“A Tree of Geese”

If you are a goose hunter, or a conservationist, a Native American tribal council member, or a wetlands manager, you know migratory geese are hard. Hard to maintain. Hard to re-introduce. In general, when migratory geese are gone, they are gone for good.

Knowing how geese diversified and hybridized and are ‘related’ could save all extant sub-species from premature extinction. That the Hāwaiʻian goose (nēnē) and the Canada goose have a common, direct progenitor may be significant for their survival.

So, understanding the historical nature of the goose, and the sub-species in question can aid in problem-solving for the present.

In this 12-page article from Academia, we want to decipher and extract the main points for the layperson, be her a hunter, or a mother, or both. Fortunately we are blessed with a free press. You can download the article yourself (below), and those interested should read it.

I am not Wikipedia, nor a geneticist by training, so I leave most genetics terms to the reader to look-up on their own if they are not familiar with them.

Why this article? It resolves many outstanding issues in the descent of geese; it both references publications of a well-respected Ducks Unlimited research scientist, Prof. Dr. Phil Lavretsky of the U of Texas, El Paso, and actually uses his methodology and Mallard data for its standard. So, let’s get our feet wet!

Summary – Rapid Speciation and Hybridization during Global Climate Change

The phylogeny of the True Geese (tribe Anserini, Anatidae, Anseriformes) has, until now, been contentious, i.e., the phylogenetic relationships and the timing of divergence between the different goose species could not be fully resolved. In addition, two main clades of Anser species could be identified, the White Geese and the Grey Geese.

The objectives of this study are threefold:

(1) to unravel the phylogenetic relationships within the Anserini tribe using phylogenomic tools for species tree estimation,

(2) to assess the timing of for the extant goose species by means of genomic and fossil data and,

(3) to discuss these findings in a framework of ecological, biogeographic and climatic events. 

The results from the consensus method suggest that the diversification of the genus Anser is heavily influenced 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 temperate grasslands.

“Certain supertree methods incorporate the multi-species coalescent model to estimate the species tree from a set of heterogeneous gene trees (Knowles, 2009). The multi-species coalescent model extends the classical coalescent (Kingman, 1980) to multiple populations and describes gene trees as independent random variables generated from the coalescence process occurring along lineages of the species tree (Liu et al., 2015). A number of coalescent based methods have been developed to estimate the species tree from multigene sequence data, including Bayesian (e.g., BUCKy, Ane et al., 2007; BEAST, Drummond et al., 2012) and likelihood approaches (e.g., STEM, Kubatko et al., 2009; STELLS, Wu, 2012).

“Coalescent-based methods have been successfully implemented to disentangle the complex evolutionary history of several closely related bird species (Carling et al., 2010; Hung et al., 2012; Lavretsky et al., 2014)…

“In accordance with the lack of a well supported phylogeny, the timing of origin of the extant goose species is unknown too. Fossil evidence indicates that geese were present during the Miocene and Pliocene (Brodkorb, 1964) and several phylogeographic studies reported Pleistocene origins of certain goose subspecies (Avise et al., 1992; Shields, 1990; Van Wagner and Baker, 1990). More over, a mtDNA study of the genus Anser dated speciation events to the late Pliocene and early Pleistocene (Ruokonen et al., 2000)…

Based on the available evidence, the authors further hypothesize that the diversification of modern goose species was initiated in the Pliocene, then accompanied by further diversification into distinct subspecies during the Pleistocene. 

“Paired-end reads {(100bp) were also mapped to the Swan Goose (Anser cygnoides) genome (Lu et al, 2015) using BWA (Li and Durbin, 2009). Over 95% of the reads were mapped successfully for all species. However, mapping to the genome of a species that is included in the phylogenetic analysis (in this case the Swan Goose) potentially leads to an inherent bias that could interfere with the phylogenetic analysis. For instance, mean mapping quality is higher for species belonging to the same genus (Anser) as the reference genome compared to species of the other genus (Bmnta)…

Therefore they decided to use the variant calls based on the mapped reads to a more distantly related reference genome, the Mallard (A platyrhynchos). 

“Although this choice leads to a reduction in the amount of data, it avoids the bias introduced by mapping to the Swan Goose genome. Why? Because all species are equally distantly related to the Mallard. So the Mallard was used as a “standard” of sorts. A similar approach has been used to reconstruct the phylogeny of Cichlid fish {lives and Lopez Fernandez, 2014)…

Molecular Clock Analyses 

“Ideally, a molecular clock analysis is run with multiple calibration points (fossils or biogeographic events) using a relaxed clock (Parham et al., 2012). Unfortunately, the fossil record for geese is too sparse to use multiple calibration points (see Section 4). Therefore, we followed the method outlined below. The resulting divergence times should thus not be interpreted as the exact dates of divergence, but rather as rough guiding estimates that allow us to formulate testable hypotheses on the biogeographical and eco logical drivers of goose speciation… 

They “estimated divergence times using an approximate likelihood method as implemented in MCMCtree (in PAML version 4, Yang, 2007), with a global clock and birth death sampling. 

Discussion 

“Whole genome analyses have recently been used to unravel the phylogenetic relations between the major bird orders (Jarvis et al., 2014; Prum et al., 2015), but our study presents one of the first phylogenomic analyses of a group of closely related bird species (DaCosta and Sorenson, 2016; Nater et al., 2015). As both concate nation and consensus methods resulted in the same topology and all nodes on the concatenation tree are supported by high boot strap values, it is likely that the resulting phylogeny closely approaches the actual species tree for the Anserini. We firmly resolve several incongruences among previous studies. 

“Monophyly of the genera Anser and Branta was already well established (Delacour and Mayr, 1945). However, the timing of separation of these genera is still a matter of debate. Fossil evidence suggested that these two groups of geese have a common ancestor between 5 and 4 Mya (Brodkorb, 1964; Wetmore, 1956), and this date has been used to calibrate the molecular clock in birds (Shields and Wilson, 1987). The consistency of this molecular clock has been questioned (van Tuinen and Hedges, 2001; Weir and Schluter, 2008), because subsequent molecular studies reported older dates for the Anser Branta split ranging from 23 to 9 million years ago (Brown et al., 2008; Fulton et al., 2012; Gonzalez et al., 2009; Jetz et al., 2012; Jiang et al., 2010; Pereira and Baker, 2006).

“They decided to use 9 million years to calibrate the mutation rate, based on recent estimates (Fulton et al., 2012; Jetz et al., 2012). Moreover, they used a fossil constraint between 20 and 4 million years ago to reflect reports of goose fossils in this time period (Brodkorb, 1964). The resulting wide confidence interval for the Anser Branta split in our molecular clock analysis, ranging from 15.1 to 4.2 Mya, indicates that there is still considerable uncertainty for this estimate. This uncertainty is a consequence of the lack of proper fossil calibration points for the Anserini tribe. Although there are numerous goose fossils (Brodkorb, 1964), it is not possible to confidently determine the phylogenetic position of these fossils.

Some Conclusions and A First Step

“Using a phylogenomic approach we were able to resolve the contentious phylogenetic history of the True Geese. Furthermore, taking advantage of the many contrasting gene histories, we gained more insight into the effects of complex speciation processes, such as rapid diversification and hybridization, in certain clades.

“The relative importance of hybridization in the evolutionary history of the True Geese remains to be investigated. The wide spread occurrence of hybridization in birds (Ottenburghs et al., 2015), and specifically waterfowl (Kraus et al., 2012; Randler, 2008; Ottenburghs et al., 2016), suggests that hybridization can act as an important component in avian speciation (Rheindt and Edwards, 2011). “

By integrating over the full exon set of genes we made a first step to quantitatively describe both species and gene histories. Their approach will be a fruitful strategy for resolving many other complex evolutionary histories at the level of genera, species, and subspecies.

Fig. 4. An overview of the evolutionary history of the True Geese combining phylogenetic tree, divergence times and current distributions of all species. Distributions based on BirdLife’s species range maps. Drawings used with permission of the Handbook of Birds of the World.

Leave a Reply

Please log in using one of these methods to post your comment:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s