Where are the pseudogenes in bacterial genomes?

Most bacterial genomes have very few pseudogenes; notable exceptions include the genomes of the intracellular parasites Rickettsia prowazekii and Mycobacterium leprae. As DNA can be introduced into microbial genomes in many ways, the compact nature of these genomes suggests that the rate of DNA influx is balanced by the rate of DNA deletion. We propose that the influx of dangerous genetic elements such as transposons and bacteriophages selects for the maintenance of relatively high deletion rates in most bacteria; the sheltered lifestyle of intracellular parasites removes this threat, leading to reduced deletion rates and larger pseudogene loads.     

Where are the Subtropics?

The tropics are clearly defined while ‘subtropics’ and ‘subtropical’ have been applied to a variety of zones, climates, and ecosystems. However, in the recent terrestrial biology literature, they have been used mainly for the zones between the tropics (±23.4^o C) and ±30.0^o. Adopting this standard would facilitate pan‐subtropical comparisons.     

When do parasites fail to speciate in response to host speciation?

Cospeciation generally increases the similarity between host and parasite phylogenies. Incongruence between host and parasite phylogenies has previously been explained in terms of host switching, sorting, and duplication events. Here, we describe an additional process, failure of the parasite to speciate in response to host speciation, that may be important in some host-parasite systems. Failure to speciate is likely to occur when gene flow among parasite populations is much higher than that of their hosts. We reconstructed trees from mitochondrial and nuclear DNA sequences for pigeons and doves (Aves: Columbiformes) and their feather lice in the genus Columbicola (Insecta: Phthiraptera). Although comparisons of the trees from each group revealed a significant amount of cospeciation, there was also a significant degree of incongruence. Cophylogenetic analyses generally indicated that host switching may be an important process in the history of this host-parasite association. Using terminal sister taxon comparisons, we also identified three apparent cases where the host has speciated but the associated parasite has not. In two of these cases of failure to speciate, these comparisons involve allopatric sister taxa of hosts whose lice also occur on hosts sympatric with both of the allopatric sisters. These additional hosts for generalist lice may promote gene flow with lice on the allopatric sister species. Relative rate comparisons for the mitochondrial cytochrome oxidase I gene indicate that molecular substitution occurs about 11 times faster in lice than in their avian hosts.     

Where are the missing pieces of the schizophrenia genetics puzzle?

On the basis of recent data from candidate region/gene and genome-wide association studies (GWAS) and their follow-up investigations, the number of genes potentially implicated in schizophrenia has been estimated to be over 1000. However, with regard to the identified odds ratio, it is likely that genetic variants with more definitive effect on schizophrenia phenotype are still missing. The hunt therefore remains open for the genetic variants that would explain the majority of the missing heritability of schizophrenia. This review aims at summarizing data from recent DNA microarray and target gene/region resequencing in order to propose new insights of where to look next. The review is divided into three sections: GWAS, copy-number variations and rare variant--candidate gene resequencing.     

Predator migration in response to prey density: What are the consequences?

A predator-prey metapopulation model with two identical patches and only migration of the predator is investigated. Local predator-prey interaction is described by the so-called Rosenzweig-MacArthur model, while the migration term of the predator is put in a nonlinear form, which is derived by extending the Holling time budget argument to migration. In particular, a dimensionless parameter theta is introduced to quantify the migration tendency of predators while they are handling their prey, which gives rise to a family of models connecting two extremes: predators have no inclination to migrate while handling prey (theta = 0) and standard diffusion (theta = 1). Various aspects of the model, including changes in the number and the stability of equilibria and limit cycles, are investigated. We then focus on the key question: "Does spatial structure lead to a substantial damping of the violent oscillations exhibited by many predator-prey models?". It is known that the answer is "yes" if one adopts standard diffusion (theta = 1). However, we present substantial evidence that the answer is "no" if one takes theta = 0. We conclude that the migration submodel is an important constituent of a spatial predator-prey model and that the issue deserves scrutiny, both experimentally and theoretically.     

Genetic research in osteoporosis: Where are we? Where should we go next?

Fractures resulting from low bone mass and excessive skeletal fragility (osteoporosis) are common worldwide both in males and females, particularly in later years of life. Both fractures, and the most important predictor of fractures, bone mass, are now known to be strongly heritable. This fact, plus the current growth in genetic science, has led to a surge of genetic research in osteoporosis, mostly in the search for genes and their polymorphisms that are responsible for variation in bone mass. Finding the genetic basis underlying variation in bone mass will lead us to deeper understanding of the biology of bone mass accumulation, maintenance and adaptation to load. This, plus finding the genetic basis for overall variation in fracture risk per se, will facilitate the development of interventions, both pharmaceutical and non-pharmaceutical, to prevent and/or treat osteoporosis successfully. This research has produced a rather large number of gene loci that seem to influence bone mass. The challenge now is to refine the statistical genetics and the phenotypes involved so that we can confidently identify those gene loci that truly influence bone mass, and to find ways to study the genetic basis for the most direct disease outcome of interest, fracture.     

Where are the Caribs? Ancient DNA from ceramic period human remains in the Lesser Antilles

The identity and history of the indigenous groups who occupied the Lesser Antilles during the ceramic periods remain highly controversial. Although recent archaeological evidence has challenged hypotheses concerning the organization of human groups in this region, more biological data are needed to fully inform the discussion. Our study provides, to our knowledge, the first palaeogenetic data for Late Ceramic groups of the Guadeloupe archipelago, yielding crucial information concerning the identities of these groups. Despite the generally poor DNA preservation in the tested remains, we were able to retrieve Hypervariable Region 1 sequences from 11 individuals and mitochondrial single-nucleotide polymorphisms from 13 individuals. These novel data provide interesting preliminary results in favour of a common origin for all Saladoid Caribbean communities, i.e. the first ceramic groups of the region, as well as for a local continuity between the Saladoid and post-Saladoid groups. A combination of the genetic data obtained and several pieces of cultural evidence allows us to propose that two different groups inhabited the Guadeloupe archipelago during the Late Ceramic period, with the possible occupation of the La Désirade and Marie-Galante islands by groups affiliated with the Taíno communities. The working hypotheses proposed here appear consistent with recent archaeological evidence.     

Where are the survivors? Tracking relictual populations of endangered frogs in Costa Rica

Aim We used abiotic environmental variables and historical locality records to infer distributions of endangered anuran species of Costa Rica to promote efficient strategies for future amphibian surveys. Location Costa Rica. Methods We used a Maximum Entropy Algorithm (Maxent) to predict potential distribution maps for 17 species of endangered anurans and create a consensus map of species richness. We compared the environmental conditions from localities where relictual amphibian populations were recently rediscovered with the conditions across their historical range to evaluate the possibility that these relictual populations might occur in specific climatic conditions that could explain their persistence. We used a multicriteria analysis considering the following factors: the intersection zones between the consensus map, conservation areas, potential Batrachochytrium dendrobatidis (Bd) distribution, collecting effort and areas within the precipitation range at which reappearances had occurred to locate sites for future surveys. Results The resulting predictions suggest that suitable areas for the highest number of species occur between 1300 and 2500 m.a.s.l and are concentrated along the Pacific slopes of the Cordillera de Talamanca and Cordillera Volcánica Central. Around 45% of the high potential richness area is under protection. Relictual populations of declined species seem to persist mainly in highly humid localities (2500–3500 mm of mean annual precipitation). Around 240 km² has an ideal environment for the rediscovery of relictual populations. The multicriteria analysis showed that around 0.5% of the Costa Rican territory should be surveyed exhaustively for frogs. Main conclusions Many of the potential refugia we identified here have not been surveyed since 2000, the areas identified by the best model predictions correspond well with the localities of the relictual populations recently reported. We suggest future surveys of missing amphibian species should focus on these areas. The discovery of populations of endangered species can be used to propose conservation areas.     

Did life history evolve in response to parasites in invasive populations of Melanoides tuberculata?

Enemy release and rapid evolution are often assumed to promote biological invasions. In the parthenogenetic snail Melanoides tuberculata, one invasive strain (MAD) was assumed to benefit from enemy release until a heavily parasitized population was found in Colombia (in the area of introduction). This population is prosperous despite important losses in the reproductive potential due to a high prevalence of a trematode that castrates snails. We studied genetic variation in life-history traits among five populations from the invaded area to test whether life histories had recently evolved in the parasitized population in such a way that snails have more chance to reproduce before being parasitized. We find significant genetic differences among populations, though they are not in the expected direction. Individuals from the parasitized population were smaller at birth, grew slower, and reproduced later and at a bigger size than individuals from the non-parasitized populations. We conclude that the life-history traits of this snail strain did not need to evolve in order to allow population renewal in the invaded area, even in the presence of parasites. This implies that enemy release and/or rapid evolution were not necessary for this strain to invade.