Isolation by resistance

Despite growing interest in the effects of landscape heterogeneity on genetic structuring, few tools are available to incorporate data on landscape composition into population genetic studies. Analyses of isolation by distance have typically either assumed spatial homogeneity for convenience or applied theoretically unjustified distance metrics to compensate for heterogeneity. Here I propose the isolation-by-resistance (IBR) model as an alternative for predicting equilibrium genetic structuring in complex landscapes. The model predicts a positive relationship between genetic differentiation and the resistance distance, a distance metric that exploits precise relationships between random walk times and effective resistances in electronic networks. As a predictor of genetic differentiation, the resistance distance is both more theoretically justified and more robust to spatial heterogeneity than Euclidean or least cost path-based distance measures. Moreover, the metric can be applied with a wide range of data inputs, including coarse-scale range maps, simple maps of habitat and nonhabitat within a species' range, or complex spatial datasets with habitats and barriers of differing qualities. The IBR model thus provides a flexible and efficient tool to account for habitat heterogeneity in studies of isolation by distance, improve understanding of how landscape characteristics affect genetic structuring, and predict genetic and evolutionary consequences of landscape change.     

Different Surrounding Landscapes may Result in Different Fish Assemblages in East African Seagrass Beds

Few studies have considered how seagrass fish assemblages are influenced by surrounding habitats. This information is needed for a better understanding of the connectivity between tropical coastal ecosystems. To study the effects of surrounding habitats on the composition, diversity and densities of coral reef fish species on seagrass beds, underwater visual census surveys were carried out in two seagrass habitat types at various locations along the coast of Zanzibar (Tanzania) in the western Indian Ocean. Fish assemblages of seagrass beds in a marine embayment with large areas of mangroves (bay seagrasses) situated 9 km away from coral reefs were compared with those of seagrass beds situated on the continental shelf adjacent to coral reefs (reef seagrasses). No differences in total fish density, total species richness or total juvenile fish density and species richness were observed between the two seagrass habitat types. However, at species level, nine species showed significantly higher densities in bay seagrasses, while eight other species showed significantly higher densities in reef seagrasses. Another four species were exclusively observed in bay seagrasses. Since seagrass complexity could not be related to these differences, it is suggested that the arrangement of seagrass beds in the surrounding landscape (i.e. the arrangement on the continental shelf adjacent to the coral reef, or the arrangement in an embayment with mangroves situated away from reefs) has a possible effect on the occurrence of various reef-associated fish species on seagrass beds. Fish migration from or to the seagrass beds and recruitment and settlement patterns of larvae possibly explain these observations. Juvenile fish densities were similar in the two types of seagrass habitats indicating that seagrass beds adjacent to coral reefs also function as important juvenile habitats, even though they may be subject to higher levels of predation. On the contrary, the density and species richness of adult fish was significantly higher on reef seagrasses than on bay seagrasses, indicating that proximity to the coral reef increases density of adult fish on reef seagrasses, and/or that ontogenetic shifts to the reef may reduce adult density on bay seagrasses.     

Sequence determinants of protein folding rates: positive correlation between contact energy and contact range indicates selection for fast folding

In comparison with intense investigation of the structural determinants of protein folding rates, the sequence features favoring fast folding have received little attention. Here, we investigate this subject using simple models of protein folding and a statistical analysis of the Protein Data Bank (PDB). The mean-field model by Plotkin and coworkers predicts that the folding rate is accelerated by stronger-than-average interactions at short distance along the sequence. We confirmed this prediction using the Finkelstein model of protein folding, which accounts for realistic features of polymer entropy. We then tested this prediction on the PDB. We found that native interactions are strongest at contact range l = 8. However, since short range contacts tend to be exposed and they are frequently formed in misfolded structures, selection for folding stability tends to make them less attractive, that is, stability and kinetics may have contrasting requirements. Using a recently proposed model, we predicted the relationship between contact range and contact energy based on buriedness and contact frequency. Deviations from this prediction induce a positive correlation between contact range and contact energy, that is, short range contacts are stronger than expected, for 2/3 of the proteins. This correlation increases with the absolute contact order (ACO), as expected if proteins that tend to fold slowly due to large ACO are subject to stronger selection for sequence features favoring fast folding. Our results suggest that the selective pressure for fast folding is detectable only for one third of the proteins in the PDB, in particular those with large contact order.     

Teaching about Scientific Origins: Taking Account of Creationism

The purpose of this study was to develop a model for measuring experimental design ability based on functional magnetic resonance imaging (fMRI) during biological inquiry. More specifically, the researchers developed an experimental design task that measures experimental design ability. Using the developed experimental design task, they measured both the paper experimental design ability and the fMRI experimental design ability of subjects. Subjects’ paper experimental design ability was measured using the quotient equation of experimental design ability, and their fMRI experimental design ability using the brain connectivity coefficient. According to the fMRI results, differences in design ability existed among subjects in terms of brain connectivity coefficient level during the experimental design task. The experimental design ability brain connectivity coefficient level and quotient for each subject were analysed. Statistically significant correlations between subjects’ connectivity strength level among brain activation regions and quotient value guided the establishment of a measuring model. The model measured experimental design ability and could predict an individual’s experimental design ability quotient using his or her brain connectivity coefficient. Hence, the model developed for this study for measuring experimental design ability based on fMRI may serve as a practical measurement of students’ scientific experimental design ability. Furthermore, this study could serve as a founding theory for measuring models of other scientific processing abilities such as observation, question generation, classification, hypothesis generation and hypothesis evaluation.     

Obligate crayfish burrow use and core habitat requirements of crawfish frogs

Crawfish frogs (Lithobates areolatus) have experienced declines across large portions of their former range. These declines are out of proportion to syntopic wetland-breeding amphibian species, suggesting losses are resulting from unfavorable aspects of non-breeding upland habitat. Crawfish frogs get their common name from their affinity for crayfish burrows, although the strength of this relationship has never been formally assessed. We used radiotelemetry to address 4 questions related to upland burrow dwelling in crawfish frogs: 1) what burrow types are used and how do they function to affect crawfish frog survivorship; 2) what are the physical characteristics and habitat associations of crawfish frog burrows; 3) what are the home range sizes of crawfish frogs when burrow dwelling; and 4) where are crawfish frog burrows situated with respect to breeding wetlands? We tracked crawfish frogs to 34 burrows, discovered another 7 occupied burrows, and therefore report on 41 burrows. Crawfish frogs exclusively occupied crayfish burrows as primary burrows, which they inhabited for an average of 10.5 months of the year. With one exception, crawfish frogs also used crayfish burrows as secondary burrows—temporary retreats occupied while exhibiting breeding migrations or ranging forays. Burrows were exclusively located in grassland habitats, although crawfish frogs migrated through narrow woodlands and across gravel roads to reach distant grassland primary burrow sites. Home range estimates while inhabiting burrows were 0.05 m² (the area of the burrow entrance plus the associated feeding platform) or 0.01 m³ (the estimated volume of their burrow). Crawfish frog burrows were located at distances up to 1,020 m from their breeding wetlands. To protect crawfish frog populations, we recommend a buffer (core habitat plus terrestrial buffer) of at least 1.2 km around each breeding wetland. Within this buffer, at least 3 critical habitat elements must be present: 1) extensive grasslands maintained by prescribed burning and/or logging, 2) an adequate number of upland crayfish burrows, and 3) no soil disturbance of the sort that would destroy crayfish burrow integrity. © 2012 The Wildlife Society.     

A spatial analytical approach for selecting reintroduction sites for burbot in English rivers

1. Availability of suitable habitat is a prerequisite for species reintroduction success, and to ensure population persistence, investigations of a species’ habitat utilisation throughout its life history should be conducted as part of a feasibility study. 2. Habitat utilisation models for burbot, Lota lota, developed using data from field studies conducted in France and Germany and information from the literature were used to assess the feasibility of reintroducing burbot into rivers of its former native range in eastern England. 3. Per cent tree roots, aquatic vegetation and flow types were important predictors of adult burbot abundance. Furthermore, the habitat utilisation models were supplemented with information from the literature, which suggested that off‐channel habitat such as wetlands and backwaters is important for spawning and nursery stages. 4. An assessment of the habitat availability in the rivers of the burbot’s former native range using variables related to spawning and nursery and adult life stages showed that although adult habitat was widely distributed, the availability of spawning and nursery habitat was less abundant, potentially limiting successful reestablishment. 5. Potential suitable habitat was concentrated in the central and southern areas of the species’ former English distribution. Overall, rivers of the burbot’s former range potentially afford suitable habitat to sustain a reintroduced population. However, sites should be preferentially selected on the basis of having appropriate spawning and nursery areas.     

Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow

Understanding patterns of connectivity among populations of marine organisms is essential for the development of realistic, spatially explicit models of population dynamics. Two approaches, empirical genetic patterns and oceanographic dispersal modelling, have been used to estimate levels of evolutionary connectivity among marine populations but rarely have their potentially complementary insights been combined. Here, a spatially realistic Lagrangian model of larval dispersal and a theoretical genetic model are integrated with the most extensive study of gene flow in a Caribbean marine organism. The 871 genets collected from 26 sites spread over the wider Caribbean subsampled 45.8% of the 1900 potential unique genets in the model. At a coarse scale, significant consensus between modelled estimates of genetic structure and empirical genetic data for populations of the reef-building coral Montastraea annularis is observed. However, modelled and empirical data differ in their estimates of connectivity among northern Mesoamerican reefs indicating that processes other than dispersal may dominate here. Further, the geographic location and porosity of the previously described east-west barrier to gene flow in the Caribbean is refined. A multi-prong approach, integrating genetic data and spatially realistic models of larval dispersal and genetic projection, provides complementary insights into the processes underpinning population connectivity in marine invertebrates on evolutionary timescales.     

Nonsignificant isolation by distance implies limited dispersal

Understanding the scale of dispersal is an important consideration in the conservation and management of many species. However, in species in which the high‐dispersal stage is characterized by tiny gametes or offspring, it may be difficult to estimate dispersal directly. This is the case for many marine species, whose pelagic larvae are dispersed by ocean currents by several days or weeks before beginning a benthic, more sedentary, adult stage. As consequence of the high‐dispersal larval stage, many marine species have low genetic structure on large spatial scales (Waples 1998 ; Hellberg 2007 ). Despite the high capacity for dispersal, some tagging studies have found that a surprising number of larvae recruit into the population they were released from (self‐recruitment). However, estimates of self‐recruitment are not informative about mean dispersal between subpopulations. To what extent are limited dispersal estimates from tagging studies compatible with high potential for dispersal and low genetic structure? In this issue, a study on five species of coral reef fish used isolation by distance (IBD) between individuals to estimate mean dispersal distances (Puebla et al. 2012 ). They found that mean dispersal was unexpectedly small (<50 km), given relatively low IBD slopes and long pelagic durations. This study demonstrates how low genetic structure is compatible with limited dispersal in marine species. A comprehensive understanding of dispersal in marine species will involve integrating methods that estimate dispersal over different spatial and temporal scales. Genomic data may increase power to resolve these issues but must be applied carefully to this question.