyses of molecular or combined data show a split of the Neotropical species into two clades, which we use to reassign genera. Epiperipatus, as currently understood, is non-monophyletic, because it includes species of monotypic genera. To avoid paraphyly of Epiperipatus, the following new combinations are proposed: Epiperipatus bouvieri (Fuhrmann, 1913), Epiperipatus hitoyensis (Oliveira et al., 2012a), Epiperipatus solorzanoi (Morera-Brenes & Monge-Nájera, 2010) and Epiperipatus sucuriuensis (Oliveira et al., 2015).

Systematics of the Peripatopsis clavigera species complex (Onychophora : Peripatopsidae) reveals cryptic cladogenic patterning, with the description of five new species

During the present study, DNA sequence data, gross morphology and scanning electron microscopy (SEM) were used to examine cryptic species boundaries in the velvet worm, Peripatopsis clavigera species complex, from the southern Cape Afrotemperate forest belt in South Africa. Sequence data were generated for the mitochondrial COI and the nuclear 18S rRNA loci and phylogenetically analysed using both a Bayesian inference and a maximum-likelihood approach. Both the COI data and the combined DNA sequence topology (COI+18S) revealed the presence of five clades within the Peripatopsis clavigera species complex, and revealed that specimens from Tulbagh were distantly related and represented a sixth clade. The evolutionary distinction of the five clades was corroborated to varying degrees by the four species-delimitation methods (ABGD, PTP, GMYC and STACEY); however, both the gross morphological data and the SEM provided limited diagnostic differences between the five clades. Furthermore, the COI haplotype network and phylogeographic analyses provided evidence of genetic isolation between lineages that are currently syntopic. The distribution of genealogically exclusive and widespread maternal lineages was atypical among velvet worms and did not reflect the general trend of genetic and geographical isolation. Instead, lineages exhibited admixture among localities, a result most likely due to fluctuations in climatic conditions affecting the southern Cape Afrotemperate forest during the Pliocene–Pleistocene period as evident from our divergence time estimations. Four novel, narrow-range endemic species – P. ferox, sp. nov., P. mellaria, sp. nov., P. edenensis, sp. nov. and P. mira, sp. nov. – are described within the P. clavigera species complex, whereas the Tulbagh specimens are described as P. tulbaghensis, sp. nov. Collectively, these results demonstrate that Peripatopsis likely contains several undescribed species.

Cryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora : Peripatopsidae : Kumbadjena)

There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.

Diversity of tortricid moths in apple orchards: evidence for a cryptic species of Grapholita (Lepidoptera: Tortricidae) from China

Understanding herbivore diversity both at the species and genetic levels is a key to effective pest management. We examined moth samples from multiple locations from a major apple growing region in China. For specimen collection, we used a pheromone trap designed to attract Grapholita molesta (Busck) (Lepidoptera: Tortricidae). Surprisingly, we found a second species captured at high proportions. Its external morphology (e.g., male genitalia and forewing coloration) was the same as for Grapholita funebrana Treitschke (Lepidoptera: Tortricidae) specimens from Europe. However, the barcode sequence of the mitochondrial gene cytochrome oxidase I (COI) diverged markedly between specimens from China and Europe, and the genetic distance value between the specimens from the two regions as estimated using the Juke-Cantor (JC) model amounted to 0.067. These morphological and molecular findings together point to a cryptic species in G. funebrana from China. Further molecular analyses based on COI and COII genes revealed its extremely high genetic diversity, indicating that the origin of this species includes the sampling region. Moreover, molecular data suggest that this species passed through a recent population expansion. This is the first report on a cryptic species in G. funebrana, as well as the first report on its genetic diversity.

Molecular analyses reveal the occurrence of three new sympatric lineages of velvet worms (Onychophora: Peripatidae) in the eastern Amazon basin

In the present study, we investigated the possible existence of new lineages of peripatids through comparisons between known Neotropical species and specimens obtained from two locations in Pará, a state in eastern Brazilian Amazonia using a molecular approach based on sequences of the mtDNA genes COI, 16Sr RNA, and 18S RNA. The analyses included also sequences of Asian and African taxa for a more systematic understanding of the phylogenetic relationships within the group. The analysis of the COI, 16S rRNA and 18S RNA sequences permitted the identification of three distinct lineages (A, B and C) based on two different phylogenetic approaches (Bayesian methods and ML). The three lineages presented here are completely distinct from all other peripatid taxa so far defined by molecular data. The presence of specimens of three independent onychophoran lineages occurring in sympatry in the Amazon basin was confirmed in all the analyses, providing consistent support for the phylogenies presented in this study. These findings reinforce the importance of the Amazon region in the diversification of Neotropical peripatids, and indicate that onychophoran diversity is much greater than previously thought, given that the number of taxa found at a single site was equivalent to the total number of allopatric species described for the entire region.

Contrasting the population genetic structure of two velvet worm taxa (Onychophora : Peripatopsidae : Peripatopsis) in forest fragments along the south-eastern Cape, South Africa

During the present study, we examined the phylogeography and systematics of two species of velvet worm (Peripatopsis Pocock, 1894) in the forested region of the southern Cape of South Africa. A total of 89 P. moseleyi (Wood-Mason, 1879) and 65 P. sedgwicki (Purcell, 1899) specimens were collected and sequenced for the cytochrome c oxidase subunit I mtDNA (COI). In addition, a single P. sedgwicki specimen per sample locality was sequenced for the 18S rRNA locus. Furthermore, morphological variation among P. sedgwicki sample localities were explored using traditional alpha taxonomic characters. DNA sequence data were subjected to phylogenetic analyses using Bayesian inference and population genetic analyses using haplotype networks and analyses of molecular variance (AMOVAs). Phylogenetic results revealed the presence of four and three clades within P. moseleyi and P. sedgwicki respectively. Haplotype networks were characterised by the absence of shared haplotypes between clades, suggesting genetic isolation, a result corroborated by the AMOVA and highly significant FST values. Specimens from Fort Fordyce Nature Reserve were both genetically and morphologically distinct from the two remaining P. sedgwicki clades. The latter result suggests the presence of a novel lineage nested within P. sedgwicki and suggests that species boundaries within this taxon require re-examination.

Fifteen into Three Does Go: Morphology, Genetics and Genitalia Confirm Taxonomic Inflation of New Zealand Beetles (Chrysomelidae: Eucolaspis)

Eucolaspis Sharp 1886 is a New Zealand native leaf beetle genus (Coleoptera: Chrysomelidae: Eumolpinae) with poorly described species and a complex taxonomy. Many economically important fruit crops are severely damaged by these beetles. Uncertain species taxonomy of Eucolaspis is leaving any biological research, as well as pest management, tenuous. We used morphometrics, mitochondrial DNA and male genitalia to study phylogenetic and geographic diversity of Eucolaspis in New Zealand. Freshly collected beetles from several locations across their distribution range, as well as identified voucher specimens from major museum collections were examined to test the current classification. We also considered phylogenetic relationships among New Zealand and global Eumolpinae (Coleoptera: Chyrosomelidae). We demonstrate that most of the morphological information used previously to define New Zealand Eucolaspis species is insufficient. At the same time, we show that a combination of morphological and genetic evidence supports the existence of just 3 mainland Eucolaspis lineages (putative species), and not 5 or 15, as previously reported. In addition, there may be another closely related lineage (putative species) on an offshore location (Three Kings Islands, NZ). The cladistic structure among the lineages, conferred through mitochondrial DNA data, was well supported by differences in male genitalia. We found that only a single species (lineage) infests fruit orchards in Hawke’s Bay region of New Zealand. Species-host plant associations vary among different regions.

Genome size and chromosome number in velvet worms (Onychophora)

The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5-19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results.

DNA barcoding methods for invertebrates

Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.

Phylogeography of the Cape velvet worm (Onychophora: Peripatopsis capensis) reveals the impact of Pliocene/Pleistocene climatic oscillations on Afromontane forest in the Western Cape, South Africa

Habitat specialists such as soft-bodied invertebrates characterized by low dispersal capability and sensitivity to dehydration can be employed to examine biome histories. In this study, the Cape velvet worm (Peripatopsis capensis) was used to examine the impacts of climatic oscillations on historical Afromontane forest in the Western Cape, South Africa. Divergence time estimates suggest that the P. capensis species complex diverged during the Pliocene epoch. This period was characterized by dramatic climatic and topographical change. Subsequently, forest expansion and contraction cycles led to diversification within P. capensis. Increased levels of genetic differentiation were observed along a west-to-south-easterly trajectory because the south-eastern parts of the Cape Fold Mountain chain harbour larger, more stable fragments of forest patches, have more pronounced habitat heterogeneity and have historically received higher levels of rainfall. These results suggest the presence of three putative species within P. capensis, which are geographically discreet and genetically distinct.

Pitfalls in comparisons of genetic distances: a case study of the avian family Acrocephalidae

Genetic distances are increasingly being used for identification and species delimitation, especially since the introduction of "barcoding". While for phylogenetic inferences great care is generally taken to choose the best-fit evolutionary model, this is usually neglected in calculating genetic distances. Moreover, distances obtained from others than best-fit models, different lengths of sequences, and even different loci are often freely compared. We examined the influence of different methods on calculating genetic distances using mitochondrial cytochrome b sequences for the passerine family Acrocephalidae. We found substantial differences between: (1) corrected distances based on the best-fit model (TrN+Γ) vs. uncorrected p-distances; (2) distances calculated based on different parts of the same gene; and (3) distances calculated using the methods of "complete deletion" vs. "pairwise deletion" for sequences that included uncertain nucleotides. All these methodological differences affected comparisons between species and potential taxonomical conclusions. We suggest that (1) different loci are incomparable. (2) Only perfectly homologous regions (same length, same part of locus) should be compared. (3) In the case of sequences with some uncertain nucleotides, only distances calculated by the method of "complete deletion" are fully comparable. (4) Only distances based on the optimal substitution model should be used. (5) Even within the same locus, corrected genetic distances are unique to the study in which they are calculated, as they are conditional on the particular dataset and model selected for that dataset.

The Invertebrate Life of New Zealand: A Phylogeographic Approach

Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand's invertebrates.

Cryptic speciation in Brazilian Epiperipatus (Onychophora: Peripatidae) reveals an underestimated diversity among the peripatid velvet worms

Background

Taxonomical studies of the neotropical Peripatidae (Onychophora, velvet worms) have proven difficult, due to intraspecific variation and uniformity of morphological characters across this onychophoran subgroup. We therefore used molecular approaches, in addition to morphological methods, to explore the diversity of Epiperipatus from the Minas Gerais State of Brazil.

Methodology/Principal Findings

Our analyses revealed three new species. While Epiperipatus diadenoproctussp. nov. can be distinguished from E. adenocryptussp. nov. and E. paurognostussp. nov. based on morphology and specific nucleotide positions in the mitochondrial cytochrome c oxidase subunit I (COI) and small ribosomal subunit RNA gene sequences (12S rRNA), anatomical differences between the two latter species are not evident. However, our phylogenetic analyses of molecular data suggest that they are cryptic species, with high Bayesian posterior probabilities and bootstrap and Bremer support values for each species clade. The sister group relationship of E. adenocryptussp. nov. and E. paurognostussp. nov. in our analyses correlates with the remarkable morphological similarity of these two species. To assess the species status of the new species, we performed a statistical parsimony network analysis based on 582 base pairs of the COI gene in our specimens, with the connection probability set to 95%. Our findings revealed no connections between groups of haplotypes, which have been recognized as allopatric lineages in our phylogenetic analyses, thus supporting our suggestion that they are separate species.

Conclusions/Significance

Our findings suggest high cryptic species diversity and endemism among the neotropical Peripatidae and demonstrate that the combination of morphological and molecular approaches is helpful for clarifying the taxonomy and species diversity of this apparently large and diverse onychophoran group.

'Moa's Ark' or 'Goodbye Gondwana': is the origin of New Zealand's terrestrial invertebrate fauna ancient, recent or both?

Evaluating the hypothesis of New Zealand’s total submersion during the Oligocene requires the strictest tests, including sound phylogenetic data and dating of phylogenies. Although New Zealand has been traditionally considered to host ancient biota that originated by vicariance after it separated from Australia ~80 Mya, the ancient origins of its biota have been recently questioned, with some authors even suggesting that all current land organisms had to arrive to the islands after it re-emerged from the ocean 22 million years ago. Here we examine examples of short-range endemic soil-dwelling invertebrates and find compelling evidence that at least some of them are the result of old lineages that diversified in New Zealand before the hypothesised submersion event 22 million year ago. We conclude that New Zealand indeed has old lineages as well as recently diversified lineages and compare this situation with that of other more stable areas of the Neotropics.

Evolution of New Zealand's terrestrial fauna: a review of molecular evidence

New Zealand biogeography has been dominated by the knowledge that its geophysical history is continental in nature. The continental crust (Zealandia) from which New Zealand is formed broke from Gondwanaland ca 80 Ma, and there has existed a pervading view that the native biota is primarily a product of this long isolation. However, molecular studies of terrestrial animals and plants in New Zealand indicate that many taxa arrived since isolation of the land, and that diversification in most groups is relatively recent. This is consistent with evidence for species turnover from the fossil record, taxonomic affinity, tectonic evidence and observations of biological composition and interactions. Extinction, colonization and speciation have yielded a biota in New Zealand which is, in most respects, more like that of an oceanic archipelago than a continent.

Species concepts and species reality: salvaging a Linnaean rank

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.

Biological identifications through DNA barcodes

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

[Natural hybridization between 2 sympatric species of mice, Mus musculus domesticus L. and Mus spretus Lataste]

Using protein loci and DNA markers, we show by a multilocus genetic analysis that certain populations of the two sympatric mouse species Mus musculus domesticus and Mus spretus show clear signs of partial introgression. Given the sterility of F1 males and the known partial genetic incompatibilities between the genomes of the two species, our finding does not invalidate the biological species complex, but allows to think that very limited genetic exchanges remain possible even long after the divergence of taxa. This may have some consequences on the dynamics of certain kinds of invasive or advantageous DNAs like transposable elements or pathogen resistance genes.

Bridging the "beech-gap": New Zealand invertebrate phylogeography implicates Pleistocene glaciation and Pliocene isolation

The existence of areas of lower endemism and disjunction of New Zealand biota is typified by Nothofagus beech trees (hence "beech-gap") and have been attributed to a variety of causes ranging from ancient fault-mediated displacement (20-25 million years ago) to Pleistocene glacial extirpation (< 1.8 million years ago). We used cytochrome oxidase I and 12S mtDNA sequence data from a suite of endemic invertebrates to explore phylogeographic depth and patterns in South Island, New Zealand, where the "beech-gap" occurs. Phylogeographic structure and genetic distance data are not consistent with ancient vicariant processes as a source of observed pattern. However, we also find that phylogeographic patterns are not entirely congruent and appear to reflect disparate responses to fragmentation, which we term "gap," "colonization," and "regional." Radiations among congenerics, and in at least one instance within a species, probably took place in the Pliocene (2-7 million years ago), possibly under the influence of the onset of mountain building. This orogenic phase may have had a considerable impact on the development of the biota generally. Some of the taxa that we studied do not appear to have suffered range reduction during Pleistocene glaciation, consistent with their survival throughout that epoch in alpine habitats to which they are adapted. Other taxa have colonized the beech-gap recently (i.e., after glaciation), whereas few among our sample retain evidence of extirpation in the most heavily glaciated zone.

Phylogenetics of Planipapillus, lawn-headed onychophorans of the Australian Alps, based on nuclear and mitochondrial gene sequences

We addressed phylogenetic relationships among species of Planipapillus, a clade of oviparous onychophorans from southeastern mainland Australia, to create a framework for understanding the evolution of the modified male head papillae used in mating in this clade. We sequenced fragments of two mitochondrial genes, COI and 12S rRNA, and a nuclear intron from the fushi tarazu gene, for individuals from 14 putative species of Planipapillus and six outgroups. We analyzed these data under both parsimony and likelihood criteria, incorporating heterogeneous parameter fitting guided by likelihood ratio tests. These analyses result in strong, congruent support for many clades. We infer multiple independent origins of spikes in Planipapillus male head structures.

Phylogenetics and speciation

Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales.

Chromosome races with Pliocene origins: evidence from mtDNA

There are eight distinct chromosomal races of the New Zealand weta Hemideina thoracica. We used mtDNA sequence data to test the hypothesis that these races originated on islands during the early Pliocene (7--4 million years ago). Nine major mitochondrial lineages were identified from 65 cytochrome oxidase I sequences. Phylogenetic analysis of these lineages suggests that they arose at approximately the same time. The geographical distribution of some lineages coincides with areas that were islands during the Pliocene. Overall, hierarchical AMOVA analysis shows that chromosomal races and Pliocene islands describe only 28% and 24%, respectively, of the total current mtDNA variation. However, removing one widespread (A) and one putatively introgressed (F) lineage increases these estimates to 65% and 80%, respectively. Intraspecific sequence divergence was very high, reaching a maximum of 9.5% (uncorrected distance) and GC content was high compared to other insect mtDNA sequences. Average corrected distance among mtDNA lineages supports the Pliocene origins of this level of genetic diversity. In the southern part of the species range there is reduced mtDNA variation, probably related to local extinction of H. thoracica populations from recent volcanic activity and subsequent re-colonization from a leading edge. In contrast, in this southern part there are five chromosome races, suggesting that chromosome races here may be younger than those in the north.