The mass digitisation of natural history collections has the power to document the past, present, and future of biodiversity in higher resolution than ever before. At the same time, the resulting increase in digital data has created an urgent need for standardised methods of automated phenotyping. As part of the Center for Computational Evolutionary Morphometry (CCEM), our goal is to model evolutionary changes in infinite dimensional shape space along branches of the phylogenetic tree using stochastic processes. PhD student Michael Lind Severinsen is helping us do that by applying the developed methods to biological images, such as 2D butterfly wings and 3D bird beaks. Visit the CCEM website for more details.
High throughput phenotyping
Marine mammal neurobiology
As climate change causes sea ice to melt and freshwater to flood into marine systems, Arctic animals face increasing stress. Global warming predictions suggest that the Arctic may become ice-free during summer within the 21st century, with dire impacts on the animals that depend on the ice to hunt, rest, socialise, give birth, and rear their young. This recently started project aims to identify the impacts of glacial melting on Arctic marine mammal neurobiology using cranial endocasts – 3D representations of the space in the skull filled in life by the brain. By taking advantage of high throughput 3D bioimaging and The Natural History Museum of Denmark’s extensive marine mammal collections, we are quantifying changes in brain anatomy over time related to cognitive functions critical for Arctic survival, such as those related to sociality, mating, behaviour, diet, feeding strategy, and sensory systems.
While scientists agree that dogs are descended from wolves, where and when during their human association did domestication occur? This project integrates novel genomic and phenotypic data from ancient to modern canids to resolve a fundamental debate in human history – the origin of dogs. Data collection overlaps with our research on wolf population structure, the results of which will allow us to better place controversial Pleistocene canids in an evolutionary framework.
Wolves (Canis lupus) were once widespread across Eurasia and North America, before being reduced by humans to about 1/3 of their original range. Today wolves are making a comeback in parts of Fennoscandia, where they are thought to be immigrants from eastern Europe and/or hybridised with dogs. As part of a PhD project by Dominika Bujnáková at University of Oulu, Finland, we aim to understand how wolf population structure and morphology varies across their range, and the consequences of that variation for their reestablishment in Europe.
Wolf population structure
Turtle shell asymmetry
Over half of the living 360 turtle and tortoise species are threatened with extinction – a higher proportion than in any other major vertebrate group. Of those, the majority are freshwater turtles. This project aims to identify deformations in freshwater turtle shells using fluctuating asymmetry, or random deviations from bilateral symmetry that can arise through developmental disturbance. PhD student Merin Joji analyses digital 3D models of turtle shells using geometric morphometrics, to quantify fluctuating asymmetry in relation to environmental variables. This summer she will travel to India to surface scan living turtles in the wild, in hopes of developing a conservation tool to monitor the health of India’s many endangered freshwater turtle species.
Humans belong to the family Hominidae together with the other great apes. Although chimpanzees are our closest living relatives, we also share many genes with gorillas that are not present in chimps. This patterns can arise from incomplete lineage sorting, or ILS, when ancestral gene copies fail to segregate following species divergence patterns. In collaboration with Professor Guojie Zhang from Zhejiang University in China, PhD student Stine Keibel Blom is studying how ILS manifests in the phenotypes of great apes, and if we can detect its signatures in shared characteristics of the hard and soft tissues of humans, chimps, and gorillas.
Incomplete lineage sorting in hominids
Many large meat-eating marsupials roamed Australia over the past millions of years, but the thylacine, or Tasmanian tiger, was the only one to survive into modern times. Together with Andrew Pask at University of Melbourne, we are using cutting-edge techniques to reconstruct the life, growth and death of this recently extinct predator, including 3D digital imaging and ancient genome assembly. These methods provide new insights into the thylacine’s extraordinary position among mammals, such as its uncanny resemblance to wolves and dingos, its poor genetic health prior to the arrival of humans, and its relationship to other marsupials like the Tasmanian devil and numbat.
Our previous work established the marsupial thylacine as a model of phenotypic convergence with placental canids, despite the two groups being separated since the Jurassic, some 160-180 million years ago. We later determined, by reconstructing skeletal development of the thylacine using bone measurements from CT scans of all known pouch young specimens in the world, that thylacines grew, and also likely moved, similar to a large cursorial (running) predator. Finally, we identified how and when during development thylacine skulls diverged from their conserved marsupial trajectory to take on proportions similar to a wolf, particularly regarding their elongated snout, widened zygomatic arches, and pronounced sagittal crest. We continue to mine this integrated phenome-genome dataset to learn more about this fascinating animal.
Australian herpetofaunal fossil record
Reptiles and amphibians, known as herpetofauna, constitute half of Australia’s terrestrial vertebrate diversity and serve as important indicators of environmental change. While many reptiles thrive in hot dry conditions, amphibians, being dependent on water for reproduction, tend to suffer. Global decreases in lizard and frog populations indicate that present-day environmental stress is already affecting the biology of these species, principally through shifts in range size, life history, and disease epidemics. What is still unclear, however, are the impacts of these changes on the evolutionary processes underlying their diversification — namely adaptation, speciation, and extinction. This project aims to identify evolutionary responses to climate change in the Australian fossil record by comparing variation in composition, abundance, and morphology of lizards and frogs over geological time. PhD student Till Ramm is contributing to this knowledge by documenting Australian herpetofaunal dynamics in the past, present, and into the future, using a combination of methods in vertebrate paleontology, molecular phylogenetics, geometric morphometrics, and species niche modeling.
The transition from a quadrupedal to a snake-like body form is one of the most dramatic transformations in vertebrate history. Among squamate reptiles (the clade containing lizards and snakes), limblessness has evolved in at least 25 lineages, with snakes representing only one such instance. Other groups such as skinks and amphisbaenians have lost their limbs numerous times during evolutionary history, with multiple intermediate forms existing today. This makes them excellent model systems for understanding the evolutionary steps and ecological contexts that make such transformations possible, including changes in skull morphology required for head-first diggging. PI Christy Hipsley and PhD student Marco Camaiti are currently studying patterns of limb loss in these groups, by describing their morphological variation and mapping relevant traits onto phylogenetic trees.