Numts: A Challenge for Avian Systematics and Population Biology

Sorenson, Michael D.; Quinn, Thomas W.

doi:10.2307/4089130

Cited by 412 publications

(317 citation statements)

References 24 publications

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“…We found no evidence of nuclear copies (or Numts; see Sorenson and Quinn 1998) in our sequences. No double peaks were found when examining the electropherograms and DNA extracts from tissues that differ in the relative number of mtDNA and nuclear copies (e.g., blood and muscle tissue) provided equally clean and identical sequences.…”

Section: Molecular Techniquesmentioning

confidence: 62%

Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala

et al. 2006

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The white-headed duck is a globally threatened species native to the Palaearctic with a range extending from Spain in the west to the western edge of China in the east. Its populations have become fragmented and undergone major declines in recent decades. To study genetic differences between populations across the range and change in genetic diversity over time, we sequenced a portion of the mitochondrial DNA control region from 67 museum specimens (years 1861-1976) as well as 39 contemporary samples from Spain and seven from Greece (years 1992Greece (years -2003. In the historical sample, we found a lack of significant genetic structure between populations in different areas. We found evidence that the species experienced a rapid expansion in the past, perhaps from glacial refugia centred around the Mediterranean following the last ice age. In Spain, the population went through a dramatic bottleneck in the 1970s and early 1980s, when only a few dozens individuals remained in the wild. Although population size has since recovered to a few thousand individuals, we found a highly significant loss of mitochondrial haplotype diversity between the historical and contemporary samples. Given ongoing declines in other areas, losses in genetic diversity that may reduce the adaptive potential of white-headed ducks in the future are a continuing concern throughout the geographic range of this species.

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Section: Molecular Techniquesmentioning

confidence: 62%

Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala

et al. 2006

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“…Third, all haplotypes obtained from feather samples were also encountered in blood samples, compatible with an identical genomic origin. Hardened feather quiUs have earlier been suggested to be particidarly good sources of mitochondrial DNA sequences (Sorenson & Quinn, 1998). Fourth, the observation of a transition-transversion ratio around 7 (see Table 1 and Fig.…”

Section: Polymerase Chain Reaction (Pcr) Amplification and Dna Sequenmentioning

confidence: 98%

“…Fifth, identical sequences were obtained on amplifying fragment sizes between 416 and 1990 bp. Since nuclear insertions of mtDNA tend to be of rather restricted length (Sorenson & Quinn, 1998), this also suggests that the analysed fragment is mitochondrial.…”

Section: Polymerase Chain Reaction (Pcr) Amplification and Dna Sequenmentioning

confidence: 99%

Phylogeography of the white‐tailed eagle, a generalist with large dispersal capacity

Hailer

Helander

Folkestad³

et al. 2007

Journal of Biogeography

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Aim Late Pleistocene glacial changes had a major impact on many boreal and temperate taxa, and this impact can still be detected in the present-day phylogeographic structure of these taxa. However, only minor effects are expected in species with generalist habitat requirements and high dispersal capabihty. One such species is the white-tailed eagle, Haliaeetus albicilla, and we therefore tested for the expected weak population structure at a continental level in this species. This also allowed us to describe phylogeographic patterns, and to deduce Ice Age refugia and patterns of postglacial recolonization of Eurasia.Location Breeding populations from the easternmost Nearctic (Greenland) and across the Palaearctic (Iceland, continental Europe, central and eastern Asia, and Japan).Methods Sequencing of a 500 base-pair fragment of the mitochondrial DNA control region in 237 samples from throughout the distribution range.Results Our analysis revealed pronounced phylogeographic structure. Overall, low genetic variability was observed across the entire range. Haplotypes clustered in two distinct haplogroups with a predominantly eastern or western distribution, and extensive overlap in Europe. These two major lineages diverged during the late Pleistocene. The eastern haplogroup showed a pattern of rapid population expansion and colonization of Eurasia around the end of the Pleistocene. The western haplogroup had lower diversity and was absent from the populations in eastern Asia. These results suggest survival during the last glaciation in two refugia, probably located in central and western Eurasia, followed by postglacial population expansion and admixture. Relatively high genetic diversity was observed in northern regions that were ice-covered during the last glacial maximum. This, and phylogenetic relationships between haplotypes encountered in the north, indicates substantial population expansion at high latitudes. Areas of glacial meltwater runoff and proglacial lakes could have provided suitable habitats for such population growth.Main conclusions This study shows that glacial climate fluctuations had a substantial impact on white-tailed eagles, both in terms of distribution and demography. These results suggest that even species with large dispersal capabilities and relatively broad habitat requirements were strongly affected by the Pleistocene climatic shifts.

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“…At times large parts of mtDNA have been copied into the nuclear genome, where, on losing the unique properties of mtDNA, they can mimic genuine mtDNA and mislead analyses (Sorenson and Quinn 1998). Heteroplasmy occurs when genetically different copies of mtDNA occur within a single organism, tissue or cell.…”

Section: Box 1: Mitochondrial Dna: a Remindermentioning

confidence: 99%

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

Joseph

Omland

2009

Emu - Austral Ornithology

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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.

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Numts: A Challenge for Avian Systematics and Population Biology

Cited by 412 publications

References 24 publications

Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala

Population structure and loss of genetic diversity in the endangered white-headed duck, Oxyura leucocephala

Phylogeography of the white‐tailed eagle, a generalist with large dispersal capacity

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

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