The alluring simplicity and complex reality of genetic rescue

A series of important new theoretical, experimental and observational studies demonstrate that just a few immigrants can have positive immediate impacts on the evolutionary trajectory of local populations. In many cases, a low level of immigration into small populations has produced fitness benefits that are greater than those predicted by theoretical models, resulting in what has been termed 'genetic rescue'. However, the opposite result (reduced fitness) can also be associated with immigration of genetically divergent individuals. Central to our understanding of genetic rescue are complex interactions among fundamental concepts in evolutionary and population biology, including both genetic and non-genetic (environmental, behavioral and demographic) factors. Developing testable models to predict when genetic rescue is likely to occur is a daunting challenge that will require carefully controlled, multi-generation experiments as well as creative use of information from natural 'experiments'.     

Assignment methods: matching biological questions with appropriate techniques

Assignment methods, which use genetic information to ascertain population membership of individuals or groups of individuals, have been used in recent years to study a wide range of evolutionary and ecological processes. In applied studies, the first step of articulating the biological question(s) to be addressed should be followed by selection of the method(s) best suited for the analysis. However, this first step often receives less attention than it should, and the recent proliferation of assignment methods has made the selection step challenging. Here, we review assignment methods and discuss how to match the appropriate methods with the underlying biological questions for several common problems in ecology and conservation (assessing population structure; measuring dispersal and hybridization; and forensics and mixture analysis). We also identify several topics for future research that should ensure that this field remains dynamic and productive.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).     

Simple life-history traits explain key effective population size ratios across diverse taxa

Effective population size (N_e) controls both the rate of random genetic drift and the effectiveness of selection and migration, but it is difficult to estimate in nature. In particular, for species with overlapping generations, it is easier to estimate the effective number of breeders in one reproductive cycle (N_b) than N_e per generation. We empirically evaluated the relationship between life history and ratios of N_e, N_b and adult census size (N) using a recently developed model (agene) and published vital rates for 63 iteroparous animals and plants. N_b/N_e varied a surprising sixfold across species and, contrary to expectations, N_b was larger than N_e in over half the species. Up to two-thirds of the variance in N_b/N_e and up to half the variance in N_e/N was explained by just two life-history traits (age at maturity and adult lifespan) that have long interested both ecologists and evolutionary biologists. These results provide novel insights into, and demonstrate a close general linkage between, demographic and evolutionary processes across diverse taxa. For the first time, our results also make it possible to interpret rapidly accumulating estimates of N_b in the context of the rich body of evolutionary theory based on N_e per generation.     

DIETS OF COASTAL BOTTLENOSE DOLPHINS FROM THE U. S. MID-ATLANTIC COAST DIFFER BY HABITAT

We recorded 31 species in the stomachs of 146 coastal bottlenose dolphins ( Tursiops truncatus ) from North Carolina, U. S. A. Sciaenid fishes were the most common prey (frequency of occurrence = 95%). By mass, Atlantic croaker ( Micropogonias undulatus ) dominated the diet of dolphins that stranded inside estuaries, whereas weakfish ( Cynosicon regalis ) was most important for dolphins in the ocean. Inshore squid ( Loligo sp.) was eaten commonly by dolphins in the ocean, but not by those in the estuaries. There was no significant pattern in prey size associated with dolphin demography, but the proportion of the diet represented by croaker was higher for males than for females, and mature dolphins ate more croaker than did juveniles. Dietary differences between dolphins that stranded in the estuaries and those that stranded on ocean beaches support the hypothesis that some members of the population inhabit the ocean primarily while others reside principally in estuaries. The overwhelming majority of prey were soniferous species (75% of numerical abundance), which is consistent with the hypothesis that bottlenose dolphins use passive listening to locate noise-making fishes. However, spatiotemporal patterns in consumption of Sciaenid fishes did not coincide with their spawning, which is when peak sound production is thought to occur.     

Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates

Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, bayesass , which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi-allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and F _ST more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low ( F _ST ≥ 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low ( m  = 0.01) and genetic differentiation is high ( F _ST ≥ 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.