Recent history of the European Nassarius nitidus (Gastropoda): phylogeographic evidence of glacial refugia and colonization pathways

Because marine species respond differentially to factors governing survival and gene flow, closely related taxa may display dissimilar phylogeographic histories. New data for the patchily distributed gastropod Nassarius nitidus throughout its Atlantic–Mediterranean range (collected during 2008 and 2009) were used to investigate its phylogeography and recent demography. Results based on mitochondrial COI sequences of 422?N. nitidus individuals from 15 localities revealed contrasting phylogeographic and demographic patterns among N. nitidus populations from each basin. Data suggest the existence of two glacial refugia, one in the Atlantic, around the Iberian Peninsula, and the other in the Paleo-Mediterranean Sea (Adriatic). Bayesian skyline reconstructions suggest that the Adriatic population of N. nitidus remained largely unaffected by the Last Glacial Maximum (LGM), whereas the Iberian Atlantic region experienced dramatic exponential growth after its conclusion. Contemporary North Sea populations of N. nitidus are the endpoint of a leading-edge recolonization process from a southern position. Additionally, a reanalysis of pre-existing material for the continuously distributed close congener N. reticulatus was used to compare both species in the late histories. In contrast to N. nitidus, N. reticulatus prospered during the LGM and experienced an earlier Atlantic expansion during the previous interglacial period. Despite similar life history and dispersal potential, the results here presented suggest that subtle differences in microhabitat requirements between the two species have had important consequences for their particular distribution in response to glacial events.     

Clonal architecture in an intertidal bed of the dwarf eelgrass <Emphasis Type="Italic">Zostera noltii</Emphasis> in the Northern Wadden Sea: persistence through extreme physical perturbation and the importance of a seed bank

Genotypic structure and temporal dynamics of the dwarf seagrass, Zostera noltii, were studied in an intertidal meadow that has persisted since prior to 1936 near the Wadden Sea island of Sylt. Samples were collected from two 10 × 10 m plots separated by 250 m from May 2002 to June 2005 and from four 1 × 1 m plots from June 2003 to September 2004. All the samples were genotyped with nine microsatellite loci. No genotypes were shared between the plots separated by 250 m. Genetic diversity was higher in the Wadden Sea than in the other regions of its geographic range. The average clone size (genets) (SD) in the two plots was 1.38 (0.26) and 1.46 (0.4) m2, respectively, with a range up to 9 m2 and <20% persisted for >4 years. A high genetic and genotypic diversity was maintained by annual recruitment of seedlings despite a dramatic decrease in ramet density that coincided with the severe heat stress event of 2003. Fine-scale (1 m2) analysis suggested that extensive loss of seagrass cover precluded space competition among the genets, while a persistent seed bank prevented local extinction. Long-term persistence of Z. noltii meadows in the intertidal Wadden Sea was achieved by high genet turnover and frequent seedling recruitment from a seed bank, in contrast to the low diversity observed in large and long-living clones of Z. noltii and other seagrasses in subtidal habitats.     

Biocultural diversity in traditional rice-based agroecosystems: indigenous research and conservation of mavo (Oryza sativa L.) upland rice landraces of eastern Indonesia

Traditional crop landraces play dynamic roles in the expression of native biological and cultural diversity via their central position in the genetic resource base, agroecosystems and social heritage of indigenous peoples. Farmer varieties provide farmers with an “agricultural survival kit” for household welfare and for adaptation to changing conditions. These varieties meet local cultural practices and environmental constraints, and play an intrinsic role in cultural survival by constituting a living repository of ancestral customs including cultivar-specific recipes, songs, handicrafts, stories of origin, and unique planting, harvesting, processing, and storage rituals and techniques. The centrality of rice in Southeast Asian agricultural and social systems, contrasted with the significant erosion of rice-based biological and cultural diversity in native communities, calls for increased attention to the links between traditional rice varieties and indigenous rice-based customs. This study represents the research efforts of rice farmers pertaining to the Tado clan, a Kempo Manggarai community on Flores␣Island, in association with USA academicians. Research results demonstrate: (i) a complex suite of upland rice-based ethnobotanical traditions; (ii) significant and␣dynamic regional flux and dissemination of “old” and “new” landraces; (iii)␣community-level maintenance of distinct genotypes across a range of microenvironments; (iv) localized “extinctions” of ancestral landraces within 1–2 generations and a concomitant loss of related traditions; and (v) the contributions of a collaborative (indigenous and academic) approach to ethnographic and agronomic research.     

ASSESSING LAND USE IMPACTS ON WATER QUALITY USING MICROBIAL SOURCE TRACKING1

ABSTRACT: A renewed emphasis on source water protection and watershed management has resulted from recent amendments and initiatives under the Safe Drinking Water Act and the Clean Water Act. Knowledge of the impact of land use choices on source water quality is critical for efforts to properly manage activities within a watershed. This study evaluated qualitative relationships between land use and source water quality and the quantitative impact of season and rainfall events on water quality parameters. High levels of specific conductance tended to be associated with dense residential development, while organic carbon was elevated at several forested sites. Turbidity was generally higher in more urbanized areas. Source tracking indicators were detected in samples where land use types would predict their presence. Coliform levels were statistically different at the 95 percent confidence levels for winter versus summer conditions and dry versus wet weather conditions. Other water quality parameters that varied with season were organic carbon, turbidity, dissolved oxygen, and specific conductance. These results indicate that land use management can be effective for mitigating impacts to a water body; however, year‐ round, comprehensive data are necessary to thoroughly evaluate the water quality at a particular site.     

Preconception and preimplantation diagnosis for cystic fibrosis

Preimplantation diagnosis provides couples at high genetic risk the possibility of avoiding genetic disease without the need for prenatal diagnosis and selective abortion of the affected pregnancy. Following extensive background work on the reliability of genetic diagnosis in a single cell, we offered on a research basis preimplantation diagnosis to five couples at risk for offspring with the delta-F508 mutation (the major mutation causing cystic fibrosis). There was no detrimental effect from polar body removal on either fertilization or preimplantation development. Genetic analysis, undertaken in 22 polar bodies and 15 corresponding blastomeres, identified 21 embryos of which ten were transferred.     

Evaluation and classification of severity for 176 genes on an expanded carrier screening panel

Background

Disease severity is important when considering genes for inclusion on reproductive expanded carrier screening (ECS) panels. We applied a validated and previously published algorithm that classifies diseases into four severity categories (mild, moderate, severe, and profound) to 176 genes screened by ECS. Disease traits defining severity categories in the algorithm were then mapped to four severity-related ECS panel design criteria cited by the American College of Obstetricians and Gynecologists (ACOG).

Methods

Eight genetic counselors (GCs) and four medical geneticists (MDs) applied the severity algorithm to subsets of 176 genes. MDs and GCs then determined by group consensus how each of these disease traits mapped to ACOG severity criteria, enabling determination of the number of ACOG severity criteria met by each gene.

Results

Upon consensus GC and MD application of the severity algorithm, 68 (39%) genes were classified as profound, 71 (40%) as severe, 36 (20%) as moderate, and one (1%) as mild. After mapping of disease traits to ACOG severity criteria, 170 out of 176 genes (96.6%) were found to meet at least one of the four criteria, 129 genes (73.3%) met at least two, 73 genes (41.5%) met at least three, and 17 genes (9.7%) met all four.

Conclusion

This study classified the severity of a large set of Mendelian genes by collaborative clinical expert application of a trait-based algorithm. Further, it operationalized difficult to interpret ACOG severity criteria via mapping of disease traits, thereby promoting consistency of ACOG criteria interpretation.

     

Modeling population effects of the Deepwater Horizon oil spill on a long-lived species

The 2010 Deepwater Horizon (DWH) oil spill exposed common bottlenose dolphins (Tursiops truncatus) in Barataria Bay, Louisiana to heavy oiling that caused increased mortality and chronic disease and impaired reproduction in surviving dolphins. We conducted photographic surveys and veterinary assessments in the decade following the spill. We assigned a prognostic score (good, fair, guarded, poor, or grave) for each dolphin to provide a single integrated indicator of overall health, and we examined temporal trends in prognostic scores. We used expert elicitation to quantify the implications of trends for the proportion of the dolphins that would recover within their lifetime. We integrated expert elicitation, along with other new information, in a population dynamics model to predict the effects of observed health trends on demography. We compared the resulting population trajectory with that predicted under baseline (no spill) conditions. Disease conditions persisted and have recently worsened in dolphins that were presumably exposed to DWH oil: 78% of those assessed in 2018 had a guarded, poor, or grave prognosis. Dolphins born after the spill were in better health. We estimated that the population declined by 45% (95% CI 14–74) relative to baseline and will take 35 years (95% CI 18–67) to recover to 95% of baseline numbers. The sum of annual differences between baseline and injured population sizes (i.e., the lost cetacean years) was 30,993 (95% CI 6607–94,148). The population is currently at a minimum point in its recovery trajectory and is vulnerable to emerging threats, including planned ecosystem restoration efforts that are likely to be detrimental to the dolphins’ survival. Our modeling framework demonstrates an approach for integrating different sources and types of data, highlights the utility of expert elicitation for indeterminable input parameters, and emphasizes the importance of considering and monitoring long-term health of long-lived species subject to environmental disasters. Article impact statement: Oil spills can have long-term consequences for the health of long-lived species; thus, effective restoration and monitoring are needed.