scholarly journals Ecology and genomic background shape the probability of parallel adaptation to climate

2021 ◽  
Author(s):  
Samridhi Chaturvedi ◽  
Zachariah Gompert ◽  
Jeffrey Feder ◽  
Owen Osborne ◽  
Moritz Muschick ◽  
...  
Keyword(s):  
Natural Selection ◽  
Bayesian Modeling ◽  
Parallel Evolution ◽  
Cuticular Hydrocarbon ◽  
Randomization Tests ◽  
Phenotypic Data ◽  
Standing Variation ◽  
Stick Insects ◽  
Shed Light ◽  
Genomic Similarity

Abstract Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar, because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental, and phenotypic data with randomization tests and Bayesian modeling to quantify the degree of parallelism and study its relationship with ecology and genetics. Our results show that the probability of parallel adaptation to climate among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the probability of genetic parallelism decays with divergence in climatic (i.e., ecological) conditions and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits, and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

scholarly journals Why many Batesian mimics are inaccurate: evidence from hoverfly colour patterns

2016 ◽  
Vol 283 (1842) ◽  
pp. 20161585 ◽  
Author(s):  
Christopher H. Taylor ◽  
Tom Reader ◽  
Francis Gilbert
Keyword(s):  
Natural Selection ◽  
Multiple Model ◽  
Wild Populations ◽  
Model Species ◽  
Trade Off ◽  
Binary Images ◽  
Classic Problem ◽  
Pattern Similarity ◽  
Colour Patterns ◽  
Shed Light

Mimicry is considered a classic example of the elaborate adaptations that natural selection can produce, yet often similarity between Batesian (harmless) mimics and their unpalatable models is far from perfect. Variation in mimetic accuracy is a puzzle, as natural selection should favour mimics that are hardest to distinguish from their models. Numerous hypotheses exist to explain the persistence of inaccurate mimics, but most have rarely or never been tested against empirical observations from wild populations. One reason for this is the difficulty in measuring pattern similarity, a key aspect of mimicry. Here, we use a recently developed method, based on the distance transform of binary images, to quantify pattern similarity both within and among species for a group of hoverflies and their hymenopteran models. This allowed us to test three key hypotheses regarding inaccurate mimicry. Firstly, we tested the prediction that selection should be more relaxed in less accurate mimics, but found that levels of phenotypic variation are similar across most hoverfly species. Secondly, we found no evidence that mimics have to compromise between accuracy to multiple model species. However, we did find that darker-coloured hoverflies are less accurate mimics, which could lead to a trade-off between mimicry and thermoregulation in temperate regions. Our results shed light on a classic problem concerning the limitations of natural selection.

scholarly journals Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

2014 ◽  
Vol 281 (1783) ◽  
pp. 20140012 ◽  
Author(s):  
Devon E. Pearse ◽  
Michael R. Miller ◽  
Alicia Abadía-Cardoso ◽  
John Carlos Garza
Keyword(s):  
Life History ◽  
Rainbow Trout ◽  
Parallel Evolution ◽  
Genomic Region ◽  
Life History Strategies ◽  
Strong Linkage Disequilibrium ◽  
Rapid Adaptation ◽  
Life History Variation ◽  
Standing Variation ◽  
Genomic Regions

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. Such changes may be population-specific or, alternatively, may involve parallel evolution of the same genomic region in multiple populations, if that region contains genes or co-adapted gene complexes affecting the selected trait(s). Both quantitative and population genetic approaches have identified associations between specific genomic regions and the anadromous (steelhead) and resident (rainbow trout) life-history strategies of Oncorhynchus mykiss . Here, we use genotype data from 95 single nucleotide polymorphisms and show that the distribution of variation in a large region of one chromosome, Omy5, is strongly associated with life-history differentiation in multiple above-barrier populations of rainbow trout and their anadromous steelhead ancestors. The associated loci are in strong linkage disequilibrium, suggesting the presence of a chromosomal inversion or other rearrangement limiting recombination. These results provide the first evidence of a common genomic basis for life-history variation in O. mykiss in a geographically diverse set of populations and extend our knowledge of the heritable basis of rapid adaptation of complex traits in novel habitats.

scholarly journals Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

2019 ◽  
Author(s):  
Colin R. Mahony ◽  
Ian R. MacLachlan ◽  
Brandon M. Lind ◽  
Jeremy B. Yoder ◽  
Tongli Wang ◽  
...  
Keyword(s):  
Spatial Scale ◽  
Local Adaptation ◽  
Lodgepole Pine ◽  
Genomic Data ◽  
Genomic Variation ◽  
Similar Species ◽  
Adaptive Variation ◽  
Phenotypic Data ◽  
Standing Variation ◽  
Climatic Drivers

AbstractThe need for tools to cost-effectively identify adaptive variation within ecologically and economically important plant species is mounting as the detrimental effects of climate change become increasingly apparent. For crop and wild populations alike, mismatches between adaptive variation and climatic optima will reduce health, growth, survival, reproduction, and continued establishment. The ease with which land managers can quantify the relative importance of different climate factors or the spatial scale of local adaptation to climate will have direct implications for the potential of mitigating or resolving such risks. Using seed collected from 281 provenances of lodgepole pine (Pinus contorta) from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that genomic and climate data are nearly equivalent for describing local adaptation in seedling traits. We also find strong agreement between the climate variables associated with genomic variation and with 20-year heights from a long-term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with cold injury occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than are indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.

Bayesian inference of natural selection from spatiotemporal phenotypic data

2020 ◽  
Vol 131 ◽  
pp. 100-109
Author(s):  
Olivier David ◽  
Gaëlle van Frank ◽  
Isabelle Goldringer ◽  
Pierre Rivière ◽  
Michel Turbet Delof
Keyword(s):  
Natural Selection ◽  
Bayesian Inference ◽  
Phenotypic Data

Cooperation and Altruism

2001 ◽  
Author(s):  
David Sloan Wilson
Keyword(s):  
Natural Selection ◽  
Evolutionary Theory ◽  
Opposite Direction ◽  
Social Adaptation ◽  
Herbivore Damage ◽  
Individual Level ◽  
Cryptic Coloration ◽  
The Subject ◽  
The Individual ◽  
Shed Light

People have always been fascinated by cooperation and altruism in animals, in part to shed light on our own propensity or reluctance to help others. Darwin’s theory added a certain urgency to the subject because the principle of “nature red in tooth and claw” superficially seems to deny the possibility of altruism and cooperation altogether. Some evolutionary biologists have accepted and even reveled in this vision of nature, giving rise to statements such as “the economy of nature is competitive from beginning to end . . . scratch an ‘altruist’ and watch a hypocrite bleed”. Others have gone so far in the opposite direction as to proclaim the entire earth a unit that cooperatively regulates its own atmosphere (Lovelock 1979). The truth is somewhere between these two extremes; cooperation and altruism can evolve but only if special conditions are met. As might be expected from the polarized views outlined above, achieving this middle ground has been a difficult process. Science is often portrayed as a heroic march to the truth, but in this case, it is more like the Three Stooges trying to move a piano. I don’t mean to underestimate the progress that been made—the piano has been moved—but we need to appreciate the twists, turns, and reversals in addition to the final location. To see why cooperation and altruism pose a problem for evolutionary theory, consider the evolution of a nonsocial adaptation, such as cryptic coloration. Imagine a population of moths that vary in the degree to which they match their background. Every generation, the most conspicuous moths are detected and eaten by predators while the most cryptic moths survive and reproduce. If offspring resemble their parents, then the average moth will become more cryptic with every generation. Anyone who has beheld a moth that looks exactly like a leaf, right down to the veins and simulated herbivore damage, cannot fail to be impressed by the power of natural selection to evolve breathtaking adaptations at the individual level. Now consider the same process for a social adaptation, such as members of a group warning each other about approaching predators.

scholarly journals How does adaptation sweep through the genome? Insights from long-term selection experiments

2012 ◽  
Vol 279 (1749) ◽  
pp. 5029-5038 ◽  
Author(s):  
Molly K. Burke
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Population Biology ◽  
De Novo ◽  
Whole Genome ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Laboratory Selection ◽  
Standing Variation ◽  
New Mutations

A major goal in evolutionary biology is to understand the origins and fates of adaptive mutations. Natural selection may act to increase the frequency of de novo beneficial mutations, or those already present in the population as standing genetic variation. These beneficial mutations may ultimately reach fixation in a population, or they may stop increasing in frequency once a particular phenotypic state has been achieved. It is not yet well understood how different features of population biology, and/or different environmental circumstances affect these adaptive processes. Experimental evolution is a promising technique for studying the dynamics of beneficial alleles, as populations evolving in the laboratory experience natural selection in a replicated, controlled manner. Whole-genome sequencing, regularly obtained over the course of sustained laboratory selection, could potentially reveal insights into the mutational dynamics that most likely occur in natural populations under similar circumstances. To date, only a few evolution experiments for which whole-genome data are available exist. This review describes results from these resequenced laboratory-selected populations, in systems with and without sexual recombination. In asexual systems, adaptation from new mutations can be studied, and results to date suggest that the complete, unimpeded fixation of these mutations is not always observed. In sexual systems, adaptation from standing genetic variation can be studied, and in the admittedly few examples we have, the complete fixation of standing variants is not always observed. To date, the relative frequency of adaptation from new mutations versus standing variation has not been tested using a single experimental system, but recent studies using Caenorhabditis elegans and Saccharomyces cerevisiae suggest that this a realistic future goal.

Gesture–speech unity

2014 ◽  
Vol 5 (2) ◽  
pp. 137-184 ◽  
Author(s):  
David McNeill
Keyword(s):  
Prefrontal Cortex ◽  
Natural Selection ◽  
Language Evolution ◽  
The Other ◽  
Shared Intentionality ◽  
Origin Of Language ◽  
Child Speech ◽  
The Brain ◽  
Shed Light ◽  
Selection Of

This paper outlines an argument for how development in child speech and gesture could shed light on language evolution: child acquisition can be thought of as two types of acquisition, one of which goes extinct (gesture-first, Acquisition 1) and is replaced by another (gesture–speech unity, Acquisition 2). For ontogenesis, this implies that children acquire two languages, one of which is extinct, and which again goes extinct in ontogenesis (it continues as “gestures of silence” rather than as gestures of speech). There is no way to get from Acquisition 1 to Acquisition 2. They are on different tracks. Even when they converge in the same sentence, as they sometimes do, they alternate and do not combine. I propose that the 3~4 year timing of Acquisition 2 relates to the natural selection of a kind of gestural self–response I call “Mead’s Loop”, which took place in a certain psychological milieu at the origin of language. This milieu emerges now in ontogenesis at 3~4 years and with it Mead’s Loop. It is self-aware agency, on which a self-response depends. Other developments, such as theory of mind and shared intentionality, likewise depend on it and also emerge around the same time. The prefrontal cortex, anchoring a ring of language centers in the brain, matures at that point as well, another factor influencing the late timing. On the other hand, a third acquisition, speech evoking adult attachment, begins at (or even before) birth, as shown by a number of studies, and provides continuity through the two acquisitions and extinction.

scholarly journals The genetic basis of the human-cannabis relationship

2018 ◽  
Author(s):  
Philippe Henry
Keyword(s):  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Diagnostic Process ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Single Nucleotide ◽  
Web Based ◽  
Genome Wide ◽  
A Genome ◽  
Shed Light

AbstractCannabis can elicit various reactions in different consumers. In order to shed light on the mechanisms underlying the human-cannabis relationship, we begin to investigate the genetic basis of this differential response. The web-based platform OpenSNP was used to collect selfreported genetic and phenotypic data. Participants either reported a positively or negative affinity to cannabis. A total of 26 individuals were retained, 10 of which indicated several negative responses and the remaining 16 indicating strong affinity for Cannabis. A total of 325’895 single nucleotide polymorphisms (SNPs) were retained. The software TASSEL 5 was used to run a genome-wide association study (GWAS), with a generalized liner model (GLM) and1000 permutations. The analysis yielded a set of 45 SNPs that were significantly associated with the reported affinity to cannabis, including one strong outlier found in the MYO16 gene. A diagnostic process is proposed by which individuals can be assessed for their affinity to cannabis. We believe this type of tool may be helpful in alleviating some of the stigma associated with cannabis use in individuals sensitive to THC and other cannabis constituents such as myrcene, which may potentiate negative responses.

scholarly journals Pleistocene stickleback genomes reveal the constraints on parallel evolution

2020 ◽  
Author(s):  
Melanie Kirch ◽  
Anders Romundset ◽  
M. Thomas P. Gilbert ◽  
Felicity C. Jones ◽  
Andrew D. Foote
Keyword(s):  
Parallel Evolution ◽  
Threespine Stickleback ◽  
Founder Effects ◽  
Freshwater Sediments ◽  
Adaptive Changes ◽  
Stochastic Nature ◽  
Standing Variation ◽  
Genome Wide ◽  
Founder Populations ◽  
Freshwater Adaptation

Parallel evolution is typically studied by comparing modern populations from contrasting environments, therefore the chronology of adaptive changes remains poorly understood. We applied a paleogenomics approach to investigate this temporal component of adaptation by sequencing the genomes of 11-13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes, and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord. The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects. We found modern lake stickleback had lost freshwater-adaptive alleles found in the ancient stickleback genomes, and showed incomplete adaptation, revealing the hitherto underappreciated stochastic nature of selection on standing variation present in founder populations.One Sentence Summary‘Pleistocene threespine stickleback genomes reveal insights into the earliest stages of freshwater adaptation’

scholarly journals Natural selection drives genome-wide evolution via chance genetic associations

2021 ◽  
Author(s):  
Zachariah Gompert ◽  
Jeffrey Feder ◽  
Patrik Nosil
Keyword(s):  
Natural Selection ◽  
Field Experiments ◽  
Indirect Selection ◽  
Direct Selection ◽  
Deer Mice ◽  
Major Theme ◽  
Genetic Associations ◽  
Genome Wide ◽  
Stick Insects ◽  
Causal Variants

Abstract Understanding selection's impact on the genome is a major theme in biology. Functionally-neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here we use field experiments and genomic data to show that widespread statistical associations with genes known to affect fitness in stick insects, deer mice and stickleback fish cause many genetic loci across the genome to be impacted indirectly by selection. We then show that statistical associations with other, unknown causal variants make aspects of evolution more predictable in stick insects. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations.

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