Genetic variability,local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South‐East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South‐East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. F_ST and principal components analysis revealed striking divergence between South‐East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South‐East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South‐East Asia during mid‐Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid‐Pleistocene.     

Contributions to the Cladocera fauna from Papua New Guinea

Twenty-eight taxa of the Cladocera are identified in collections from Papua New Guinea, 17 being new records for New Guinea, bringing the total number of Cladocera taxa reported for this region to 39. Most of the taxa are circumtropical. One species (Sarsilatona papuana) is endemic to Papua New Guinea and northern Australia. The species list includes two species that are normally listed as Holarctic:Alonella nana andAlona rustica. Widespread genera such asDaphnia, Pleuroxus, Disparalona, Acroperus were strikingly absent from the Papua New Guinean material.     

COLOR PATTERN EVOLUTION,ASSORTATIVE MATING,AND GENETIC DIFFERENTIATION IN BRIGHTLY COLORED BUTTERFLYFISHES (CHAETODONTIDAE)

In butterflyfishes (Chaetodontidae), color pattern evolves rapidly and is often the only morphological trait separating closely related species. Vivid coloration is frequently assumed to provide critical signals for mate recognition and mate choice, but few direct experimental tests are available. Here we analyze the relationship between color pattern change, mate choice, and genetic differentiation in a group of three very closely related allopatric butterflyfishes. We found that in only one member of this group, Chaetodon multicinctus, is color pattern evolution associated with mate preference and genetic divergence. For its two sister species, C. punctatofasciatus and C. pelewensis, color pattern change has not resulted in assortative mating (based on laboratory pairing experiments and field observations) or in significant mtDNA or allozyme differentiation. In a contact zone on reefs in the Solomon Islands and Papua New Guinea, hybridization between the two forms has nearly homogenized color pattern differences. Outside these areas, however, color pattern remains distinct. Genetic variation is homogeneous over a much larger geographic scale. Sequence variation in the tRNA-proline end of the mitochondrial control region and allozyme variation was distributed widely within C. punctatofasciatus and C. pelewensis, which suggests few constraints to mitochondrial or nuclear gene flow across the color pattern boundary. These contrasting patterns strongly suggest that selection is maintaining color pattern differences in allopatry in the face of potentially homogenizing levels of gene flow. The mating pattern data show that this selection is not operating on mate recognition in the strictest sense, but probably on some other aspect of the social system of these territorial fish. In this case, divergence in mating preference can follow color pattern evolution, but is not contemporaneous with it.     

Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity

New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria‐transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.     

Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South‐West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high‐elevation, semi‐aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each situated on islands on either side of Wallace's Line. One radiation is composed of Philippine species of Platymantis and the other contains all taxa from the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian archipelagos. Several additional genera (Batrachylodes, Discodeles, Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of these Batrachylodes and Discodeles are nonmonophyletic. To address the widespread paraphyly of the genus Platymantis and several additional nomenclatural issues, we undertook a wholesale nomenclatural reorganization of the family. Given our partially unresolved phylogeny, and in order to impart a conservative, stable taxonomy, involving a minimal number of genus‐species couplet changes, we propose a conservative classification representing a few compromises. These changes are designed to preserve maximally the presumed original intent of taxonomy (widely used group names associated with morphological and ecological diversity of particular species or groups of species) while implementing a hierarchical system that is consistent with the estimate of phylogeny based on new molecular data. © 2015 The Linnean Society of London     

Molecular Relationships of the New Guinean Bandicoot Genera Microperoryctes and Echymipera (Marsupialia: Peramelina)

The complete 12S rRNA gene was sequenced for multiple exemplars of the New Guinean bandicoot genera Microperoryctes and Echymipera representing many of the currently recognized subspecies. These two genera are resolved as monophyletic sister taxa but there was no genetic support for the family Peroryctidae proposed by Groves and Flannery (1990). Within Microperoryctes, M. papuensis was sister to M. longicauda. Although there was only weak support for recognition of the subspecies M. l. magnus, our results demonstrate the need for further genetic and morphological studies of variation among populations of Microperoryctes. Haplotype relationships within Echymipera did not reflect current species boundaries. Although E. clara was the most divergent species, no clear separation could be made between E. rufescens and E. kalubu (E. kalubu samples from New Britain were consistently more closely allied with the E. rufescens exemplars collected from north and east of the Central Cordillera than with their congeners). We suggest the need for a major morphological reassessment of New Guinean bandicoot relationships.     

High species richness and genetic diversity of the genus Caloglossa (Delesseriaceae,Rhodophyta) in New Ireland,Papua New Guinea

Distribution patterns and genetic diversity of Caloglossa species have been studied in various regions but are still poorly understood around the tropical western Pacific where many marine organisms show high species richness. We explored the diversity of Caloglossa species in New Ireland, Papua New Guinea using morphological and genetic analyses. Seven species of Caloglossa (C. adhaerens, C. leprieurii, C. ogasawaraensis, C. bengalensis, C. postiae, C. saigonensis and C. vieillardii) were collected from eight sites; the latter four species are new records in Papua New Guinea. All specimens collected were cultured to compare their morphology under the same culture condition. Reproductive structures of gametophytes and/or sporophytes were described for the first time in some species from these collections. In C. leprieurii, gall‐like structure appeared in most gametophyte strains but not in tetrasporophytes. Such galls were produced from wing cells, and spermatangia and/or procarps were formed on many galls. The LSU rDNA and rbcL analyses revealed high intraspecific diversity in many species although the number of samples was limited and the sampling sites were within 200 km. We revealed high species richness and intraspecific genetic variation in Papua New Guinea, suggesting a hot spot for the diversity of Caloglossa.     

Two unusual species of <Emphasis Type="Italic">Physalacria</Emphasis> (Basidiomycetes,Agaricales) collected in New Zealand and Papua New Guinea during mycological expeditions by the National Science Museum,Tokyo

Two unusual species of Physalacria from New Zealand and Papua New Guinea are described and illustrated. Physalacria pseudotropica from South Island in New Zealand and P. tropica from Papua New Guinea are recorded for the first time.     

Multilocus population genetic analysis of the Southwest Pacific malaria vector Anopheles punctulatus

The population structure and history of the cryptic malaria vector species, Anopheles punctulatus (Doenitz), was investigated throughout Papua New Guinea and the Solomon Islands with the aim of detailing genetic subdivisions and the potential for movement through this biogeographically complex region. We obtained larval collections from over 80 sites and utilised a diverse array of molecular markers that evolve through different processes. Individuals were initially identified to species and genotyped using the ribosomal DNA second internal transcribed spacer. DNA sequencing of a single copy nuclear ribosomal protein S9 and the mitochondrial cytochrome oxidase I loci were then investigated and 12 nuclear microsatellite markers were developed and analysed. Our data revealed three genetically distinct populations – one in Papua New Guinea, the second on Buka Island (Bougainville Province, Papua New Guinea), and the third on Guadalcanal Island (Solomon Islands). Genetic differentiation within Papua New Guinea was much lower than that found in studies of other closely related species in the region. The data does suggest that A. punctulatus has undergone a population bottleneck followed by a recent population and range expansion in Papua New Guinea. Humans and regional economic growth may be facilitating this population expansion, as A. punctulatus is able to rapidly occupy human modified landscapes and traverse unsealed roads. We therefore anticipate extensive movement of this species through New Guinea – particularly into the highlands, with a potential increase in malaria frequency in a warming climate – as well as relatively unrestricted gene flow of advantageous alleles that may confound vector control efforts.     

The Strongylophthalmyiidae (Diptera) of Papua New Guinea,with descriptions of five new species and a world checklist

Eight species of the Strongylophthalmyiidae are reported from Papua New Guinea. Of these, five species (Strongylophthalmyia gigantica sp. nov., S. papuana sp. nov., S. rubella sp. nov., S. sedlaceki sp. nov. and S. shatalkini sp. nov.) are described as new to science. Strongylophthalmyia puncticollis Frey is recorded for the first time from Papua New Guinea. Faunistic remarks, a key to the species of the Strongylophthalmyia in Papua New Guinea and a world checklist are provided.     

A remarkable new genus of Braconini (Hymenoptera: Braconidae: Braconinae) from Papua New Guinea,reared from fallen fruit

During an investigation of the insect food web in Papua New Guinea several specimens of a new genus and species of large, black and orange braconine braconid wasp were reared from fruits of Rubiaceae. These are described here as Karposibracon papuensis Quicke & Butcher gen. et sp. nov. Karposibracon gen. nov. appears to belong to the tribe Braconini and is the largest known species in this group, with body length up to 12?mm. The new genus is illustrated photographically, distinguished from other genera, and comments are on its likely biology provided.     

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.     

A revision of Ptychopyxis (Euphorbiaceae) in southeast Asia

Ptychopyxis is a genus comprised of 11 species. Nine are found in southeast Asia mainland and west Malesia and two species are endemic to New Guinea. One of the endemic New Guinean species is newly described here, viz. P. esdras Stoops sp. nov.     

Local versus regional species richness in tropical insects: one lowland site compared with the island of New Guinea

1. The overlap in species composition of Cercopoidea (Aphrophoridae, Cercopidae, and Machaerotidae), Flatidae, and Ricaniidae between two data sets, an almost exhaustive census from 13 Ficus species and a sample from diverse vegetation in the same area, led to the estimate for local species richness of 111 (SE 11.5) species (45 species of Cercopoidea, 36 species of Flatidae, and 30 species of Ricaniidae) at a lowland rainforest site in New Guinea. 2. Samples restricted to 13 species of Ficus contained 66 species, i.e. 59% of the estimated local species richness. This high proportion probably results from the high proportion of polyphagous and tourist (transient) species in the Cercopoidea, Flatidae, and Ricaniidae. 3. The two largest museum collections of New Guinean insects contained 327 species of Cercopoidea from New Guinea, including 23 of the 34 species collected in the field samples. This overlap led to the estimate of 483 (SE 97.2) species of Cercopoidea present in New Guinea. 4. The species found in the field samples were also 2.6 times more likely to be found in the museum collection than other species. This sampling bias can be due to a positive correlation between species local abundance and geographic distribution and/or similar patterns of species abundance at different sites. 5. The estimate of species richness of Cercopoidea in New Guinea increased to 1222 species when corrected for this sampling bias. Thus, only 4% of the New Guinean species were present locally, in the study area. Such high beta diversity is probably a consequence of the exceptional habitat and vegetation diversity in New Guinea, as well as its complex geological history.     

Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae)

Bryant, L. M., Donnellan, S. C., Hurwood, D. A. & Fuller, S. J. (2011). Phylogenetic relationships and divergence date estimates among Australo‐Papuan mosaic‐tailed rats from the Uromys division (Rodentia: Muridae). —Zoologica Scripta, 40, 433–447. We inferred phylogenetic relationships and divergence date estimates among four genera of mosaic‐tailed rats from the Uromys division in Australia, New Guinea and the Solomon Islands from both mitochondrial (16S rRNA) and nuclear (AP5 and DHFR introns) nucleotide sequence data. Phylogenetic analysis of our combined data shows that Melomys species from Australia and New Guinea are monophyletic to the exclusion of Paramelomys, which last shared a common ancestor with other members of the Uromys division approximately 3 MYA. However, Melomys was found to be paraphyletic with respect to the Solomon Islands endemic Solomys, suggesting the taxonomic distinction of the latter may need revision. The radiation of this group was estimated to have occurred between 2.1 MYA and 900 000 years ago. A currently undescribed taxon, species nova, which is apparently morphologically indistinguishable from sympatric M. cervinipes, was found to be a highly distinctive lineage and was not monophyletic with Melomys from Australia or New Guinea. Australian Uromys share a sister group relationship with sp. n. and the Melomys/Solomys clade. Australian Melomys were not monophyletic with respect to New Guinean Melomys. The New Guinean M. lutillus and Australian M. burtoni appear to be conspecific, supporting a previous suggestion that M. burtoni has an extralimital distribution encompassing New Guinea as M. lutillus. This also suggests sustained contact between these taxa, most likely enabled through historical landbridges that linked the two landmasses during periods of lower sea level. Melomys rubicola, found only on Bramble Cay, 50 km south of New Guinea, is more closely related to Australian Melomys, particularly M. capensis, than to any of the New Guinean species. Results suggest that M. rubicola and M. capensis last shared a common ancestor in the early Pleistocene, a time when land bridges existed connecting Bramble Cay to Cape York. Finally, polyphyly within M. cervinipes was also detected, corresponding to reciprocally monophyletic northern and southern clades. The northern M. cervinipes clade diverged from the M. capensis/rubicola clade approximately 1.2 MYA, with this split possibly resulting from isolation across the Normanby gap in far north Queensland.     

Musaespora,a genus of pyrenocarpous lichens with campylidia,and other additions to the foliicolous lichen flora of New Guinea

Abstract: The new lichen genus Musaespora is described from Java and Papua New Guinea. It is the first known pyrenocarpous lichen genus with campylidia, and appears to belong to the Aspidotheliaceae. Three species are described, two foliicolous species from Papua New Guinea and one corticolous species from Java. In addition, a list is given of the foliicolous lichen flora of the site in Papua New Guinea, where the foliicolous Musaespora species have been found, two more new foliicolous species are described, Echinoplaca hispida and Sporopodium lucidum, and 19 species are recorded for the first time form Papua New Guinea.     

Characterization of population structure from the mitochondrial DNA vis‐à‐vis language and geography in Papua New Guinea

Situated along a corridor linking the Asian continent with the outer islands of the Pacific, Papua New Guinea has long played a key role in understanding the initial peopling of Oceania. The vast diversity in languages and unique geographical environments in the region have been central to the debates on human migration and the degree of interaction between the Pleistocene settlers and newer migrants. To better understand the role of Papua New Guinea in shaping the region's prehistory, we sequenced the mitochondrial DNA (mtDNA) control region of three populations, a total of 94 individuals, located in the East Sepik Province of Papua New Guinea. We analyzed these samples with a large data set of Oceania populations to examine the role of geography and language in shaping population structure within New Guinea and between the region and Island Melanesia. Our results from median‐joining networks, star‐cluster age estimates, and population genetic analyses show that while highland New Guinea populations seem to be the oldest settlers, there has been significant gene flow within New Guinea with little influence from geography or language. The highest genetic division is between Papuan speakers of New Guinea versus East Papuan speakers located outside of mainland New Guinea. Our study supports the weak language barriers to genetic structuring among populations in close contact and highlights the complexity of understanding the genetic histories of Papua New Guinea in association with language and geography. Am J Phys Anthropol 142:613–624, 2010. © 2010 Wiley‐Liss, Inc.     

Bats Without Borders: Long-Distance Movements and Implications for Disease Risk Management

Fruit bats of the genus Pteropus (commonly known as flying-foxes) are the natural hosts of several recently emerged zoonotic viruses of animal and human health significance in Australia and Asia, including Hendra and Nipah viruses. Satellite telemetry was used on nine flying-foxes of three species (Pteropus alecto n = 5, P. vampyrus n = 2, and P. neohibernicus n = 2) to determine the scale and pattern of their long-distance movements and their potential to transfer these viruses between countries in the region. The animals were captured and released from six different locations in Australia, Papua New Guinea, Indonesia, and Timor-Leste. Their movements were recorded for a median of 120 (range, 47–342) days with a median total distance travelled of 393 (range, 76–3011) km per individual. Pteropus alecto individuals were observed to move between Australia and Papua New Guinea (Western Province) on four occasions, between Papua New Guinea (Western Province) and Indonesia (Papua) on ten occasions, and to traverse Torres Strait on two occasions. Pteropus vampyrus was observed to move between Timor-Leste and Indonesia (West Timor) on one occasion. These findings expand upon the current literature on the potential for transfer of zoonotic viruses by flying-foxes between countries and have implications for disease risk management and for the conservation management of flying-fox populations in Australia, New Guinea, and the Lesser Sunda Islands.     

The phylogenetic relationships of the bilby, Macrotis lagotis (Peramelimorphia: Thylacomyidae), to the bandicoots- DNA sequence evidence

Partial sequencing of the 12S ribosomal RNA gene was used to test two competing hypotheses concerning the phylogenetic relationship of the bilby (Macrotis lagotis) to the Australian and New Guinean species of bandicoot. The first hypothesis proposes that the Australian and New Guinean bandicoots are in a monophyletic clade to the exclusion of the bilbies, whereas the second hypothesis proposes that the bilby is monophyletic with the Australian bandicoots to the exclusion of the New Guinean bandicoots. Phylogenies determined by both maximum-likelihood and neighbour-joining approaches supported the first hypothesis in which the bilby is excluded from the clade represented by the Australian and New Guinean bandicoots. Monophyly of the Australian and New Guinean bandicoots is consistent with the biogeographical scenario in which Australia and Papua New Guinea have undergone repeated connection and disconnection over the last 20 million years.     

Comparative developmental and reproductive biology of geographical populations from two cryptic species in Brontispa longissima (Coleoptera: Chrysomelidae)

Brontispa longissima is a serious pest of the coconut palm Cocos nucifera, presumed to have originated in Papua New Guinea and Indonesia. It recently invaded Southeast and East Asia, where outbreaks have been reported. Mitochondrial DNA analysis reveals two cryptic species in B. longissima: one is distributed over a wide area including Asia and the Pacific region (the Asian clade) and the other in a limited area in the Pacific region (the Pacific clade). Recent invasions and outbreaks have been reported only from the area where the Asian clade has been found, suggesting that this clade has become a pest in Asia. To infer if the Asian clade has the ability to establish, spread and outbreak in novel habitats more effectively than the Pacific clade, we compared life‐history traits between the two populations of different clades. The net reproduction rate (R₀) was 130.0 and 94.0, the mean length of a generation (T) was 57.7 and 54.7 days, and the intrinsic rate of natural increase (r) was 0.084 and 0.083 per day for the population from Ishigaki Island, Japan (ISH) (the Asian clade) and for the population from Papua New Guinea (PNG) (the Pacific clade), respectively. Although the difference in r was little, the simulated population growth showed that the ISH population can be 1.6 times larger than that of the PNG after ten generations. The rapid population growth of the Asian clade would be partly responsible for its establishment, spread and frequent outbreaks in Asia.