Testing advances in molecular discrimination among Chinook salmon life histories: evidence from a blind test.

The application of DNA-based markers toward the task of discriminating among alternate salmon runs has evolved in accordance with ongoing genomic developments and increasingly has enabled resolution of which genetic markers associate with important life-history differences. Accurate and efficient identification of the most likely origin for salmon encountered during ocean fisheries, or at salvage from fresh water diversion and monitoring facilities, has far-reaching consequences for improving measures for management, restoration and conservation. Near-real-time provision of high-resolution identity information enables prompt response to changes in encounter rates. We thus continue to develop new tools to provide the greatest statistical power for run identification. As a proof of concept for genetic identification improvements, we conducted simulation and blind tests for 623 known-origin Chinook salmon (Oncorhynchus tshawytscha) to compare and contrast the accuracy of different population sampling baselines and microsatellite loci panels. This test included 35 microsatellite loci (1266 alleles), some known to be associated with specific coding regions of functional significance, such as the circadian rhythm cryptochrome genes, and others not known to be associated with any functional importance. The identification of fall run with unprecedented accuracy was demonstrated. Overall, the top performing panel and baseline (HMSC21) were predicted to have a success rate of 98%, but the blind-test success rate was 84%. Findings for bias or non-bias are discussed to target primary areas for further research and resolution.

Identification of three single nucleotide polymorphisms in Anopheles gambiae immune signaling genes that are associated with natural Plasmodium falciparum infection.

BACKGROUND: Laboratory studies have demonstrated that a variety of immune signaling pathways regulate malaria parasite infection in Anopheles gambiae, the primary vector species in Africa. METHODS: To begin to understand the importance of these associations under natural conditions, an association mapping approach was adopted to determine whether single nucleotide polymorphisms (SNPs) in selected immune signaling genes in A. gambiae collected in Mali were associated with the phenotype of Plasmodium falciparum infection. RESULTS: Three SNPs were identified in field-collected mosquitoes that were associated with parasite infection in molecular form-dependent patterns: two were detected in the Toll5B gene and one was detected in the gene encoding insulin-like peptide 3 precursor. In addition, one infection-associated Toll5B SNP was in linkage disequilibrium with a SNP in sequence encoding a mitogen-activated protein kinase that has been associated with Toll signaling in mammalian cells. Both Toll5B SNPs showed divergence from Hardy-Weinberg equilibrium, suggesting that selection pressure(s) are acting on these loci. CONCLUSIONS: Seven of these eight infection-associated and linked SNPs alter codon frequency or introduce non-synonymous changes that would be predicted to alter protein structure and, hence, function, suggesting that these SNPs could alter immune signaling and responsiveness to parasite infection.

Geographic and taxonomic distribution of a positive interaction: ant-tended homopterans indirectly benefit figs across southern Africa.

Although species pairs and assemblages often occur across geographic regions, ecologists know very little about the outcome of their interactions on such large spatial scales. Here, we assess the geographic distribution and taxonomic diversity of a positive interaction involving ant-tended homopterans and fig trees in the genus Ficus. Previous experimental studies at a few locations in South Africa indicated that Ficus sur indirectly benefited from the presence of a homopteran (Hilda patruelis) because it attracted ants (primarily Pheidole megacephala) that reduced the effects of both pre-dispersal ovule gallers and parasitoids of pollinating wasps. Based on this work, we evaluated three conditions that must be met in order to support the hypothesis that this indirect interaction involves many fig species and occurs throughout much of southern Africa and Madagascar. Data on 429 trees distributed among five countries indicated that 20 of 38 Ficus species, and 46% of all trees sampled, had ants on their figs. Members of the Sycomorus subgenus were significantly more likely to attract ants than those in the Urostigma subgenus, and ant-colonization levels on these species were significantly greater than for Urostigma species. On average, each ant-occupied F.sur tree had 37% of its fig crop colonized by ants, whereas the value was 24% for other Ficus species. H. patruelis was the most common source for attracting ants, although figs were also attacked by a range of other ant-tended homopterans. P. megacephala was significantly more common on figs than other ant species, being present on 58% of sampled trees. Ant densities commonly exceeded 4.5 per fig, which a field experiment indicated was sufficient to provide protection from ovule gallers and parasitoids of pollinators. Forty-nine percent of all colonized F. sur trees sampled had ant densities equal to or greater than 4.5 per fig, whereas this value was 23% for other Ficus species. We conclude that there is considerable evidence to suggest that this indirect interaction occurs across four southern African countries and Madagascar, and involves many Ficus species.

Sediment quality assessment in tidal salt marshes in northern California, USA: an evaluation of multiple lines of evidence approach.

The objective of this study was to evaluate the efficacy of integrating a traditional sediment quality triad approach with selected sublethal chronic indicators in resident species in assessing sediment quality in four salt marshes in northern California, USA. These included the highly contaminated (Stege Marsh) and relatively clean (China Camp) marshes in San Francisco Bay and two reference marshes in Tomales Bay. Toxicity potential of contaminants and benthic macroinvertebrate survey showed significant differences between contaminated and reference marshes. Sublethal responses (e.g., apoptotic DNA fragmentation, lipid accumulation, and glycogen depletion) in livers of longjaw mudsucker (Gillichthys mirabilis) and embryo abnormality in lined shore crab (Pachygrapsus crassipes) also clearly distinguished contaminated and reference marshes, while other responses (e.g., cytochrome P450, metallothionein) did not. This study demonstrates that additional chronic sublethal responses in resident species under field exposure conditions can be readily combined with sediment quality triads for an expanded multiple lines of evidence approach. This confirmatory step may be warranted in environments like salt marshes in which natural variables may affect interpretation of toxicity test data. Qualitative and quantitative integration of the portfolio of responses in resident species and traditional approach can support a more comprehensive and informative sediment quality assessment in salt marshes and possibly other habitat types as well.