Morphological clocks: Quantifying module- and lineage-specific variation in rates of morphological evolution in the primate skull

Lead Research Organisation: University College London
Department Name: Anthropology

Abstract

An animal's body (its phenotype) is the vehicle through which its genes interact with the environment in which it lives. The shape of the body is constrained developmentally by the animal's genes (it cannot grow into a shape that is not coded for by its genome) and put to the test by the environment in which it lives, leading to evolution through Natural Selection (characteristics of the body can make the difference between life and death, and only phenotypes that survive for long enough to reproduce can pass on their genetic blueprint to subsequent generations). We can, consequently, view the shape of a phenotype as the result of interactions between the effects of the environment in which a species evolved and the constraints imposed by its evolutionary relationships with other species. We can also expect different elements of the phenotype to differentially reflect these relationships. In other words, some elements of morphology (the shape of the phenotype) will reflect evolutionary relationships more directly, while others will primarily reflect adaptation to specific environmental challenges or functions. We further predict that elements of morphology that tend to reflect adaptation will evolve more quickly, and in line with changes in the environment, whereas elements of morphology which are not primarily influenced by adaptation will evolve more slowly. In the first instance, our proposed research aims to quantify the extent to which environmental and evolutionary history are reflected in the shape of the primate skull and of different elements of the primate skull and, more specifically, in the rate at which different evolutionary lineages and different parts of the skull have changed over evolutionary time. In a second step, we aim to develop a new and improved framework for inferring evolutionary relationships between extinct species and between extinct and living species that takes that information into account. The skull is an ideal focus for this research for two main reasons. First, it is the most complex hard-tissue element of the body in terms of the range of functions through which the body interacts with its natural environment. It contains all the major sensory organs (vision, hearing, smell and taste) as well as the brain, and it performs key elements of the feeding process including locating, seizing and initial processing (chewing) of food items. Its complexity means that it is the most likely part of the skeleton to reflect measurable degrees of evolutionary and environmental influences. Second, elements of the skull are the most frequently recovered body parts in the fossil record, making them the focus of the vast majority of research on the evolution of extinct species. Primates provide a good model group of species because their natural history is relatively well known, allowing for the testing of hypotheses that relate aspects of the species' natural history to the shape of their skulls and to the rate with which that shape changed over evolutionary time. In the longer term, this research will contribute to solving some of the most interesting outstanding questions in primate and human evolution. For example, which known fossil species are the earliest members of the lineage that led to the 'higher primates' (anthropoids: monkeys, apes and humans)? Which known fossil is the earliest member of the hominins (the evolutionary lineage, which ultimately led to modern humans, after its divergence from that of the chimpanzees)? Which fossil hominin is the closest relative of our own genus, Homo? These questions are not only interesting in their own right, but have to be answered, in order to correctly interpret the sequence in which important characteristics of a species, or group of species, evolved and, ultimately, are key to defining our own fundamental biological identity.

Publications

10 25 50
publication icon
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

publication icon
Smaers JB (2013) Laterality and the evolution of the prefronto-cerebellar system in anthropoids. in Annals of the New York Academy of Sciences

publication icon
Smaers JB (2012) Comparative analyses of evolutionary rates reveal different pathways to encephalization in bats, carnivorans, and primates. in Proceedings of the National Academy of Sciences of the United States of America

 
Description The quality of inferences of evolutionary processes are necessarily constrained by the assumptions made in models that are used to map evolutionary change back trough time. The key central success of this grant has been the development, from idea to fully automatised and computationally efficient software package, of a new, more flexible (i.e., implying fewer assumptions) model of evolution for mapping character traits over evolutionary trees.
A second key achievement has been the acquisition of the largest available standardised dataset of 3D cranial landmarks for strepsirrhine primates (lemurs, lorises and bushbabies).
Exploitation Route Both the database and the phylogenetic analysis software will become freely available and will be instrumental in supporting further research on strepsirrhine primates in particular and organismic evolution in general, with the latter increasingly supporting a broad range of fields including, for example conservation and medicine. Part of the software developed for the project has now been published as open source.
Sectors Education,Environment,Pharmaceuticals and Medical Biotechnology,Other

 
Description Graduate Research Scholarship for Cross Disciplinary Training
Amount £21,126 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 09/2013 
End 09/2014
 
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 "PhyloMap" (beta): A geometric modelling approach to phylogenetic trait mapping 
Description R package "PhyloMap" that includes computational methods to estimate patterns of evolutionary change in deep time, as well as visualization techniques for phylogenetic 'trait mapping'. The focus lies on the applications of the method of Independent Evolution; a geometric modelling approach to inferring deep time branch-directional evolutionary changes. Applications include the estimation of ancestral values, variable rates, mechanisms of change through time, and evolutionary 'snapshots' of morphospace. 
Type Of Material Data analysis technique 
Year Produced 2013 
Provided To Others? Yes  
Impact The package is currently in beta version, is being presented in a podium presentation and a workshop at the Linnean Society on 10-11 November 2014, and is scheduled for publication in January 2016. To date, the method has been made available to other research groups on a collaborative basis. 
 
Title 3D morphometric landmark data of strepsirrhine primate crania 
Description 3D landmark data collected with a Microscribe MX: 65 landmarks for 1633 specimens in 35 species, 20 genera and 7 families of strepsirrhine primates (Lemuriformes and Lorisiformes). 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact The data were collected as part of the PhD research studentship associated with the project. Once the PhD research has been published, the database will be made publicly available. 
 
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 evomap: R package for the evolutionary mapping of continuous traits 
Description R package for evolutionary mapping of continuous traits. This software estimates branch-specific evolutionary trajectories of biological traits across a large temporal scale, and makes available several plotting options to visualize how biological traits are estimated to have evolved across a phylogenetic landscape. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact Specifically, the methods made available in the new software package have been used in numerous publications already as a beta version was introduced to the wider scientific community on the occasion of an international workshop at the Linnean Society, London, in 2014. More generally, the accurate documentation of temporal patterns of change in biological traits are of paramount importance to understanding the nature of the evolutionary process. By making available procedures to estimated evolutionary trajectories of biological traits and intuitively visualize such evolutionary change across a phylogenetic space, this software provides tools to help increase public scientific literacy on the understanding of the concept of evolution. 
URL https://github.com/JeroenSmaers/evomap
 
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