Analysis of coprolites from the extinct mountain goat Myotragus balearicus

Humans colonized the Balearic Islands 5-4 ka ago. They arrived in a uniquely adapted ecosystem with the Balearic mountain goat Myotragus balearicus (Bovidae, Antilopinae, Caprini) as the only large mammal. This mammal went extinct rapidly after human arrival. Several hypotheses have been proposed to explain the extinction of M. balearicus. For the present study ancient DNA analysis (Sanger sequencing, Roche-454, Ion Torrent), and pollen and macrofossil analyses were performed on preserved coprolites from M. balearicus, providing information on its diet and paleo-environment. The information retrieved shows that M. balearicus was heavily dependent on the Balearic box species Buxus balearica during at least part of the year, and that it was most probably a browser. Hindcast ecological niche modelling of B. balearica shows that local distribution of this plant species was affected by climate changes. This suggests that the extinction of M. balearicus can be related to the decline and regional extinction of a plant species that formed a major component of its diet. The vegetation change is thought to be caused by increased aridity occurring throughout the Mediterranean. Previous hypotheses relating the extinction of M. balearicus directly to the arrival of humans on the islands must therefore be adjusted. (C) 2013 University of Washington. Published by Elsevier Inn All rights reserved.

Mycobacterium ulcerans persistence at a village water source of Buruli ulcer patients

Buruli ulcer (BU), a neglected tropical disease of the skin and subcutaneous tissue, is caused by Mycobacterium ulcerans and is the third most common mycobacterial disease after tuberculosis and leprosy. While there is a strong association of the occurrence of the disease with stagnant or slow flowing water bodies, the exact mode of transmission of BU is not clear. M. ulcerans has emerged from the environmental fish pathogen M. marinum by acquisition of a virulence plasmid encoding the enzymes required for the production of the cytotoxic macrolide toxin mycolactone, which is a key factor in the pathogenesis of BU. Comparative genomic studies have further shown extensive pseudogene formation and downsizing of the M. ulcerans genome, indicative for an adaptation to a more stable ecological niche. This has raised the question whether this pathogen is still present in water-associated environmental reservoirs. Here we show persistence of M. ulcerans specific DNA sequences over a period of more than two years at a water contact location of BU patients in an endemic village of Cameroon. At defined positions in a shallow water hole used by the villagers for washing and bathing, detritus remained consistently positive for M. ulcerans DNA. The observed mean real-time PCR Ct difference of 1.45 between the insertion sequences IS2606 and IS2404 indicated that lineage 3 M. ulcerans, which cause human disease, persisted in this environment after successful treatment of all local patients. Underwater decaying organic matter may therefore represent a reservoir of M. ulcerans for direct infection of skin lesions or vector-associated transmission.

Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage.

Zoonoses, diseases affecting both humans and animals, can exert tremendous pressures on human and veterinary health systems, particularly in resource limited countries. Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria. Here we describe the genetic diversity of Bacillus anthracis in Nigeria and compare it to Chad, Cameroon and a broader global dataset based on the multiple locus variable number tandem repeat (MLVA-25) genetic typing system. Nigerian B. anthracis isolates had identical MLVA genotypes and could only be resolved by measuring highly mutable single nucleotide repeats (SNRs). The Nigerian MLVA genotype was identical or highly genetically similar to those in the neighboring countries, confirming the strains belong to this unique West African lineage. Interestingly, sequence data from a Nigerian isolate shares the anthrose deficient genotypes previously described for strains in this region, which may be associated with vaccine evasion. Strains in this study were isolated over six decades, indicating a high level of temporal strain stability regionally. Ecological niche models were used to predict the geographic distribution of the pathogen for all three countries. We describe a west-east habitat corridor through northern Nigeria extending into Chad and Cameroon. Ecological niche models and genetic results show B. anthracis to be ecologically established in Nigeria. These findings expand our understanding of the global B. anthracis population structure and can guide regional anthrax surveillance and control planning.

Adaptive behavioural syndromes due to strategic niche specialization

BACKGROUND: Behavioural syndromes, i.e. consistent individual differences in behaviours that are correlated across different functional contexts, are a challenge to evolutionary reasoning because individuals should adapt their behaviour to the requirements of each situation. Behavioural syndromes are often interpreted as a result of constraints resulting in limited plasticity and inflexible behaviour. Alternatively, they may be adaptive if correlated ecological or social challenges functionally integrate apparently independent behaviours. To test the latter hypothesis we repeatedly tested helpers in the cooperative breeder Neolamprologus pulcher for exploration and two types of helping behaviour. In case of adaptive behavioural syndromes we predicted a positive relationship between exploration and aggressive helping (territory defence) and a negative relationship between these behaviours and non-aggressive helping (territory maintenance). RESULTS: As expected, helpers engaging more in territory defence were consistently more explorative and engaged less in territory maintenance, the latter only when dominant breeders were present. Contrary to our prediction, there was no negative relationship between exploration and territory maintenance. CONCLUSION: Our results suggest that the three behaviours we measured are part of behavioural syndromes. These may be adaptive, in that they reflect strategic specialization of helpers into one of two different life history strategies, namely (a) to stay and help in the home territory in order to inherit the breeding position or (b) to disperse early in order to breed independently.

Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys

Hatchery fish stocking for stock enhancement has been operated at a massive and global scale. However, the use of hatchery fish as a means of stock enhancement is highly controversial, and little is known about its effects on wild stock and consequences for stock enhancement. Here we review the scientific literature on this subject in order to address a fundamental - question is hatchery stocking a help or harm for wild stock and stock enhancement? We summarized 266 peer-reviewed papers that were published in the last 50 years, which describe empirical case studies on ecology and genetics of hatchery stocks and their effects on stock enhancement. Specifically, we asked whether hatchery stock and wild stock differed in fitness and the level of genetic variation, and whether stocking affected population abundance. Seventy studies contained comparisons between hatchery and wild stocks, out of which 23 studies showed significantly negative effects of hatchery rearing on the fitness of stocked fish, and 28 studies showed reduced genetic variation in hatchery populations. None of these studies suggested a positive genetic effect on the fitness of hatchery-reared individuals after release. These results suggest that negative effects of hatchery rearing are not just a concern but undeniably present in many aquaculture species. In a few cases, however, no obvious effect of hatchery rearing was observed, and a positive contribution of hatchery stock to the abundance of fish populations was indicated. These examples suggest that there is a chance to improve hatchery practices and mitigate the negative effects on wild stocks, although scientific data supporting the positive effect on stock enhancement are largely missing at this moment. Technically, microsatellite-based parentage assignments have been proven as a useful tool for the evaluation of reproductive fitness in natural settings, which is a key for stock enhancement by hatchery-based stocking. We discuss implications of these results, as well as their limitations and future directions. (C) 2010 Elsevier B.V. All rights reserved.

Occurrence, finger printing and ecological risk assessment of polycyclic aromatic hydrocarbons (PAHs) in the Chenab River, Pakistan

Seventeen polycyclic aromatic hydrocarbons (PAHs) were studied in surface waters (including particulate phase) from the Chenab River, Pakistan and ranged from 289-994 and 437-1290 ng l-1 in summer and winter (2007-09), respectively. Concentrations for different ring-number PAHs followed the trend: 3-rings > 2-rings > 4-rings > 5-rings > 6-rings. The possible sources of PAHs are identified by calculating the indicative ratios; appropriating petrogenic sources of PAHs in urban and sub-urban regions with pyrogenic sources in agricultural region. Factor analysis based on principal component analysis identified the origins of PAHs from industrial activities, coal and trash burning in agricultural areas and municipal waste disposal from surrounding urban and sub-urban areas via open drains into the riverine ecosystem. Water quality guidelines and toxic equivalent factors highlighted the potential risk of low molecular weight PAHs to the aquatic life of the Chenab River. The flux estimated for PAHs contaminants from the Chenab River to the Indus River was >50 tons/year.

Thermal adaptation and ecological speciation

Ecological speciation is defined as the emergence of reproductive isolation as a direct or indirect consequence of divergent ecological adaptation. Several empirical examples of ecological speciation have been reported in the literature which very often involve adaptation to biotic resources. In this review, we investigate whether adaptation to different thermal habitats could also promote speciation and try to assess the importance of such processes in nature. Our survey of the literature identified 16 animal and plant systems where divergent thermal adaptation may underlie (partial) reproductive isolation between populations or may allow the stable coexistence of sibling taxa. In many of the systems, the differentially adapted populations have a parapatric distribution along an environmental gradient. Isolation often involves extrinsic selection against locally maladapted parental or hybrid genotypes, and additional pre- or postzygotic barriers may be important. Together, the identified examples strongly suggest that divergent selection between thermal environments is often strong enough to maintain a bimodal genotype distribution upon secondary contact. What is less clear from the available data is whether it can also be strong enough to allow ecological speciation in the face of gene flow through reinforcement-like processes. It is possible that intrinsic features of thermal gradients or the genetic basis of thermal adaptation make such reinforcement-like processes unlikely but it is equally possible that pertinent systems are understudied. Overall, our literature survey highlights (once again) the dearth of studies that investigate similar incipient species along the continuum from initial divergence to full reproductive isolation and studies that investigate all possible reproductive barriers in a given system.