Complete mitochondrial DNA geonome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis

Abstract

The ratites have stimulated much debate as to how such large £ightless birds came to be distributed across the southern continents, and whether they are a monophyletic group or are composed of unrelated lineages that independently lost the power of £ight. Hypotheses regarding the relationships among taxa di¡er for morphological and molecular data sets, thus hindering attempts to test whether plate tectonic events can explain ratite biogeography. Here, we present the complete mitochondrial DNA genomes of two extinct moas from New Zealand, along with those of ¢ve extant ratites (the lesser rhea, the ostrich, the great spotted kiwi, the emu and the southern cassowary) and two tinamous from di¡erent genera. The non-stationary base composition in these sequences violates the assumptions of most tree-building methods. When this bias is corrected using neighbour-joining with log-determinant distances and nonhomogeneous maximum likelihood, the ratites are found to be monophyletic, with moas basal, as in morphological trees. The avian sequences also violate a molecular clock, so we applied a non-parametric rate smoothing algorithm, which minimizes ancestor^descendant local rate changes, to date nodes in the tree. Using this method, most of the major ratite lineages ¢t the vicariance biogeography hypothesis, the exceptions being the ostrich and the kiwi, which require dispersal to explain their present distribution.

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

“…This was long after Africa separated from Gondwana around 100 Ma [47,48]. A mixture of dispersal and continental drift were invoked to explain the ostrich's presence in Africa and Asia [3,5]. By contrast, the much older ostrich divergence time we derived borders on the time of rifting of Africa from Gondwana, and thus dispersal need not be invoked.…”

“…Ratites are a group of large flightless birds that lack a keel on their sternum, and include emu (Australia), cassowaries (Australia and New Guinea), rheas (South America), ostrich (Africa and formerly Asia), kiwis (New Zealand) and extinct moas (New Zealand) and elephant birds (Madagascar). Many studies using morphological and molecular data supported the monophyly of ratites and placed them sister to tinamous, although no consensus was achieved on relationships among ratites [1][2][3][4][5]. Their flightless condition and disjunct distribution on southern land masses led to a widely accepted biogeographic theory that their evolution and distribution was shaped by the break-up of Gondwana [1,3,5].…”

“…Unlike DNA sequences, retroposon insertion analysis avoids problems of model misspecification, taxon sampling, long-branch attraction and base compositional biases. Both long-branch attraction and base compositional biases have been implicated in making phylogenetic analyses of the palaeognaths so problematic using mitochondrial genomes [3,8]. Although retroposon insertions avoid many of the pitfalls of DNA sequences, they are not exempt from incomplete lineage sorting.…”

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa

“…1) phyly of the Australian freshwater mussel genera has been 500 reported previously (Baker et al, 2003(Baker et al, , 2004 vicariance -e.g., southern beeches (Knapp et al, 2005), ratite birds 521 (Haddrath and Baker, 2001), and galaxiid fishes (Burridge et al,522 2012). This is not the case with the disjunct distribution of the and the fossil taxa in those areas are assigned to their respective 552 modern taxa (Martínez and Figueiras, 1991;Hocknull, 2000;553 Perea et al, 2009;Thompson and Stilwell, 2010;Parras and 554 Griffin, 2013).…”

Comparative digesta retention patterns in ratites

“…Various phylogenetic relationships among ratites have been proposed, differing specifically in whether Common Ostriches (Struthio camelus, hereafter Ostriches) or Rheas (Rhea spp.) are more closely related to Emus (Dromaius novaehollandiae; van Tuinen et al 1998, Cooper et al 2001, Haddrath and Baker 2001, Mitchell et al 2014). This phylogenetic debate also includes flighted Tinamous (Tinamou spp.…”