Confianza en el conocimiento experto

Intron markers have great potential to provide complementary data for population genetics and phylogenetic relationships within penguins, as demonstrated through this study. One of the five markers had not been used previously for either population genetics or phylogenetics (UCHL3). Within Adélie penguins, the five intron markers used showed no evidence for the presence of the two mitochondrial lineages (A and RS), most likely due to lower mutation rates and larger effective population sizes for the intron markers relative to mitochondrial DNA, as well as gene flow between these lineages. The markers also indicated a population expansion event 1.95 to 6.14 million years ago. These introns are probably not applicable to finer-scale population genetics analyses than those carried out here; wider sampling within Adélie penguins is needed to assess their utility in this context fully. These markers will very likely prove useful within other penguin species, as this study also showed the cross- amplification of the primers and amplification conditions across all extant penguin genera.

Four intron markers individually did not provide enough resolution for phylogenetic analysis among penguins, due to the lack of topological resolution and low statistical support. The concatenated phylogeny, however, successfully recovered the majority of splits as reported in a robust phylogeny based on mitochondrial DNA and one nuclear exon (BAKER et al. 2006). While introns are still not as widely used in

phylogenetics as mitochondrial DNA markers or even certain nuclear coding genes (eg RAG-1), a number of recent studies have used introns to resolve difficult phylogenies (CREER et al. 2006; DALEBOUT et al. 2008; JACOBSEN et al. 2010; YU et

al. 2011) successfully. While individual introns frequently do not provide enough resolution individually, concatenation of different intron markers provides more power (JACOBSEN et al. 2010; YU et al. 2011). Working with introns is, however, not

straightforward, due to difficulty in acquiring their sequences, phasing heterozygotes, gap-filled alignments, recombination, among others. In the past these difficulties were perhaps reason enough to avoid using introns, however new sequencing and bioinformatics developments are making using introns more feasible.

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6

Chapter Six

RECOVERING ANCIENT NUCLEAR INTRONS OF ADÉLIE