Modularity and Metamorphosis: the effect of complex life history on cranial integration

Lead Research Organisation: University College London
Department Name: Genetics Evolution and Environment

Abstract

What drives large-scale patterns of morphological evolution? Natural selection acts upon existing variation, the raw material of evolution, to shape the diverse organisms that we see and study today, but what shapes variation? Development is often presented as a major influence on morphological variation, but linking developmental effects into large-scale models of evolution is difficult because comparative developmental data is relatively uncommon. Quantitative data, specifically measurements of the shapes of organisms and the interactions among parts of an organism, has the potential unify disparate fields of evolutionary study, from genetics to development and morphology, into a single framework. Quantification of organismal shape (morphology), during development has been hindered by difficulties in obtaining measurements from small, immature specimens, which often can lose their shape during preparation. However, in recent years, increased access to high-resolution imaging machines, such as CT scanners, and advanced visualization and digitising software has improved the possibility of gathering large volumes for rigorous statistical analyses of changes during development.

The topic of morphological integration is among those that are highly quantitative and will benefit from the incorporation of comparative developmental data. These terms relate to the intuitive idea that complex organisms have many parts with varying interrelationships. Simply, a change in a foot bone would be expected to have more effect on other parts of the foot than they do on, for example, the nose. Delineating the relationships of different parts of an organism can provide novel and unpredicted information on the genetic, developmental, and functional influences on an organism's morphology, and these patterns of trait relationships are termed morphological integration.

Much research on morphological integration has focused on the mammalian skull and jaws and has shown a number of interesting results. First, mammal skulls are formed of six relatively distinct regions, and this pattern of skull integration is observed across mammals, from monkeys to mice. Second, this pattern may reflect developmental interactions, such as tissue origin, as the skull is a developmentally complex structure. Third, patterns of skull integration change through development, from the early stages immediately after birth until subadulthood or adulthood. This last feature is complicated, but there is some evidence that differences in reproductive strategies, specifically between marsupials (such as kangaroos) and placentals (such as dogs or humans) are reflected in the changes in skull integration that occur during ontogeny.

While most research on morphological integration in vertebrates has been conducted on mammals, especially primates and rodents, there is little comparative data on other vertebrates with which to judge whether mammalian patterns are unusual, or simply reflect a more ancestral condition. Furthermore, the diversity of developmental strategies in mammals is far less than that observed across vertebrates. In this study, we will examine morphological integration in the skull of a vertebrate with a very different developmental strategy to that seen in mammals: the African clawed frog, which undergoes metamorphosis from a larval tadpole to a froglet to an adult frog. We will use CT scanning to gather large numbers of specimens from three stages of development to test if skull integration is similar in frogs and mammals, if skull integration changes during frog development, including metamorphosis, and if skull integration in adult frogs reflects whether bones are formed before, during or after metamorphosis.

The results of this study, in comparison with existing data for mammals, will form the basis for a more comprehensive study of developmental integration across tetrapods.

Planned Impact

We will engage with the academic community by publishing results in high-impact peer-reviewed journals (e.g Proceedings of the Royal Society, Evolution, Biology Letters), presentation of results at relevant conferences (e.g. Society of Integrative and Comparative Biology) and through active participation in an online web resource, recently developed by colleagues at UCL and Hull York Medical School for sharing of 3-D image data with the international community.

We will engage with the wider, non-academic community by using the familiar frog and its metamorphosis, a common topic in pre-university science education, to introduce the public to the cutting edge biological imaging methods and research bridging genetic and developmental to evolutionary questions.

We will disseminate our results and conclusions to the wider public via the following means
(1) Press releases. UCL has a very proactive press office, which links between researchers and the media. We will announce the results of our work via press releases through the UCL and NERC press offices. The PI's recent work has been featured in the international news, including the BBC and Washington Post.

(2) Presentations/talks. The PI has extensive experience of direct engagement with the general public via talks, open days and other events. For example, the PI has presented her work on mammalian evolution to the general public at 'Darwin Live' sessions at the Natural History Museum, at 'Brain Food' lunchtime lectures at UCL, and at public debates in the Grant Museum at UCL and the Horniman Museum. She has also been featured on National Geographic, Discovery, BBC News, BBCRadio4, and BBCWales to discuss various aspects of evolutionary biology, paleontology, and science funding. We will seek opportunities to continue this level of engagement, including offering talks during Science Week.

(3) Teaching. The results of our research will be integrated into existing lecture courses at UCL on vertebrate evolution and evolutionary development. This keeps the course content fresh and up-to-date, and inspires students to consider the links between fields and the utility of imaging methods to get more out of anatomical specimens. This research should also produce 'spin-off work that could form the basis for Masters and PhD projects.

(4) Museum workshop: We will use the reconstructed CT-scans to develop a museum workshop with Grant Museum professionals that clearly visualize in 3-D view the profound changes that occur during frog metamorphosis. This image-based workshop would be focused at primary to early secondary school children but would interest the general public as well. It could be easily transferred to other museums and schools, or even developed into an e-learning tool.

Publications

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Goswami A (2016) EMMLi: A maximum likelihood approach to the analysis of modularity. in Evolution; international journal of organic evolution

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Goswami A (2014) The macroevolutionary consequences of phenotypic integration: from development to deep time. in Philosophical transactions of the Royal Society of London. Series B, Biological sciences

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Goswami Anjali (2016) The macroevolutionary consequences of phenotypic integration: from development to deep time in INTEGRATIVE AND COMPARATIVE BIOLOGY

 
Description Variation is the raw material for natural selection, but the factors that limit or shape possible morphological variation are still poorly understood. Genetic and developmental interactions are suggested to direct variation along "paths of least resistance", but there has been little empirical analysis of this fundamental hypothesis. This study provided the first comparative data on phenotypic integration and modularity through ontogeny in a lissamphibian species, representing a much-needed foundation for integrating genetic and developmental hypotheses into rigorous deep-time studies of organismal evolution that exploit the full breadth of phenomic data. The development of tools for comparative and phylogenetic analyses of trait integration and modularity that were tested with this dataset also will provide a valuable bridge across disparate fields of evolutionary biology, from genomics to palaeobiology.

Phenotypic integration and modularity are topics of growing interest in recent decades, as they have to potential to bridge genetic and developmental models of trait relationships with macroevolutionary data on organismal diversity. Phenotypic integration is based on the intuitive concept that morphological traits covary, and that their patterns of covariance reflect their intrinsic genetic, developmental, and functional relationships. Furthermore, the differential relationships among traits leads to evolution of modularity, or the fragmentation of traits into sets of highly correlated traits that have little to no correlation with traits outside of their set, or module. These relationships among traits allow for the deciphering of developmental and genetic shifts from phenotypic data alone, such as those available from rare or extinct taxa, and they also have substantial consequences for the evolutionary trajectories of phenotypic change. Thus far, the vast majority of work in phenotypic integration of vertebrates has focused on mammals, characterising patterns of integration and modularity through ontogeny and across mammal phylogeny. While the focus on mammals is understandable for providing better baseline understanding of genetics, development, ecology, and phylogeny than is available for other animals, mammals are far less diverse developmentally than most other vertebrate clades. This conservation and relative simplicity of development is even more striking when one considers that repeated repatterning of trait covariances through ontogeny that has been observed in many mammals.

Among vertebrates, few display as extreme morphological changes through ontogeny as is observed in frogs, which for the most part, hatch as fully aquatic larvae and later undergo extensive and rapid metamorphosis that involves changes to the entire musculo-skeletal, respiratory, digestive, and sensory systems. Frogs also provide important model systems for medial and biological research, and characterizing the changes in phenotypic integration through frog ontogeny is important for better understanding amphibian biology and evolution as well as phenotypic integration more generally. In this study, we analysed three stages of development in the model organism Xenopus laevis (African clawed frog) to identify patterns of cranial trait covariation and changes in these patterns through postmetamorphic ontogeny.

Our preliminary analyses of 125 specimens representing three stages (late metamorphosis, early post-metamorphosis, and adult) demonstrate that, as in mammals, patterns of integration change significantly through frog ontogeny and that the trajectory of this change results in a decrease in integration, and an increase in modularity, through time. There was also a significant correlation between symmetric (all variation) and asymmetric (developmental variation) components in all stages, suggesting that developmental integration is a large contributor to overall phenotypic integration. Moreover, variance in cranial shape decreased with increasing age, such that the highest variance is observed in the youngest stage of development. This pattern of variance is similar to that observed in placental mammals, but differs from that observed in marsupials. Patterns of cranial modularity also change significantly through ontogeny, with RV coefficient analysis strongly supporting a two-module model in earlier stages, but supporting a more complex six-module pattern in adult samples. This result contrasts with a recent analysis of caecilians that found strong support for a two-module model, but did not test more complex models. We also developed a new information theoretic approach to the study of modularity, which was tested in this sample of Xenopus, and both confirmed the general result of the RV coefficient analysis, but also suggested that the precise model was less parametrized that previous methods allowed us to test. This work was presented at the European Evolutionary Developmental Biology conference in July 2014 and is currently in review for publication.

This work provides the much-meeded foundation for expanding analyses of modularity to other lissamphibians, which is central to establishing if modularity does shift in this clade and to understanding its relationship to reproductive and developmental strategy, life history, ecology, and morphological evolution, thereby establishing its utility and significance in evolutionary biology. These differences in results also highlight the need for model selection tests that can meaningfully compare more and less complex models of modularity, which, as noted above, we have recently developed and tested with this model dataset for Xenopus.



In addition to the methodological advances and important new analyses that resulted from this project, we have begun to archive our original 3-D scans and associated data on a new online database, www.phenome10K.org, which will jumpstart the field of phenomics and serve as a model and resource for international researchers.
Exploitation Route The information theoretic methods developed in this project will be widely applicable, both for the study of modularity and also for other types of network analyses. The study of modularity through ontogeny will also be widely relevant, as there is limited information on this topic in non-mammalian taxa at present, and this study will serve as a foundation for further work in lissamphibians. Furthermore, we have developed a free online repository for 3-D data, www.phenome10k.org, such as those gathered in this study, for use by international researchers, which will jumpstart the field of evolutionary and developmental phenomics.
Sectors Digital/Communication/Information Technologies (including Software),Education,Environment

URL http://www.goswamilab.com
 
Description The results from this study have been presented in an invited symposium presentation at the European Evolutionary Developmental Biology meeting in Vienna, Austria in July 2014. As the first study of modularity through ontogeny in a non-mammalian tetrapod, these results represented an important point of comparison with the numerous studies of mammals and a foundation for future studies. In particular, these finding have further formed the basis for a new grant application focused on expanding this work across lissamphibians, which received a score of 8 in the January 2014 NERC Standard grant found and is being resubmitted in the next round. I further used the data and system from this award to develop a new information theoretic approach to the analysis of modularity, which represents an important step forward for this fundamental field of evolutionary developmental biology and can be applied to diverse ecological and evolutionary systems. The paper describing this method is in review and will form the first output from this study (this submission was delayed by my maternity leave for much of 2013). Once this study is accepted, we will submit the second paper detailing the specific patterns observed in Xenopus laevis. This work also influenced ideas that I developed and described in a recently published study in Philosophical Transactions of the Royal Society B, although the bulk of that work was supported by a NERC standard grant on a related topic. Lastly, we have begun uploading the raw data from this study to a new free online repository that I have developed, www.phenome10k.org, for sharing of 3-D data with the international education and research communities.
First Year Of Impact 2014
Sector Digital/Communication/Information Technologies (including Software),Education
 
Description Research Grant
Amount $220,180 (USD)
Organisation National Science Foundation (NSF) 
Sector Public
Country United States
Start 08/2014 
End 08/2017
 
Description Research Project Grant
Amount £122,319 (GBP)
Funding ID RPG-2014-364 
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2015 
End 09/2017
 
Description Research Project Grant
Amount £219,910 (GBP)
Funding ID RPG-2013-124 
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2014 
End 01/2017
 
Description Starting Grant
Amount € 1,482,818 (EUR)
Funding ID 637171 
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 06/2015 
End 06/2020
 
Title Evaluating Modularity with Maximum Likelihood (EMMLi) 
Description This is a new method for the analysis of phenotypic modularity that was developed to apply maximum likelihood and information theoretic approaches to the study of modularity. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2014 
Provided To Others? Yes  
Impact The publication describing this method is currently in review, but I presented it at a conference in July 2014 where it was met with great interest from other researchers. 
 
Title Phenome10K 
Description This is a new free online repository for 3-D images and associated data and publications. I developed this site so that international researchers and educators could easily upload and download 3-D images and associated files, as many of us have terabytes of data sitting uselessly in our labs once we finish our project of interest. With only a minute or two of effort, one can upload a file and make it available to the global community. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact The site was only completed in October 2014, and a few bugs remain to be fixed, but international research labs have already begun uploading their own datafiles, and I expect that within a year, this will be a major resource for the international community. 
URL http://www.phenome10k.org
 
Title EMMLi 
Description R package for analysis of modularity using maximum likelihood 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Use of product by international scientists 
 
Description Cambridge Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Panel member presenting on the importance of palaeobiological data for evolutionary developmental biology.
Year(s) Of Engagement Activity 2014
 
Description Cheltenham Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Science panel on unusual evolutionary stories
Year(s) Of Engagement Activity 2016
 
Description Cheltenham Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact I was a speaker on a high-profile event on the tree of life and organismal evolution at the Cheltenham Science Festival
Year(s) Of Engagement Activity 2015
URL http://www.cheltenhamfestivals.com/science/
 
Description Public Lecture Linnean Society of London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Talk sparked discussion on development and macroevolution of diversity

Additional requests for public talks
Year(s) Of Engagement Activity 2014
 
Description Radiations and Extinctions: Clade Dynamics in Deep Time 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation workshop facilitator
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I organised this symposium and workshop on methods to analyse biodiversity through deep time, which sparked extensive discussion and debate on new approaches, data selection, and parameters of interest. We trained 50 postgraduates in these methods, which will ensure that the new quantitative approaches will be more widely applied.

Both the symposium and workshop were fully booked months in advance, and dozens have asked for me to organise an annual session to improve training in these cutting-edge approaches.
Year(s) Of Engagement Activity 2014
URL http://www.linnean.org/Meetings-and-Events/Events/Radiation+and+Extinction+-+Investigating+Clade+Dyn...