Genome scans and elusive candidate genes: detecting the variation that matters for speciation

Next‐generation sequencing is providing us with vast amounts of genetic data, yet we are currently struggling in our attempts to make sense of them. In particular, it has proven difficult to link phenotypic divergence and speciation to genome level divergence. In the current issue of Molecular Ecology, Ruegg et al. ( 2014 ) present new empirical results from two closely related bird taxa. They use a promising approach combining genome scan and candidate gene analysis. Their results suggest that we may have been looking in vain for candidate speciation genes by focusing only on genes found within genomic islands of divergence. This is because genes important in divergence and speciation may not be detected by genome scans and because features of the genomic architecture per se may have a large effect on the pattern of genome divergence.     

Autochthonous outer ramp sedimentation: The Alamogordo Member of the Lake Valley Formation,New Mexico

Summary Paleozoic carbonate ramp sedimentation has generally been described in terms of downlapping clinoforms composed of allochthonous sediment derived from shallower environments. However, during transgressive episodes when carbonate sediment production is low and down slope sediment transport by gravity becomes inactive, autochthonous carbonate sediment accumulates in vertical stacks of essentially in situ sediment. Autochthonous outer ramp deposition is probably a part of many Paleozoic ramp strata, but has heretofore not been recognized because of the general absence of adequate exposures. Evidence of autochthonous, in situ deposition and preservation of sediments in a starved setting is well displayed in the Alamogordo Member of the Lake Valley Formation in south central New Mexico. This evidence includes: 1) beds and bed sets that are individually continuous and traceable along ramp slope for 32 km, 2) down-ramp sequential distributions of depth-sensitive organisms and assemblages but patchy distribution of rock types, 3) lack of sedimentary structures indicative of transport, 4) well preserved, unabraded fossils, 5) the common occurrence of fossils in life position, 6) beds traceable into and through mounds 7) bed thickness trends ascribed to biotic productivity, and 8) geopetal structures in original position. Integrated paleontologic, sedimentologic, and stratigraphic data provide information about depositional processes and setting. The depositional slope was approximately 0.5^o based on the distribution of fossil algae; this is comparable to dips reported for other Mississippian homoclinal ramps. An oxygen minimum zone may have impinged on the ramp during a major flooding event. Shifts in biotic gradients from bed to bed reveal transgressive-regressive patterns that would not be resolvable without detailed paleontological evidence. The Alamogordo Member formed as a result of transgressive and early highstand starved carbonate sedimentation along a narrow, homoclinal outer ramp. The surface of maximum flooding and the boundary between the TST and HST are within the Alamogordo Member.     

The impacts of climate change on the annual cycles of birds

Organisms living today are descended from ancestors that experienced considerable climate change in the past. However, they are currently presented with many new, man-made challenges, including rapid climate change. Migration and reproduction of many avian species are controlled by endogenous mechanisms that have been under intense selection over time to ensure that arrival to and departure from breeding grounds is synchronized with moderate temperatures, peak food availability and availability of nesting sites. The timing of egg laying is determined, usually by both endogenous clocks and local factors, so that food availability is near optimal for raising young. Climate change is causing mismatches in food supplies, snow cover and other factors that could severely impact successful migration and reproduction of avian populations unless they are able to adjust to new conditions. Resident (non-migratory) birds also face challenges if precipitation and/or temperature patterns vary in ways that result in mismatches of food and breeding. Predictions that many existing climates will disappear and novel climates will appear in the future suggest that communities will be dramatically restructured by extinctions and changes in range distributions. Species that persist into future climates may be able to do so in part owing to the genetic heritage passed down from ancestors who survived climate changes in the past.     

<Emphasis Type="Italic">Psathyrella turcosomarginata</Emphasis>, a new species with cheilocystidia possessing mucoid deposits staining bluish green in ammonia solution

Psathyrella turcosomarginata is described and illustrated as a new species from Japan (Fukuoka Prefecture, Kyushu). This species is assigned to section Spintrigerae because of its lack of pleurocystidia and basidiome habit. It is characterized by having fairly large basidiomes, a distinct sulcate-striate pileal margin, and cheilocystidia with mucoid deposits that stain bluish green in ammonia solution.     

New developments in MRI: System characterization,technical advances and radiotherapy applications

A Special Issue of Physica Medica – European Journal of Medical Physics, focused on some important points of contact between the world of magnetic resonance and that of medical physics, was published during 2021. This Editorial describes and comments on the content of this Focus Issue, which contains articles from leading groups invited by the Guest Editors.     

Local or global? Biogeography of some primitive Lepidoptera in New Zealand

Abstract

Distribution maps are presented for 30 species of small forest moths representing two genera of Micropterigidae and one genus of Mnesarchaeidae. Evolutionary patterns are interpreted by means of the panbiogeographic method in order to seek a relationship between dispersal patterns within New Zealand and the overseas links of the taxa in question. It is established that different evolutionary lines indeed exhibit different geographic dispersal patterns within New Zealand. Moreover, certain characteristics of these patterns can be attributed to the overseas affinities of the groups, i.e., groups of organisms with New Caledonian or Australian affinities have a western disjunct pattern, whereas those with circum-Pacific affinities have a different pattern in which the taxa occupying a basal position in the phylogeny are to be found in the eastern South Island. However, both groups have overlapping centres of diversity, particularly in NW Nelson.     

Comparison of point counts and territory mapping for detecting effects of forest management on songbirds

Point counts are commonly used to assess changes in bird abundance, including analytical approaches such as distance sampling that estimate density. Point‐count methods have come under increasing scrutiny because effects of detection probability and field error are difficult to quantify. For seven forest songbirds, we compared fixed‐radii counts (50 m and 100 m) and density estimates obtained from distance sampling to known numbers of birds determined by territory mapping. We applied point‐count analytic approaches to a typical forest management question and compared results to those obtained by territory mapping. We used a before–after control impact (BACI) analysis with a data set collected across seven study areas in the central Appalachians from 2006 to 2010. Using a 50‐m fixed radius, variance in error was at least 1.5 times that of the other methods, whereas a 100‐m fixed radius underestimated actual density by >3 territories per 10 ha for the most abundant species. Distance sampling improved accuracy and precision compared to fixed‐radius counts, although estimates were affected by birds counted outside 10‐ha units. In the BACI analysis, territory mapping detected an overall treatment effect for five of the seven species, and effects were generally consistent each year. In contrast, all point‐count methods failed to detect two treatment effects due to variance and error in annual estimates. Overall, our results highlight the need for adequate sample sizes to reduce variance, and skilled observers to reduce the level of error in point‐count data. Ultimately, the advantages and disadvantages of different survey methods should be considered in the context of overall study design and objectives, allowing for trade‐offs among effort, accuracy, and power to detect treatment effects.