New Guinea highland origin of a widespread arthropod supertramp

The biologically and geologically extremely diverse archipelagos of Wallacea, Australasia and Oceania have long stimulated ecologists and evolutionary biologists. Yet, few molecular phylogenetic analyses of the terrestrial fauna have been carried out to understand the evolutionary patterns. We use dense taxon and character sampling of more than 7000 bp DNA sequence data for a group of diving beetles ranging from the Holarctic throughout Asia to as far east as French Polynesia. We here show that an ecologically diverse, common and widespread (Portugal to New Zealand) arthropod supertramp species originated in the highlands of New Guinea, ca 6.0–2.7 Myr ago. The approximately 25 closely related species are narrow endemics in Australasia/Oceania. The ancestor of this clade colonized that region from Eurasia ca 9–7 Myr ago. Our finding contradicts the widely held view of local endemism as an evolutionary dead end, as we find multiple peripatric speciation events within the Pleistocene and complex colonization patterns between the Oriental and Australian zoogeographic regions, including the recolonization of Eurasia, jumping across Wallace''s line and colonization of continental Australia out of New Guinea. Our study strongly highlights the importance of dispersal over water gaps in shaping biogeographic patterns.     

Australian biogeographical connections and the phylogeny of large genera in the plant family Myrtaceae

Aim To compare the phylogeny of the eucalypt and melaleuca groups with geological events and ages of fossils to discover the time frame of clade divergences. Location Australia, New Caledonia, New Guinea, Indonesian Archipelago. Methods We compare published molecular phylogenies of the eucalypt and melaleuca groups of the plant family Myrtaceae with geological history and known fossil records from the Cretaceous and Cenozoic. Results The Australasian eucalypt group includes seven genera, of which some are relictual rain forest taxa of restricted distribution and others are species‐rich and widespread in drier environments. Based on molecular and morphological data, phylogenetic analyses of the eucalypt group have identified two major clades. The monotypic Arillastrum endemic to New Caledonia is related in one clade to the more species‐rich Angophora, Corymbia and Eucalyptus that dominate the sclerophyll vegetation of Australia. Based on the time of rifting of New Caledonia from eastern Gondwana and the age of fossil eucalypt pollen, we argue that this clade extends back to the Late Cretaceous. The second clade includes three relictual rain forest taxa, with Allosyncarpia from Arnhem Land the sister taxon to Eucalyptopsis of New Guinea and the eastern Indonesian archipelago, and Stockwellia from the Atherton Tableland in north‐east Queensland. As monsoonal, drier conditions evolved in northern Australia, Arnhem Land was isolated from the wet tropics to the east and north during the Oligocene, segregating ancestral rain forest biota. It is argued also that the distribution of species in Eucalyptopsis and Eucalyptus subgenus Symphyomyrtus endemic in areas north of the stable edge of the Australian continent, as far as Sulawesi and the southern Philippines, is related to the geological history of south‐east Asia‐Australasia. Colonization (dispersal) may have been aided by rafting on micro‐continental fragments, by accretion of arc terranes onto New Guinea and by land brought into closer proximity during periods of low sea‐level, from the Late Miocene and Pliocene. The phylogenetic position of the few northern, non‐Australian species of Eucalyptus subgenus Symphyomyrtus suggests rapid radiation in the large Australian sister group(s) during this time frame. A similar pattern, connecting Australia and New Caledonia, is emerging from phylogenetic analysis of the Melaleuca group (Beaufortia suballiance) within Myrtaceae, with Melaleuca being polyphyletic. Main conclusion The eucalypt group is an old lineage extending back to the Late Cretaceous. Differentiation of clades is related to major geological and climatic events, including rifting of New Caledonia from eastern Gondwana, development of monsoonal and drier climates, collision of the northern edge of the Australian craton with island arcs and periods of low sea level. Vicariance events involve dispersal of biota.     

Phylogeny and biogeography of Chinese and Australasian Polystichum ferns as inferred from chloroplast trnL-F and rps4-trnS sequence data

Polystichum, one of the largest genera of ferns, occurs worldwide with the greatest diversity in southwest China and adjacent regions. Although there have been studies of Chinese Polystichum on its traditional classification, geographic distributions, and even a few on its molecular systematics, its relationships to other species outside China remain little known. Here, we investigated the phylogeny and biogeography of the Polystichum species from China and Australasia. The evolutionary relationships among 42 Polystichum species found in China (29 taxa) and Australasia (13 taxa) were inferred from phylogenetic analyses of two chloroplast DNA sequence data sets: rps4-trnS and trnL-F intergenic spacers. The divergence time between Chinese and Australasian Polystichum was estimated. The results indicated that the Australasian species comprise a monophyletic group that is nested within the Chinese diversity, and that the New Zealand species are likewise a monophyletic group nested within the Australasian species. The divergence time estimates suggested that Chinese Polystichum migrated into Australasia from around 40 Ma ago, and from there to New Zealand from about 14 Ma. The diversification of the New Zealand Polystichum species began about 10 Ma. These results indicated that Polystichum probably originated in eastern Asia and migrated into Australasia: first into Australia and then into New Zealand.     

The origin and evolution of Indomalesian,Australasian and Pacific island biotas: insights from Aglaieae (Meliaceae,Sapindales)

Aim The role of long‐distance dispersal in the Indomalesian, Australasian and Pacific flora is currently hotly debated. The lack of well‐resolved phylogenetic trees for Pacific plants has been a major limitation for biogeographical analysis. Here, we present a well‐resolved phylogenetic tree for the tribe Aglaieae in the mahogany family, Meliaceae, and use it to investigate the origin, evolution and dispersal history of biotas in this area. The subfamily Melioideae, including the tribe Aglaieae (Meliaceae, Sapindales), is a plant group with good representation in the region in terms of biomass and species numbers, wide ecological attributes and known animal vectors. The family has a good fossil record (especially from North America and Europe). Genera and species in the tribe Aglaieae therefore provide an excellent model group for addressing this debate. Location Indomalesia, Australasia, Pacific islands. Methods Results from nuclear internal transcribed spacer ribosomal DNA analyses of 82 taxa, based on sequence alignment guided by secondary structure models, were combined with evidence from fossils and distribution data. We used strict and relaxed molecular clock approaches to estimate divergence times within Aglaieae. Putative ancestral areas were investigated through area‐based and event‐based biogeographical approaches. Information on dispersal routes and their direction was inferred from the investigation of dispersal asymmetries between areas. Results Our study indicates that the crown group of Aglaieae dates back at least to the Late Eocene, with major divergence events occurring during the Oligocene and Miocene. It also suggests that dispersal routes existed during Miocene–Pliocene times from the area including Peninsular Malaysia, Sumatra and Borneo to Wallacea, India and Indochina, and from the area including New Guinea, New Ireland and New Britain further east to the Pacific islands at the peripheries of the distribution range. The origin of the Fijian species dates back to the Pliocene. Main conclusions Dispersal over oceanic water barriers has occurred during geological time and seems to have been a major driving force for divergence events in Aglaieae, with some old Gondwanan land masses (e.g. Australia) colonized only during recent times. Movement from the ancestral area was predominantly towards the east. Extant Fijian species of Aglaia are monophyletic and share morphological features rarely found in species of other areas, suggesting speciation within an endemic clade. Divergence of living taxa from their closest living relatives took place during both the Miocene and the Pliocene, and peaked in the Pliocene. The present‐day distribution of many species in the tribe must therefore have arisen as a result of dispersal rather than vicariance events. Furthermore, colonization from Indomalesia to Australasia and the Pacific has frequently been followed by speciation.     

Phylogeography of the pademelons (Marsupialia: Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio‐Pleistocene

Aim Alternative hypotheses concerning genetic structuring of the widespread endemic New Guinean forest pademelons (Thylogale) based on current taxonomy and zoogeography (northern, southern and montane species groupings) and preliminary genetic findings (western and eastern regional groupings) are investigated using mitochondrial sequence data. We examine the relationship between the observed phylogeographical structure and known or inferred geological and historical environmental change during the late Tertiary and Quaternary. Location New Guinea and associated islands. Methods We used primarily museum specimen collections to sample representatives from Thylogale populations across New Guinea and three associated islands. Mitochondrial cytochrome b and control region sequence data were used to construct phylogenies and estimate the timing of population divergence. Results Phylogenetic analyses indicated subdivision of pademelons into ‘eastern’ and ‘western’ regional clades. This was largely due to the genetic distinctiveness of north‐eastern and eastern peninsula populations, as the ‘western’ clade included samples from the northern, southern and central regions of New Guinea. Two tested island groups were closely related to populations north of the Central Cordillera; low genetic differentiation of pademelon populations between north‐eastern New Guinea and islands of the Bismarck Archipelago is consistent with late Pleistocene human‐mediated translocations, while the Aru Islands population showed divergence consistent with cessation of gene flow in the mid Pleistocene. There was relatively limited genetic divergence between currently geographically isolated populations in subalpine and nearby mid‐montane or lowland regions. Main conclusions Phylogeographical structuring does not conform to zoogeographical expectations of a north/south division across the cordillera, nor to current species designations, for this generalist forest species complex. Instead, the observed genetic structuring of Thylogale populations has probably been influenced by geological changes and Pleistocene climatic changes, in particular the recent uplift of the north‐eastern Huon Peninsula and the lowering of tree lines during glacial periods. Low sea levels during glacial maxima also allowed gene flow between the continental Aru Island group and New Guinea. More work is needed, particularly multi‐taxon comparative studies, to further develop and test phylogeographical hypotheses in New Guinea.     

Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus,Gekkonidae, Squamata)

Oliver, P.M., Richards, S.J. & Sistrom, M. (2012). Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata). —Zoologica Scripta, 41, 437–454. The systematics and biogeographical history of the diverse fauna of New Guinea and surrounding islands (Melanesia) remain poorly known. We present a phylogeny for 16 of the 21 recognised Melanesian bent‐toed geckos in the genus Cyrtodactylus based on mitochondrial sequence data. These analyses reveal two divergent lineages of Cyrtodactylus within Melanesia. One includes a single recognised species with clear affinities to sampled taxa from Asia. The other comprises a relatively diverse radiation (likely 30+ species), not closely related to sampled extralimital taxa and centred on the Melanesian region (including Australia). Many taxa within this second lineage are endemic to islands surrounding New Guinea, and dispersal and speciation on peripheral islands appears to have played an important role in the accumulation of species diversity within this clade. In contrast, little diversity is centred upon montane areas, although we do identify at least one lineage closely associated with hill and lower montane forest that probably dates to at least the late Miocene. Our phylogenetic analyses also reveal numerous divergent lineages that require taxonomic attention, including at least two widespread taxa that are likely to be composite, additional specimens of Cyrtodactylus capreoloides (until recently known only from the holotype) and several divergent and completely novel lineages, two of which we introduce herein: Cyrtodactylus arcanus sp. n. and Cyrtodactylus medioclivus sp. n.     

Sphagnum in peatlands of Australasia: Their distribution,utilisation and management

In comparison to the northern hemisphere, Sphagnum peatlands are an unusual andinfrequent component of the Australasianlandscape. Most peatlands in Australasiaare primarily composed of eitherRestionaceous or Cyperaceous peats. Sphagnum peatlands in Australia and PapuaNew Guinea/Irian Jaya (now West Papua) arelargely located in montane and alpineenvironments, but also occur down to sealevel in New Zealand and as moss patches onsome subantarctic islands. Fire is a majordeterminant of the characteristics ofpeatlands in Australasia. Peatlandmanagement in Australasia is hindered bythe need for increased understanding ofpeatland processes to enable a sustainablebalance of conservation of a small resourcewith localised utilisation. Themanagement focus in Australasia has largelybeen on ensuring ecologically sustainable Sphagnum moss harvesting, withlimited peat mining. We have found thatgeneral recovery of Sphagnum after moss harvesting canbe enhanced by harvesting larger peatlands,and by leaving one-third of the acrotelm toregenerate. The largest upland peat swampin mainland Australia, Wingecarribee Swamp,suffered a major collapse in 1998 followingpeat mining. Environmental and managementconsequences of this collapse have majorramifications for rehabilitation options. Sphagnum peatlands in Australasia arelikely to be adversely affected bydrainage, burning, grazing, trampling,global warming and peat mining.     

Zoogeography and relationships of Australasian skates (Chondrichthyes: Rajidae)

Aim To investigate distributional patterns and derivation of skates in the Australasian realm. Location Australasia. Methods Genus‐group skate taxa were defined for this region for the first time and new systematic information, as well as bathymetric and geographical data, used to identify distribution patterns. Results The extant skate fauna of Australasia (Australia, New Zealand, New Caledonia and adjacent subAntarctic dependencies) is highly diverse and endemic with sixty‐two species from twelve currently recognized, nominal genus‐group taxa. These include the hardnose skate (rajin) groups Anacanthobatis, Amblyraja, Dipturus, Okamejei, Rajella and Leucoraja, and softnose skate (arhynchobatin) genera Arhynchobatis, Bathyraja, Insentiraja, Irolita, Pavoraja and Notoraja. Additional new and currently unrecognized nominal taxa of both specific and supraspecific ranks also occur in the region. The subfamily Arhynchobatinae is particularly speciose in Australasia, and the New Zealand/New Caledonian fauna is dominated by undescribed supraspecific taxa and species. The Australian fauna, although well represented by arhynchobatins, is dominated by Dipturus‐like skates and shows little overlap in species composition with the fauna of New Zealand and New Caledonia. Similarly, these faunas exhibit no overlap with the polar faunas of the Australian subAntarctic dependencies (Heard and Macdonald Islands) to the south. Skates appear to be absent from the Macquarie Ridge at the southern margin of the New Zealand Plateau. Their absence off New Guinea probably reflects inadequate sampling and the subsequent poor knowledge of that region's deepwater fish fauna. Main conclusions Skates appear to have existed in the eastern, Australasian sector of Gondwana before fragmentation in the late Cretaceous. The extant fauna appears to be derived from elements of Gondwanan origin, dispersal from the eastern and western Tethys Sea, and intraregional vicariance speciation.     

Mitochondrial DNA variability of West New Guinea populations.

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.     

Population structure and biogeography of Hemiphaga pigeons (Aves: Columbidae) on islands in the New Zealand region

Aim The New Zealand avifauna includes lineages that lack close relatives elsewhere and have low diversity, characteristics sometimes ascribed to long geographic isolation. However, extinction at the population and species levels could yield the same pattern. A prominent example is the ecologically important pigeon genus Hemiphaga. In this study, we examined the population structure and phylogeography of Hemiphaga across islands in the region. Location New Zealand, Chatham Islands and Norfolk Island. Methods Mitochondrial DNA was sequenced for all species of the genus Hemiphaga. Sixty‐seven individuals from mainland New Zealand (Hemiphaga novaeseelandiae novaeseelandiae), six of the Chatham Islands sister species (Hemiphaga chathamensis), and three of the extinct Norfolk Island subspecies (Hemiphaga novaeseelandiae spadicea) were included in this study. Novel D‐loop and cytochrome b primers were designed to amplify DNA from museum samples. Additionally, five other mitochondrial genes were used to examine placement of the phylogenetic root. Results Analyses of mitochondrial DNA sequences revealed three Hemiphaga clades, consistent with the allopatric populations of recognized (sub)species on oceanic islands. Of the 23 D‐loop haplotypes among 67 New Zealand pigeons (Hemiphaga n. novaeseelandiae), 19 haplotypes were singletons and one haplotype was common and widespread. Population genetic diversity was shallow within and between New Zealand populations, indicating range expansion with high inter‐population exchange. Tentative rooting of the Hemiphaga clade with cyt b data indicates exchange between mainland New Zealand and the Chatham Islands prior to colonization of Norfolk Island. We found low genetic divergence between populations on New Zealand, the Chatham Islands and Norfolk Island, but deep phylogenetic divergence from the closest living relatives of Hemiphaga. Main conclusions The data are consistent with the hypothesis of population reduction during the Pleistocene and subsequent expansion from forest refugia. Observed mobility of Hemiphaga when feeding helps explain the shallow diversity among populations on islands separated by many hundreds of kilometres of ocean. Together with comparison of distribution patterns observed among birds of the New Zealand region, these data suggest that endemicity might represent not long occupancy of an area, but descent from geologically recent colonizations. We consider the role of lineage pruning in creating the impression of old endemicity.     

Diploid hybrid origin of Hippophaë gyantsensis (Elaeagnaceae) in the western Qinghai–Tibet Plateau

Homoploid hybrid speciation, the origin of a hybrid species without change in chromosome number, is currently considered to be a rare form of speciation. In the present study, we examined the phylogenetic origin of Hippophaë gyantsensis, a diploid species occurring in the western Qinghai–Tibet Plateau. Some of its morphological and molecular traits suggest a close relationship to H. rhamnoides ssp. yunnanensis while others indicate H. neurocarpa. We conducted phylogenetic analyses of sequence data of two maternally inherited chloroplast (cp) DNA fragments and the bi‐parentally inherited nuclear ribosomal internal transcribed spacer (ITS) from 17 populations of H. gyantsensis, 15 populations of H. rhamnoides ssp. yunnanensis and 27 populations of H. neurocarpa across their distributional ranges, and modelled the niche differentiation of the three taxa. Multiple lines of evidence suggested that H. gyantsensis is a morphologically stable, genetically independent and ecologically distinct species. The inconsistent phylogenetic placements of the H. gyantsensis clade that comprised the dominant cpDNA haplotypes and ITS ribotypes suggested a probable diploid hybrid origin from multiple crosses between H. rhamnoides ssp. yunnanensis and H. neurocarpa. This tentative hypothesis is more parsimonious than alternative explanations according to the data available, although more evidence based on further testing is needed.     

Scrophularia arguta,a widespread annual plant in the Canary Islands: a single recent colonization event or a more complex phylogeographic pattern?

Many studies have addressed evolution and phylogeography of plant taxa in oceanic islands, but have primarily focused on endemics because of the assumption that in widespread taxa the absence of morphological differentiation between island and mainland populations is due to recent colonization. In this paper, we studied the phylogeography of Scrophularia arguta, a widespread annual species, in an attempt to determine the number and spatiotemporal origins of dispersal events to Canary Islands. Four different regions, ITS and ETS from nDNA and psbA‐trnH and psbJ‐petA from cpDNA, were used to date divergence events within S. arguta lineages and determine the phylogenetic relationships among populations. A haplotype network was obtained to elucidate the phylogenetic relationships among haplotypes. Our results support an ancient origin of S. arguta (Miocene) with expansion and genetic differentiation in the Pliocene coinciding with the aridification of northern Africa and the formation of the Mediterranean climate. Indeed, results indicate for Canary Islands three different events of colonization, including two ancient events that probably happened in the Pliocene and have originated the genetically most divergent populations into this species and, interestingly, a recent third event of colonization of Gran Canaria from mainland instead from the closest islands (Tenerife or Fuerteventura). In spite of the great genetic divergence among populations, it has not implied any morphological variation. Our work highlights the importance of nonendemic species to the genetic richness and conservation of island flora and the significance of the island populations of widespread taxa in the global biodiversity.     

Population genetic analyses of Plasmodium falciparum chloroquine receptor transporter gene haplotypes reveal the evolutionary history of chloroquine-resistant malaria in India

Inferring the origin and dispersal of the chloroquine-resistant (CQR) malaria parasite, Plasmodium falciparum, is of academic and public health importance. The Pfcrt gene of P. falciparum is widely known as the CQR gene and two major haplotypes of this gene (CVIET and SVMNT) occur widely across CQR-endemic regions of the globe. In India, studies to date of the Pfcrt gene have indicated the widespread prevalence of the SVMNT haplotype (prevalent in the South America and Papua New Guinea), whereas the CVIET haplotype, primarily found in southeast Asia, was not detected at a high frequency in India. This distribution pattern of the two most common CQR-Pfcrt haplotypes in India is quite surprising. Thus, in order to understand probable evolutionary and migration patterns of the CQR-Pfcrt haplotypes into India, we generated new sequence data of exon 2 of the Pfcrt gene and collected published information on the CQR-Pfcrt haplotype data from India, Papua New Guinea, southeast Asia and South America, and performed several population and evolutionary genetic analyses. Among several interesting findings, statistically significant longitudinal clines for the CVIET and SVMNT haplotypes (in opposite directions) in India, and the clustering of India and Papua New Guinea under the SVMNT-specific clade in the phylogenetic tree, are the two most remarkable aspects of the data. It also appears that both the SVMNT and CVIET haplotypes in India have migrated from southeast Asia. In particular, whereas the Indian CVIET haplotype has a southeast Asian origin, the SVMNT haplotype, prevalent in India, seems to have originated in Papua New Guinea and entered India through southeast Asia.     

Genetic structure of Micromeria (Lamiaceae) in Tenerife,the imprint of geological history and hybridization on within‐island diversification

Geological history of oceanic islands can have a profound effect on the evolutionary history of insular flora, especially in complex islands such as Tenerife in the Canary Islands. Tenerife results from the secondary connection of three paleo‐islands by a central volcano, and other geological events that further shaped it. This geological history has been shown to influence the phylogenetic history of several taxa, including genus Micromeria (Lamiaceae). Screening 15 microsatellite markers in 289 individuals representing the eight species of Micromeria present in Tenerife, this study aims to assess the genetic diversity and structure of these species and its relation with the geological events on the island. In addition, we evaluate the extent of hybridization among species and discuss its influence on the speciation process. We found that the species restricted to the paleo‐islands present lower levels of genetic diversity but the highest levels of genetic differentiation suggesting that their ranges might have contracted over time. The two most widespread species in the island, M. hyssopifolia and M. varia, present the highest genetic diversity levels and a genetic structure that seems correlated with the geological composition of the island. Samples from M. hyssopifolia from the oldest paleo‐island, Adeje, appear as distinct while samples from M. varia segregate into two main clusters corresponding to the paleo‐islands of Anaga and Teno. Evidence of hybridization and intraspecific migration between species was found. We argue that species boundaries would be retained despite hybridization in response to the habitat's specific conditions causing postzygotic isolation and preserving morphological differentiation.     

South Pacific biogeography,tectonic calibration,and pre‐drift tectonics: cladogenesis in Abrotanella (Asteraceae)

Abrotanella is the basal genus in the large tribe Senecioneae (Asteraceae) and has a disjunct distribution in Australasia and South America. A recent molecular phylogeny of the genus was used to investigate whether the main biogeographical patterns in the group could be related to the region's tectonic history in a coherent way. The phylogenetic/biogeographical breaks and overlaps in the genus imply a series of vicariance and range expansion events. Each of these can be related to one of the main tectonic events in the region, including assembly of the New Zealand terranes, crustal extension, and magmatism in Gondwana that preceded seafloor spreading, opening of the Tasman and Pacific basins, and transcurrent movement on the New Zealand Alpine fault. The coincident sequence indicates that pre‐drift tectonics and magmatism have been more important for the origin of trans‐Tasman and trans‐Pacific groups than the final rifting of Gondwana that led to their disjunction. For example, during the pre‐drift phase of break‐up, the Whitsunday volcanic province of Australia and the Median Batholith of New Zealand formed a large, active igneous belt. Its distribution is aligned with the break between New Zealand–south‐eastern Australia clades, and New Zealand–New Guinea clades. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Genetic differentiation in the Trinidad endemic Mannophryne trinitatis (Anura: Aromobatidae): Miocene vicariance,in situ diversification and lack of geographical structuring across the island

Trinidad offers a unique study system within the Caribbean to assess the processes and patterns of amphibian speciation. We used mitochondrial DNA sequences to investigate the phylogenetic relationships and patterns of intraspecific genetic variation of Mannophryne trinitatis from Trinidad. Molecular clock estimates point to a genetic split between M. trinitatis and its sister species, M. venezuelensis, dating to the Late Miocene (c. 7–8 Mya), suggesting vicariance as a means of speciation when Trinidad pulled apart from northern Venezuela. M. trinitatis phylogenetic population analyses from ten Northern Range and four Central Range localities recovered three well‐resolved clades: a larger clade formed by haplotypes from Northern Range localities and two additional clades, one formed by haplotypes from the Central Range and another including haplotypes from Northern Range localities and one haplotype from the Central Range. Overall, our results show that the genetic diversity in M. trinitatis is not geographically structured but it is distributed among the various Northern and Central Range localities. In congruence with the vicariance speciation hypothesis, we attribute M. trinitatis present distribution and lack of genetic structure to multiple admixture events caused by climate changes that severely affected the topology of Trinidad throughout the Pliocene/Pleistocene periods.     

A curious coincidence: mosquito biodiversity and the limits of the Japanese encephalitis virus in Australasia

Background  

The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is the major vector of endemic arboviruses in Australia and is also responsible for the establishment of the Japanese encephalitis virus (JEV) in southern Papua New Guinea (PNG) as well as its incursions into northern Australia. Papua New Guinea and mainland Australia are separated by a small stretch of water, the Torres Strait, and its islands. While there has been regular JEV activity on these islands, JEV has not established on mainland Australia despite an abundance of Cx. annulirostris and porcine amplifying hosts. Despite the public health significance of this mosquito and the fact that its adults show overlapping morphology with close relative Cx. palpalis Taylor, its evolution and genetic structure remain undetermined. We address a hypothesis that there is significant genetic diversity in Cx. annulirostris and that the identification of this diversity will shed light on the paradox that JEV can cycle on an island 70 km from mainland Australia while not establishing in Australia itself.     

Vicariance of Pyrocoelia fireflies (Coleoptera: Lampyridae) in the Ryukyu islands,Japan

We performed molecular phylogenetic analyses based on the mitochondrial COI gene (687 bp) and the nuclear 28S rRNA gene (715 bp) and reconstructed phylogenetic trees of the Pyrocoelia fireflies in the Ryukyu Islands and eastern Asia. Age calibration was done using a robust geological constraint: the Okinawa trough and associated straits began to rift at 1.55 Ma, isolating the Ryukyu Islands from the Chinese continent, Japanese islands, Taiwan island and some of the islands from each other. We suggest that the physical isolation of these islands began to generate the allopatric speciation within these islands, so the timing of this isolation was assigned to an appropriate node. The topology is completely concordant among phylogenetic trees reconstructed using MEGA (maximum‐likelihood), raxmlGUI (maximum‐likelihood) and BEAST (Bayesian inference; including combined analysis of COI and 28S rRNA genes). Two lineages are recognized, related to their emergence time; spring to summer, and autumn. In each lineage, vicariance is inferred to have begun at 1.55 Ma from our phylogenetic and geological analyses. In lineage 1, P. oshimana (Amami), P. matsumurai (Okinawa), P. discicollis (W. Japan), P. fumosa (E. Japan) and P. abdominalis (Yaeyama) were differentiated. In lineage 2, P. rufa (Tsushima and Korea), P. miyako (Miyako‐jima), P. atripennis (Ishigaki‐jima) and P. praetexta (Taiwan and HongKong) were differentiated. Pyrocoelia analis (Taiwan and China) emerges throughout the year except for winter, and constitutes another lineage. We suggest that Pyrocoelia fireflies differentiated at 2 Ma to generate these three lineages. The base substitution rate for the COI gene is estimated as 4.48% Myr^–1 and that for the 28S rRNA gene is 0.394%  Myr^–1, and these rates were used in a combined BEAty analysis in BEAST.     

Connectivity,small islands and large distances: the Cellana strigilis limpet complex in the Southern Ocean

The Southern Ocean contains some of the most isolated islands on Earth, and fundamental questions remain regarding their colonization and the connectivity of their coastal biotas. Here, we conduct a genetic investigation into the Cellana strigilis (limpet) complex that was originally classified based on morphological characters into six subspecies, five of which are endemic to the New Zealand (NZ) subantarctic and Chatham islands (44–52°S). Previous genetic analyses of C. strigilis from six of the seven island groups revealed two lineages with little or no within‐lineage variation. We analysed C. strigilis samples from all seven island groups using two mitochondrial (COI and 16S), one nuclear (ATPase β) and 58 loci from four randomly amplified polymorphic DNA markers (RAPDs) and confirmed the existence of two distinct lineages. The pronounced genetic structuring within each lineage and the presence of private haplotypes in individual islands are the result of little genetic connectivity and therefore very high self‐recruitment. This study supports the significance of the subantarctic islands as refugia during the last glacial maximum and adds to the knowledge of contemporary population connectivity among coastal populations of remote islands in large oceans and the distance barrier to gene flow that exists in the sea (despite its continuous medium) for most taxa.     

Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea

We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.