Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation.
TL;DR: The various attributes of these three potential sources of adaptive variation are compared, 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, and mimicry genes in Heliconius butterflies are examined.
Abstract: 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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TL;DR: Genetic rescue is a tool that can stem biodiversity loss more than has been appreciated, provides population resilience, and will become increasingly useful if integrated with molecular advances in population genomics.
Abstract: Genetic rescue can increase the fitness of small, imperiled populations via immigration. A suite of studies from the past decade highlights the value of genetic rescue in increasing population fitness. Nonetheless, genetic rescue has not been widely applied to conserve many of the threatened populations that it could benefit. In this review, we highlight recent studies of genetic rescue and place it in the larger context of theoretical and empirical developments in evolutionary and conservation biology. We also propose directions to help shape future research on genetic rescue. Genetic rescue is a tool that can stem biodiversity loss more than has been appreciated, provides population resilience, and will become increasingly useful if integrated with molecular advances in population genomics.
560 citations
TL;DR: The nature of the species boundary is explored, defined as the phenotypes/genes/genome regions that remain differentiated in the face of potential hybridization and introgression, and it is emphasized that species boundaries are semipermeable, with permeability (gene exchange) being a function of genome region.
Abstract: Species can be defined as populations that are diagnosably distinct, reproductively isolated, cohesive, or exclusive groups of organisms. Boundaries between species in sympatry are maintained by intrinsic barriers to gene exchange; these boundaries may not be uniform in space, in time, or across the genome. Here, we explore the nature of the species boundary, defined as the phenotypes/genes/genome regions that remain differentiated in the face of potential hybridization and introgression. We emphasize that species boundaries are semipermeable, with permeability (gene exchange) being a function of genome region. The early evidence for semipermeable species boundaries came from data on differential introgression in hybrid zones. This “genic view” of species was common in the hybrid zone literature even when few molecular markers were available to characterize genome-wide patterns of variation. Now, molecular tools allow detailed characterization of differentiation between diverging lineages and patterns of variation across natural hybrid zones, but the questions being asked by evolutionary biologists have remained much the same. Recent data (from DNA sequences and genotypes) reinforce earlier conclusions about the semipermeable nature of most species boundaries. However, debate persists over the nature and extent of genome divergence that accompanies speciation.
519 citations
Cites background from "Adaptive introgression in animals: ..."
...In fact, many evolutionary biologists in that era recognized continuity in degree of divergence, viewed reproductive isolation and barriers to gene exchange as potentially incomplete, and argued that species boundaries can be semipermeable....
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...…theory, globally advantageous alleles will tend to introgress easily (“adaptive introgression”; e.g., see Whitney et al. 2006; Pardo-Diaz et al. 2012; Hedrick 2013); neutral alleles will introgress to varying extents, but linkage to genes that contribute to local adaptation or reproductive…...
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TL;DR: An overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments is provided.
Abstract: As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.
463 citations
TL;DR: Many groups of closely related species have reticulate phylogenies, showing that some sexual compatibility may exist among them and can affect all parts of the tree of life, not just the recent species at the tips.
Abstract: Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.
436 citations
Cites background from "Adaptive introgression in animals: ..."
...The relative importance of selection in introgression across the genome is still not known, and is an area of active research [83], but many introgression events are now known to have involved adaptation....
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TL;DR: Pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non‐chemical pest‐control methods.
Abstract: Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.
356 citations
Cites background from "Adaptive introgression in animals: ..."
...Interbreeding may include adaptive introgression, in which hybridisation between a ‘donor’ species and a target species is followed by back-crosses with the target species during which positive selection results in the retention of a specific gene from the donor species (Hedrick, 2013)....
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References
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Book•
01 Jan 1983
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
Abstract: Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. He first proposed the theory in 1968 to explain the unexpectedly high rate of evolutionary change and very large amount of intraspecific variability at the molecular level that had been uncovered by new techniques in molecular biology. The theory - which asserts that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants - has caused controversy ever since. This book is the first comprehensive treatment of this subject and the author synthesises a wealth of material - ranging from a historical perspective, through recent molecular discoveries, to sophisticated mathematical arguments - all presented in a most lucid manner.
7,874 citations
Max Planck Society1, Broad Institute2, University of California, Berkeley3, European Bioinformatics Institute4, National Institutes of Health5, University of Massachusetts Medical School6, University of Washington7, Spanish National Research Council8, University of Montana9, Croatian Academy of Sciences and Arts10, University of Oviedo11, University of Bonn12, Emory University13, University College Cork14, Harvard University15
TL;DR: The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
3,575 citations
"Adaptive introgression in animals: ..." refers background in this paper
...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....
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...…in humans One of the most provocative findings from human molecular genomics is that 1–4% of the modern Eurasian genome originated from Neanderthals (Green et al. 2010) © 2013 John Wiley & Sons Ltd and that 4–6% of the modern Melanesian genome originated from Denisovans (Reich et al. 2010; for a…...
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...Neanderthal or Denisovan ancestry in humans One of the most provocative findings from human molecular genomics is that 1–4% of the modern Eurasian genome originated from Neanderthals (Green et al. 2010) © 2013 John Wiley & Sons Ltd 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)....
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TL;DR: It is stated that these sequences differed in the cytochromes c of various species to an extent that seemed unnecessary from the standpoint of their function.
Abstract: IN 1966, I became interested in the amino acid sequences of cytochrome c molecules ([Jukes 1966][1]). I noted that these sequences differed in the cytochromes c of various species to an extent that seemed unnecessary from the standpoint of their function. I stated, “The changes produced in
3,011 citations
"Adaptive introgression in animals: ..." refers background in this paper
...By definition, there is no waiting time for standing variation, while the expected waiting time for a new mutation is approximately 1/u generations (Kimura 1983) where u is the mutation rate per generation to a favourable mutant....
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...waiting time for standing variation, while the expected waiting time for a new mutation is approximately 1/u generations (Kimura 1983) where u is the mutation rate...
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