Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution

Abstract

The origin of the ratites, large flightless birds from the Southern Hemisphere, along with their flighted sister taxa, the South American tinamous, is central to understanding the role of plate tectonics in the distributions of modern birds and mammals. Defining the dates of ratite divergences is also critical for determining the age of modern avian orders. To resolve the ratite phylogeny and provide biogeographical data to examine these issues, we have here determined the first complete mitochondrial genome sequences of any extinct taxa--two New Zealand moa genera--along with a 1,000-base-pair sequence from an extinct Madagascan elephant-bird. For comparative data, we also generated 12 kilobases of contiguous sequence from the kiwi, cassowary, emu and two tinamou genera. This large dataset allows statistically precise estimates of molecular divergence dates and these support a Late Cretaceous vicariant speciation of ratite taxa, followed by the subsequent dispersal of the kiwi to New Zealand. This first molecular view of the break-up of Gondwana provides a new temporal framework for speciation events within other Gondwanan biota and can be used to evaluate competing biogeographical hypotheses.

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

“…Recently, complete mitochondrial genome sequences (usually 16–17 kbp among vertebrate species) have proven useful in clarifying phylogenetic relationships among species (Arnason et al., 2008; Cooper et al., 2001; Coulson, Marshall, Pepin, & Carr, 2006; Horai, Hayasaka, Kondo, Tsugane, & Takahata, 1995; Inoue, Miya, Tsukamoto, & Nishida, 2001; Miya, Kawaguchi, & Nishida, 2001; Miya et al., 2003). Following extensive use in human population and evolutionary genetics (Horai et al., 1995; Ingman, Kaessmann, Pääbo, & Gyllensten, 2000; Mishmar et al., 2003; Pope, Carr, Smith, & Marshall, 2011; Tanaka et al., 2004), increasing use has been made in intraspecific studies of fish (Carr & Marshall, 2008a; Feutry et al., 2014; Teacher, André, Merilä, & Wheat, 2012) and other mammals (Carr et al., 2015; Knaus, Cronn, Liston, Pilgrim, & Schwartz, 2011; Stone et al., 2010).…”

Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims

“…DNA extractions on the powdered samples followed a standard phenol/chloroform method modified for aDNA samples, as described by Cooper et al (2001).…”

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].…”