The effect of migratory behaviour on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon Salmo salar

The genetic diversity of anadromous and freshwater Atlantic salmon ( Salmo salar ) populations from north-west Russia and other north European locations was compared using microsatellite variation to evaluate the importance of anadromous migration, population size and population glacial history in determining population genetic diversity and divergence. In anadromous Atlantic salmon populations, the level of genetic diversity was significantly higher and the level of population divergence was significantly lower than among the freshwater Atlantic salmon populations, even after correcting for differences in stock size. The phylogeographic origin of the populations also had a significant effect on the genetic diversity characteristics of populations: anadromous populations from the basins of the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than anadromous populations from the Baltic Sea basin. Among the freshwater populations, the result was the opposite: the Baltic freshwater populations were more variable. The results of this study imply that differences in the level of long-term gene flow between freshwater populations and anadromous populations have led to different levels of genetic diversity, which was also evidenced by the hierarchical analysis of molecular variance. Furthermore, the results emphasize the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash. Hence, high conservation status is warranted in order to ensure the long-term survival of the limited number of European populations with this life-history strategy.     

Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses

Journal of Plant Research - Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of...     

Trematode infections in freshwater snails and cattle from the Kafue wetlands of Zambia during a period of highest cattle-water contact

A total of 984 snails, comprising nine species, were collected from six areas in the Kafue wetlands between August and October 2003 to assess larval trematode infections. Of these, 135 (13.7%) were positive. Most trematode infections were recorded from Lymnaea natalensis (42.8%), which harboured four of the five morphologically different cercariae found. No trematodes were recovered from Bellamya capillata, Biomphalaria pfeifferi, Melanoides tuberculata, Physa acuta and Cleopatra nswendweensis. One snail (0.2%) of 416 Bulinus snails shed brevifurcate-apharyngeate distome cercariae while three (0.7%) shed amphistomes. Gymnocephalous and longifurcate-pharyngeate distome were the commonest types of cercariae recorded while xiphidiocercaria was the least common. The highest prevalence rates of F. gigantica (68.8%) and amphistomes (50.0%) in cattle (n = 101) were in Chiyasa while those in Kaleya had the lowest (9.1 and 18.2%, respectively). In most habitats, infections were recorded in both cattle and snails. Critical determinants of infection may have been the distance of settlements and/or cattle kraals, the number of animals in nearby homesteads and the presence of susceptible host snails. This study suggests that fascioliasis and amphistomiasis could be major constraints of cattle production in the Kafue wetlands because favourable factors were available to introduce and maintain the infections. It further provides a starting point for some comprehensive studies on snail-related aspects of transmission and snail host ecology in Zambia.     

Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bamboo.

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics (Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice (Oryza sativa) and sugarcane (Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.     

Temporal changes of genetic population structure and diversity in the endangered Blakiston's fish owl (Bubo blakistoni) on Hokkaido Island, Japan, revealed by microsatellite analysis

The Blakiston's fish owl (Bubo blakistoni) population on Hokkaido Island, Japan, decreased to less than one hundred individuals over the last century due to habitat disruption by human activity. Although the ongoing conservation management has slightly restored the population, it remains endangered. In order to assess the genetic variation and population structure of the Blakiston's fish owl in Hokkaido, we genotyped eight microsatellite loci on 120 individuals sampled over the past three decades. The genotype data set showed low levels of genetic variation and gene flow among the geographically isolated five subpopulations. Comparative analysis of past and current populations indicated that some alleles shared by past individuals had been lost, and that genetic variation had declined over the last three decades. The result suggests that the genetic decline may have resulted from inbreeding and/or genetic drift due to bottlenecks in the Hokkaido population. The present study provides invaluable genetic information for the conservation and management of the endangered Blakiston's fish owl in Hokkaido.     

Notocotylus ikutai n. sp. (Digenea: Notocotylidae) from lymnaeid snails and anatid birds in Hokkaido,Japan

An unknown species of the genus Notocotylus (Digenea: Notocotylidae) was found as the larval stage from the lymnaeid snail, Radix auricularia, in a static water area of the Chubetsu River, Hokkaido, the northernmost island of Japan. A DNA barcoding identification system was applied to detect the adult stage. Through the inspection of anatid game birds in Hokkaido, Anas crecca, Anas platyrhynchos, Anas zonorhyncha, and Mareca penelope were demonstrated to serve as the definitive hosts. The detailed morphological features of the species were characterized using adults raised experimentally in immunosuppressed mice and naturally developed larvae in R. auricularia. Although the species is morphologically similar to Notocotylus attenuatus and Notocotylus magniovatus in both adult and larval stages, its taxonomic independence was confirmed by a comprehensive study based on molecular phylogeny, morphology, and ecology. Here we propose Notocotylus ikutai n. sp. for this species. The migratory behavior of the anatid hosts and the North-Eurasian distribution of R. auricularia suggest that the new species is widely distributed in the northern Far East.     

The Ong Be language-speaking population in Hainan Island: genetic diversity,phylogenetic characteristics and reflections on ethnicity

Molecular Biology Reports - The Ong Be language-speaking population (Lingao population) settled in the north-central coast of Hainan Island and has attracted little attention because of its small...     

Methotrexate-resistance in plants: genetic,molecular and cytological analyses

Abstract

Carrot cell lines resistant to methotrexate were selected and, upon analysis, shown to overproduce dihydrofolate reductase, the target anzyme of the antifolic agent, as the main biochemical alteration. This feature behaves as a dominant trait as judged by somatic hybridization. Using this selective marker, asymmetric fertile somatic hybrids between carrot and tobacco were obtained by protoplast fusion using the gamma-irradiation technique. Dihydrofolate reductase was purified and characterized as regard kinetic and structural properties and shown to be a bifunctional protein associated with thymidylate synthase. The pure protein was injected into a rabbit to obtain polyclonal antibodies which were used for the screning of an expression library in the vector lambda gt11 and the subcellular localization of the bifunctional polypeptide.     

Drivers of symbiont diversity in freshwater snails: a comparative analysis of resource availability,community heterogeneity,and colonization opportunities

Decades of community ecology research have highlighted the importance of resource availability, habitat heterogeneity, and colonization opportunities in driving biodiversity. Less clear, however, is whether a similar suite of factors explains the diversity of symbionts. Here, we used a hierarchical dataset involving 12,712 freshwater snail hosts representing five species to test the relative importance of potential factors in driving symbiont richness. Specifically, we used model selection to assess the explanatory power of variables related to host species identity, resource availability (average body size, host density), ecological heterogeneity (richness of hosts and other taxa), and colonization opportunities (wetland size and amount of neighboring wetland area) on symbiont richness in 146 snail host populations in California, USA. We encountered a total of 23 taxa of symbionts, including both obligatory parasites such as digenetic trematodes as well as more commensal, mutualistic, or opportunistic groups such as aquatic insect larvae, annelids, and leeches. After validating richness estimates per host population using species accumulative curves, we detected positive effects on symbiont richness from host body size, total richness of the aquatic community, and colonization opportunities. Neither snail density nor the richness of snail species accounted for significant variation in symbiont diversity. Host species identity also affected symbiont richness, with higher gamma and average alpha diversity among more common host species with higher local abundances. These findings highlight the importance of multiple, concurrent factors in driving symbiont richness that extend beyond epidemiological measures of host abundance or host diversity alone.     

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging,but endangered,freshwater mussel

Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure throughout its range. Mitochondrial DNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in most populations; however, all populations have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.     

Environmental and climatic determinants of molecular diversity and genetic population structure in a coenagrionid damselfly

Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean F_ST = 0.06, D_est = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. F_ST-and D_est-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats.     

Minimum population size,genetic diversity,and social structure of the Asian elephant in Cat Tien National Park and its adjoining areas,Vietnam, based on molecular genetic analyses

Vietnam’s elephant population that has suffered severe declines during the past three decades is now believed to number 60–80 individuals in the wild. Cat Tien National Park is thought to be one of the key areas for the recovery of Vietnam’s elephants. We carried out a molecular genetic study of elephants in Cat Tien National Park and its adjoining areas with the objectives of estimating minimum population size, assessing genetic diversity, and obtaining insights into social organization. We obtained a minimum population size of 11 elephants based on a combination of unique nuclear microsatellite genotypes and mitochondrial haplotypes. While mitochondrial diversity based on a 600-base pair segment was high in this small sample of individuals, the six microsatellite loci examined showed low diversity and the signature of a recent population bottleneck. Along with nuclear genetic depauperation of Cat Tien’s elephants, we also report disruption of normal social organization, with different matrilines having coalesced into a single social group because of anthropogenic disturbance. The results emphasize the critical condition of this elephant population and the need for urgent conservation measures if this population is to be saved.     

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

A total of 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 150 accessions of cultivated rice (Oryza sativa L.) from Korea, China, and Japan. A total of 375 alleles were detected with an average of 12.9 per locus. The averaged values of gene diversity and polymorphism information content (PIC) for each SSR locus were 0.7001 and 0.6683, respectively. Alleles per locus in Korean rice were 8.8, whereas 8.1 and 7.2 alleles per locus were found in Chinese and Japanese rice, respectively. The mean gene diversity in Korean, Chinese, and Japanese rice was 0.6058, 0.6457, and 0.5174, respectively, whereas the mean PIC values for each SSR locus were 0.5759, 0.6138, and 0.4881, respectively. The genetic diversity of the Korean and Chinese cultivars was higher than that of the Japanese cultivars, and the genetic diversity ofjaponica was higher than that ofindica. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 22% in contrast to 78% for the within-population component. The overallFST value was 0.2180, indicating a moderate differentiation among groups. The results could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.     

Taxonomic revision of three species of the genus Genarchopsis (Digenea: Hemiuroidea: Derogenidae) in Japan by molecular phylogenetic analyses

The taxonomic status of three nominal species of Genarchopsis (G. goppo Ozaki, 1925; G. gigi Yamaguti 1939; and G. fellicola Shimazu, 1995) (Digenea: Hemiuroidea: Derogenidae) was investigated by molecular phylogenetic analyses using partial sequences of the genomic ITS-1 region and the mitochondrial COI. The analyzed samples were divided into four groups: Lake Biwa, West Japan, Central Japan and G. fellicola. The Lake Biwa group, a sister taxon to the other three groups, was interpreted as G. gigi, so we concluded that G. gigi is valid; thus, this species is resurrected taxonomically. The specimens from the type host caught near the type locality of G. goppo were included in the West Japan group, so this group was regarded as G. goppo sensu stricto. Because the phylogenetic position of the Central Japan group could not be confirmed, it was identified tentatively as G. goppo, even though this species thus becomes paraphyletic. The taxonomic validity of G. fellicola was reconfirmed. The divergence time of G. gigi is discussed in relation to the geological history of Lake Biwa and the origin of host species.     

Genetic diversity, population structure and phylogenetic inference among Italian Orchids of the Serapias genus assessed by AFLP molecular markers

The means by which new species arise remain a fundamental question in the Orchid family evolution. Even if the Orchid-pollinator interactions are highly specific, events of cross-hybridization in Serapias are possible and represent a central issue of the plant's evolutionary biology. Italian Orchids have a wide variety of pollination systems and highly diverse floral traits, considered as some of the main tools for activating the speciation processes. The assess of diversity in Serapias taxa and eventual phylogenetic relationships among Serapias lingua, S. parviflora, S. vomeracea, S. apulica, S. nurrica, S. neglecta, S. cordigera, S. politisii, and some putative inter-specific hybrids were investigated at the DNA level by AFLP markers. The present molecular study on Serapias populations (1) confirms some previous finding, (2) opens new hypotheses on the possible evolutionary and taxonomic relationships existing among the Serapias species, and (3) gives indications about the real consistence of hybrid individuals in a genus characterized by a relevant gene flow.     

Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish,Bagrus docmak,in East Africa

The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak ). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N  = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (?3.769 and ?5.049; p  < .05). Heterozygosity deficiencies and restricted effective population size (N _eLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (?_ST = 0.62 for mtDNA; p  < .001) and contemporary (microsatellite F _ST = 0.460; p  < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro‐ and micro‐evolutionary forces in the formation of the East African teleost fauna.