Mitochondrial ATPase 6/8 genes reveal genetic divergence in the Coilia dussumieri (Valenciennes, 1848) populations of north east and northwest coasts of India

The golden anchovy, Coilia dussumieri, though possessing discontinuous distribution along northeast and northwest coasts of India, it is being managed as unit stock for fishery assessment purposes. By considering the need for stock specific management of the species, mitochondrial ATP synthase 6 and 8 (ATPase 6/8) genes were analyzed for delineating genetic stock structure of the species. Sequence analysis revealed a total of 34 haplotypes across four populations from both the east and west coasts of India. Haplotype diversity (h) was found in the range of 0.7421–0.9368. Similarly, nucleotide diversity (π) varied from 0.0012 to 0.0025. AMOVA results indicated a high total variance of 72.66 % between east and west coast populations and less (1.34 %) among populations within the respective coast. Phylogenetic tree constructed using pair wise F_ST also indicated the genetic divergence of populations of east and west coasts of India. The findings of the present study will be helpful in developing stock specific management measures for conservation and sustainable utilization of the species.     

Microsatellite Markers to Determine Population Genetic Structure in the Golden Anchovy,Coilia dussumieri

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F _ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.     

Absence of shared mitochondrial DNA haplotypes between sea lamprey from North American and Spanish rivers

Sea lamprey Petromyzon marinus from the River Miño and Sella, Spain, showed an almost identical frequency for three observed haplotypes. None of these haplotypes were found among three North American populations. These results indicate an absence of exchange among sea lamprey populations spawning in the west and south‐east Atlantic coasts. The similarity between the collections from the two Spanish rivers suggests that homing does not occur in anadromous sea lamprey.     

A new species of Gastrosaccus (Crustacea,Mysidacea) from beaches in Madagascar

Gastrosaccus madagascariensis sp.nov. is common in thesurfzone of sandy beaches along the east and south coasts ofMadagascar. Morphologically, it is characterised by having sevenlateral spines along each side of the telson; with spines 2–4 andthe penultimate spine being dorso-lateral in origin. One or twospinules are interspersed between the fifth and terminal spines.The fourth exopod segment of pleopod 3 in the male is bulbous, bearing twoterminal barbed unequal spines. A robust and naked seta is alsopresent on the same segment in the male.     

Phylogeography of the mallard Anas platyrhynchos from Eurasia inferred from sequencing of the mtDNA control region

Phylogenetic relationships, demographic history, and geographic distribution of the mtDNA haplotypes of the mallard Anas platyrhynchos were examined in three populations, Indian, Northern European, and Far Eastern. Two divergent halotype groups, A and B, were found in the Far Eastern population, while haplotypes identified in Northern European and Far Eastern populations were exclusively of the A group. The presence of B group haplotypes in the Far Eastern population can be explained either in terms of hybridization of the mallard with spot-billed duck Anas zonorhyncha at the south of the Russian Far East, or by the mtDNA paraphyly in mallards. In general, mallards from Eurasia were characterized by low genetic population differentiation along with slightly expressed phylogeographic structure. The most differentiated was the population from India (??_st = 0.076?0.077), while the difference between Northern European and Far Eastern populations was extremely low (??_st = 0.0029). Differentiation of Anas platyrhynchos Indian population was determined by the fact that a part of the population, inhabiting southern and eastern coasts of the Hindustan Peninsula, was resident.     

Habitat and population size of the coelacanth Latimeria chalumnae at Grand Comoro

Synopsis In 1987 and 1989 coelacanths were observed for the first time in their natural habitat with the help of submersibles. Coelacanths were found between 150–253 m depth, their preferential depth seems to be around 200 m; the water temperature ranged between 16.5–22.8° C. During the day coelacanths aggregate in small non-aggressive groups in sheltered lava-caves. Caves might be a limiting factor for distribution. At night they leave the caves for hunting by drifting singly along the steep lava slopes. They migrate between different caves located within a large home range covering more than 8 km coastline. Coelacanths are site-attached, some for a period of at least 2 years. Our own observations and earlier catch records show that only the west coast of Grand Comoro is a suitable coelacanth habitat with more structural complexity and prey fish abundance than other coastlines of the island. From our survey we estimated a total coelacanth population off Grand Comoro to be 150–210 individuals; a saturated population would be 370–510 individuals. This small relict population seems to be stable. International protection of coelacanths against commercial interests is needed     

Patterns of nitrogen accumulation and cycling in riparian floodplain ecosystems along the Green and Yampa rivers

Patterns of nitrogen (N) accumulation and turnover in riparian systems in semi-arid regions are poorly understood, particularly in those ecosystems that lack substantial inputs from nitrogen fixing vegetation. We investigated sources and fluxes of N in chronosequences of riparian forests along the regulated Green River and the free-flowing Yampa River in semi-arid northwestern Colorado. Both rivers lack significant inputs from N-fixing vegetation. Total soil nitrogen increased through time along both rivers, at a rate of about 7.8 g N m^–2 year^–1 for years 10–70, and 2.7 g N m^–2year^–1 from years 70–170. We found that the concentration of N in freshly deposited sediments could account for most of the soil N that accumulated in these floodplain soils. Available N (measured by ion exchange resin bags) increased with age along both rivers, more than doubling in 150 years. In contrast to the similar levels of total soil N along these rivers, N turnover rates, annual N mineralization, net nitrification rates, resin-N, and foliar N were all 2–4 times higher along the Green River than the Yampa River. N mineralization and net nitrification rates generally increased through time to steady or slightly declining rates along the Yampa River. Along the Green River, rates of mineralization and nitrification were highest in the youngest age class. The high levels of available N and N turnover in young sites are not characteristic of riparian chronosequences and could be related to changes in hydrology or plant community composition associated with the regulation of the Green River.     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Complex genetic origin of Indian populations and its implications

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000?years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.     

Species structure, contemporary distribution and status of the Siberian surgeon Acipenser baerii

A detailed analysis of the historical and contemporary range of the Siberian sturgeon, Acipenser baerii, shows that the contemporary status of its populations and forms can be described as threatened or endangered. Recently, the abundance of the nominal subspecies, A. b. baerii, which inhabits mainly the Ob River basin, decreased sharply. Due to construction of hydroelectric dams, up to 40% of the spawning grounds became inaccessible for migrating sturgeon of this subspecies. The Lake Baikal subspecies, A. baerii baicalensis, is extremely rare and was included in the Russian Federation Red Data Book in 1983. The abundance of the east Siberian subspecies, A. baerii stenorrhynchus, inhabiting the basins of the east Siberia rivers, has also significantly decreased during the last few years. Its range in the Yenisey and Lena River basins is gradually being reduced. Gametogenesis is anomalous in a high number of females from all populations of this subspecies (in the Kolyma and Indigirka river stocks 80–100% of females were anomalous in 1987–1989). These anomalies seem to be caused by high levels of water pollution.     

Genetic heterogeneity in the Indian stocks of seahorse (<Emphasis Type="Italic">Hippocampus kuda</Emphasis> and <Emphasis Type="Italic">Hippocampus trimaculatus</Emphasis>) inferred from mtDNA cytochrome b gene

Genetic stock structure analysis of two seahorse species from the south east and south west coasts of India (37 samples of Hippocampus kuda and 39 samples of Hippocampus trimaculatus from Kollam (Kerala) and Mandapam (Tamil Nadu)) was carried out through sequence variation analysis of a 350 bp cytochrome b fragment of mitochondrial DNA. This was taken up to support the breeding and restocking programme of these species in natural habitats for conservation purpose. The occurrence of strong genetic subdivision among the samples, detected by the analysis of molecular variance (AMOVA), and significant Φ_ST values indicated that stocks of both the species in the two Indian coasts are distinct. The findings of the present study have important implications for conservation and management of these two species and we recommend stock-specific, breeding assisted sea-ranching programme for H. kuda and H. trimaculatus along the Indian coasts. Handling editor: K. Martens     

First report of Perkinsus beihaiensis in Crassostrea madrasensis from the Indian subcontinent

Protozoan parasites of the genus Perkinsus are considered important pathogens responsible for mass mortalities in many wild and farmed bivalve populations. The present study was initiated to screen populations of the Indian edible oyster Crassostrea madrasensis, a promising candidate for aquaculture along the Indian coasts, for the presence of Perkinsus spp. The study reports the presence of P. beihaiensis for the first time in C. madrasensis populations from the Indian subcontinent and south Asia. Samples collected from the east and west coasts of India were subjected to Ray's fluid thioglycollate medium (RFTM) culture and histology which indicated the presence of Perkinsus spp. PCR screening of the tissues using specific primers amplified the product specific to the genus Perkinsus. The taxonomic affinities of the parasites were determined by sequencing both internal transcribed spacer (ITS) and actin genes followed by basic local alignment search tool (BLAST) analysis. Analysis based on the ITS sequences showed 98 to 100% identity to Perkinsus spp. (P. beihaiensis and Brazilian Perkinsus sp.). The pairwise genetic distance values and phylogenetic analysis confirmed that 2 of the present samples belonged to the P. beihaiensis clade while the other 4 showed close affinities with the Brazilian Perkinsus sp. clade. The genetic divergence data, close affinity with the Brazilian Perkinsus sp., and co-existence with P. beihaiensis in the same host species in the same habitat show that the remaining 4 samples exhibit some degree of variation from P. beihaiensis. As expected, the sequencing of actin genes did not show any divergence among the samples studied. They probably could be intraspecific variants of P. beihaiensis having a separate lineage in the process of evolution.     

The biogeographic and tectonic history of India

Aim To present an up to date account of the Mesozoic history of India and its relationship to the other Gondwana continents and to Eurasia. Location Continents surrounding the Western Indian Ocean. Methods Utilization of recent evidence of continental relationships based upon research in stratigraphy, palaeomagnetism, palaeontology, and contemporary biotas. Results The physical data revealed a sequence of events as India moved northward: (1) India–Madagascar rifted from east Africa 158–160 Ma (million years ago), (2) India–Madagascar from Antarctica c. 130 Ma, (3) India–Seychelles from Madagascar 84–96 Ma, (4) India from Seychelles 65 Ma, (5) India began collision with Eurasia 55–65 Ma and (6) final suturing took place c. 42–55 Ma. However, data from fossil and contemporary faunas indicate that, throughout the late Cretaceous, India maintained exchanges with adjacent lands. There is an absence in the fossil record of peculiar animals and plants that should have evolved, had India undergone an extended period of isolation just before its contact with Eurasia. Main conclusions The depiction of India in late Cretaceous as an isolated continent is in error. Most global palaeomaps, including the most recent one, show India, as it moves northward, following a track far out in the Indian Ocean. But the evidence now indicates that India's journey into northern latitudes cannot have taken place under such isolated circumstances. Although real breaks among the lands were indicated by the physical data, faunal links were maintained by vagile animals that were able to surmount minor marine barriers. India, during its northward journey, remained close to Africa and Madagascar even as it began to contact Eurasia.     

The Systematics and Reproductive Biology of the Galeus arae Subspecific Complex (Chondrichthyes: Scyliorhinidae)

Galeus arae is currently classified as a complex of three subspecies (Galeus arae arae, Galeus arae antillensis, and Galeus arae cadenati). Morphometric and meristic analyses, size at maturity, and variation in color patterns, support the recognition of these taxa as distinct species. All species have well-developed nidamental glands and are oviparous. Galeus arae comprises two geographically disjunct populations that are not distinguishable by the characters we examined. A northern population occurs along the east and Gulf coasts of North America from South Carolina to the Mississippi delta, and the northern coast of Cuba to the north-eastern tip of the Yucatan. A southern population occurs along the Caribbean coasts of Honduras, Nicaragua, and Costa Rica, and some neighboring islands. Galeus antillensis occurs on the northern coasts of Hispaniola and Puerto Rico, and off many of the Leeward Islands. Galeus cadenati occurs off the Caribbean coasts of Panama and Colombia. Distributional data suggest that the three species are distributed allopatrically.     

Landscape Genetic Structure of a Streamside Tree Species Euptelea pleiospermum (Eupteleaceae): Contrasting Roles of River Valley and Mountain Ridge

We used landscape genetics and statistical models to test how landscape features influence connectivity or create barriers to dispersal for a mountain riparian tree species, Euptelea pleiospermum. Young leaves from 1078 individuals belonging to 36 populations at elevations of 900–2000 m along upper reaches of four rivers were genotyped using eight nuclear microsatellite markers. We found no evidence for the unidirectional dispersal hypothesis in E. pleiospermum within each river. The linear dispersal pattern along each river valley is mostly consistent with the “classical metapopulaton” model. Mountain ridges separating rivers were genetic barriers for this wind-pollinated tree species with anemochorous seeds, whereas river valleys provided important corridors for dispersal. Gene flow among populations along elevational gradients within each river prevails over gene flow among populations at similar elevations but from different rivers. This pattern of gene flow is likely to promote elevational range shifts of plant populations and to hinder local adaptation along elevational gradients. This study provides a paradigm to determine which of the two strategies (migration or adaptation) will be adopted by mountain riparian plants under climate warming.     

Phylogeny of rheusus monkeys (Macaca mulatta) as revealed by mitochondrial DNA restriction enzyme analysis

Mitochondrial DNA, purified from 36 samples of 23 local populations which are widely distributed in Vietnam, Burma, and 10 provinces of China, has been analyzed to model the phylogeny of rhesus monkeys. The 20 local populations of China may represent nearly all major populations in China. Using 20 restriction endonucleases of 6-bp recognition, we observed a total of 50–61 sites in the various samples. By combining the cleavage patterns for each enzyme, the 36 samples were classified into 23 restriction types, each of which was found exclusively in the respective population from which samples were obtained. By combining the earlier study of Indian rheusus monkeys, phylogenetic trees, which have been constructed on the basis of genetic distance, indicate that rhesus monkeys in China, Vietnam, India, and Burma can be divided into seven groups. Integrating morphological and geographical data, we suggest that rhesus monkeys in China, Vietnam, and Burma may be classified into six subspecies—M. m. mulatta, M. m. brevicaudus, M. m. lasiotis, M. m. littoralis, M. m. vestita, and M. m. tcheliensis-and rhesus monkeys in India may be another valid subspecies.M. m. tcheliensis is the most endangered subspecies in China. Divergence among subspecies may have begun 0.9–1.6 Ma. The radiation of rhesus monkeys in China may have spread from the southwest toward the east. The taxonomic status of the Hainan monkey and the Taiwan monkey require further investigation.     

Genetic differentiation and trade among populations of peach palm (Bactris gasipaes Kunth) in the Peruvian Amazon—implications for genetic resource management

Peach palm (Bactris gasipaes Kunth) is cultivated for fruit and heart of palm, and is an important component of agroforestry systems in the Peruvian Amazon. In this study, AFLP was used to compare genetic diversity among domesticated populations along the Paranapura and Cuiparillo rivers, which are managed by indigenous and colonist farming communities, respectively. Gene diversity was 0.2629 for the populations in indigenous communities and 0.2534 in colonist communities. Genetic differentiation among populations (G_st) was 0.0377–0.0416 (P<0.01) among populations along both rivers. There was no relation between genetic differentiation and the geographical location of populations along the rivers. Since natural seed dispersal by birds and rodents is thought to occur only across relatively short distances (100–200 m), it is likely that exchange of material by farmers and commercial traders is responsible for most of the long-distance (over more than 20 km) gene flow among populations along the two rivers studied. This exchange of material may be important to counteract the effects of selection as well as genetic drift in small groups of trees in farmers fields, much as in a metapopulation, and may account for the weak genetic differentiation between the two rivers (G_st=0.0249, P<0.01). A comparison with samples from other landraces in Peru and Brazil showed the existence of an isolation-by-distance structure up to 3,000 km, consistent with gene flow on a regional scale, likely mediated by trade in the Amazon Basin. Results are discussed with regard to practical implications for the management of genetic resources with farming communities.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by H.F. Linskens     

The historic biogeography of India: isolation or contact?

Geophysical maps depicting continental movement have consistently shown India, as it moved northward, to be located far out in the Tethys Sea. India split off from the African east coast about 148 m.y.a. From that time onward, according to almost all geophysical accounts, India was isolated from all of other continents until the early Miocene when it made contact with Eurasia. But the biological data, both fossil and Recent, indicate that this concept cannot be correct. If India had really existed as an isolated, oceanic continent for about 100 m.y., it should have developed a peculiar biota with many endemic genera and families in its terrestrial and shallow marine habitats. But there are virtually no remains of organisms indicating that India was isolated for any substantial time (millions of years). Instead, we find that almost all Indian taxa were possessed in common with other continents. As time went on, the northern relationships became stronger and the southern ones weaker. Most of the recent geophysical accounts show India not making contact with Eurasia until the early Miocene, but fossil materials show that this event must have taken place by the early Eocene. It has been postulated that, as India moved northward, it created a biogeographic barrier that separated marine fish populations and resulted in the east-west provinces that are now apparent in the Indian Ocean. At the same time, the barrier effect was supposed to have resulted in the formation of sister species that are now located far apart. Information currently available indicates that most living, tropical marine species are probably not over 3 m.y. old. Consequently, the northward movement of India, which took place primarily between 148 and 50 m.y.a., could have no bearing on the relationships of modern species.     

Genetic Structure of Capelin (Mallotus villosus) in the Northwest Atlantic Ocean

Capelin (Mallotus villosus) is a commercially exploited, key forage-fish species found in the boreal waters of the North Pacific and North Atlantic Oceans. We examined the population structure of capelin throughout their range in the Canadian northwest Atlantic Ocean using genetic-based methods. Capelin collected at ten beach and five demersal spawning locations over the period 2002 through 2008 (N = 3,433 fish) were genotyped using six polymorphic microsatellite loci. Temporally distinct samples were identified at three beach spawning locations: Chance Cove, Little Lawn and Straitsview, Newfoundland. Four capelin stocks are assumed for fisheries management in the northwest Atlantic Ocean based on meristics, morphometrics, tag returns, and seasonal distribution patterns. Our results suggested groupings that were somewhat different than the assumed structure, and indicate at least seven genetically defined populations arising from two ancestral populations. The spatial mosaic of capelin from each of the two basal cluster groups explains much of the observed geographic variability amongst neighbouring samples. The genetic-defined populations were resolved at Jost’s D _est ≥ 0.01 and were composed of fish collected 1) in the Gulf of St. Lawrence, 2) along the south and east coasts of Newfoundland, 3) along coastal northern Newfoundland and southern Labrador, 4) along coastal northern Labrador, 5) near the Saguenay River, and at two nearshore demersal spawning sites, 6) one at Grebes Nest off Bellevue Beach on the east coast of Newfoundland, and 7) one off the coast of Labrador at Domino Run. Moreover, the offshore demersal spawners on the Scotian Shelf and Southeast Shoal appeared to be related to the inshore demersal spawners at Grebes Nest and in Domino Run and to beach spawners from the Gulf of St. Lawrence.