An integrative approach to studying evolutionary radiation, hybridisation and biodiversity: the Cervidae (deer) as an example

white tailed deer in a field — A white-tailed deer. Image © Paul Tessier/Shutterstock

This project will gather genomic and morphological data allowing total evidence to produce the most thorough combined phylogenetic analysis to date for all extant and recently extinct cervids.

Project background

Despite recent advances in phylogenetic analysis of the deer (Cervidae), many genera remain taxonomically confused. This is particularly true among New World taxa, which represent a recent adaptive radiation (Heckeberg et al. 2020). Mixed evolutionary ancestry (polyphyly) has been suggested in multiple genera, including huemul (Hippocamelus), tailed deer (Odocoileus), brocket (Mazama) and pudu (Pudu).

To date, most studies have focused on cytogenetic and mitochondrial DNA sequence data, and genomic data are severely lacking. Extensive morphological diversity, particularly in antler form, also exists, but has never been investigated using objective morphological analysis. This PhD would first investigate radiation and diversity in morphology, including antler structure and genomics to reassess New World cervid systematics. 

A recent study on antler variation and genomic diversity in red deer (Peters et al 2022) suggests that antler morphology has high heritability, a polygenic architecture and traits that are positively genetically correlated with pleiotropic loci. The evolutionary dynamics of targeted genomic regions implicated in antler growth will therefore be sequenced alongside morphological analysis.

Genomic analysis is increasingly highlighting that hybridisation and introgression are involved in the evolution of many vertebrate taxa. Hybridisation occurs in black-tailed deer and reindeer, introgression is thought to have occurred between Eld’s deer and sambar in the origin of white-lipped deer, and is suspected in Père David’s deer where mitochondrially, it is sister to Eld’s deer but for nuclear DNA is sister to wapiti. Therefore, for this PhD, genomic analysis of E. davidianus (Père David’s deer) will secondly focus on establishing its evolutionary origin and history of admixture (reference genome already available). 

The above elements of the PhD will gather much of the genomic and morphological data which will then finally be complemented by character-scoring on deer skulls, allowing total evidence to produce the most thorough combined phylogenetic analysis to date for all extant and recently extinct cervids.

Project aims and methods

Methods will include genome sequencing and resequencing using established ancient and modern DNA analyses from museum specimens of New World deer in the NHM collection and the CryoArks biobank.

Samples will be taken for all relevant members of the Odocoileini (Heckeberg 2020), which currently includes 11 species, of which a high-quality reference genome already exists for both white tailed and mule deer (Russell et al 2019) for reference-based alignment. A Père David’s deer assembly also already exists (Zhu et al 2018) as do genomes for sika and red deer. Thus, additional reference genome production should be a relatively straightforward exercise, and this will be carried out for all available species up to 30x coverage. Up to ten additional individuals per species will be resequenced to low genomic coverage (10x). Phylogenomic analysis will comprise approaches described in Fan et al (2020) for New World camelids and will enable the pinpointing of hybridization and admixture events, including their timing.

Comparative genomic analysis will also be used to understand the evolutionary trajectories of each species (changes in population size over time), to pinpoint regions of the genome possessing selection signatures, unusual levels of genomic diversity and for evolution in genes linked to antler growth and morphology. A series of morphometric measurements to be taken on skulls and mandibles of New World Deer from the NHM and other collections. Antler diversity in New World deer will be explored by 3D laser scanning and extracting geometric measurements for use in a PCA and homology analyses.

Ontogeny would also be examined to see how much antler growth differs across ‘simple-antlered’ Mazama and Pudu and the branched/palmated antlers of Alces, Rangifer etc. Global cervid morphological character-scoring will encompass skulls, postcrania and skins.