A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species

We aimed to clarify phylogenetic relationships within the pantropical genus Diospyros (Ebenaceae sensu lato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA sequences from eight plastid regions (rbcL, atpB, matK, ndhF, trnK intron, trnL intron, trnL-trnF spacer, and trnS-trnG spacer) and included 149 accessions representing 119 Diospyros species in our analysis. Results from this study confirmed the monophyly of Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that Diospyros colonized New Caledonia multiple times. The four lineages of Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.     

Origin and post-colonization evolution of the Chatham Islands skink (Oligosoma nigriplantare nigriplantare)

Island ecosystems provide an opportunity to examine a range of evolutionary and ecological processes. The Chatham Islands are an isolated archipelago situated approximately 800 km east of New Zealand. Geological evidence indicates that the Chatham Islands re-emerged within the last 1-4 million years, following a prolonged period of marine inundation, and therefore the resident flora and fauna is the result of long-distance overwater dispersal. We examine the origin and post-colonization evolution of the Chatham Islands skink, Oligosoma nigriplantare nigriplantare, the sole reptile species occurring on the archipelago. We sampled O. n. nigriplantare from across nine islands within the Chatham Islands group, and representative samples from across the range of its closest relative, the New Zealand mainland common skink (Oligosoma nigriplantare polychroma). Our mitochondrial sequence data indicate that O. n. nigriplantare diverged from O. n. polychroma 5.86-7.29 million years ago. This pre-dates the emergence date for the Chatham Islands, but indicates that O. n. nigriplantare colonized the Chatham Islands via overwater dispersal on a single occasion. Despite the substantial morphological variability evident in O. n. nigriplantare, only relatively shallow genetic divergences (maximum divergence approximately 2%) were found across the Chatham Islands. Our analyses (haplotypic diversity, Phi(ST), analysis of molecular variance, and nested clade phylogeographical analysis) indicated restricted gene flow in O. n. nigriplantare resulting in strong differentiation between islands. However, the restrictions to gene flow might have only arisen recently as there was also a significant pattern of isolation by distance, possibly from when the Chatham Islands were a single landmass during Pleistocene glacial maxima when sea levels were lower. The level of genetic and morphological divergence between O. n. nigriplantare and O. n. polychroma might warrant their recognition as distinct species.     

Review of the New Caledonian species of Acritoptila Wells, 1982 (Trichoptera,Insecta), with descriptions of 3 new species

We review the New Caledonian representatives of the Australasian endemic hydroptiline genus Acritoptila, based on examination of a considerable collection of material in the Swedish Museum of Natural History and of types of previously established species. A key for identification of males is given and includes 3 species newly described here: A. parallelasp. n., A. forficatasp. n. and A. macrospinasp. n. For all New Caledonian species, male genitalia are illustrated, and for 5 associated females, distinctive features are illustrated and described.     

Association and description of males, females and larvae of two New Caledonian Xanthochorema species (Trichoptera: Hydrobiosidae) based on mitochondrial 16S and COI sequences

A method for associating larvae, females and males of Trichoptera is demonstrated for New Caledonian Hydrobiosidae species of the genus Xanthochorema, using cytochrome oxidase subunit I (COI) and 16S mitochondrial gene sequences. Two species, X. caledon Kimmins, 1953 and X. celadon Schmid, 1989 , previously with unknown larvae and undescribed females, were associated, and males, females and larvae of both species are described. Mitochondrial COI and 16S gene fragments are demonstrated to be useful for association of sexes and life stages of the two species, and distance measures show that the method is likely to also be useful for other species within the genus. The associations are well supported by high bootstrap and jackknife values.     

The evolution of South American endemic canids: a history of rapid diversification and morphological parallelism

The origin of endemic South American canid fauna has been traditionally linked with the rise of the Isthmus of Panama, suggesting that diversification of the dog fauna on this continent occurred very rapidly. Nevertheless, despite its obvious biogeographic appeal, the tempo of Canid evolution in South America has never been studied thoroughly. This issue can be suitably tackled with the inference of a molecular timescale. In this study, using a relaxed molecular clock method, we estimated that the most recent common ancestor of South American canids lived around 4 Ma, whereas all other splits within the clade occurred after the rise of the Panamanian land bridge. We suggest that the early diversification of the ancestors of the two main lineages of South American canids may have occurred in North America, before the Great American Interchange. Moreover, a concatenated morphological and molecular analysis put some extinct canid species well within the South American radiation, and shows that the dental adaptations to hypercarnivory evolved only once in the South American clade.     

The anatomy and systematics of the New Caledonian land snail genus Draparnaudia Montrouzier, 1859 (Pulmonata: Orthurethra)

A comprehensive study of the anatomy, ecology and distribution of the orthurethran genus Draparnaudia confirms its family-group status, and suggests a probable sister-group relationship with another Pacific family, the Partulidae; its previous position as a subfamily of the Enidae is refuted. Draparnaudia is endemic to New Caledonia, but records from the New Hebrides are thought to result from introductions. A total of six species are recognized in the taxonomic revision, including two new species. Spermatophores are recorded for the first time.     

Ancient differentiation in the single-island avian radiation of endemic Hispaniolan chat-tanagers (Aves: Calyptophilus)

The simple geographic structure of island systems often makes them tractable for studies of the patterns and processes of biological diversification. The Calyptophilus chat-tanagers of Hispaniola are of general evolutionary interest because their multiple lineages might have arisen on a single island, of conservation concern because several isolated populations are nearly extinct, and taxonomically ambiguous because they have been variously lumped or split into one to four species. To explore the context of diversification of the seven extant Calyptophilus populations, we conducted a multilocus coalescent analysis based on sequences of mitochondrial ND2 and three nuclear intron loci. We then compared patterns of phylogeographic genetic variation with the morphological differences that distinguish these populations. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by a large magnitude of nucleotide divergence. Intron structure largely paralleled the geographic grouping pattern of the mitochondrial DNA (mtDNA), but these groups were only reciprocally monophyletic at one of the three introns. Also, the magnitude of between-group divergence was much lower in the introns than mtDNA genealogies. Multilocus coalescent analyses inferred a nonzero divergence time between these two major geographic groups, but suggested that they have experienced a low level of gene flow. All four markers showed substantial allele sharing within each of the two groups, demonstrating that many now separated montane populations do not have long histories of isolation. Considered in concert, our multilocus phylogeographic reconstructions support the recognition of two species within the Calyptophilus complex, and raise the possibility that these taxa differentiated prior to the fusion of the two palaeo-islands that form present-day Hispaniola.     

Evolution of distribution and habitat patterns in endemic millipedes of the genus Dolichoiulus (Diplopoda: Julidae) on the Canary Islands, with notes on distribution patterns of other Ganarian species swarms

Forty-six species of the genus Dolichoiulus , all endemic, occur on the Canary Islands The highest number of species occur on the largest, highest island (Tenerife); fewest occur on Lanzarote, Fuerteventura (low, xeric), El Hierro and La Palma (small, remote). Most of the Dolichoiulus species live on one island only, as in other endemic Canarian species swarms. The scarcity of pluri-insular Dolichoiulus species, in connection with information on phylogeny, suggests that speciation has mainly taken place within individual islands. Distribution patterns are partly governed by habitat differences between species, but vicariance patterns between species living in the same kind of habitat are evident on La Gomera and Tenerife. Dolichoiulus species occur in all kinds of natural habitats. Laurisilva and cave species are generally paler than other species. In the laurisilva of eastern Tenerife, microhabitat differentiation between species is pronounced. In some, but far from all, cases, species coexisting in the same microhabitat are of different sizes. The ancestral colonizing species of Dolichoiulus is/are hypothesized to have been small and to have lived in coastal habitats. Colonization of higher altitudes was usually accompanied by an increase in body size. Invasion of the laurisilva was usually accompanied by a habitat shift from the ground layer to logs.     

Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: evidence for a single origin of the endemic skinks of Tasmantis

We use approximately 1900bp of mitochondrial (ND2) and nuclear (c-mos and Rag-1) DNA sequence data to recover phylogenetic relationships among 58 species and 26 genera of Eugongylus group scincid lizards from New Caledonia, Lord Howe Island, New Zealand, Australia and New Guinea. Taxon sampling for New Caledonian forms was nearly complete. We find that the endemic skink genera occurring on New Caledonia, New Zealand and Lord Howe Island, which make up the Gondwanan continental block Tasmantis, form a monophyletic group. Within this group New Zealand and New Zealand+Lord Howe Island form monophyletic clades. These clades are nested within the radiation of skinks in New Caledonia. All of the New Caledonian genera are monophyletic, except Lioscincus. The Australian and New Guinean species form a largely unresolved polytomy with the Tasmantis clade. New Caledonian representatives of the more widespread genera Emoia and Cryptoblepharus are more closely related to the non-Tasmantis taxa than to the endemic New Caledonian genera. Using ND2 sequences and the calibration estimated for the agamid Laudakia, we estimate that the diversification of the Tasmantis lineage began at least 12.7 million years ago. However, using combined ND2 and c-mos data and the calibration estimated for pygopod lizards suggests the lineage is 35.4-40.74 million years old. Our results support the hypothesis that skinks colonized Tasmantis by over-water dispersal initially to New Caledonia, then to Lord Howe Island, and finally to New Zealand.     

Origin and evolution of the endemic Canary Island shrews (Mammalia: Soricidae)

Until recently the North Atlantic Islands were believed to house only mammals introduced by humans. Recent work has demonstrated that at least the Canary Islands house(d) a native mammal fauna. New data including chromosome numbers, genetic distances and analysis of vocalizations are given for the two extant shrew species, Crocidura canariensis and C. osorio , and their possible sister taxa are evaluated. Evidence is presented for the hypothesis that the two island species originated from two different lineages of the Palaearctic branch of the genus Crocidura. The data support the present status of the Canary Island shrews as local endemics of high conservation priority.     

On the genetic diversity in the mitochondrial 12S rRNA gene of Platymantis frogs from Western New Guinea (Anura: Ceratobatrachidae)

Platymantis is a group of neobatrachian frogs that occurs from the Philippines to New Guinea – an area situated at the interface between the Australian and Asian biogeographical region that is highly fragmented by stretches of open sea. Partial sequences of the mitochondrial 12S rRNA gene are herein used to infer the relationships of species from the Indonesian part of New Guinea (Papua and West Papua Province). The phylogenetic trees reveal a deep bifurcation between the Asian and Western New Guinean clades being consistent with phylogeographic patterns observed in various other faunal groups. While most species are well differentiated in the examined locus, low interspecific genetic distances between one and three percent were observed in the New Guinean species Platymantis papuensis and P. cryptotis as well as P. pelewensis from Palau. Platymantis papuensis and P. pelewensis are geographically separated from each other by a 1100 km stretch of open sea. The minor degree of genetic differentiation between both species points to a recent event of transmarine dispersal as causation for the occurrence of P. pelewensis on Palau. The low genetic differentiation between P. cryptotis and the sympatric P. papuensis, two species that are bioacoustically and morphologically distinct, may indicate its possibly recent evolutionary origin or, alternatively, yet undetected hybridization between the two species. The same may also hold true for frogs from Yapen that exhibit calls different from the sympatric P. papuensis. Tentatively referred to as Platymantis spec., these frogs are also genetically not well differentiated. It is furthermore concluded that the partly low genetic differentiation of the New Guinean Platymantis species render this group one of the cases in which DNA barcoding would likely fail to produce reliable results.     

New genera of Copepoda (Poecilostomatoida) from the scleractinian coral Psammocora in New Caledonia

Three new monotypic genera of copepods (Poecilostomatoida) are associated with the hermatypic shallow-water coral Psammocora (Stephanaria) logianensis near Noumea, New Caledonia: in the Anchimolgidae, Lipochaetes extrusus (antenna 4-segmented, endopods absent in legs 3 and 4) and Dumbeana undulatipes (antenna 3-segmcntcd, endopod of leg 3 with formula 0 1; 0–2; 1,11,2; leg 4 endopod with 0 1:1); and in the Rhynchomolgidae; Emunoa proknta (leg 4 endopod with 0 1;II, antenna 4-segmented, mandible witli outer pointed process and inner row of spines). Copepoda (primarily Poecilostomatoida and Siphonostomatoida, but also relatively few Cyclopoida and Harpacticoida) are very frequent associates or parasites of Scleractinia. At present 245 species from 48 scleractinian coral genera are known. Species of these copepod associates, their host genera, and localities, described since (and those not included in) previous publications of the author are listed.     

Sequencing of whole plastid genomes and nuclear ribosomal DNA of Diospyros species (Ebenaceae) endemic to New Caledonia: many species,little divergence

Background and Aims Some plant groups, especially on islands, have been shaped by strong ancestral bottlenecks and rapid, recent radiation of phenotypic characters. Single molecular markers are often not informative enough for phylogenetic reconstruction in such plant groups. Whole plastid genomes and nuclear ribosomal DNA (nrDNA) are viewed by many researchers as sources of information for phylogenetic reconstruction of groups in which expected levels of divergence in standard markers are low. Here we evaluate the usefulness of these data types to resolve phylogenetic relationships among closely related Diospyros species.Methods Twenty-two closely related Diospyros species from New Caledonia were investigated using whole plastid genomes and nrDNA data from low-coverage next-generation sequencing (NGS). Phylogenetic trees were inferred using maximum parsimony, maximum likelihood and Bayesian inference on separate plastid and nrDNA and combined matrices.Key Results The plastid and nrDNA sequences were, singly and together, unable to provide well supported phylogenetic relationships among the closely related New Caledonian Diospyros species. In the nrDNA, a 6-fold greater percentage of parsimony-informative characters compared with plastid DNA was found, but the total number of informative sites was greater for the much larger plastid DNA genomes. Combining the plastid and nuclear data improved resolution. Plastid results showed a trend towards geographical clustering of accessions rather than following taxonomic species.Conclusions In plant groups in which multiple plastid markers are not sufficiently informative, an investigation at the level of the entire plastid genome may also not be sufficient for detailed phylogenetic reconstruction. Sequencing of complete plastid genomes and nrDNA repeats seems to clarify some relationships among the New Caledonian Diospyros species, but the higher percentage of parsimony-informative characters in nrDNA compared with plastid DNA did not help to resolve the phylogenetic tree because the total number of variable sites was much lower than in the entire plastid genome. The geographical clustering of the individuals against a background of overall low sequence divergence could indicate transfer of plastid genomes due to hybridization and introgression following secondary contact.     

Resurrection of New Caledonian maskray Neotrygon trigonoides (Myliobatoidei: Dasyatidae) from synonymy with N. kuhlii, based on cytochrome-oxidase I gene sequences and spotting patterns

The maskray from New Caledonia, Neotrygon trigonoides Castelnau, 1873, has been recently synonymized with the blue-spotted maskray, N. kuhlii (Müller and Henle, 1841), a species with wide Indo-West Pacific distribution, but the reasons for this are unclear. Blue-spotted maskray specimens were collected from the Indian Ocean (Tanzania, Sumatra) and the Coral Triangle (Indonesia, Taiwan, and West Papua), and N. trigonoides specimens were collected from New Caledonia (Coral-Sea). Their partial COI gene sequences were generated to expand the available DNA-barcode database on this species, which currently comprises homologous sequences from Ningaloo Reef, the Coral Triangle and the Great Barrier Reef (Coral-Sea). Spotting patterns were also compared across regions. Haplotypes from the Coral-Sea formed a haplogroup phylogenetically distinct from all other haplotypes sampled in the Indo-West Pacific. No clear-cut geographic composition relative to DNA-barcodes or spotting patterns was apparent in N. kuhlii samples across the Indian Ocean and the Coral Triangle. The New Caledonian maskray had spotting patterns markedly different from all the other samples. This, added to a substantial level of net nucleotide divergence (2.6%) with typical N. kuhlii justifies considering the New Caledonian maskray as a separate species, for which we propose to resurrect the name Neotrygon trigonoides.     

New Zealand phylogeography: evolution on a small continent

New Zealand has long been a conundrum to biogeographers, possessing as it does geophysical and biotic features characteristic of both an island and a continent. This schism is reflected in provocative debate among dispersalist, vicariance biogeographic and panbiogeographic schools. A strong history in biogeography has spawned many hypotheses, which have begun to be addressed by a flood of molecular analyses. The time is now ripe to synthesize these findings on a background of geological and ecological knowledge. It has become increasingly apparent that most of the biota of New Zealand has links with other southern lands (particularly Australia) that are much more recent than the breakup of Gondwana. A compilation of molecular phylogenetic analyses of ca 100 plant and animal groups reveals that only 10% of these are even plausibly of archaic origin dating to the vicariant splitting of Zealandia from Gondwana. Effects of lineage extinction and lack of good calibrations in many cases strongly suggest that the actual proportion is even lower, in keeping with extensive Oligocene inundation of Zealandia. A wide compilation of papers covering phylogeographic structuring of terrestrial, freshwater and marine species shows some patterns emerging. These include: east–west splits across the Southern Alps, east–west splits across North Island, north–south splits across South Island, star phylogenies of southern mountain isolates, spread from northern, central and southern areas of high endemism, and recent recolonization (postvolcanic and anthropogenic). Excepting the last of these, most of these patterns seem to date to late Pliocene, coinciding with the rapid uplift of the Southern Alps. The diversity of New Zealand geological processes (sinking, uplift, tilting, sea level change, erosion, volcanism, glaciation) has produced numerous patterns, making generalizations difficult. Many species maintain pre‐Pleistocene lineages, with phylogeographic structuring more similar to the Mediterranean region than northern Europe. This structure reflects the fact that glaciation was far from ubiquitous, despite the topography. Intriguingly, then, origins of the flora and fauna are island‐like, whereas phylogeographic structure often reflects continental geological processes.     

Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae)

Reticulate, or non-bifurcating, evolution is now recognized as an important phenomenon shaping the histories of many organisms. It appears to be particularly common in plants, especially in ferns, which have relatively few barriers to intra- and interspecific hybridization. Reticulate evolutionary patterns have been recognized in many fern groups, though very few have been studied rigorously using modern molecular phylogenetic techniques in order to determine the causes of the reticulate patterns. In the current study, we examine patterns of branching and reticulate evolution in the genus Dryopteris, the woodferns. The North American members of this group have long been recognized as a classic example of reticulate evolution in plants, and we extend analysis of the genus to all 30 species in the New World, as well as numerous taxa from other regions. We employ sequence data from the plastid and nuclear genomes and use maximum parsimony (MP), maximum likelihood (ML), Bayesian inference (BI), and divergence time analyses to explore the relationships of New World Dryopteris to other regions and to reconstruct the timing and events which may have led to taxa displaying reticulate rather than strictly branching histories. We find evidence for reticulation among both the North and Central/South American groups of species, and our data support a classic hypothesis for reticulate evolution via allopolyploid speciation in the North America taxa, including an extinct diploid progenitor in this group. In the Central and South American species, we find evidence of extensive reticulation involving unknown ancestors from Asia, and we reject deep coalescent processes such as incomplete lineage sorting in favor of more recent intercontinental hybridization and chloroplast capture as an explanation for the origin of the Latin American reticulate taxa.