Habitat fragmentation and biodiversity: testing for the evolutionary effects of refugia

Concordant areas of endemism among taxa have important implications both for understanding mechanisms of speciation and for framing conservation priorities. Here we discuss the need for careful testing of phylogeographic data for evidence of such concordance, with particular reference to the Indonesian island of Sulawesi. This is because there are good reasons to question whether concordance between taxa is likely to be a common pattern, and because of the serious implications of incorrectly concluding that the biodiversity of a given area can be partitioned in this way.     

Population genomics and speciation

The process of speciation begins with genomically-localised barriers to gene exchange associated with loci for local adaptation, intrinsic incompatibility or assortative mating. The barrier then spreads until reproductive isolation influences the whole genome. The population genomics approach can be used to identify regions of reduced gene flow by detecting loci with greater differentiation than expected from the average across many loci. Recently, this approach has been used in several systems. I review these studies, concentrating on the robustness of the approach and the methods available to go beyond the simple identification of differentiated markers. Population genomics has already contributed significantly to understanding the balance between gene flow and selection during the evolution of reproductive isolation and has great future potential both in genome species and in non-model organisms.     

Avian predation on a parasitic fly of cervids during winter: can host‐related cues increase the predation risk?

The deer ked (Lipoptena cervi) is an ectoparasitic fly on cervids that has expanded its distribution rapidly in Northern Europe. However, the regulating biotic factors such as predation remain unknown. The host‐independent pupal stage of the fly lasts for several months. Blackish pupae are visible against snow, especially on the bedding sites of hosts, and are thus exposed to predators. To evaluate the role of predation on the invasion dynamics and evolution of L. cervi, we monitored pupal predation on artificial bedding sites in three geographical areas in Finland during winter. We explored: (1) possible predators; (2) magnitude of predation; and (3) whether predation risk is affected by host‐derived cues. We demonstrate that pupae are predated by a number of tit species. Any reddish brown snow discoloration on bedding sites, indicating heavy infestation of the host, serves as an exploitable cue for avian predators, thereby increasing the risk of pupal predation. The ability of tits to use this host‐derived cue seems to be dependent on the prevalence of L. cervi and the period of invasion history, which suggests that it may be a learned behavioural response. Predation by tits may potentially affect the L. cervi population dynamics locally. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 275–286.     

Habitat association and seasonality in a mosaic and bimodal hybrid zone between Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae)

Understanding why some hybrid zones are bimodal and others unimodal can aid in identifying barriers to gene exchange following secondary contact. The hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi contains a mix of allopatric parental populations and inter-mingled bimodal and unimodal sympatric populations, and provides an ideal system to examine the roles of local selection and gene flow between populations in maintaining bimodality. However, it is first necessary to confirm, over a larger spatial scale, previously identified associations between population composition and season and habitat. Here we use cline-fitting of one morphological and one song trait along two valley transects, and intervening mountains, to confirm previously identified habitat associations (mountain versus valley) and seasonal changes in population composition. As expected from previous findings of studies on a smaller spatial scale, C. jacobsi dominated mountain habitats and mixed populations dominated valleys, and C. brunneus became more prevalent in August. Controlling for habitat and incorporating into the analysis seasonal changes in cline parameters and the standard errors of parental trait values revealed wider clines than previous studies (best estimates of 6.4 to 24.5 km in our study versus 2.8 to 4.7 km in previous studies) and increased percentage of trait variance explained (52.7% and 61.5% for transects 1 and 2 respectively, versus 17.6%). Revealing such strong and consistent patterns within a complex hybrid zone will allow more focused examination of the causes of variation in bimodality in mixed populations, in particular the roles of local selection versus habitat heterogeneity and gene flow between differentiated populations.     

Interleukin-8 is the single most up-regulated gene in whole genome profiling of <Emphasis Type="Italic">H. pylori</Emphasis> exposed gastric epithelial cells

Background  

The association between Helicobacter pylori infection and upper gastrointestinal disease is well established. However, only a small fraction of H. pylori carriers develop disease, and there are great geographical differences in disease penetrance. The explanation to this enigma lies in the interaction between the bacterium and the host. H. pylori Outer Membrane Phospholipase A (OMPLA) has been suggested to play a role in the virulence of this bacterium. The aim of this study was to profile the most significant cellular pathways and biological processes affected in gastric epithelial cells during 24 h of H. pylori exposure, and to study the inflammatory response to OMPLA⁺ and OMPLA^- H. pylori variants.     

The Littorina sequence database (LSD)--an online resource for genomic data

We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.     

An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error

Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fragment locations (loci) within the fingerprint. Our method uses thresholds of AFLP-polymerase chain reaction-product fluorescence intensity (peak height) in order to: (i) exclude AFLP loci that are likely to contribute high rates of error to data sets, and (ii) determine the AFLP phenotype (fragment presence or absence) at the retained loci. Error rate analysis is an integral part of this process and is used to determine optimal thresholds that minimize genotyping error, while maximizing the numbers of retained loci. We show that application of this method to a large AFLP data set allows genotype calls that are rapid, objective and repeatable, facilitating the extraction of reliable genotype data for molecular ecological studies.     

Measuring dispersal and detecting departures from a random walk model in a grasshopper hybrid zone

Abstract. 1. The grasshopper species Chorthippus brunneus and C. jacobsi form a complex mosaic hybrid zone in northern Spain. Two mark–release–recapture studies were carried out near the centre of the zone in order to make direct estimates of lifetime dispersal.
2. A model framework based on a simple random walk in homogeneous habitat was extended to include the estimation of philopatry and flying propensity. Each model was compared with the real data, correcting for spatial and temporal biases in the data sets.
3. All four data sets (males and females at each site) deviated significantly from a random walk. Three of the data sets showed strong philopatry and three had a long dispersal tail, indicating a low propensity to move further than predicted by the random walk model.
4. Neighbourhood size estimates were 76 and 227 for the two sites. These estimates may underestimate effective population size, which could be increased by the long tail to the dispersal function. The random walk model overestimates lifetime dispersal and hence the minimum spatial scale of adaptation.
5. Best estimates of lifetime dispersal distance of 7–33 m per generation were considerably lower than a previous indirect estimate of 1344 m per generation. This discrepancy could be influenced by prezygotic isolation, an inherent by-product of mosaic hybrid zone structure.     

Inter and intra‐population variation in shoaling and boldness in the zebrafish (Danio rerio)

Population differences in anti‐predator behaviour have been demonstrated in several species, although less is known about the genetic basis of these traits. To determine the extent of genetic differences in boldness (defined as exploration of a novel object) and shoaling within and between zebrafish ( Danio rerio ) populations, and to examine the genetic basis of shoaling behaviour in general, we carried out a study that involved laboratory‐raised fish derived from four wild‐caught populations. Controlling for differences in rearing environment, significant inter‐population differences were found in boldness but not shoaling. A larger shoaling experiment was also performed using one of the populations as the basis of a North Carolina type II breeding design (174 fish in total) to estimate heritability of shoaling tendency. A narrow‐sense heritability estimate of 0·40 was obtained, with no apparent dominance effects.