A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Abstract

a b s t r a c tPhylogenetic incongruence can be caused by analytical shortcomings or can be the result of biological processes, such as hybridization, incomplete lineage sorting and gene duplication. Differentiation between these causes of incongruence is essential to unravel complex speciation and diversification events. The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) was, until now, con tentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. We sequenced nineteen goose genomes (representing seventeen spe cies of which three subspecies of the Brent Goose, Branta bernicla) and used an exon based phylogenomic approach (41,736 exons, representing 5887 genes) to unravel the evolutionary history of this bird group. We thereby provide general guidance on the combination of whole genome evolutionary analyses and analytical tools for such cases where previous attempts to resolve the phylogenetic history of several taxa could not be unravelled. Identical topologies were obtained using either a concatenation (based upon an alignment of 6,630,626 base pairs) or a coalescent based consensus method. Two major lineages, corre sponding to the genera Anser and Branta, were strongly supported. Within the Branta lineage, the White cheeked Geese form a well supported sub lineage that is sister to the Red breasted Goose (Branta ruficol lis). In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese. The results from the consensus method suggest that the diversification of the genus Anser is heavily influ enced by rapid speciation and by hybridization, which may explain the failure of previous studies to resolve the phylogenetic relationships within this genus. The majority of speciation events took place in the late Pliocene and early Pleistocene (between 4 and 2 million years ago), conceivably driven by a global cooling trend that led to the establishment of a circumpolar tundra belt and the emergence of tem perate grasslands. Our approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

Flyway structure in the circumpolar greater white‐fronted goose

“…The greater white‐fronted goose is the only representative of the “gray” geese in North America and is thought to have a Eurasian origin (Ottenburghs et al., ). Our isolation‐with‐migration analysis suggests that North American and Eurasian populations began diverging at least 50,000 years ago, with post‐divergence gene flow biased toward movement into North America.…”

Crossing species boundaries : the hybrid histories of the true geese

“…Hybrids have been reported within each genus (Delnicki, 1974, Hatch and Shortt, 1976, Leafloor et al, 2013, Nijman et al, 2010, Trauger et al, 1971, Weckstein et al, 2002, Lehmhus and Gustavsson, 2014, but also intergeneric hybrids have been documented (Craven and Westemeier, 1979, Nelson, 1952, Prevett and Macinnes, 1973, Gustavsson, 2009). Previous studies suggested that the evolutionary history of the True Geese is heavily influenced by hybridization and rapid diversification (Ruokonen et al, 2000, Ottenburghs et al, 2016a. The Anser-clade can be regarded as an adaptive radiation and was probably affected more by hybridization compared to the more gradually diversifying Branta-clade (Ottenburghs et al, 2016a).…”

“…Previous studies suggested that the evolutionary history of the True Geese is heavily influenced by hybridization and rapid diversification (Ruokonen et al, 2000, Ottenburghs et al, 2016a. The Anser-clade can be regarded as an adaptive radiation and was probably affected more by hybridization compared to the more gradually diversifying Branta-clade (Ottenburghs et al, 2016a). In this paper, we focus on the role of hybridization during the diversification of these genera using a network approach and taking advantage of phylogenetic incongruence across the whole genome by fully re-sequencing all taxa of the True Geese clade.…”

“…To visualize this phylogenetic incongruence, we constructed a phylogenetic neighbour-joining network using the ordinary least squares method (with default settings) in SplitsTree version 4.1.4.2 (Huson and Bryant, 2006). This network was based on genetic distances, which were calculated in RAxML 8.3 with a GTR + Γ substitution model (Stamatakis, 2006, Ottenburghs et al, 2016a. We calculated the degree distributions (i.e.…”

“…The diversification of the Branta-clade was more gradual compared to the Anser-clade, which can be considered an adaptive radiation (Ottenburghs et al, 2016a). During an adaptive radiation the frequency of interspecific interactions increases, enhancing the probability of introgressive hybridization (Seehausen, 2004).…”