Genomic islands of speciation or genomic islands and speciation?

Populations of the malaria mosquito, Anopheles gambiae, are comprised of at least two reproductively isolated, sympatric populations. In this issue, White et al. (2010) use extensive sampling, high‐density tiling microarrays, and an updated reference genome to clarify and expand our knowledge of genomic differentiation between these populations. It is now clear that DNA near the centromeres of all three chromosomes are in near‐perfect disequilibrium with each other. This is in stark contrast to the remaining 97% of the assembled genome, where fixed differences between populations have not been found, and many polymorphisms are shared. This pattern, coupled with direct evidence of hybridization in nature, supports models of “mosaic” speciation, where ongoing hybridization homogenizes variation in most of the genome while loci under strong selection remain in disequilibrium with each other. However, unambiguously demonstrating that selection maintains the association of these pericentric “speciation islands” in the face of gene flow is difficult. Low recombination at all three loci complicates the issue, and increases the probability that selection unrelated to the speciation process alters patterns of variation in these loci. Here, we discuss these different scenarios in light of this new data.     

Changes in chlorophyll,polyamines and chloroplast ultrastructure of Puccinia striiformis induced ‘green islands’ on detached leaves of Triticum aestivum

Biochemical and ultrastructure features of ‘green islands’ were investigated using detached wheat leaves infected with the yellow rust Puccinia striiformis. Chlorophylls appear to culminate 10 d after inoculation at which point ‘green islands’ were fully developed. These changes were paralleled by an increase in spermidine and spermine content which play an important role in formation of ‘green islands’. Retention of chlorophyll was demonstrated in leaf tissues of wheat plants supplied with exogenous putrescine, spermidine and spermine. Putrescine was least and spermidine and spermine most effective in retarding loss of chlorophylls. Ultrastructural observation revealed that chloroplasts were regenerated in ‘green islands’ where many proplastids were detected. The regeneration of chloroplasts coincided with the high concentration of chlorophylls and polyamines particularly spermidine and spermine. The ultrastructural changes of chloroplasts in leaf cell containing infection structures were parallel to physiological changes.     

Are habitat islands islands? Woodliving beetles (Coleoptera) in deciduous forest fragments in boreal forest

Modern forestry has changed the fire dynamics in the boreal forest and as a result the size and number of deciduous forest patches have been reduced as well as the number of deciduous trees within the coniferous forest This has exaggerated the insularity of deciduous forest patches within the boreal coniferous forest zone In this paper I examine whether the diversity of beetles living in dead stems of deciduous trees follows the relationship with patch area to be predicted from island biogeographic theory, and to what extent the species assemblages differ between large and small patches and single deciduous trees within managed coniferous forests Three larger patches of deciduous forest (>120 ha) arisen as successions after forest fires in the late 1880's are compared with 6 small (<20 ha) patches of similar origin No difference in diversity could be detected between large and small patches A statistically significant difference between assembly composition was detected using matrix regression between a matrix of observed assembly similarities and a hypothetical similarity matrix based on the type of area in which the plot was situated (large- small or matrix) Finally I examined the distribution of the 56 most common beetle species over the habitat types investigated Thirty four species did not show any Significant habitat preference, 12 were found more often in clear-cut areas than expected 5 were over-represented in small patches, and 4 in large areas My explanation to this apparent lack of insularity effects is the relative recent commencement of intensive forestry in these areas and the fact that the matrix is of rather high quality that is inhabitable for numerous beetle species Thus the patches may be viewed as incipient islands still exchanging biota with their surroundings     

Why do green rods of frog and toad retinas look green?

Amphibian “green” rods express a blue-sensitive cone visual pigment, and should look yellow. However, when observing them axially under microscope one sees them as green. We used single-cell microspectrophotometry (MSP) to reveal the basis of the perceived color of these photoreceptors. Conventional side-on MSP recording of the proximal cell segments reveals no selective long-wave absorbing pigment explaining the green color. End-on MSP recording shows, in addition to the green rod visual pigment, an extra 2- to 4-fold attenuation being almost flat throughout the visible spectrum. This attenuation is absent in red (rhodopsin) rods, and vanishes in green rods when the retina is bathed in high-refractive media, and at wide illumination aperture. The same treatments change the color from green to yellow. It seems that the non-visual pigment attenuation is a result of slender green rod myoids operating as non-selective light guides. We hypothesize that narrow myoids, combined with photomechanical movements of melanin granules, allow a wide range of sensitivity regulation supporting the operation of green rods as blue receptors at mesopic-to low-photopic illumination levels. End-on transmittance spectrum of green rods looks similar to the reflectance spectrum of khaki military uniforms. So their greenness is the combined result of optics and human color vision.     

Speciation on islands: what are we learning?

Systematics and the Origin of Species from the Viewpoint of a Zoologist has remained an essential text on the bookshelves of evolutionary biologists since it was first published. Here, I expand upon several topics touched upon by Ernst Mayr to look at how our thinking has evolved, and is evolving, with particular reference to molecular phylogenetic studies on islands. At the time of publication, apart from the fossil record, inferences of temporal trends or patterns could only be speculative, deduced from the distributions of species and the patterns that these present. Much like the subject material itself, evolutionary biology evolves as a discipline, with an increasing availability of tools and resources. The development of molecular phylogenetics and molecular markers has given biologists a new window on the past and, as such, the ideas and explanations of Mayr have become more accessible to testing. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 47–52.     

Are islands the end of the colonization road?

Ecologists have, up to now, widely regarded colonization of islands from continents as a one-way journey, mainly because of widely accepted assertions that less diverse island communities are easier to invade. However, continents present large targets and island species should be capable of making the reverse journey, considering they are the direct descendants of successful colonists and provided that they have not lost their dispersal abilities. Recent mapping of geography onto molecular phylogenies has revealed several cases of 'reverse colonization' (from islands to continents). We suggest this phenomenon warrants closer attention in ecology and biogeography. Assessing its significance will contribute to understanding the role of dispersal and establishment in biogeographic distributions and the assembly of natural biotas.     

Conservation and restoration of plant–animal mutualisms on oceanic islands

Islands harbour much of the world's threatened biodiversity. Recent work has highlighted how it is not species diversity per se but rather the interactions between organisms that breathes life into ecosystems. Thus, the real challenge to preserving and restoring biodiversity on islands is not to only focus on species themselves, but more importantly on maintaining and restoring the integrity of interactions between the species. Here we argue that mutualistic plant–animal interactions play a pivotal role with regards to conservation and restoration on islands. Furthermore, these interactions are ideally suited for inter-island comparisons due to ecological and evolutionary similarities across geographical and taxonomical boundaries. The similarities include highly generalised mutualistic systems, the evolution and readjustment of plant reproductive traits, and a disharmony in taxonomic groups of mutualists, compared to continental ecosystems. We highlight past and present threats to island plant–animal mutualisms, as well as the challenges and opportunities inherent to these interactions. In particular, we (1) argue that mutualistic networks provide an ideal approach to collect information and advance our knowledge on the systems, (2) suggest the use of interactions as biodiversity monitoring and assessment tools, (3) highlight the differences and similarities between pollination and seed dispersal interactions in the context of restoration, and (4) briefly discuss the ambiguous role of alien invasive species in the management of mutualistic interactions. Finally, we highlight how a recently proposed but controversial restoration strategy, rewilding, can be gainfully applied to and further advanced in island settings.     

HpaII library indicates ‘methylation-free islands’ in wheat and barley

Summary A library of wheat genomic DNA HpaII tiny fragments (HTF), sized below 500 bp, has been constructed. Of the clones in the library 80% belong to the single/low-copy category, while 12% of the clones are nuclear repetitive sequences and 8% originate from the chloroplast and mitochondrial DNA. This result shows a substantial enrichment in the single/low-copy sequences of the wheat genome, which contains at least 80% repetitive sequences. Twenty-nine random single/lowcopy clones were analysed further for wheat chromosome location, cross-hybridisation to barley DNA and their association with rare-cutting, C-methylation-sensitive restriction sites. The results show that the HTF clones are associated more frequently than expected with NotI, MluI, NruI and PstI sites in wheat and barley genomic DNA. The 12% repetitive fraction of the clones contain both moderately and highly repetitive sequences, but no tandemly repeated sequences. The level of enrichment for single/low-copy sequences indicates that libraries of this type are a valuable source of probes for RFLP mapping. In addition, the close association of the HTF clones with rare-cutting restriction enzyme sites ensures that HTF clones will have a useful role in the construction of long-range physical maps in wheat.     

Unravelling genetics at the top: mountain islands or isolated belts?

Background and Aims

In mountain plant populations, local adaptation has been described as one of the main responses to climate warming, allowing plants to persist under stressful conditions. This is especially the case for marginal populations at their lowest elevation, as they are highly vulnerable. Adequate levels of genetic diversity are required for selection to take place, while high levels of altitudinal gene flow are seen as a major limiting factor potentially precluding local adaptation processes. Thus, a compromise between genetic diversity and gene flow seems necessary to guarantee persistence under oncoming conditions. It is therefore critical to determine if gene flow occurs preferentially between mountains at similar altitudinal belts, promoting local adaptation at the lowest populations, or conversely along altitude within each mountain.

Methods

Microsatellite markers were used to unravel genetic diversity and population structure, inbreeding and gene flow of populations at two nearby altitudinal gradients of Silene ciliata, a Mediterranean high-mountain cushion plant.

Key Results

Genetic diversity and inbreeding coefficients were similar in all populations. Substantial gene flow was found both along altitudinal gradients and horizontally within each elevation belt, although greater values were obtained along altitudinal gradients. Gene flow may be responsible for the homogeneous levels of genetic diversity found among populations. Bayesian cluster analyses also suggested that shifts along altitudinal gradients are the most plausible scenario.

Conclusions

Past population shifts associated with glaciations and interglacial periods in temperate mountains may partially explain current distributions of genetic diversity and population structure. In spite of the predominance of gene flow along the altitudinal gradients, local genetic differentiation of one of the lower populations together with the detection of one outlier locus might support the existence of different selection forces at low altitudes.     

Breeding birds on small islands: island biogeography or optimal foraging?

1. We test MacArthur and Wilson's theory about the biogeography of communities on isolated habitat patches using bird breeding records from 16 small islands off the coasts of Britain and Ireland. 2. A traditional examination of patterns of species richness on these islands suggests that area and habitat diversity are important predictors, but that isolation and latitude have a negligible impact in this system. 3. Unlike traditional studies, we directly examine the fundamental processes of colonization and local extinction (cessation of breeding), rather than higher-order phenomena such as species richness. 4. We find that many of MacArthur and Wilson's predictions hold: colonization probability is lower on more isolated islands, and extinction probability is lower on larger islands and those with a greater diversity of habitats. 5. We also find an unexpected pattern: extinction probability is much lower on more isolated islands. This is the strongest relationship in these data, and isolation is the best single predictor of colonization and extinction. 6. Our results show that examination of species richness alone is misleading. Isolation has a strong effect on both of the dynamic processes that underlie richness, and in this system, the reductions in both colonization and extinction probability seen on more distant islands have opposing influences on species richness, and largely cancel each other out. 7. We suggest that an appropriate model for this system might be optimal foraging theory, which predicts that organisms will stay longer in a resource patch if the distance to a neighbouring patch is large. If nest sites and food are the resources in this system, then optimal foraging theory predicts the pattern we observe. 8. We advance the hypothesis that there is a class of spatial systems, defined by their scale and by the taxon under consideration, at which decision-making processes are a key driver of the spatiotemporal dynamics. The appropriate theory for such systems will be a hybrid of concepts from biogeography/metapopulation theory and behavioural ecology.     

Seabirds as agents of spatial heterogeneity on New Zealand’s offshore islands

Aims

This study investigates how burrow-nesting, colonial seabirds structure the spatial patterns of soil and plant properties (including soil and leaf N) and tests whether burrow density drives these spatial patterns within each of six individual islands that vary greatly in burrow density.

Methods

Within individual islands, we compared semivariograms (SVs) with and without burrows as a spatial trend. We also used SVs to describe and compare the spatial patterns among islands for each of 16 soil and plant variables.

Results

Burrow density within a single island was only important in determining spatial structuring in one-fifth of the island-variable combinations tested. Among islands, some variables (i.e., soil pH, δ¹⁵N, and compaction; microbial biomass and activity) achieved peak spatial variance on intermediate-density islands, while others (i.e., net ammonification, net nitrification, NH₄ ⁺, NO₃ ^-) became increasingly variable on densely burrowed islands.

Conclusions

Burrow density at the within-island scale was far less important than expected. Seabirds and other ecosystem engineers whose activities (e.g., nutrient subsidies, soil disturbance) influence multiple spatial scales can increase spatial heterogeneity even at high densities, inconsistent with a “hump-shaped” relationship between resource availability and heterogeneity.     

Intercropping green manure crops—effects on rooting patterns

Greater productivity under intercropping has been attributed to the complementary use of environmental resources. However, the rooting pattern of component species under intercropping, which is an important morphological feature considering the complementary uptake of nutrients, has been studied only rarely under field conditions because of inherent technical difficulties. We examined rooting patterns of three green manure species, both sole cropped and intercropped, using a newly developed multi-color staining technique. Species were chosen from different functional groups: sorghum (Sorghum bicolor (L.) Moench.), a C4 grass; crotalaria (Crotalaria juncea L.), a legume; and sunflower (Helianthus annuus L.), a C3 dicot. We also investigated these species’ aboveground biomass and N uptake. Sorghum distributed roots deeper under intercropping than under sole cropping; it was the most important contributor to increased biomass under intercropping. Crotalaria had a deep rooting system under both sole cropping and intercropping. Sunflower, with a shallow rooting system, was suppressed extremely under intercropping, possibly because of water deficiency in late in the season. The rooting patterns of green manure species examined using multi-color staining were related closely to the aboveground performance of these species under intercropping.