The Anseriform Genome Project


In natural sciences progress and new insights are often triggered by new technologies, which allow a deeper and more detailed analysis of the material world. In biology, a breakthrough was triggered by the possibility to sequence not only few marker genes but also complete genomes. In the last ten years, DNA technology has seen the advent of new sequencing technologies (Next Generation Sequencing; NGS) which allow the parallel sequencing of millions of DNA molecules. With NGS, complete genomes can now be sequenced in a relatively short time and at costs realistic for research groups with a normal research budget.

Very recently, a breakthrough has been achieved in avian genetics on the biggest possible scale: avian genomics. A special issue in the journal Science has been released at the end of 2014, that features the analysis of 48 (or more in some of the papers) genome sequences of birds. The Science issue introduced genome data in a comparative framework as to understand the evolution of birds and their genomes. In addition more than 20 further articles were published concertedly in other journals. This project spear-headed by three internationally renowned genomics experts: Guojie Zhang (Associate Director of National Genbank, BGI-Shenzhen, China), Tom Gilberts (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark) and Erich Jarvis (Duke University Medical Center, Durham, USA). The same consortium has now moved forward to a bigger ambition project Bird 10K (B10K), which aims to sequence all >10,000 bird species in next few years.

Evolution and Speciation in the Anseriformes: Ducks, Geese and Swans as Model Species
“Nothing in Biology makes sense except in the light of evolution” is a central dogma of modern science. Evolution is the study of genetic change over time in the basal biological unit, the population. The definition of a population is in theory straight forward: The smallest set of individuals that constitutes a randomly mating group. However, in practice this turns out to be more difficult because subtle structure within a population can emerge purely through the effect of geographic distance. When genetic distances within a population become sufficiently large and render its sub-populations to evolve in an increasingly independent manner, genetic drift and local adaptation lead to differentiation. Genetically well understood systems of naturally occurring examples for such speciation events are crater lake cichlid fishes. There, a very rapid speciation occurred (and likely still occurs) and the resulting species are phenotypically well distinguishable, yet so young as to complicate an inference of genetic differentiation. This is expected as genetic drift and selection take time to operate and lead to recognisable genomic differences between species.

What, then, is a species? Again this is a complicated question that also needs to take into account taxonomic context; species in bacteria might be something else than in a sexually reproducing organism. For avian biology the most widely accepted concept is one in which species are treated as reproducing units (Biological Species Concept) with due respect for, and integration of the recognition of incomplete reproductive barriers between species that evolve independently, nevertheless (Phylogenetic Species Concept). This pragmatic fusion of species concepts holds most promise to arrive at a consensus between groups of biologists who might have different operational needs for their questions, and it conceptually allows to study questions regarding speciation and hybridisation in a more natural way.
For several years it is known that hybridisation in the animal kingdom is more widespread than previously acknowledged and that among birds the Anseriformes constitute an exceptional case of elevated hybridisation rates. Anseriformes are a relatively basal order of birds and contain the waterbird family ducks, geese and swans (Anatidae; ~150 species), as well as the basal families of the screamers (Anhimidae, with only two species) and the magpie geese (Anseranatidae, one species). Even though they are a particularly interesting group regarding Ecology and Evolution, they have received quite limited attention for molecular investigations compared to other groups of birds.

In ducks, I have recently shown that rampant hybridisation among waterfowl is likely not an exception but happens frequently enough to leave traces in evolutionary time frames. In many bird models the study of speciation is complicated by the young age of evolved lines and biased by allopatry. However, ducks (but also geese and swans) constitute a very promising emerging model for speciation research. Among the many pairwise species/hybridisation relationships they harbour a great variety of divergence times from less than one million to beyond five million years in sympatry. Therefore, within Anatidae a wide range of pairwise comparisons is available where some groups exhibit a great propensity to hybridise but not others. This opens the possibility to comparatively study speciation and hybridisation in a common framework of multi-dimensional genomic space.

The Anseriform Genome Project

I currently establish a research line in evolutionary genetics and disease ecology. In this framework I study the genomics of speciation and hybridisation in their own right, and also their bearings on concerted evolution (e.g. of the immune system). Continuing hybridisation could lead to a supra-population of some species complexes of ducks or geese. Such a species complex with porous genomes due to hybridisation might therefore share evolutionary potential. Also very recently it has been shown that genes acquired from other species, through introgressive hybridisation and subsequent horizontal gene transfer (HGT), are a key component in metazoan evolution. One species of ducks could therefore evolve an allele of an immune gene in response to parasite pressure which can subsequently spread not only within but also among species by HGT; i.e., the evolution of the immune system acts across species boundaries. A similar scenario is described in Frank Hailer’s startling commentary on several years of brown bear/polar bear research finding exactly this: “brown bears as vectors for polar bear alleles”.

There has been comparatively little work in genomics of Anseriformes. However, I was part of the early efforts of using genome-scale data in this group with marker-based research and contributed to the mallard genome analysis and paper. With my further efforts in comparative genetic screens of the porous genomes of hybridising waterfowl species it is therefore consequent to establish reference genome resources for my whole study group, the Anseriformes. Besides my published papers on the subject (see above) I am currently collaborating with Jente Ottenburghs et al. from Wageningen University, The Netherlands, who study hybridisation in geese on a genomic scale. They collected whole genome sequencing data of all 20 goose species and subspecies recognised in the most recent world list of birds, the data of which are available to me by collaboration (no results published yet). Completion of whole genome sequencing of my study group will be carried out in my upcoming projects. The power of comparative genomics in the Anseriformes lies in the richness of possible hierarchical comparisons between species within genera (e.g. mallard vs. pintail), between genera within families (e.g. barnacle goose vs. greyleg goose), and between all Anatidae as a whole vs. their outgroups in the same taxonomic order, the Anhimidae and Anseranatidae. Further, different evolutionary ages of taxa can be incorporated in comparisons as well as distributional patterns (sympatry vs. parapatry vs. allopatry).

With new sequencing technologies and global efforts of collaborations towards common goals the B10K consortium (see above) offers a great opportunity to frame my plans into broader international cooperation. B10K works closely with BGI, the biggest genome sequencing centre in the world. Guojie Zhang, the proposed mentor, is an Associate Director at BGI and has pulled the special issue about avian genomics of the journal Science to a success with eight papers published in this journal at once and >20 others in different journals on the same day. Since autumn 2014 I have been in regular contact with him and his team (Tom Gilbert and Erich Jarvis) about the possibilities of collaborating with B10K on creating my Anseriform Genome framework. Together, we plan to write grant proposals for acquiring funds to sequence the remaining species of the ~160 Anseriforms; potentially in two steps: 1) genus level, 2) species level. B10K has successfully published its papers on bird order level at the end of 2014 and currently prepares family level analyses, e.g. another 200+ genomes – one per bird family. The genus level is the logical next step. The proposed meetings with Guojie Zhang will help me to achieve a better connection to B10K in order achieve my scientific goals.

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