Phylogeography: its development and impact in Australo-Papuan ornithology with special reference to paraphyly in Australian birds

Abstract

Abstract.With examples from Australo-Papuan ornithology, we examine the technical and theoretical roots of molecular phylogeography and review its development. We describe the progression from ad hoc interpretation of gene trees in single species phylogeographic studies through to comparative phylogeography and currently advocated model-testing approaches. Mitochondrial DNA (mtDNA) sequences have provided most advances to date, although we demonstrate and advocate the future use of multilocus datasets analysed with coalescent methods. We examine interrelationships among speciation research, historical biogeography, phylogeography and landscape genetics. Mitochondrial paraphyly, in which individuals of one species or population have mtDNA that is more closely related to that of another than to their own, emerges in 44% of Australian studies to date as a common, important result in Australian avian phylogeography. Accordingly, we explore at length its most common causes and its impact on case studies in Australo-Papuan avian phylogeography. The impact of so much paraphyly on avian phylogeography and taxonomy is a major theme of the review. We suggest a full research agenda for avian phylogeography in the AustraloPapuan region that spans diverse topics: the need for more studies of pelagic birds, spatio-temporal links between New Guinea and Australia, island populations, testing of long-established biogeographical hypotheses, and integration of molecular and non-molecular datasets into integrated evolutionary understanding of species and populations. Studying the full continuum of divergences from landscape genetics, to phylogeography, to recently diverged species with evidence of paraphyly, to highly divergent species with many fixed differences will lead to a more complete understanding of the processes and patterns of avian evolution.

Towards modelling persistence of woodland birds: the role of genetics

“…Phylogeography, the study of how evolutionary lineages are distributed in geographical space and time, makes important contributions to wildlife management (Joseph and Omland 2009). Its role in identifying and mapping the distribution of biodiversity was outlined above (see 'Identification of management units').…”

“…As well as delimiting potential units for management purposes and quantifying levels of migration among them as an objective and meaningful metric of distinctiveness, work like this can shed light on the impacts of previous climate change and environmental influences, including fire, on biodiversity (Lee and Edwards 2008). The number of good-quality studies in the Australian avifauna is growing (Balakrishnan and Edwards 2009;Joseph and Omland 2009;Pavlacky et al 2009).…”

“…Genetic approaches have shown that subspecies boundaries are often discordant with evolutionary history or function, or both. Although such assessments are sometimes based for pragmatic reasons on only mitochondrial DNA (mtDNA), well known to be risky (for Australian birds, see Joseph and Omland 2009), there are many cases where morphology, other traits and geography do not mirror evolutionary lineages (e.g. Palm Cockatoos (Probosciger aterrimus), Murphy et al 2007;Australian Magpie, Toon et al 2007).…”

An Update of Wallace’s Zoogeographic Regions of the World

“…Additionally, we included information from a range of studies for the deep branching between major clades, orders, and some families (65,(68)(69)(70)(71)(72)(73)(74)(75)(76)(77)(78)(79)(80)(81). Within each major clade, we give additional references and major taxonomic changes (relative to 38) below (Table S5).…”

Prehistoric Birds and Bats from the Atiahara Site, Tubuai, Austral Islands, East Polynesia

“…However, a few fossil taxa, little different from G. philippensis but still flightless, make G. philippensis as currently construed appear to be paraphyletic. Reasons for such paraphyly among distinctive taxa can include recent or past hybridization events and incomplete lineage sorting, as reviewed by Joseph and Omland (2009), and were in part invoked by Kirchman (2009) to explain the data. Gallirallus steadmani, described herein, is another flightless taxon that is about as distinct from G. philippensis as the various Marianas species (Kirchman andSteadman 2006a, Kirchman 2009), so it may conceivably be closely related to the G. philippensis radiation, or more likely because of its geographic location it may be a sister species to G. ripleyi of Mangaia and G. huiatua of Niue and derived from an earlier spreading volant ancestor.…”