Genetic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) in the Gulf of Thailand

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered, small cetacean species which is widely distributed in rivers, estuaries, and coastal waters throughout the tropical and subtropical Indo-Pacific. Despite the extensive distribution of this species, little is known of individual movements or genetic exchange among regions in Thailand. Here, we evaluate the genetic diversity and genetic structure of O. brevirostris in the eastern, northern and western Gulf of Thailand, and Andaman Sea. Although phylogenetic relationships and network analysis based on 15 haplotypes obtained from 32 individuals reveal no obvious divergence, significant genetic differentiation in mitochondrial DNA (overall F_ST = 0.226, P < 0.001; Φ_ST = 0.252, P < 0.001) is apparent among regions. Of 18 tested microsatellite loci, 10 are polymorphic and successfully characterized in 28 individuals, revealing significant genetic differentiation (overall F_ST = 0.077, P < 0.05) among the four sampling sites. Structure analysis reveals two inferred genetic clusters. Additionally, Mantel analysis demonstrates individual-by-individual genetic distances and geographic distances follow an isolation-by-distance model. We speculate that the significant genetic structure of O. brevirostris in Thailand is associated with a combination of geographical distribution patterns, environmental and anthropogenic factors, and local adaptations.     

Ontogenetic variation in diet and habitat of Irrawaddy dolphins (Orcaella brevirostris) in the Gulf of Thailand and the Andaman Sea

Irrawaddy dolphins (Orcaella brevirostris) are threatened, little‐known cetaceans primarily jeopardized by fishing gear entanglement. Information regarding life history, foraging ecology, and movement are crucial to determine management units and conservation regions. This is the first analysis of the ontogenetic changes in diet and habitat of Irrawaddy dolphins from the Gulf of Thailand and the Andaman Sea using stable isotopes from skin and teeth. Results suggest limited age and sex structure indicated by weak ontogenetic and sexual variability in δ¹⁵N and δ¹³C in teeth. Significant variation in δ¹³C and δ¹⁵N values were observed between three Gulf regions and the Andaman Sea, indicating distinct regional groups. Isotope mixing models run on soft tissues from the eastern Gulf revealed a diet based primarily on fishes and secondarily on crustaceans, suggesting overlap with fishery targets. Conservation strategies that focus on reducing regional competition with humans and bycatch mortality are proposed. Fishing gear improvements and monitoring of fishing operations are a potential immediate response to reduce anthropogenic impact.     

Description of whistles of Irrawaddy dolphins (Orcaella brevirostris) from the waters of Matang,Peninsular Malaysia

The whistles of Irrawaddy dolphins (Orcaella brevirostris) from the waters of Matang, western Peninsular Malaysia are described. Duration, frequency and frequency modulation variables were measured from 163 whistles recorded using a broadband towed hydrophone. Irrawaddy dolphins produced whistles with a mean duration of 0.366 s (S.D. ± 0.217 s). The fundamental frequency of whistles extended from 3040 to 17,123 Hz with low levels of frequency modulation. These dolphins produced whistles that were comparable to those of conspecifics recorded from the waters of Kalimantan, but were generally different from the related Australian snubfin dolphin (O. heinsohni). They also differed from the whistles of the sympatric Indo-Pacific humpback dolphin (Sousa chinensis). Characteristics of Irrawaddy dolphin whistles may be useful in future passive acoustic monitoring studies to investigate differences in sympatric species and their habitat.     

Passive acoustic monitoring of the distribution patterns of Irrawaddy dolphins (Orcaella brevirostris) in the middle reaches of the Ayeyarwady River,Myanmar

The Irrawaddy dolphins (Orcaella brevirostris) are an endangered species. Thus, up-to-date information on the distribution pattern of dolphins is critical for its proper management and conservation. Using a towed passive acoustic monitoring device, the distribution pattern of the Irrawaddy dolphins in the middle reaches of the Ayeyarwady River, Myanmar, was investigated during a vessel-based survey between Mingun and Katha. This region was successively divided into segments 1–4 from upstream to downstream. Sixteen echolocation encounters, with a series of click trains separated by <8 min and 26 dolphin acoustic trajectories were recorded. The mean dolphin detection rate (animals/kilometer) across the four segments progressively increased from upstream to downstream. High relative abundance was observed in segment 4 (46%) and segment 1 (23%) which was consistent with findings from historical boat-based visual surveys. The averaged interclick intervals of each click train in segment 2 and 4 was significantly shorter than that in segment 3, indicating that the dolphins in these segments frequently use shorter-ranged biosonar. More frequent and consistent surveys with a systematic sampling track design that incorporates other factors and covering the whole distribution range along the Ayeyarwady River and at varied water levels are needed in the future.     

Likely future extirpation of another Asian river dolphin: The critically endangered population of the Irrawaddy dolphin in the Mekong River is small and declining

The population of Irrawaddy dolphins that occupies the Mekong River in southern Lao People's Democratic Republic and Cambodia is classified as Critically Endangered by the IUCN. Based on capture‐recapture of photo‐identified individuals, we estimated that the total population numbered 93 ±  SE 3.90 individuals (95% CI 86–101), as of April 2007. The combined photo‐identification and carcass recovery program undertaken from 2001 to 2007 established that the Irrawaddy dolphin population inhabiting the Mekong River has reached a critical point with regards to its continued survival, where immediate research and management actions are required to greatly reduce adult mortality, and establish the cause of newborn mortality. In addition, community consultation is required to initiate, and evaluate, urgently required conservation measures. An ongoing well‐designed combined program of abundance estimation (i.e., photo‐identification) and carcass recovery is required to monitor total population size and mortality rates, to inform and evaluate management initiatives. The conclusions of this paper are likely generic to river dolphin populations, particularly where photo‐identification is possible.     

Mitochondrial DNA diversity and population structure among southern right whales (Eubalaena australis)

The population structure and mitochondrial (mt) DNA diversity of southern right whales (Eubalaena australis) are described from 146 individuals sampled on 4 winter calving grounds (Argentina, South Africa, Western Australia, and the New Zealand sub-Antarctic) and 2 summer feeding grounds (South Georgia and south of Western Australia). Based on a consensus region of 275 base pairs of the mtDNA control region, 37 variable sites defined 37 unique haplotypes, of which only one was shared between regional samples of the Indo-Pacific and South Atlantic Oceans. Phylogenetic reconstruction of the southern right whale haplotypes revealed 2 distinct clades that differed significantly in frequencies between oceans. An analysis of molecular variance confirmed significant overall differentiation among the 4 calving grounds at both the haplotype and the nucleotype levels (F(ST) = 0.159; Phi(ST) = 0.238; P < 0.001). Haplotype diversity was significantly lower in the Indo-Pacific (h = 0.701 +/- 0.037) compared with the South Atlantic (h = 0.948 +/- 0.013), despite a longer history of exploitation and larger catches in the South Atlantic. In fact, the haplotype diversity in the Indo-Pacific basin was similar to that of the North Atlantic right whale that currently numbers about 300 animals. Multidimensional scaling of genetic differentiation suggests that gene flow occurred primarily between adjacent calving grounds within an ocean basin, with mixing of lineages from different calving grounds occurring on feeding grounds.     

Multi‐methods approach to characterizing the magnitude,impact, and spatial risk of Irrawaddy dolphin (Orcaella brevirostris) bycatch in small‐scale fisheries in Malampaya Sound,Philippines

Addressing the urgent conservation threat of marine mammal bycatch in small‐scale fisheries requires information on bycatch magnitude, gear types, population impacts, and risk. However, data on these proximate attributes are widely lacking in developing countries. This study used a multi‐methods approach integrating boat surveys and interviews with fishermen (n = 526) to assess proximate attributes of bycatch for the Critically Endangered subpopulation of Irrawaddy dolphins (Orcaella brevirostris) in Malampaya Sound, Philippines. Given an updated population estimate of 35 individuals (CV = 22.9%), the estimated rate of bycatch fatalities exceeds the potential biological removal rate. Spatial overlap scores were calculated to characterize overlap between dolphins and fisheries as a proxy of bycatch risk. These scores identified particularly high risk areas that could be prioritized for gear bans. However, completely reducing bycatch risk would require more widespread bans beyond these high risk areas. Implementing gear restrictions will be immensely challenging, given serious obstacles to fisheries management at this site. The multi‐methods approach describes the urgency of the bycatch problem and the changes required for mitigation, setting the stage for identifying and evaluating potential solutions. It can be readily applied to developing country sites to guide more efficient and complete data collection and conservation efforts.     

Evolution of the common cetacean highly repetitive DNA component and the systematic position of Orcaella brevirostris

Summary The common cetacean highly repetitive DNA component was analyzed with respect to its evolution and value for establishing phylogenetic relationships. The repeat length of the component, which is tandemly organized, is 1750 by in all cetaceans except the delphinids, in which the repeat length is 1580 bp.The evolution of the component was studied after sequencing the component in different odontocetes representing the Delphinidae (delphinids), Monodontidae (narwhals), and Ziphiidae (beaked whales). The evolution of this component is very slow, and comparisons showed that sequence divergence among species corresponds closely to their generally accepted phylogenetic relationships and that the component evolves in a concerted manner.The phylogenetic information obtained in this study identified the Irrawaddy dolphin (Orcaella brevirostris) as a delphinid and did not support a close relationship of this species with the Monodontidae.Offprint requests to: S. Gretarsdottir     

Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin (Pontoporia blainvillei)

The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F‐statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex‐biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long‐term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.     

Mitochondrial DNA diversity, population structure, and gender association in the gynodioecious plant Silene vulgaris

A highly variable mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) locus is used to assess the population structure of mitochondrial genomes in the gynodioecious plant Silene vulgaris at two spatial scales. Thirteen mtDNA haplotypes were identified within 250 individuals from 18 populations in a 20-km diameter region of western Virginia. The population structure of these mtDNA haplotypes was estimated as thetaST = 0.574 (+/- 0.066 SE) and, surprisingly, genetic differentiation among populations was negatively correlated with geographic distance (Mantel r = -0.246, P < 0.002). Additionally, mtDNA haplotypes were spatially clumped at the scale of meters within one population. Gender in S. vulgaris is determined by an interaction between autosomal male fertility restorers and cytoplasmic male sterility (CMS) factors, and seed fitness is affected by an interaction between gender and population sex ratio; thus, selection acting on gender could influence the distribution of mtDNA RFLP haplotypes. The sex ratio (females:hermaphrodites) varied among mtDNA haplotypes across the entire metapopulation, possibly because the haplotypes were in linkage disequilibrium with different CMS factors. The gender associated with some of the most common haplotypes varied among populations, suggesting that there is also population structure in male fertility restorer genes. In comparison with reports of mtDNA variation from other published studies, we found that S. vulgaris exhibits a large number of mtDNA haplotypes relative to that observed in other species.     

Mitochondrial DNA diversity and population differentiation in southern East Asia

Mitochondrial DNA (mtDNA) polymorphism has been studied systematically in the Han, Tibeto-Buman, and Hmong-Mien ethnic families of southern East Asia. Only two families in this region, Daic and Austro-Asiatic, were still uninvestigated. Daic is a major ethnic family in South China and Southeast Asia and has a long history. To study mtDNA polymorphism within this family, all the Daic populations of China and some of Vietnam (774 individuals from 30 populations) were typed by HVS-1 region sequencing and by PCR-RFLP assays. The observed high Southern type frequencies (B, F, M7, R) confirmed Daic as a typical Southern group. mtDNAs of other populations (126 individuals from 14 populations) from Austro-Asiatic ethnic families neighboring the Daic were also typed. Networks of mtDNA haplogroups in South China were traced from these new data and those from the literature. Ethnic families share many haplogroups, indicating their common origin. However, the two largest families in South China, Daic, and Hmong-Mien, polarized into several ethnic family specific haplogroups. Haplogroup ages were estimated in the networks of high-frequency haplogroups (B, F, M7, R), and they were found to originate about 50,000 years ago. In contrast, ethnic family specific haplogroups all originated around 20,000 years ago. We therefore conclude that modern humans have lived in South China for a long time, inside-ethnogenesis was a rather late event, and frequent inmixing was taking place throughout. MtDNA data of Daic, Austro-Asiatic and other populations in South China has therefore proven pivotal for studying the human history of East Asia.     

BarredDanio species from the Irrawaddy River drainage (Teleostei, Cyprinidae)

The three barredDanio species known from the Irrawaddy River drainage are redescribed. Two species are known from southwestern Yunnan:Danio interruptus in the Husa He and Longchuan, Jian watersheds, andD. apogon abundantly in the main river and tributaries of the Daying Jiang basin. The third species,D. shanensis, occurs in the Myitnge basin of northern Shan State, Myanmar.Danio interruptus differs from other barredDanio species by having a short, incomplete lateral line, a deeper head, and shorter thicker dark vertical bars or blotches anteriorly on the sides.Danio shanensis has the lateral line either complete or incomplete, lesser head depth, and a series of deeper narrower vertical bars.Danio apogon has no lateral line, narrow or indistinct dark vertical bars, and a wide, but indistinct, horizonatal P stripe.Danio choprae, previously considered, as a barredDanio species, is more closely related to theD. dangila species group.     

Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish,rock carp (Procypris rabaudi) in upper Yangtze River drainage

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, π = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit.     

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos)

Two sections of the control region and the genes coding for NADH dehydrogenase sub-units 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.     

Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum)

The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.     

Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study, the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximatel...     

Genetic structure and diversity of Shorea obtusa (Dipterocarpaceae) in Thailand

Shorea obtusa is a keystone species of the dry deciduous dipterocarp forest in Thailand. In this study, the genetic structure and diversity of this species were evaluated by means of five microsatellite markers. A total of 146 trees were collected from five populations encompassing major forest regions of Thailand. High levels of genetic diversity were found among the five populations with the average He of 0.664. Genetic differentiations between populations, although significant, were low with approximately 3% of genetic variation partitioned among populations. This may indicate that the populations sampled were recently part of a continuous population. A tree constructed using the unweighted pair group method with arithmetic average, based on Nei's genetic distance, divided the populations into three groups. This separation was consistent with the altitudinal zonation of the populations, thus indicating that altitude might play a significant role in the genetic structure of S. obtusa. Areas of high genetic diversity were identified which could be considered priorities for conservation.