Shaping up? A direct comparison between 2D and low-cost 3D shape analysis using African Cichlid mandibles

Shape is a complex trait which can be investigated through a variety of methods that have been developed over the past century. Currently, ecologists and evolutionary biologists employ the use of geometric morphometrics on 2D images as their standard approach. Recently, there has been increased interest in the use of 3D methods. However, while low-cost 3D methods of data collection are becoming available their potential benefits are often more implied rather than quantified. Using the mandibles from two species of African cichlids (Maylandia zebra and Tropheops “Red Cheek”), this study aimed to evaluate the use of a low-cost 3D method of shape capture versus a range of 2D data sets (termed ‘standard’, ‘even’, and ‘extended’). Our findings indicated that while both 2D and 3D methods could discriminate differences in species and sexes there was only a slight improvement using 3D when landmark datasets were held even. Further, the standard approaches to data collection that would be taken by most researchers clearly outperformed our 3D approach. Therefore, as 3D methods become more accessible researchers should consider a cost/benefit ratio in terms of the time required to obtain 3D data versus shape information gained

Conservation evo-devo: preserving biodiversity by understanding its origins

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields

A new methodology for the quantitative visualization of coherent flow structures in alluvial channels using multibeam echo-sounding (MBES)

In order to investigate the interactions between turbulence and suspended sediment transport in natural aqueous environments, we ideally require a technique that allows simultaneous measurement of fluid velocity and sediment concentration for the whole flow field. Here, we report on development of a methodology using the water column acoustic backscatter signal from a multibeam echo sounder to simultaneously quantify flow velocities and sediment concentrations. The application of this new technique is illustrated with reference to flow over the leeside of an alluvial sand dune, which allows, for the first time in a field study, quantitative visualization of large-scale, whole flow field, turbulent coherent flow structures associated with the dune leeside that are responsible for suspending bed sediment. This methodology holds great potential for use in a wide range of aqueous geophysical flows

Foraging environment determines the genetic architecture and evolutionary potential of trophic morphology in cichlid fishes

Phenotypic plasticity allows organisms to change their phenotype in response to shifts in the environment. While a central topic in current discussions of evolutionary potential, a comprehensive understanding of the genetic underpinnings of plasticity is lacking in systems undergoing adaptive diversification. Here, we investigate the genetic basis of phenotypic plasticity in a textbook adaptive radiation, Lake Malawi cichlid fishes. Specifically, we crossed two divergent species to generate an F3 hybrid mapping population. At early juvenile stages, hybrid families were split and reared in alternate foraging environments that mimicked benthic/scraping or limnetic/sucking modes of feeding. These alternate treatments produced a variation in morphology that was broadly similar to the major axis of divergence among Malawi cichlids, providing support for the flexible stem theory of adaptive radiation. Next, we found that the genetic architecture of several morphological traits was highly sensitive to the environment. In particular, of 22 significant quantitative trait loci (QTL), only one was shared between the environments. In addition, we identified QTL acting across environments with alternate alleles being differentially sensitive to the environment. Thus, our data suggest that while plasticity is largely determined by loci specific to a given environment, it may also be influenced by loci operating across environments. Finally, our mapping data provide evidence for the evolution of plasticity via genetic assimilation at an important regulatory locus, ptch1. In all, our data address long-standing discussions about the genetic basis and evolution of plasticity. They also underscore the importance of the environment in affecting developmental outcomes, genetic architectures, morphological diversity and evolutionary potential

Does phenotypic plasticity initiate developmental bias?

Acknowledgements We thank attendees and organizers of the “developing a theory of developmental bias” workshop for stimulating discussion on the topics in this manuscript. We are grateful to Matt Wund and an anonymous reviewer who provided thoughtful and constructive comments that helped to improve the manuscript. We also thank Calum Campbell,Joey Humble, and Iain Hill for photographing sticklebacks that were used to generate Figure 2. This paper was partially supported by NERC grant NE/N016734/1 and by an EPSRC studentship grant EP/M508056/1.Peer reviewedPublisher PD

Modularity of the Oral Jaws Is Linked to Repeated Changes in the Craniofacial Shape of African Cichlids

The African cichlids of the East-African rift-lakes provide one of the most dramatic examples of adaptive radiation known. It has long been thought that functional decoupling of the oral and pharyngeal jaws in cichlids has facilitated their explosive evolution. Recent research has also shown that craniofacial evolution from radiations in lakes Victoria, Malawi, and Tanganyika has occurred along a shared primary axis of shape divergence, whereby the preorbital region of the skull changes in a manner that is, relatively independent from other head regions. We predicted that the preorbital region would comprise a variational module and used an extensive dataset from each lake that allowed us to test this prediction using a model selection approach. Our findings supported the presence of a preorbital module across all lakes, within each lake, and for Malawi, within sand and rock-dwelling clades. However, while a preorbital module was consistently present, notable differences were also observed among groups. Of particular interest, a negative association between patterns of variational modularity was observed between the sand and rock-dwelling clades, a patter consistent with character displacement. These findings provide the basis for further experimental research involving the determination of the developmental and genetic bases of these patterns of modularity

Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations. To address these open questions, we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish ( ). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed towards a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution

An evaluation of the status of living collections for plant, environmental, and microbial research

Citation: McCluskey, K., Parsons, J. P., Quach, K., & Duke, C. S. (2017). An evaluation of the status of living collections for plant, environmental, and microbial research. Journal of Biosciences, 42(2), 321-331. https://doi.org/10.1007/s12038-017-9685-6While living collections are critical for biological research, support for these foundational infrastructure elements is inconsistent, which makes quality control, regulatory compliance, and reproducibility difficult. In recent years, the Ecological Society of America has hosted several National Science Foundation–sponsored workshops to explore and enhance the sustainability of biological research infrastructure. At the same time, the United States Culture Collection Network has brought together managers of living collections to foster collaboration and information exchange within a specific living collections community. To assess the sustainability of collections, a survey was distributed to collection scientists whose responses provide a benchmark for evaluating the resiliency of these collections. Among the key observations were that plant collections have larger staffing requirements and that living microbe collections were the most vulnerable to retirements or other disruptions. Many higher plant and vertebrate collections have institutional support and several have endowments. Other collections depend on competitive grant support in an era of intense competition for these resources. Opportunities for synergy among living collections depend upon complementing the natural strong engagement with the research communities that depend on these collections with enhanced information sharing, communication, and collective action to keep them sustainable for the future. External efforts by funding agencies and publishers could reinforce the advantages of having professional management of research resources across every discipline. © 2017 Indian Academy of Science

Limits of Principal Components Analysis for Producing a Common Trait Space: Implications for Inferring Selection, Contingency, and Chance in Evolution

<b>Background</b> Comparing patterns of divergence among separate lineages or groups has posed an especially difficult challenge for biologists. Recently a new, conceptually simple methodology called the “ordered-axis plot” approach was introduced for the purpose of comparing patterns of diversity in a common morphospace. This technique involves a combination of principal components analysis (PCA) and linear regression. Given the common use of these statistics the potential for the widespread use of the ordered axis approach is high. However, there are a number of drawbacks to this approach, most notably that lineages with the greatest amount of variance will largely bias interpretations from analyses involving a common morphospace. Therefore, without meeting a set of a priori requirements regarding data structure the ordered-axis plot approach will likely produce misleading results.<p></p> <b>Methodology/Principal Findings</b> Morphological data sets from cichlid fishes endemic to Lakes Tanganyika, Malawi, and Victoria were used to statistically demonstrate how separate groups can have differing contributions to a common morphospace produced by a PCA. Through a matrix superimposition of eigenvectors (scale-free trajectories of variation identified by PCA) we show that some groups contribute more to the trajectories of variation identified in a common morphospace. Furthermore, through a set of randomization tests we show that a common morphospace model partitions variation differently than group-specific models. Finally, we demonstrate how these limitations may influence an ordered-axis plot approach by performing a comparison on data sets with known alterations in covariance structure. Using these results we provide a set of criteria that must be met before a common morphospace can be reliably used.<p></p> <b>Conclusions/Significance</b> Our results suggest that a common morphospace produced by PCA would not be useful for producing biologically meaningful results unless a restrictive set of criteria are met. We therefore suggest biologists be aware of the limitations of the ordered-axis plot approach before employing it on their own data, and possibly consider other, less restrictive methods for addressing the same question

Oil exposure alters social group cohesion in fish

Many animal taxa live in groups to increase foraging and reproductive success and aid in predator avoidance. For fish, a large proportion of species spend all or part of their lives in groups, with group coordination playing an important role in the emergent benefits of group-living. Group cohesion can be altered by an array of factors, including exposure to toxic environmental contaminants. Oil spills are one of the most serious forms of pollution in aquatic systems, and while a range of effects of acute oil exposure on animal physiology have been demonstrated, sub-lethal effects on animal behavior are relatively under-studied. Here we used an open-field behavioral assay to explore influence of acute oil exposure on social behavior in a gregarious fish native to the Gulf of Mexico, Atlantic croaker (Micropogonias undulatus). We used two oil concentrations (0.7% and 2% oil dilution, or 6.0 ± 0.9 and 32.9 ± 5.9 μg l−1 ΣPAH50 respectively) and assays were performed when all members of a group were exposed, when only one member was exposed, and when no individuals were exposed. Shoal cohesion, as assessed via mean neighbor distance, showed significant impairment following acute exposure to 2% oil. Fish in oil-exposed groups also showed reduced voluntary movement speed. Importantly, overall group cohesion was disrupted when even one fish within a shoal was exposed to 2% oil, and the behavior of unexposed in mixed groups, in terms of movement speed and proximity to the arena wall, was affected by the presence of these exposed fish. These results demonstrate that oil exposure can have adverse effects on fish behavior that may lead to reduced ecological success