Paleopopulation Genetics

Wall, Jeffrey D.; Slatkin, Montgomery

doi:10.1146/annurev-genet-110711-155557

Cited by 17 publications

(11 citation statements)

References 103 publications

(112 reference statements)

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“…One of the most provocative findings from human molecular genomics is that 1-4% of the modern Eurasian genome originated from Neanderthals and that 4-6% of the modern Melanesian genome originated from Denisovans (Reich et al 2010; for a review of paleopopulation genetics, see Wall & Slatkin 2012). Given this level of hybridization, then some variants from Neanderthals and Denisovans might be expected to have substantial frequencies in humans by chance history although there are several variants from these hominins that have been suggested as present in modern humans because of adaptive introgression.…”

Section: Neanderthal or Denisovan Ancestry In Humansmentioning

confidence: 99%

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

2013

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Adaptive genetic variation has been thought to originate primarily from either new mutation or standing variation. Another potential source of adaptive variation is adaptive variants from other (donor) species that are introgressed into the (recipient) species, termed adaptive introgression. Here, the various attributes of these three potential sources of adaptive variation are compared. For example, the rate of adaptive change is generally thought to be faster from standing variation, slower from mutation and potentially intermediate from adaptive introgression. Additionally, the higher initial frequency of adaptive variation from standing variation and lower initial frequency from mutation might result in a higher probability of fixation of the adaptive variants for standing variation. Adaptive variation from introgression might have higher initial frequency than new adaptive mutations but lower than that from standing variation, again making the impact of adaptive introgression variation potentially intermediate. Adaptive introgressive variants might have multiple changes within a gene and affect multiple loci, an advantage also potentially found for adaptive standing variation but not for new adaptive mutants. The processes that might produce a common variant in two taxa, convergence, trans-species polymorphism from incomplete lineage sorting or from balancing selection and adaptive introgression, are also compared. Finally, potential examples of adaptive introgression in animals, including balancing selection for multiple alleles for major histocompatibility complex (MHC), S and csd genes, pesticide resistance in mice, black colour in wolves and white colour in coyotes, Neanderthal or Denisovan ancestry in humans, mimicry genes in Heliconius butterflies, beak traits in Darwin's finches, yellow skin in chickens and non-native ancestry in an endangered native salamander, are examined.

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Section: Neanderthal or Denisovan Ancestry In Humansmentioning

confidence: 99%

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

2013

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“…There are a number of excellent articles that have reviewed the literature on genome-wide studies of human history [17–23]. Here our focus is not on providing a comprehensive review but instead on highlighting promising directions for future research.…”

Section: Introductionmentioning

confidence: 99%

Toward a new history and geography of human genes informed by ancient DNA

Pickrell¹,

Reich²

2014

Trends in Genetics

230

148

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Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world’s human populations. In light of this, we argue that it is time to critically re-evaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

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“…The efficacy of targeted enrichment protocols for aDNA has been recently demonstrated with some samples yielding as many as 150 k SNPs(Carpenter et al 2013). These technologies provide the foundation for the nascent field of paleopopulation genetics(Wall & Slatkin 2012), adding to our knowledge of how species responded to environmental changes in recent geologic times (reviewed inStewart (2009) andde Bruyn et al (2011)).…”

mentioning

confidence: 99%

Natural history collections as windows on evolutionary processes

et al. 2016

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Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics, and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long-term field studies or from experimental studies in the lab, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short time scales in response to presumably strong selective pressures. In some instances evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations.

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Paleopopulation Genetics

Cited by 17 publications

References 103 publications

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

Toward a new history and geography of human genes informed by ancient DNA

Natural history collections as windows on evolutionary processes

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