Rates of Evolution in Ancient DNA from Adélie Penguins

Lambert, David M.; Ritchie, Peter A.; Millar, Craig D.; Holland, Barbara R.; Drummond, Alexei J.; Baroni, Carlo

doi:10.1126/science.1068105

Cited by 276 publications

(272 citation statements)

References 19 publications

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“…Mutation rates vary among species (see, for example, Lambert et al, 2002;de Bruyn et al, 2009;Phillips et al, 2009), and there is no precise estimate for this species. However, we used a rate that falls within the intervals of those derived from time series data and a coalescent approach for other vertebrate species (see Phillips et al, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…However, we used a rate that falls within the intervals of those derived from time series data and a coalescent approach for other vertebrate species (see Phillips et al, 2009). For example, in the Adélie penguin, Pysocelis adeliae, 9.6 × 10 − 7 s s y − 1 (Lambert et al, 2002), southern elephant seal, Mirounga leonina, 9.8 × 10 − 7 s s y − 1 (de Bruyn et al, 2009) and Steller sea lion, Eumetopias jubatus, 2.7 × 10 − 7 s s y − 1 (Phillips et al, 2009). These estimates are based on HVR1 and our control region sequence is somewhat longer, but we get similar estimates when just the HVR1 region is used (data not shown).…”

Section: Discussionmentioning

confidence: 99%

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Post-glacial habitat release and incipient speciation in the genus Delphinus

et al. 2016

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The role of ecological and changing environmental factors in the radiation of species diversity is a fundamental question in evolutionary biology. Of particular interest is the potential for these factors to determine the boundary between what we would consider differentiation among populations and incipient speciation. Dolphins in the genus Delphinus provide a useful test case, exhibiting morphological variation in beak length, coloration and body size across their wide geographic distribution, and in particular among coastal and more pelagic habitats. Two species have been proposed, D. delphis and D. capensis, but morphologically similar allopatric populations are not monophyletic, indicating that the mostly coastal 'long-beaked' D. capensis form is not a single globally distributed species. However, the sympatric populations in the Eastern North Pacific currently designated as these two species are both morphologically and genetically differentiated. Here we use microsatellite DNA and mitochondrial DNA markers to investigate the evolutionary mechanisms that led to this incipient speciation event. We used coalescent and assignment methods to investigate the timing and extent of reproductive isolation. Our data indicate that although there is some level of on-going gene flow, the putative species found in the Eastern North Pacific are reciprocally monophyletic. The timing of isolation appears to be associated with regional changes in paleoceanographic conditions within the Holocene timeframe.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Post-glacial habitat release and incipient speciation in the genus Delphinus

et al. 2016

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“…Serial samples have been previously used to estimate genetic parameters, for example, with DNA sequences from human immunodeficiency virus (Rodrigo and Felsenstein, 1999;Fu, 2001;Drummond et al, 2002) and from ancient penguin bones (Lambert et al, 2002). Our work differs in that we consider different markers, namely transposons, and because we assume that pathogen populations are monomorphic.…”

Section: Introductionmentioning

confidence: 99%

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

Rosenberg

Tsolaki

Tanaka

2003

Theoretical Population Biology

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In infectious disease epidemiology, it is useful to know how quickly genetic markers of pathogenic agents evolve while inside hosts. We propose a modular framework with which these genotype change rates can be estimated. The estimation scheme requires a model of the underlying process of genetic change, a detection scheme that filters this process into observable quantities, and a monitoring scheme that describes the timing of observations. We study a linear ''birth-shift-death'' model for change in transposable element genotypes, obtaining maximum-likelihood estimators for various detection and monitoring schemes. The method is applied to serial genotypes of the transposon IS6110 in Mycobacterium tuberculosis. The estimated birth rate of 0.0161 (events per copy of the transposon per year) and death rate of 0.0108 are both significantly larger than the estimated shift rate of 0.0018. The sum of these estimates, which corresponds to a ''half-life'' of 2.4 years for a typical strain that has 10 copies of the element, substantially exceeds a previous estimate of 0.0135 total changes per copy per year. We consider experimental design issues that enable the precision of estimates to be improved. We also discuss extensions to other markers and implications for molecular epidemiology. r

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“…For the analysis of historic populations, DNA was extracted from either toe pads of museum specimens (Heath Hens, n=21, and Attwater's prairie-chickens, n=19; see appendix A) or from wings collected during the last Greater Prairie-chicken hunting seasons (1951)(1952)(1953)(1954) in Wisconsin by Fredrick and Frances Hamerstrom (n=73;see Bellinger et al 2003;Johnson et al 2004). Historic DNA was extracted following described methods (Fleischer et al 2000;Lambert et al 2002) in sets of ten or less using phenol/chloroform methods followed by a cleaning step using a Qiagen DNeasy kit (QIAGEN) to remove PCR inhibitors.…”

Section: Samplingmentioning

confidence: 99%

Low Genetic Variation in the Heath Hen Prior to Extinction and Implications for the Conservation of Prairie-Chicken Populations

Johnson

Dunn

2006

Conserv Genet

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Low genetic variation is often considered to contribute to the extinction of species when they reach small population sizes. In this study we examined the mitochondrial control region from museum specimens of the Heath Hen (Tympanuchus cupido cupido), which went extinct in 1932. Today, the closest living relatives of the Heath Hen, the Greater (T. c. pinnatus), Attwater's (T. c. attwateri) and Lesser (T. pallidicinctus) Prairie-chicken, are declining throughout most of their range in Midwestern North America, and loss of genetic variation is a likely contributor to their decline. Here we show that 30 years prior to their extinction, Heath Hens had low levels of mitochondrial genetic variation when compared with contemporary populations of prairie-chickens. Furthermore, some current populations of Greater Prairie-chickens are isolated and losing genetic variation due to drift. We estimate that these populations will reach the low levels of genetic variation found in Heath Hens within the next 40 years. Genetic variation and fitness can be restored with translocation of individuals from other populations; however, we also show that choosing an appropriate source population for translocation can be difficult without knowledge of historic population bottlenecks and their effect on genetic structure.

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Rates of Evolution in Ancient DNA from Adélie Penguins

Cited by 276 publications

References 19 publications

Post-glacial habitat release and incipient speciation in the genus Delphinus

Post-glacial habitat release and incipient speciation in the genus Delphinus

Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis

Low Genetic Variation in the Heath Hen Prior to Extinction and Implications for the Conservation of Prairie-Chicken Populations

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