Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

Abstract

Background: The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.

Results: Charadriiformes represent a monophyletic group that consists of three monophyletic suborders Lari (i.e., Laridae [including Sternidae and Rynchopidae], Stercorariidae, Alcidae, Glareolidae, Dromadidae, and Turnicidae), Scolopaci (i.e., Scolopacidae [including Phalaropidae], Jacanidae, Rostratulidae, Thinocoridae, Pedionomidae), and Charadrii (i.e., Burhinidae, Chionididae, Charadriidae, Haematopodidae, Recurvirostridae, and presumably Ibidorhynchidae). The position of purported "gruiform" buttonquails within Charadriiformes is confirmed. Skimmers are most likely sister to terns alone, and plovers may be paraphyletic with respect to oystercatchers and stilts. The Egyptian Plover is not a member of the Glareolidae, but is instead relatively basal among Charadrii. None of the putative sisters of Charadriiformes were recovered as such.

Conclusion: Hypotheses of non-monophyly and sister relationships of shorebirds are tested by multilocus analysis. The monophyly of and interfamilial relationships among shorebirds are confirmed and refined. Lineage-specific differences in evolutionary rates are more consistent across loci in shorebirds than other birds and may contribute to the congruence of locus-specific phylogenetic estimates in shorebirds.

Figure 1

Substitution rates per locus. Pairwise distances of each of five non-coding partitions of nuclear loci plotted against combined pairwise distances with linear model regressions added, showing differences in evolutionary rates among loci. Closed diamonds, RAG-1 3^rd positions; open squares, GPD3-5; closed triangles, ADH5; open circles, FGB7; and open triangles, myo-2. Note faster rate of RAG-1 3^rd positions than introns.

Figure 2

Transition:transversion plots. Uncorrected transition and transversion pairwise distances plotted against total distance for each of four loci obtained from combined MP analysis, drawn to same scale. (a), ADH5; (b), FGB7; (c), GPD3-5; and (d), 16S rDNA, 12SrDNA, and tRNA Valine. Closed circles, transition substitutions; and open circles, transversion substitutions. Note accelerated rate of transition substitutions of mtDNA.

Figure 3

Phylogeny of Charadriiformes. Optimal maximum likelihood phylogenetic reconstruction of Charadriiformes and selected outgroups based on combined data of ADH5, GPD3-5, FGB7, 12S rDNA, 16S rDNA, and tRNA Valine using GTR + G. Both mixed model Bayesian analysis and maximum parsimony produce trees of identical topology. Bootstrap values obtained from 500 ML pseudoreplicates are indicated above branches or positioned by arrows. Asterisks indicate bootstrap values of 100%. Charadriiformes are indicated by bold font and subordinal epithets.

Figure 4

Residual plots. Residual plots of internodal distances of each of four nuclear loci obtained from regression against RAG-1 internodal distances (independent variable) on MP tree reconstructed from combined data sets of 5 nuclear loci. (a, b), FGB7; (c, d), ADH5; (e, f), GPD3-5; and (g, h), myo-2. Note the higher variance of residuals in non-Charadriiformes (left panel) than Charadriiformes (right panel), indicating better correlation of estimates of internode lengths in the latter across all loci.