Report

Teaser, summary, work performed and final results

Periodic Reporting for period 3 - ADaPTIVE (Analysing Diversity with a Phenomic approach: Trends in Vertebrate Evolution)

Teaser

What processes shape vertebrate diversity through deep time? Approaches to this question can focus on many different factors, from life history and ecology to large-scale environmental change and extinction. To date, the majority of studies on the evolution of vertebrate...

Summary

What processes shape vertebrate diversity through deep time? Approaches to this question can focus on many different factors, from life history and ecology to large-scale environmental change and extinction. To date, the majority of studies on the evolution of vertebrate diversity have focused on relatively simple metrics, specifically taxon counts or univariate measures, such as body size. However, multivariate morphological data provides a more complete picture of evolutionary and palaeoecological change. Morphological data can also bridge deep-time palaeobiological analyses with studies of the genetic and developmental factors that shape variation and must also influence large-scale patterns of evolutionary change. Thus, accurately reconstructing the patterns and processes underlying evolution requires an approach that can fully represent an organism’s phenome, the sum total of their observable traits.

Recent advances in imaging and data analysis allow large-scale study of phenomic evolution. In this project, we will quantitatively analyse the deep-time evolutionary diversity of tetrapods (amphibians, reptiles, birds, and mammals). Specifically, I will apply and extend new imaging, morphometric, and analytical tools to construct a multivariate phenomic dataset for living and extinct tetrapods from 3-D scans. We will use these data to rigorously compare extinction selectivity, timing, pace, and shape of adaptive radiations, and ecomorphological response to large-scale climatic shifts across all tetrapod clades. To do so, we will quantify morphological diversity (disparity) and rates of evolution spanning over 300 million years of tetrapod history. We will further analyse the evolution of phenotypic integration by quantifying not just the traits themselves, but changes in the relationships among traits, which reflect the genetic, developmental, and functional interactions that shape variation, the raw material for natural selection.

The overall objectives for this project are to reconstruct vertebrate evolution with dense phenotypic (anatomical) data through their evolution and use it to understand how both intrinsic factors, such as development, and extrinsic factors, such as environment and extinction, have influenced their evolution and will continue to influence their evolution in the future. By understanding how variation and diversification are controlled, we can estimate the limits to evolution and thus project how species will respond to continuing environmental changes, and whether there are any generalities in response across vertebrates or if some clades will be more susceptible to environmental changes than others.

Work performed

This first half of the project was focused on three major goals: data collection, development and testing of surface morphometric approaches and analysis of modularity, application of those methods to our newly-generated high-dimensional datasets for birds, caecilians, and squamates, and palaeontological fieldwork. We have made great progress in each of these objectives.

In addition to PI Goswami, four staff have been employed on this grant: Postdoctoral Research Assistant Dr. Ryan Felice (from August 2015), Ph.D. student Ms. Carla Bardua (from September 2015), Research Assistant Ms. Eve Noirault (from May 2016), and Postdoctoral Research Assistant Dr. Akinobu Watanabe (from July 2016 to December 2017). Each staff member is tasked with collecting and analysing data for a different clade of tetrapods, with the majority of time during this first period devoted primarily to data collection. To accomplish this purpose, we purchased three portable laser scanning systems, which we have taken to many museums across Europe and North America, as detailed below. We have further involved several undergraduate and Master’s students in data collection and analysis of intraspecific and non-cranial datasets.

Dr. Ryan Felice is leading the work on Archosauromorpha, including birds, crocodiles, dinosaurs, and turtles. He has travelled extensively to scan specimens at the following institutions: The Museum of Natural History (London), Muséum National d’Histoire Naturelle (Paris, France), National Museum of Natural History (Smithsonian Institution, Washington, D.C.), American Museum of Natural History (New York), Yale Peabody Museum of Natural History (New Haven, Connecticut), Museum of Comparative Zoology, Harvard University (Cambridge, Massachusetts), Field Museum of Natural History (Chicago, USA), Carnegie Museum of Natural History (Pittsburgh, Pennsylvania), University of Michigan Museum of Zoology (Ann Arbor, Michigan), Museum of the Rockies (Bozeman, Montana), Royal Tyrrell Museum (Drumheller, Alberta), University of California Museum of Paleontology (Berkeley, California), Natural History Museum of Utah (Salt Lake City, Utah), Burke Museum (Seattle, Washington), Denver Museum of Nature and Science (Denver, Colorado), Museo de la Plata (La Plata, Argentina), and Museo Argentino de Ciencias Naturales (Buenos Aires, Argentina). Through these trips, he has amassed a 3D image dataset of 513 species, comprising 352 species of birds (representing 192 families), 47 non-avian dinosaurs, 48 crocodylomorphs, 66 turtles, and 10 stem archosauromorphs. We have further accumulated intraspecific samples of 2 species of turtles, 2 species of birds, and one species of crocodylomorph, representing an additional 170 specimens. Analyses of these data have contributed to one published paper, with a second submitted and currently in review (see below). A third manuscript, testing hypotheses of adapative evolution in the avian skull, is also in review. These publications utilize the avian portion of the taxanomic sampling, with a dataset composed of high-resolution geometric morphometric quantification of shape (757 3D landmarks). Dr. Felice has served as a supervisor for a number of junior students (three master’s students and one Erasmus+ trainee) whose research projects utilizing this dataset. Ongoing work includes analysis of non-avian archosauromorph data.

Ms. Carla Bardua is leading the work on amphibians, including all living groups and fossils dating back to the initial terrestrialisation of vertebrates. She has travelled extensively to scan specimens to build her dataset. Extant material was collected through trips to Museum National d’Histoire Naturelle (Paris) and Florida Museum of Natural History. Fossil scans were collected through trips to the Museum of Comparative Zoology (Harvard), Carnegie Museum of Natural History (Pittsburgh), Royal Ontario Museum (Toronto), Field Museum of Natural History (Chicago), US National Museum o

Final results

\"We have gathered an unprecedented, rich, comparative dataset on phenotype and have developed and refined several new methods for gathering and analysing dense 3D data from 3D images (Figure attached). We have analysed macroevolutionary patterns of morphological evolution and modularity on a far larger scale than previously achieved, hailed as \"\"the vanguard of comparative evolutionary morphology\"\" in a commentary piece published alongside our recent publication in Proceedings of the National Academy of Sciences USA. We have used our rich data and understanding of evolutionary history of these groups to reconstruct hypothetical ancestors for our clades, which can be compared to existing fossils or provide a search image and estimate in the absence of fossils. We have identified a fundamental divide across vertebrates in where they concentrate changes in their skulls and we have proposed novel hypotheses on how these differences arise during development. As we continue on this project, we will continue to publish results of each major tetrapod clade (frogs, salamanders, dinosaurs, crocodiles, turtles, placental mammals, marsupials), and next year we anticipate combining our data in larger groupings (all reptiles, all mammals, all amphibians) and ultimately all tetrapods. In the size of our dataset, the density and quality of our phenomic data, and the depth and rigour of our analyses, we have broken extensive new ground for the study of phenomics and the understanding of skull evolution and diversity, with ramifications for understanding how species can, and cannot, respond to changes and how future environmental shifts will affect vertebrate diversity.
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Website & more info

More info: http://www.goswamilab.com.