Pinniped phylogenetic relationships inferred using AFLP markers

Abstract

Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic reconstruction in plants but their use in animal taxa has been limited, and in mammals rare. In addition, their use has been largely limited to shallow relationships amongst species or subspecies. Here, we genotype 23 pinniped species for 310 AFLP markers and find a strong phylogenetic signal, with individuals coclustering within species, and overall a good agreement between our phylogeny and those constructed using mitochondrial DNA and nuclear sequences even at nodes B15 million years old. Although supporting the existing ideas about pinniped relationships, our data shed light on relationships within the hitherto relatively unresolved Phocine species group, and provide further supporting evidence for raising two subspecies of Zalophus californianus, Z. c. californianus and Z. c. wollebaeki, to species level. Plotting AFLP divergence time estimates against those based on both mtDNA and nuclear sequences we find strong linear relationships, suggesting that the different markers are evolving in a clocklike fashion. These data further emphasize the utility of AFLP markers as general tools for phylogenetic reconstruction.

AFLPs support deep relationships among darters (Percidae: Etheostomatinae) consistent with morphological hypotheses

“…As cyt b distances are derived from truly homologous loci, a greater amount of scatter at larger distances would indicate a greater proportion of homoplasious AFLP bands. As in Dasmahapatra et al, 2009, we show a strong positive relationship between PAUP* Nei-Li distances and ML cyt b distances between 0.082 and 0.638 substitutions per position, with a seemingly negligible increase in scatter about the regression line at larger distances, especially for DiceJC distances (Figure 4). This pattern suggests the phylogenetic signal-to-noise ratio is approximately constant through this level of divergence.…”

“…These appear to be the deepest divergences analyzed using AFLPs to date (Graves, 2009;Dasmahapatra et al, 2009). We obtained a relatively robust tree with species of accepted genera and long-recognized subgenera clustering with statistical support.…”

“…In another in silico study of genomic data from Drosophila, Althoff et al (2007) reported that only 14% (2/14) of comigrating fragments from the D. simulans and D. yakuba genomes (estimated to have diverged 6 MA) were homologous. Graves (2009), however, questioned the protocol of this study, citing a robust AFLP phylogeny of pinnipeds (Dasmahapatra et al, 2009) in which authors eliminated bands that appeared to be non-homologous across all species (by only scoring those bands that amplified consistently with minimal size variation) and excluded smaller fragments. Using these methods, authors recovered moderate to strong phylogenetic signal at a divergence of B15 MA (Higdon et al, 2007;Dasmahapatra et al, 2009).…”

Snails in the desert: Species diversification of Theba (Gastropoda: Helicidae) along the Atlantic coast of NW Africa

“…This distance measure is very well suited for AFLPs, as it accounts for the sharing of present alleles, while shared absent alleles are ignored due to their potential homoplasious character (Dasmahapatra, Hoffman, & Amos, 2009; Koopman, 2005). Internal node support was assessed by nonparametric bootstrapping (1,000 replicates).…”

Population structure and speciation in the dragonfly Sympetrum striolatum/nigrescens (Odonata: Libellulidae): An analysis using AFLP markers

“…The AFLP protocol was similar to that used by Vos et al (1995) and is described in detail by Dasmahapatra et al (2009). Briefly, 100-400 ng of genomic DNA was first digested using TaqI (5 U in a 10 µl volume at 65°C for 2 h) and then with EcoRI (5 U in a 20 µl volume at 37°C for 2 h).…”