IUCN classification zones concord with, but underestimate, the population genetic structure of the zebra shark Stegostoma fasciatum in the Indo-West Pacific

The Indo-West Pacific (IWP), from South Africa in the western Indian Ocean to the western Pacific Ocean, contains some of the most biologically diverse marine habitats on earth, including the greatest biodiversity of chondrichthyan fishes. The region encompasses various densities of human habitation leading to contrasts in the levels of exploitation experienced by chondrichthyans, which are targeted for local consumption and export. The demersal chondrichthyan, the zebra shark, Stegostoma fasciatum , is endemic to the IWP and has two current regional International Union for the Conservation of Nature (IUCN) Red List classifications that reflect differing levels of exploitation: 'Least Concern' and 'Vulnerable'. In this study, we employed mitochondrial ND4 sequence data and 13 microsatellite loci to investigate the population genetic structure of 180 zebra sharks from 13 locations throughout the IWP to test the concordance of IUCN zones with demographic units that have conservation value. Mitochondrial and microsatellite data sets from samples collected throughout northern Australia and Southeast Asia concord with the regional IUCN classifications. However, we found evidence of genetic subdivision within these regions, including subdivision between locations connected by habitat suitable for migration. Furthermore, parametric F _ST analyses and Bayesian clustering analyses indicated that the primary genetic break within the IWP is not represented by the IUCN classifications but rather is congruent with the Indonesian throughflow current. Our findings indicate that recruitment to areas of high exploitation from nearby healthy populations in zebra sharks is likely to be minimal, and that severe localized depletions are predicted to occur in zebra shark populations throughout the IWP region.     

Synonymous but not the same: the causes and consequences of codon bias

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.     

Mutant p53: it’s not all one and the same

Mutation of the TP53 tumor suppressor gene is the most common genetic alteration in cancer, and almost 1000 alleles have been identified in human tumors. While virtually all TP53 mutations are thought to compromise wild type p53 activity, the prevalence and recurrence of missense TP53 alleles has motivated countless research studies aimed at understanding the function of the resulting mutant p53 protein. The data from these studies support three distinct, but perhaps not necessarily mutually exclusive, mechanisms for how different p53 mutants impact cancer: first, they lose the ability to execute wild type p53 functions to varying degrees; second, they act as a dominant negative (DN) inhibitor of wild type p53 tumor-suppressive programs; and third, they may gain oncogenic functions that go beyond mere p53 inactivation. Of these possibilities, the gain of function (GOF) hypothesis is the most controversial, in part due to the dizzying array of biological functions that have been attributed to different mutant p53 proteins. Herein we discuss the current state of understanding of TP53 allele variation in cancer and recent reports that both support and challenge the p53 GOF model. In these studies and others, researchers are turning to more systematic approaches to profile TP53 mutations, which may ultimately determine once and for all how different TP53 mutations act as cancer drivers and whether tumors harboring distinct mutations are phenotypically unique. From a clinical perspective, such information could lead to new therapeutic approaches targeting the effects of different TP53 alleles and/or better sub-stratification of patients harboring TP53 mutant cancers.Subject terms: Cancer genetics, Tumour-suppressor proteins     

Amyloid structure--one but not the same: the many levels of fibrillar polymorphism

Many proteins and peptides can form amyloid-like structures both in vivo and in vitro. Although strikingly similar fibrillar structures can be observed across a variety of amino acid sequences, the fibrils formed often exhibit a stunning wealth of polymorphisms at the level of electron or atomic force microscopy. This appears to violate the Anfinsen principle seen for globular proteins, where each protein sequence codes for just one well-defined fold. To a large extent, polymorphism reflects variable packing of a single protofilament structure in the mature fibrils. However, we and others have recently demonstrated that polymorphism can also reflect real structural differences in the molecular packing of the polypeptide chains leading to several possible protofilament structures and diverse mature fibrillar structures. Glucagon has been a particularly useful model system for studying the fibrillogenesis mechanisms that lead to the formation of structural polymorphism, thanks to its single tryptophan residue and the availability of large quantities at pharmaceutical-grade quality. Combinations of structural investigations and seed extension experiments have revealed the reproducible formation of at least five different self-propagating fibril types from subtle variations in growth conditions. These reflect the underlying complexity of the peptide conformational landscape and provide a link to natively disordered proteins, where structure is dictated by context in the form of different binding partners. Here we review some of the latest advances in the study of glucagon fibrillar polymorphism and their implications for mechanisms of fibril formation in general.     

Genetic and morphological variation of Rhizophora mangle (red mangrove) along the northern Pacific coast of Nicaragua

Red mangrove (Rhizophora mangle) dominates in tidally active areas of neotropical mangrove forests. Despite the ecological and economic importance of this species, we still know little about the genetic structure and diversity of its natural populations. In particular, Nicaraguan populations have not yet been investigated although they could be important for a better understanding of the evolutionary history of R. mangle in Mesoamerica. The aim of this study was to estimate the genetic and morphological variability of 4 populations sampled along the northwestern coast of Nicaragua. Microsatellite analysis showed higher levels of allelic diversity (30 alleles and a mean number of allele per locus per population = 6.42) than reported for the same species in other sites of tropical America. This variability could be attributed to the existence of a glacial refugium in the studied area and/or to repeated introgression among closely related species. Analysis of molecular variance (AMOVA) revealed that there was little but significant variation among the sampled sites suggesting that the studied populations cannot be considered as a single panmictic group, although they are closely related. This result was confirmed by the Bayesian analysis and UPGMA dendrogram showing three genetically distinct clusters. Bayesian analysis of migration rates showed that propagule dispersion associated with marine currents is an important factor shaping the observed genetic structure. The scatterplot from discriminant analysis indicated significant phenotypic differences between two groups, mainly related to specific leaf area variation. The morphological similarity between PR and PO was consistent with the results of molecular analysis, supporting the common origin of these two populations. Nevertheless, we did not find a significant statistical correlation between microsatellite and morphological data. In conclusion, the results reported here contribute to a better understanding of R. mangle genetic structure and would provide baseline information to guide land managers in implementing conservation initiatives in Nicaragua.     

Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species)

Species of Saccostrea are common oysters on Indo-Pacific rockyshores. The taxonomy of this genus is unclear, however, becauseof morphological plasticity among its constituent species. Oystersamples with distinct morphotypes were collected from shoresexperiencing different degrees of wave exposure in Japan, Taiwan,China, Vietnam, Singapore and Australia. Intraspecific and interspecificvariations in shell characters have been identified. Only S.kegaki could be readily differentiated from S. cucullata-B,S. cucullata-C and S. mordax by multivariate shell allometricanalyses. Phylogenetic analyses using partial mitochondrial16S DNA sequences of approximately 513 base pairs identifiedtwo clades that correspond to superspecies, i.e. putative S.cucullata and putative S. mordax, comprising nine and two lineagesfrom the Indo-West Pacific, respectively. These are S. cucullata-A,B, C, D, E, F, G, S. kegaki and S. glomerata in one clade, andS. mordax-A and B in the other. Interspecific sequence divergence(Kimura-2-parameter values) between lineages ranged from 1.02%to 11.74%. Both S. cucullata-C and S. kegaki are restrictedto the northern hemisphere, whereas S. glomerata seems to bea temperate species from the southern hemisphere. S. cucullata-Doccurs only in Taiwan. Other species, i.e. S. cucullata-A, B,D, E and F and S. mordax-A and B, have a wide range on rockyshores in the tropical and subtropical Western Pacific and inboth northern and southern hemispheres. (Received 7 January 2005; accepted 4 November 2005)     

Population fragmentation leads to isolation by distance but not genetic impoverishment in the philopatric Lesser Kestrel: a comparison with the widespread and sympatric Eurasian Kestrel

Population fragmentation is a widespread phenomenon usually associated with human activity. As a result of habitat transformation, the philopatric and steppe-specialist Lesser Kestrel Falco naumanni underwent a severe population decline during the last century that increased population fragmentation throughout its breeding range. In contrast, the ubiquitous Eurasian Kestrel Falco tinnunculus did not suffer such adverse effects, its breeding range still remaining rather continuous. Using microsatellites, we tested the effects of population fragmentation on large-scale spatial patterns of genetic differentiation and diversity by comparing these two sympatric and phylogenetically related species. Our results suggest that habitat fragmentation has increased genetic differentiation between Lesser Kestrel populations, following an isolation-by-distance pattern, while the population of Eurasian Kestrels is panmictic. Contrary to expectations, we did not detect significant evidence of reduced genetic variation or increased inbreeding in Lesser Kestrels. Although this study reports genetic differentiation in a species that has potential for long-distance dispersal but philopatry-limited gene flow, large enough effective population sizes and migration may have been sufficient to mitigate genetic depauperation. A serious reduction of genetic diversity in Lesser Kestrels would, therefore, only be expected after severe population bottlenecks following extreme geographic isolation.     

Pure species in a continuum of genetic and morphological variation: sympatric oaks at the edge of their range

Background and Aims Studies on oaks (Quercus spp.) have often been hampered by taxonomic confusion, a situation further compounded by the occurrence of extensive interspecific hybridization. In the present study, a combination of genetic and morphological analyses was used to examine sympatric populations of Q. petraea and Q. robur at the north-western edge of their ranges in Northern Ireland, since it had previously been suggested that hybridization could facilitate the apparent rapid, long-distance dispersal of oaks following the glaciations.Methods Samples were collected from 24 sites across Northern Ireland that had been previously designated as ancient or semi-natural woodland. Genotypes were obtained from a total of 950 trees using 12 nuclear microsatellite loci, and admixture coefficients were calculated based on a Bayesian clustering approach. Individuals were also classified as Q. petraea, Q. robur or hybrids based on two objective morphometric characters shown previously to delineate pure individuals effectively. Genetically ‘pure’ individuals of both species, as defined by the Bayesian clustering, were also genotyped for five chloroplast microsatellites.Key Results Genetic and morphological analyses both indicated the presence of pure individuals of both species, as well as a continuum of intermediates. There was a good agreement between the molecular and morphological classification, with a generally clear separation between pure individuals.Conclusions Despite millennia of hybridization and introgression, genetically and morphologically pure individuals of both Q. petraea and Q. robur can be found at the edge of their range, where both species occur sympatrically. The high proportion of individuals exhibiting introgression compared with previous studies may reflect the historical role of hybridization in facilitating dispersal following the glaciations. This is further supported by the significantly higher chloroplast diversity in Q. robur compared with Q. petraea.     

Patterns of genetic variation do not correlate with geographical distance in the reef-building coral Pocillopora meandrina in the South Pacific

Dispersal may be a critical factor in the ability of reef-building corals to recover after major disturbances. We studied patterns of geographical structure using four microsatellite markers in seven South Pacific populations of Pocillopora meandrina, a major coral species from Polynesia. Variation within populations showed evidence of heterozygote deficiency. Genetic differentiation between populations was detected at a large scale (2000 km) between the Tonga and the Society Islands. Within the Society Islands, four of the five studied populations from Bora Bora, Moorea and Tahiti were not significantly different from each other. Unexpectedly, one of the three populations surveyed in Moorea was genetically different from the other two populations of this island (that were 5 and 10 km apart), and from the populations of the other two surveyed islands in this archipelago. We cannot rule out the possibility that this pattern is an equilibrium state, whereby short-range dispersal is locally more differentiating than long-range dispersal, as has been suggested by similar patterns reported in other studies. An alternative explanation that is globally consistent with all observations is that this is the signature of a large-scale destruction event, as for instance a bleaching event, followed by the recent restoration of populations by new colonists.     

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.     

水源涵养与水文调节:和而不同的陆地生态系统水文服务

水与生态系统的关系是重要的科学问题,并且受到社会广泛关注。水源涵养和水文调节都是陆地生态系统所能提供的水文服务,并从生态水文和水资源角度把生态系统的健康和完整性与人类社会的持续发展紧密联系起来,从而也要求动态和综合的视角加以深入研究。基于生态水文过程原理,对水源涵养和水文调节的概念进行了辨析,认为前者是后者的有机组成部分,相对具体、应用中务求精确明晰;后者则更具包容性、客观性和广泛适用性。文章进一步简要分析了当前国内外生态系统水源涵养和水文调节服务的主导评估方法,结果表明,水源涵养的评估以储水量法为主,而水文调节则以基于降水和蒸散的水量平衡法及综合模型法(如SWAT)为主。从生态系统服务相互作用的角度考量,实际上水源涵养和水文调节及其相关的其它服务类型(如固碳、土壤保持、生物生产、淡水供给等)存在着复杂的动态权衡或协同关系,在科学研究和生态系统管理实践中必须统筹考虑,以确保对科学问题的准确把握和促进"水-生态-社会系统"的高效、可持续发展。为此,必须加强对生态水文过程的长期观测和实验研究,并且关注空间异质性及尺度效应、时间动态性和利益相关者需求的多维性。     

Similar but not the same: normobaric and hyperbaric pulmonary oxygen toxicity, the role of nitric oxide

Pulmonary manifestations of oxygen toxicity were studied and quantified in rats breathing >98% O(2) at 1, 1.5, 2, 2.5, and 3 ATA to test our hypothesis that different patterns of pulmonary injury would emerge, reflecting a role for central nervous system (CNS) excitation by hyperbaric oxygen. At 1.5 atmosphere absolute (ATA) and below, the well-recognized pattern of diffuse pulmonary damage developed slowly with an extensive inflammatory response and destruction of the alveolar-capillary barrier leading to edema, impaired gas exchange, respiratory failure, and death; the severity of these effects increased with time over the 56-h period of observation. At higher inspired O(2) pressures, 2-3 ATA, pulmonary injury was greatly accelerated but less inflammatory in character, and events in the brain were a prelude to a distinct lung pathology. The CNS-mediated component of this lung injury could be attenuated by selective inhibition of neuronal nitric oxide synthase (nNOS) or by unilateral transection of the vagus nerve. We propose that extrapulmonary, neurogenic events predominate in the pathogenesis of acute pulmonary oxygen toxicity in hyperbaric oxygenation, as nNOS activity drives lung injury by modulating the output of central autonomic pathways.     

The Chromodorididae (Opisthobranchia: Mollusca) of the Indo-West Pacific: Noumea purpurea and Chromodoris decora colour groups

Nine species of chromodorid nudibranchs are described including a new species of Durvilledoris and a new species of Noumea. The Noumea purpurea colour group consists of five species with a pink, purple or reddish-purple background and a median white line, sometimes broken. The Chromodoris decora colour group also has white longitudinal lines with a pinkish background colour and usually an orange border. A non-chromodorid juvenile, probably a species of Hexabranchus , is compared with the species of the C. decora colour group.     

Geographic variation in bird songs: examination of the effects of sympatric related species on the acoustic structure of songs

Birdsong evolution has influenced by various ecological and social factors. When related species that sing similar songs coexist, the acoustic properties of the songs of one or both species may shift, and the songs may diverge. We investigated geographic variation in the songs of the Japanese tit (Parus minor) and the varied tit (Poecile varius) in the Ryukyu Archipelago, Japan, whose islands harbor either one or both species. The songs of the two species exhibited similar structure, but acoustic measurements differed between them. For example, varied tits sang songs at higher frequency than Japanese tits did. The songs of both species varied geographically. At sites with higher relative densities of varied tits, Japanese tits sang lower frequency songs, indicating that in areas of coexistence, Japanese tits sang songs that had acoustically diverged from those of varied tits. Song variation in varied tits was not related to sympatry with Japanese tits. These asymmetric results suggest that the subordinate Japanese tit modified the acoustic characteristics of its song to avoid harassment by the dominant varied tit. We observed no effects of genetic divergence or local intraspecific density on Japanese tit or varied tit songs. This study used geographic variation to examine hypotheses of song evolution, and the results highlight the importance of character displacement.     

Patterns of population genetic structure and diversity across bumble bee communities in the Pacific Northwest

Patterns of genetic structure and diversity are largely mediated by a species’ ecological niche and sensitivity to climate variation. Some species with narrow ecological niches have been found to exhibit increased population differentiation, limited gene flow across populations, and reduced population genetic diversity. In this study, we examine patterns of population genetic structure and diversity of four bumble bee species that are broadly sympatric, but do not necessarily inhabit the same ecological niche in the Pacific Northwest of the United States. Testing for the effect of isolation by geographic distance (IBD) with linearized F _st and D _est found that Bombus sylvicola and B. mixtus exhibited significant IBD across populations. In contrast, both B. melanopygus and B. flavifrons, two species that are distributed across a broad elevation gradient, exhibited no IBD, a result further corroborated by Bayesian a priori population assignment tests. Furthermore, we discovered that B. sylvicola populations distributed on the Olympic Peninsula have significantly less average allelic diversity than populations distributed in the Cascade Mountains. Our results suggest that populations distributed in the Olympic Mountains represent a distinct genetic cluster relative to the Cascade Mountains, with B. sylvicola and B. mixtus likely experiencing the greatest degree of population genetic differentiation relative to B. flavifrons and B. melanopygus. While bumble bees are known to co-exist across a diversity of habitats, our results demonstrate that underlying population genetic structure and diversity may not necessarily be similar across species, and are largely governed by their respective niches.     

Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that populations within species are highly differentiated in terms of their morphology, behaviour, ecology and molecular genetic variation. Despite this level of variability, differences between species are sometimes small, possibly reflecting the fact that reproductive isolation is not always complete and there exists the opportunity for genetic exchange between taxa through hybridization. The present study uses sequence data from a mitochondrial gene to further investigate genetic variation in Society Island Partula. Most populations are found in this study to be highly differentiated, but within individual species there seems to be no simple relationship either between genetic distance and geographical proximity, or between variation in mitochondria and that in allozymes or morphological characteristics. Among species there appears to be no simple correlation between degrees of reproductive isolation and genetic relatedness according to mitochondrial DNA. The results suggest that past events as well as ongoing drift and selection may have been important in affecting patterns of variation. Similarities among species at specific localities suggest that there must have been some genetic exchange in the past, although this may not necessarily reflect ongoing rates of hybridization. The discrepancy between results for different markers probably reflects the differential effects of drift and selection on mitochondrial and nuclear genes.     

Quantum yield variation across the three pathways of photosynthesis: not yet out of the dark

The convergent quantum yield hypothesis (CQY) assumes that thermodynamics and natural selection jointly limit variation in the maximum energetic efficiency of photosynthesis in low light under otherwise specified conditions (e.g. temperature and CO(2) concentration). A literature survey of photosynthetic quantum yield (phi) studies in terrestrial plants from C(3), C(4), and CAM photosynthetic types was conducted to test the CQY hypothesis. Broad variation in phi values from C(3) plants could partially be explained by accounting for whether the measuring conditions were permissive or restrictive for photorespiration. Assimilatory quotients (AQ), calculated from the CO(2) phi:O(2) phi ratios, indicated that 49% and 29% of absorbed light energy was allocated to carbon fixation and photorespiration in C(3) plants, respectively. The unexplained remainder (22%) may represent diversion to various other energy-demanding processes (e.g. starch synthesis, nitrogen assimilation). Individual and cumulative effects of these other processes on photosynthetic efficiency are poorly quantified. In C(4) plants, little variation in phi values was observed, consistent with the fact that C(4) plants exhibit little photorespiration. As before, AQ values indicate that 22% of absorbed light energy cannot be accounted for by carbon fixation in C(4) plants. Among all three photosynthetic types, the phi of photosynthesis in CAM plants is the least studied, appears to be highly variable, and may present the greatest challenge to the CQY hypothesis. The high amount of energy diverted to processes other than carbon fixation in C(3) and C(4) plants and the poor characterization of photosynthetic efficiency in CAM plants are significant deficiencies in our otherwise robust understanding of the energetics of terrestrial photoautotrophy.     

Structure of rhodopsin and the superfamily of seven-helical receptors: the same and not the same

The crystal structure of rhodopsin provides significant insights concerning structure/activity relationships in visual pigments and related G-protein-coupled receptors. The specific arrangement of seven-transmembrane helices is stabilized by a series of intermolecular interactions that appear to be conserved among Family A receptors. However, the potential for structural and functional diversity among members of the superfamily of seven-helical receptors presents a significant future challenge.