Detrimental conditions affecting Xestospongia muta across shallow and mesophotic coral reefs off the southwest coast of Puerto Rico.

Sponges are fundamental components of coral reef communities and, unfortunately, like other major benthic members, they too have been impacted by epizootic and panzootic events. We report on the prevalence of disease-like conditions affecting populations of the giant barrel sponge Xestospongia muta across shallow and mesophotic coral reefs off La Parguera Natural Reserve (LPNR) and Mona Island Marine Reserve (MIMR) in Puerto Rico. Four different conditions affecting X. muta were observed during our surveys, of which 3 have been previously reported: cyclic spotted bleaching (CSB; apparently non-lethal), Xestospongia-tissue wasting disease (X-TWD; apparently lethal), and sponge orange band disease (SOB; sparsely associated with X-TWD infected individuals). Additionally, we describe a fourth condition, Xestospongia-tissue hardening condition (X-THC), a previously unreported disease recently observed along the insular shelf margin off LPNR and MIMR. Within LPNR, a total of 764 specimens of X. muta were inspected and measured. Of these, 590 sponges (72.2%) had CSB, 25 (3.27%) had signs of X-TWD, 7 (0.92%) had SOB, and the remaining 142 (18.6%) were apparently healthy. Three colonies inhabiting upper mesophotic depths on the LPNR insular shelf showed signs of CSB and X-TWD. At MIMR, video-transect surveys revealed a total of 514 colonies, of which 40 (7.78%) had signs of CSB and/or XTWD, 14 (2.72%) were affected by X-THC, while the remaining 460 (89.5%) showed no external signs of disease and appeared healthy. The presence of 4 concomitant disease-like conditions in barrel sponges of Puerto Rico is alarming, and indicative of the deteriorating status of Caribbean coral reefs.

Efficiencies of genes and accuracy of tree-building methods in recovering a known Drosophila genealogy.

Phylogenetic hypotheses generated from seven Drosophila mitochondrial genomes support a well-corroborated genealogy with a single evolutionary history. These mitochondrial data form a model system for investigating the efficiency of genes and accuracy of different tree-building methods in recovering a well-supported genealogy. We consider 15 genes (13 protein-coding and 2 rRNAs) and 83 tree-building methods (27 distance, 4 parsimony, 50 maximum likelihood, and 2 Bayesian). Among the 15 genes examined, ND4 recovered the true genealogy most efficiently (82 out of 83 methods). Generally, maximum likelihood models enforcing a clock most accurately reclaim the true genealogy. Surprisingly, however, this method fails to recover the well-supported topology for more than half of the genes. Additional studies are required to test the generality of the results presented here.

An efficient DNA extraction method for small metazoans.

The isolation of total nucleic acids from small metazoan taxa is difficult and often leads to an unacceptably large percentage of unsuccessful polymerase chain reaction (PCR) amplifications. Our work with the evolutionary genetics of harpacticoid copepods was an incentive to refine techniques such that consistent amplifications from minute marine organisms were feasible. We describe these modifications and demonstrate their utility for the amplification of multiple loci from single harpacticoid copepods.

Ecotoxicology and population genetics: the emergence of "phylogeographic and evolutionary ecotoxicology".

Genetics of ecotoxicology has recently emerged as a priority research field. The advent of polymerase chain reaction and molecular population genetics has made it possible to examine the genetics in even the smallest individuals. Although a potentially powerful technique, current approaches oversimplify the relationship of change in gene frequency to contaminant exposure. Many of these approaches cannot control for random correlation or accessory abiotic factors that impinge on the system tested. Indeed, the gestalt approaches of laboratory exposure or natural field experiments may ignore significant genome-level interactions that are important within a given system. At the very least, these approaches would benefit by a biogeographic survey of genetic variation to understand geographic microevolutionary patterns, or phylogeography, within a species to reduce spurious correlations and erroneous conclusions. Other single locus approaches can be chosen to enhance this approach if genetic/environmental interactions have been characterized for laboratory populations or for other model systems.

Differential survival of three mitochondrial lineages of a marine benthic copepod exposed to a pesticide mixture.

In South Carolina estuaries, the harpacticoid copepod Microarthridion littorale (Poppe 1881) consists of three distinct mitochondrial lineages (liI, liII, and liIII), whose distributions may be partially explained by the presence of toxic contaminants in the sampled habitats. The frequencies of liII and liIII are greatly diminished and sometimes absent in South Carolina contaminated tidal creeks where liI is omnipresent. In this study, representatives of these lineages or haplotype groups were collected from sediments of an estuarine creek containing low to undetectable levels of toxicants and then exposed to a toxic (approximately LC90) aqueous mixture containing an organophosphate (chlorpyrifos) and organochlorine pesticide (DDT, mixed isomers). A comparison was conducted for the frequency of each of the three haplotypes among the survivors of the exposed animals relative to that among the survivors of the control group. The haplotype group with the highest frequency in contaminated SC estuaries (liI) was statistically higher in frequency in survivors of the pesticide-exposed group than in the control group. The two rarer groups (liII and liIII) were less abundant among the survivors of the pesticide-exposed group than the control group. The frequencies of liI, liII, and liIII did not change significantly among the survivors of the control group. The differential survival of the three haplotype groups in the pesticide mixture may be one of the reasons that some haplotype groups are more likely to be found in clean or contaminated tidal creeks on the South Carolina coast.