Evolutionary history and identification of conservation units in the giant otter, Pteronura brasiliensis.

The giant otter, Pteronura brasiliensis, occupies a range including the major drainage basins of South America, yet the degree of structure that exists within and among populations inhabiting these drainages is unknown. We sequenced portions of the mitochondrial DNA (mtDNA) cytochrome b (612bp) and control region (383 bp) genes in order to determine patterns of genetic variation within the species. We found high levels of mtDNA haplotype diversity (h = 0.93 overall) and support for subdivision into four distinct groups of populations, representing important centers of genetic diversity and useful units for prioritizing conservation within the giant otter. We tested these results against the predictions of three hypotheses of Amazonian diversification (Pleistocene Refugia, Paleogeography, and Hydrogeology). While the phylogeographic pattern conformed to the predictions of the Refugia Hypothesis, molecular dating using a relaxed clock revealed the phylogroups diverged from one another between 1.69 and 0.84 Ma, ruling out the influence of Late Pleistocene glacial refugia. However, the role of Plio-Pleistocene climate change could not be rejected. While the molecular dating also makes the influence of geological arches according to the Paleogeography Hypothesis extremely unlikely, the recent Pliocene formation of the Fitzcarrald Arch and its effect of subsequently altering drainage pattern could not be rejected. The data presented here support the interactions of both climatic and hydrological changes resulting from geological activity in the Plio-Pleistocene, in shaping the phylogeographic structure of the giant otter.

Contrasting responses to selection in class I and class IIα major histocompatibility-linked markers in salmon.

Comparison of levels and patterns of genetic variation in natural populations either across loci or against neutral expectation can yield insight into locus-specific differences in the strength and direction of evolutionary forces. We used both approaches to test the hypotheses on patterns of selection on major histocompatibility (MH)-linked markers. We performed temporal analyses of class I and class IIα MH-linked markers and eight microsatellite loci in two Atlantic salmon populations in Ireland on two temporal scales: over six decades and 9 years in the rivers Burrishoole and Delphi, respectively. We also compared contemporary Burrishoole and Delphi samples with nearby populations for the same loci. On comparing patterns of temporal and spatial differentiation among classes of loci, the class IIα MH-linked marker was consistently identified as an outlier compared with patterns at the other microsatellite loci or neutral expectation. We found higher levels of temporal and spatial heterogeneity in heterozygosity (but not in allelic richness) for the class IIα MH-linked marker compared with microsatellites. Tests on both within- and among-population differentiation are consistent with directional selection acting on the class IIα-linked marker in both temporal and spatial comparisons, but only in temporal comparisons for the class I-linked marker. Our results indicate a complex pattern of selection on MH-linked markers in natural populations of Atlantic salmon. These findings highlight the importance of considering selection on MH-linked markers when using these markers for management and conservation purposes.

Lifetime reproductive success and longevity of queens in an annual social insect.

Although central to understanding life-history evolution, the relationship between lifetime reproductive success and longevity remains uncertain in many organisms. In social insects, no studies have reported estimates of queens' lifetime reproductive success and longevity within populations, despite the importance of understanding how sociality and associated within-group conflict affect life-history traits. To address this issue, we studied two samples of colonies of the annual bumblebee, Bombus terrestris audax, reared from wild-caught queens from a single population. In both samples, queens' lifetime reproductive success, measured as either queens' inclusive fitness or as total biomass of queen-produced sexuals (new queens and males), was significantly positively associated with queen longevity, measured from the day the first worker was produced. We suggest that a positive relationship between reproductive success and longevity was inherited from nonsocial ancestors showing parental care and maintained, at least in part, because the presence of workers buffers queens against extrinsic mortality.

A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation.

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.

Rapid evolution of the MH class I locus results in different allelic compositions in recently diverged populations of Atlantic salmon.

We compared major histocompatibility class I allelic diversity in two currently reproductively isolated Atlantic salmon (Salmo salar) populations (Irish and Norwegian) with a common postglacial origin in order to test for among-population differences in allelic composition and patterns of recombination and point mutation. We also examined the evidence for adaptive molecular divergence at this locus by analyzing the rate of amino acid replacement in relation to a neutral expectation. Contrary to our prediction, and in contrast to the situation for other genetic markers, the two populations have almost nonoverlapping sets of major histocompatibility class I alleles. Although there is a strong signal of point mutation that predates population divergence, recent recombination, acting in similar, but not identical, ways in both populations appears to be a significant force in creating new alleles. Moreover, selection acting on peptide-binding residues seems to favor new recombinant alleles and is likely to be responsible for the rapid divergence between populations.

Patterns of variability at the major histocompatibility class II alpha locus in Atlantic salmon contrast with those at the class I locus.

In order to investigate the mechanisms creating and maintaining variability at the major histocompatibility (MH) class II alpha (DAA) locus we examined patterns of polymorphism in two isolated Atlantic salmon populations which share a common post-glacial origin. As expected from their common origin, but contrary to the observation at the MH class I locus, these populations shared the majority of DAA alleles: out of 17 sequences observed, 11 were common to both populations. Recombination seems to play a more important role in the origin of new alleles at the class II alpha locus than at the class I locus. A greater than expected proportion of sites inferred to be positively selected (potentially peptide binding residues, PBRs) were found to be involved in recombination events, suggesting a mechanism for increasing MH variability through an interaction between recombination and natural selection. Thus it appears that although selection and recombination are important mechanisms for the evolution of both class II alpha and class I loci in the Atlantic salmon, the pattern of variability differs markedly between these classes of MH loci.

Phenotypic divergence despite high levels of gene flow in Galápagos lava lizards (Microlophus albemarlensis).

The extent of evolutionary divergence of phenotypes between habitats is predominantly the result of the balance of differential natural selection and gene flow. Lava lizards (Microlophus albemarlensis) on the small island of Plaza Sur in the Galápagos archipelago inhabit contrasting habitats: dense vegetation on the western end of the island thins rapidly in a transitional area, before becoming absent on the eastern half. Associated with these habitats are phenotypic differences in traits linked to predator avoidance (increased wariness, sprint speed, and endurance in lizards from the sparsely vegetated habitat). This population provides an opportunity to test the hypothesis that reduced gene flow is necessary for phenotypic differentiation. There was no evidence of any differences among habitats in allele frequencies at six out of seven microsatellite loci examined, nor was there any indication of congruence between patterns of genetic variability and the change in vegetation regime. We infer that gene flow between the habitats on Plaza Sur must be sufficiently high to overcome genetic drift within habitats but that it does not preclude phenotypic differentiation.

Odorant receptor gene expression changes during the parr-smolt transformation in Atlantic salmon.

The ability of salmon to home accurately to their natal stream to spawn has long intrigued biologists and has important consequences for the maintenance of population structure in these species. It is known that olfaction is crucial to homing, and that the transition from the freshwater to the marine environment (the parr-smolt transformation; PST) is a period of increased olfactory sensitivity and learning, resulting in a permanent memory of natal site odours that is retained, at least in part, in peripheral sensory neurones. These odours are then used as cues by sexually maturing fish on their homeward migration. We used quantitative polymerase chain reaction techniques to demonstrate transient increases in expression of odorant receptor transcripts (of up to fifty-fold over pre-PST levels) coincident with PST. Both olfactory (SORB) and vomeronasal receptors (SVRA and SVRC) are involved, which suggests that the fish learn both environmental odours and semiochemicals (pheromones). Receptor expression varies between families and changes over time indicating both genetic differences in odour stimuli and multiple periods of olfactory sensitivity. We suggest that changes in OR gene expression may have a role in homing behaviour and thus the maintenance of population structure in Atlantic salmon.

Genetic evidence reveals density-dependent mediated success of alternative mating behaviours in the European bitterling (Rhodeus sericeus).

The reproductive success of alternative mating behaviours may vary within and among populations in relation to environmental factors and demographic parameters. We used behavioural and genetic data to investigate how male density affects reproductive success of territoriality and sneaking in the European bitterling (Rhodeus sericeus, Cyprinidae), a freshwater fish that spawns on the gills of living freshwater mussels. Keeping the number of spawning sites constant, we manipulated male densities in laboratory and mesocosm experiments. We showed that sneaked fertilizations were common in R. sericeus, and that they increased significantly with male density. Territorial mating was almost 17 times more successful than sneaking at the lowest male density treatment, and still 2-3 times more successful at intermediate densities. However, both behaviours conferred the same fitness pay-off at the highest male density. While the success of territorial males declined with male density, the success of individual sneaking males remained constant across densities. Notably, the capacity of territorial males to outcompete sneakers by preoviposition sperm loading was the best predictor of male reproductive success, rather than aggression, body size or postoviposition ejaculation.

The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard.

Ancient climatic fluctuations have caused changes in the demography and distribution of many species. The genetic differentiation between populations of the same species and of sister species is often attributed largely to the more recent Pleistocene fluctuations. Recent interpretations, which implicate earlier episodes, have proved controversial. We address the timing of genetic divergence in the Iberian lizard Lacerta schreiberi by studying the phylogeography of the cytochrome b sequence. The species has a remarkable morphological uniformity, yet our evidence suggests that earlier events in the Pliocene initiated the main divergence between populations. This interpretation implies that the different populations survived through the Pleistocene in separate localities. This conclusion is robust to different molecular clock calibrations. The persistence of earlier differentiation through the Pleistocene has wide implications for our understanding of Pleistocene refugia in this species and, by extension, to the biogeography of the whole region.

New perspectives on mate choice and the MHC.

A long series of studies on mice have shown that mate choice decisions can be made on the basis of individual genotype at the major histocompatibility complex (MHC), which accords well with the importance of immunocompetence in some theories of sexual selection. Recent work on other vertebrate species, including humans, indicates that MHC-based mate choice is not restricted to the genus Mus. However, its importance may vary among species as a result of differences in social and mating system structure, and perhaps genome structure. There appears to be a general preference expressed for MHC-dissimilar mates, and such MHC-disassortative mating may be involved in maintaining MHC and/or genome-wide diversity in natural populations. The strength and direction of MHC-based mating preference can vary, and may be modulated by factors such as genetic background, sex, and early life experience.

The effectiveness of combined saquinavir and ketoconazole treatment in reducing HIV viral load.

With the advent of protease inhibitors, the treatment of persons infected with the human immunodeficiency virus (HIV) has resulted in lower levels of the virus in the blood. The first of these protease inhibitors was saquinavir, which inhibits the HIV protease enzyme responsible for post-translational processing of Gag and Gag-Po1 poly protein precursors into their functional products. Studies have suggested that ketoconazole, given in combination with saquinavir, increases the bioavailability of saquinavir. This study compared the HIV viral load in patients treated with saquinavir alone and in combination with ketoconazole. Results showed that while all patients who received saquinavir exhibited a positive response, patients who also received ketoconazole had a greater drop in viral load levels. In addition, a greater number of patients had undetectable viral levels after 3 months on the ketoconazole/saquinavir regimen. These results indicate that the combination of saquinavir/ketoconazole for the treatment of HIV requires further study.

Partner notification and focused intervention as a means of identifying HIV-positive patients.

Partner notification as a means of contact tracing human immunodeficiency virus (HIV)-infected persons remains controversial. It is argued against by many gay activists, while primary public health officials and leaders in ethnic communities continue to support this as a means of identifying unknown cases. Human immunodeficiency virus-positive patients were interviewed to determine if partner notification could be a useful instrument. Based on interviews, patients at risk of infection through heterosexual contact were able to identify most of their sexual partners; the majority of these patients were women. Twenty-two of 22 women infected heterosexually were able to identify all of their sexual partners. Five of 8 heterosexual men were able to identify all of their sexual partners, but these men were infected through intravenous drug use. Six of 44 homosexual men interviewed were able to make these identifications. Two focus groups of homosexual men who were HIV-positive patients were organized; each was asked one question. Men in group B were asked if they could identify HIV-positive persons whom they suspected were not in a treatment program. Men in group A were asked if they they thought they knew HIV-positive persons still practicing unsafe sex. Thirteen of the 14 patients in group A were able to identify 30 persons they felt were still practicing unsafe sex; 17 of 30 tested HIV-positive and 9 were unaware of their status. The 14 patients in group B identified 15 persons they felt were HIV-positive; 11 were found to be HIV-positive and 8 were unaware of their status. These findings suggest that partner notification definitely has a role in heterosexual contact tracing, and focused intervention is a more cost-effective approach to early intervention.

New perspectives on mate choice and the MHC.

A long series of studies on mice has shown that mate choice decisions can be made on the basis of individual genotype at the major histocompatibility complex (MHC), which accords well with the importance of immunocompetence in some theories of sexual selection. Recent work on other vertebrate species, including humans, indicates that MHC-based mate choice is not restricted to the genus Mus. However, its importance may vary among species as a result of differences in social and mating system structure, and perhaps genome structure. There appears to be a general preference expressed for MHC-dissimilar mates, and such MHC-disassortative mating may be involved in maintaining MHC and/or genome-wide diversity in natural populations. The strength and direction of MHC-based mating preference can vary, and may be modulated by factors such as genetic background, sex, and early life experience.

The effectiveness of intermittent hyperbaric oxygen in relieving drug-induced HIV-associated neuropathy.

This 3-month study evaluated the effects of hyperbaric oxygen on drug-induced neuropathies in 22 patients with human immunodeficiency virus. All patients included in the study had been taking an antiretroviral medication for at least 12 months and had subjective symptoms of numbness or tingling, lethargy, and a decrease in deep tendon reflex. Patients with an active substance abuse history or Kaposi's sarcoma were excluded. Of the 20 patients who completed the series, 17 had significant improvement, 2 had a demyelinating disorder that may have affected the outcome, and 1 had no change.

Clarithromycin prophylaxis against Cryptosporidium enteritis in patients with AIDS.

Cryptosporidium enteritis (CE) in patients with acquired immunodeficiency syndrome (AIDS) can be a life-threatening opportunistic infection. A retrospective review of 471 charts of patients with AIDS in our clinic, prior to the availability of clarithromycin for the treatment of Mycobacterium avium complex (MAC), revealed that seven patients with CD4 counts < 25/mm3 developed CE. The median survival period from diagnosis to death in these patients was 10.6 days. The incidence of CE in patients with CD4 counts < 50/mm3 treated with clarithromycin prophylaxis for MAC was compared with patients not receiving clarithromycin prophylaxis. Of 136 patients with AIDS, 63 received clarithromycin 500 mg twice daily, and 73 patients not treated with clarithromycin represented the control group. None of the patients who received clarithromycin developed CE compared with four patients who developed CE in the control group. All four patients in the control group who developed CE had CD4 counts < 25/mm3. All patients who received clarithromycin remained stool negative for Cryptosporidium. In a subsequent 2-year follow-up of an additional 217 AIDS patients with CD4 counts < 50/mm3 receiving clarithromycin 500 mg twice daily as MAC prophylaxis, no patient developed CE. These results provide strong evidence supporting the use of clarithromycin as prophylaxis against cryptosporidium enteritis in patients with AIDS.