Description of ten new Lobophora species from the Bismarck Sea (Papua New Guinea)

Sampling in the framework of the research program called ‘La Planète Revisitée’ in Kavieng and Madang (Papua New Guinea) brought thus far unknown diversity of the brown algal genus Lobophora to the surface. DNA‐assisted alpha taxonomy allowed identifying the presence of 16 species Lobophora from these two localities, which only share four species in common. Ten species are newly described, including four, which are only known to the Bismarck Sea. A more exhaustive sampling across the Bismarck Sea, and more largely across the Coral Triangle, will very likely unveil an even greater diversity. The present study underscores the fragmentary nature of our knowledge of macroalgal diversity in this region.     

Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across,but not within,basins of the Indo‐Pacific based on mitochondrial DNA

Genetic stock structure is atypical in tuna species, with most species demonstrating geographically‐broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo‐Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D‐loop) gene region. One hundred and thirty‐nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ?_ST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo‐Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.     

Microsatellite and mitochondrial DNA analyses of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea

Genetic variation was surveyed at nine microsatellite loci and the mitochondrial control region (868 bp) to test for the presence of genetic stock structure in young-of-the-year Atlantic bluefin tuna (Thunnus thynnus thynnus) from the Mediterranean Sea. Bluefin tuna were sampled over a period of 5 years from the Balearic and Tyrrhenian seas in the western basin of the Mediterranean Sea, and from the southern Ionian Sea in the eastern basin of the Mediterranean Sea. Analyses of multilocus microsatellite genotypes and mitochondrial control region sequences revealed no significant heterogeneity among collections taken from the same location in different years; however, significant spatial genetic heterogeneity was observed across all samples for both microsatellite markers and mitochondrial control region sequences (FST=0.0023, P=0.038 and PhiST=0.0233, P=0.000, respectively). Significant genetic differentiation between the Tyrrhenian and Ionian collections was found for both microsatellite and mitochondrial markers (FST=0.0087, P=0.015 and PhiST=0.0367, P=0.030, respectively). These results suggest the possibility of a genetically discrete population in the eastern basin of the Mediterranean Sea.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Altitude,language, and class I HLA allele frequencies in Papua New Guinea

Class I HLA gene frequencies show considerable variation over short geographical distances in Papua New Guinea. Hypotheses to account for this invoke natural selection, population structure, the pattern of population movement, or past demographic changes. To determine the role of the various factors in shaping this distribution, we have studied correlations between HLA-based genetic distances, geographical distances, altitude, and linguistic differences in Papua New Guinea. Linguistic differences at the family or stock level within the Trans-New Guinea Phylum generally correspond to genetic differences. However, on the basis of their HLA gene frequencies, speakers of Austronesian (AN) languages do not form a distinct group of populations. Linguistic variation and spatial autocorrelation do not fully account for the altitudinal cline differences noted in gene frequencies, particularly at the HLA-A locus. We propose that the distribution of HLA gene frequencies in Papua New Guinea is partially under the control of selection operating differentially along the altitude gradient. © 1994 Wiley-Liss, Inc.     

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.     

Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia

As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).     

Oceanographic Currents and Local Ecological Knowledge Indicate,and Genetics Does Not Refute,a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster,Panulirus ornatus in the South-East Asian Archipelago

Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences Φ_ST = -0.008; microsatellite loci F_ST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.     

Discrimination of juvenile yellowfin (Thunnus albacares) and bigeye (T. obesus) Tunas using mitochondrial DNA control region and liver morphology

Yellowfin tuna, Thunnus albacares (Bonnaterre, 1788) and bigeye tuna, Thunnus obesus (Lowe, 1839) are two of the most economically important tuna species in the world. However, identification of their juveniles, especially at sizes less than 40 cm, is very difficult, often leading to misidentification and miscalculation of their catch estimates. Here, we applied the mitochondrial DNA control region D-loop, a recently validated genetic marker used for identifying tuna species (Genus Thunnus), to discriminate juvenile tunas caught by purse seine and ringnet sets around fish aggregating devices (FADs) off the Southern Iloilo Peninsula in Central Philippines. We checked individual identifications using the Neighbor-Joining Method and compared results with morphometric analyses and the liver phenotype. We tested 48 specimens ranging from 13 to 31 cm fork length. Morpho-meristic analyses suggested that 12 specimens (25%) were bigeye tuna and 36 specimens (75%) were yellowfin tuna. In contrast, the genetic and liver analyses both showed that 5 specimens (10%) were bigeye tuna and 43 (90%) yellowfin tuna. This suggests that misidentification can occur even with highly stringent morpho-meristic characters and that the mtDNA control region and liver phenotype are excellent markers to discriminate juveniles of yellowfin and bigeye tunas.     

Population genetics of Atlantic bluefin tuna,Thunnus thynnus (Linnaeus, 1758), in the Mediterranean: implications for its conservation management

The movement of Atlantic bluefin tuna (ABFT) across international boundaries necessitates traceability strategies that would provide more accurate information needed for stock assessment. The Mediterranean Sea is one of the main contributors to ABFT reproduction and global population genetic diversity. In the present study this genetic variability was investigated using 193 samples of adult bluefin tuna from Spain, Turkey and Malta – a longitudinal distance of 3400 km. Analysed were 13 microsatellite loci (eight of which were newly‐tested) as genetic markers for the population study. Allele richness measured per locus and sampling location varied from 1.89 to 8.88, taking into account rarefaction. ABFT private alleles were detected in each of the three sampling sites. No significant spatial genetic divergence was found between pairs at the studied locations (F_ST values <0.0001; P‐values >0.05). Bayesian clustering analysis corroborated a single and panmictic ABFT population in the Mediterranean Sea. Statistical power analyses indicated a high probability of detecting genetic differentiation and population structure with the sample size and microsatellites used, even at an F_ST value of 0.005. From the results it may be postulated that migrating ABFT during the spawning season are allowing gene flow within the Mediterranean Sea. The complex interplay of movements, including plasticity in the selection of spawning sites with increasing age and environmental conditions, require multiple and new fisheries monitoring and management techniques in order to target the ABFT long‐term conservation effectively.     

Haemaphysalis (Garnhamphysalis) rusae (Ixodoidea: Ixodidae): identity, deer and pig hosts, and distribution in Luzon and Mindanao

Haemaphysalis (Garnhamphysalis) rusae Kohls, previously known only from three male ticks from Mindanao, Philippines, is a seldom collected but probably common parasite of the Philippine deer, Cervus (Rusa) philippinus, and wild pig, Sus celebensis philippensis, in forests of Mindanao and Luzon. A single female taken from a wallaby in Papua New Guinea is presumed to result from an introduction with the Philippine deer. The male, originally briefly described, is redescribed to provide criteria for comparing this species and other members of the subgenus Garnhamphysalis. The female and nymph are described for the first time. The male H. (G.) rusae and H. (G.) calvus Nuttall and Warburton are structurally quite similar, differing only in palpal length:breadth ratio and size of the trochanter IV spur. Females differ more widely in the presence (rusae) or absence (calvus) of a large retrograde spur extending from the posteroventral margin of palpal segment 2. Conversely, qualitative and quantitative structural differences between most Haemaphysalis species are greater in males than in females.     

The genetic population structure of Thunnus thynnus (Linnaeus, 1758) in the Mediterranean Sea,a controversial issue

The Atlantic bluefin tuna (ABFT), Thunnus thynnus (Linnaeus, 1758), is an important commercial species managed as two different stocks, western and eastern Atlantic, with their spawning grounds in the Gulf of Mexico and in the Mediterranean Sea, respectively. The eastern Atlantic stock has been overexploited in the last decades, leading to the application of specific management measures introduced by the International Commission for the Atlantic Tuna (ICCAT). A clear understanding of the genetic structure of ABFT Mediterranean population should be pursued in order to support management decisions. To date the genetic studies on the Mediterranean ABFT, carried out with different molecular markers and sampling procedures, have produced unclear results. Here, we analysed ABFT samples from central and western Mediterranean Sea with mitochondrial sequences and 11 microsatellite loci to investigate, among the others, the area of the Strait of Messina, where environmental conditions seem to support a resident population of ABFT. Furthermore, genetic analyses of mitochondrial sequences were carried out including nucleotide sequences of Adriatic ABFT wild larvae retrieved from GenBank. Among the investigated areas a genetic differentiation was detected between the Strait of Messina and the Tyrrhenian Sea with microsatellite loci according to the exact G test, but not to the Bayesian analyses carried out with STRUCTURE. The analyses with mitochondrial sequences do not reveal any differentiation among sampled areas, however, a highly significant genetic divergence was observed between the Adriatic mitochondrial sequences retrieved from GenBank and the central‐western Mediterranean sequences obtained in the present work. Our results provide some evidence of population structure of Mediterranean ABFT adding pieces to a still unclear picture.     

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.     

Population genetics of tunas

Population genetic studies on tunas are reviewed. These studies have focused on phylogenetic reconstructions, species identifications and stock delineation, and have used tools ranging from blood group and allozyme analysis to PCR-aided examination of mitochondrial DNA variation. Both allozyme and mtDNA approaches show tunas in the genus Thunnus to be very closely related to one another, but also indicate that the two presently recognized subspecies of northern bluefin tuna, Thunnus thynnus thynnus and T. t. orientalis , in fact may be worthy of species status. These techniques also permit the unequivocal recognition of specimens, which is not always possible on morphological grounds. However, it is arguable that, until recently, tunas have not received their due attention from geneticists given their commercial significance and the need for information on stock structure to ensure sustainable management. This may be because tunas are known to be highly vagile and therefore levels of population differentiation are expected to be low. None the less, population subdivision has been recorded in several species (skipjack, yellowfin, albacore), although this tends to be on a broad (intra- or inter-oceanic) rather than on a more local scale. New molecular tools, including the PCR-based analyses of nuclear genes and microsatellite loci, are yielding new, highly polymorphic markers, and will enable more powerful analyses of stock structure than have hitherto been possible.     

Multiple population structure of the giant mottled eel, Anguilla marmorata

The population structure of the giant mottled eel, Anguilla marmorata, was investigated with mitochondrial and microsatellite DNA analyses using 449 specimens from 13 localities throughout the species range. Control region F-statistics indicated the North Pacific (Japan, Taiwan, Philippines, Sulawesi), South Pacific (Tahiti, Fiji, New Caledonia, Papua New Guinea), eastern Indian Ocean (Sumatra), western Indian Ocean (Réunion, Madagascar), Ambon, and Guam regions were significantly different (Phi(ST) = 0.131-0.698, P < 0.05) while only a few differences were observed between localities within the South Pacific. These regions were roughly clustered in the neighbour-joining tree, although Ambon individuals were mainly divided into North and South Pacific groups. Analysis with eight microsatellite loci showed almost identical results to those of the control region, except no genetic difference was observed between the western and eastern Indian Ocean (F(ST) = 0.009, P > 0.05). The Bayesian cluster analysis of the microsatellite data detected two genetic groups. One included four North Pacific localities, and the other included eight localities in the South Pacific, Indian Ocean, and Guam, but Ambon individuals were evenly assigned to these two groups. These results showed that A. marmorata has four genetically different populations (North Pacific, South Pacific, Indian Ocean, Guam region). The North Pacific population is fully panmictic whereas the South Pacific and Indian Ocean populations have a metapopulation structure. Interestingly, Guam was suggested to be inhabited by a reproductive population restricted to that region, and the individuals from the North and South Pacific populations co-exist in Ambon.     

Microsatellite DNA markers for population‐genetic studies of Atlantic bluefin tuna (Thunnus thynnus thynnus) and other species of genus Thunnus

Twenty‐five microsatellites from Atlantic bluefin tuna (Thunnus thynnus thynnus) were characterized. All 25 microsatellites were polymorphic; the number of alleles among up to 56 individuals surveyed ranged from two to 23. Atlantic bluefin tuna are highly exploited and major questions remain as to stock structure and abundance in the eastern and western North Atlantic. The microsatellites will be useful in testing stock‐structure hypotheses and in generating estimates of effective population size. The polymerase chain reaction primer sets developed also amplified identifiable alleles in three other species of genus Thunnus: T. albacares (yellowfin tuna), T. alalunga (albacore tuna) and T. obesus (bigeye tuna).     

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 new Indo-Australian genus of Braconinae (Insecta, Hymenoptera, Braconidae)

Bicarinibracon gen.n. (type species Atanyco1us tricolor . Szépligeti from Papua New Guinea and Irian Jaya). Bicarinibracon luteus gen. et. 3p.n. from India and Malaya and B. lepicius gen. et. sp.n. from Thailand and the Philippines are described and illustrated. A key to the specics of Bicarinibracon is provided and its systematic placement is discussed.     

Mitochondrial DNA analysis reveals three stocks of yellowfin tuna Thunnus albacares (Bonnaterre, 1788) in Indian waters

Yellowfin tuna (Thunnus albacares) is an epipelagic, oceanic species of family Scombridae found in tropical and subtropical region of Pacific, Indian and Atlantic Ocean. It is commercially important fish and accounts for 19 % of total tuna catches in Indian waters. In present study, population structure of yellowfin tuna was examined using sequence analysis of mitochondrial DNA from seven geographically distinct locations along the Indian coast. A 500 bp segment of D-loop region was sequenced and analysed for 321 yellowfin samples. Hierarchical analysis of molecular variance showed significant genetic differentiation among three groups (VE); (AG); (KO, TU, PO, VI, PB) analyzed (Φ _ST  = 0.03844, P ≤ 0.001). In addition, spatial analysis of molecular variance identified three genetically heterogeneous groups of yellowfin tuna in Indian waters. Results were further corroborated by significant value of nearest neighbour statistic (S _nn = 0.261, P ≤ 0.001). Thus finding of this study rejects the null hypothesis of single panmictic population of yellowfin tuna in Indian waters.