What Do We Really Know About Adaptation at Range Edges?

2020 ◽  
Vol 51 (1) ◽  
pp. 341-361
Author(s):  
Amy L. Angert ◽  
Megan G. Bontrager ◽  
Jon Ågren
Keyword(s):  
Sequence Data ◽  
Genetic Load ◽  
Indirect Evidence ◽  
Recent Theory ◽  
Adaptive Genetic Variation ◽  
Genetic Constraints ◽  
Trait Divergence ◽  
Positive Effects ◽  
Evolutionary Forces ◽  
Edge Populations

Recent theory and empirical evidence have provided new insights regarding how evolutionary forces interact to shape adaptation at stable and transient range margins. Predictions regarding trait divergence at leading edges are frequently supported. However, declines in fitness at and beyond edges show that trait divergence has sometimes been insufficient to maintain high fitness, so identifying constraints to adaptation at range edges remains a key challenge. Indirect evidence suggests that range expansion may be limited by adaptive genetic variation, but direct estimates of genetic constraints at and beyond range edges are still scarce. Sequence data suggest increased genetic load in edge populations in several systems, but its causes and fitness consequences are usually poorly understood. The balance between maladaptive and positive effects of gene flow on fitness at range edges deserves further study. It is becoming increasingly clear that characterizations about degree of adaptation based solely on geographical peripherality are unsupported.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

scholarly journals Coral settlement and recruitment responses to reef fish foraging and trait diversity

2021 ◽  
Author(s):  
Cher F Y Chow ◽  
Caitlin Bolton ◽  
Nader Boutros ◽  
Viviana Brambilla ◽  
Luisa Fontoura ◽  
...  
Keyword(s):  
Reef Fish ◽  
Fish Assemblages ◽  
Reef Fishes ◽  
Foraging Strategies ◽  
Coral Recruitment ◽  
Coral Settlement ◽  
Trait Divergence ◽  
Positive Effects ◽  
Recruitment Success ◽  
Trait Diversity

The process of coral recruitment is crucial to the healthy functioning of coral reef ecosystems, as well as recovery following disturbances. Fishes are key modulators of this process by feeding on algae and other benthic taxa that compete with corals for benthic space. However, foraging strategies within reef fish assemblages are highly diverse and the effect of foraging diversity on coral recruitment success remains poorly understood. Here, we test how the foraging traits of reef fishes affect coral settlement and juvenile success at Lizard Island, Great Barrier Reef. Using a multi-model inference approach incorporating six metrics of fish assemblage foraging diversity (foraging rates, trait richness, trait evenness, trait divergence, herbivore abundance, and benthic invertivore abundance), we found that herbivore abundance had positive effects on both coral settlement and recruitment success. However, foraging trait diversity had a negative effect on coral settlement but not on recruitment. Coral settlement was higher at sites with less trait diverse fish assemblages, specifically in trait divergence and richness. Moreover, these two trait diversity metrics were stronger predictors of coral settlement success compared to herbivore abundance. Our findings provide evidence that impacts mediated by fish foraging on coral juveniles can potentially be harmful during settlement, but the space-clearing effect overall remains advantageous. We show here that the variation of fish biodiversity across reefs can be a partial driver to spatially uneven patterns of coral recruitment and reef recovery.

scholarly journals Evolutionary lessons from California plant phylogeography

2016 ◽  
Vol 113 (29) ◽  
pp. 8064-8071 ◽  
Author(s):  
Victoria L. Sork ◽  
Paul F. Gugger ◽  
Jin-Ming Chen ◽  
Silke Werth
Keyword(s):  
Genetic Variation ◽  
Spatial Distribution ◽  
Plant Traits ◽  
Sequence Data ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Adaptive Genetic Variation ◽  
Local Selection ◽  
Isolation By Environment ◽  
The Impact

Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.

scholarly journals Genomic Evidences Support an Independent History of Grapevine Domestication in the Levant

2020 ◽  
Author(s):  
Aviad Sivan ◽  
Oshrit Rahimi ◽  
Mail Salmon-Divon ◽  
Ehud Weiss ◽  
Elyashiv Drori ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genetic Load ◽  
Whole Genome Sequence ◽  
Local Varieties ◽  
Caucasus Region ◽  
Demographic Models ◽  
Comprehensive Survey ◽  
History Of ◽  
Distinct Lineage ◽  
Pedigree Relationship

AbstractThe ancient grapevines of the Levant have inspired beliefs and rituals in human societies which are still practiced today in religious and traditional ceremonies around the world. Despite their importance, the original Levantine wine-grapes varieties were lost due to cultural turnovers commencing in the 7th century CE, which lead to the collapse of a flourishing winemaking industry in this region. Recently, a comprehensive survey of feral grapevines was conducted in Israel in an attempt to identify local varieties, yet the origin of these domesticated accessions is unclear. Here we study the origin of Levantine grapevines using whole-genome sequence data generated for a diversity panel of wild and cultivated accessions. Comparison between Levantine and Eurasian grapevines indicated that the Levantine varieties represent a distinct lineage from the Eurasian varieties. Demographic models further supported this observation designating that domestication in the Caucasus region predated the emergence of the Levantine samples in circa 5000 years and that authentic descendants of ancient varieties are represented among the Levantine samples. We further explore the pedigree relationship among cultivated grapevines, identify footprints of selective sweeps, and estimate the extent of genetic load in each group. We conclude that the Levantine varieties are distinct from the Eurasian varieties and that resistance to disease and abiotic stress are key traits in the development of both Eurasian and Levantine varieties.

scholarly journals Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte

PLoS Genetics ◽  
2021 ◽  
Vol 17 (12) ◽  
pp. e1009797
Author(s):  
Luis Fernando Samayoa ◽  
Bode A. Olukolu ◽  
Chin Jian Yang ◽  
Qiuyue Chen ◽  
Markus G. Stetter ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Rare Variants ◽  
Sequence Data ◽  
Genetic Load ◽  
Population History ◽  
Additional Contribution ◽  
Wild Relative ◽  
Small Individual ◽  
Maize Population ◽  
Close Relatives

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte.

scholarly journals Population genomics of East Asian ethnic groups

Hereditas ◽  
2020 ◽  
Vol 157 (1) ◽  
Author(s):  
Ziqing Pan ◽  
Shuhua Xu
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Ethnic Groups ◽  
Population Genomics ◽  
Sequence Data ◽  
East Asian ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Evolutionary Forces ◽  
Asian Populations

AbstractEast Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.

scholarly journals Recombination in diverse maize is stable, predictable, and associated with genetic load

2015 ◽  
Vol 112 (12) ◽  
pp. 3823-3828 ◽  
Author(s):  
Eli Rodgers-Melnick ◽  
Peter J. Bradbury ◽  
Robert J. Elshire ◽  
Jeffrey C. Glaubitz ◽  
Charlotte B. Acharya ◽  
...  
Keyword(s):  
Practical Importance ◽  
Genetic Load ◽  
Gc Content ◽  
Genotyping By Sequencing ◽  
Resolving Power ◽  
Nested Association Mapping ◽  
Evolutionary Forces ◽  
Recombination Hotspots ◽  
Quantitative Trait Mapping ◽  
Wide Scale

Among the fundamental evolutionary forces, recombination arguably has the largest impact on the practical work of plant breeders. Varying over 1,000-fold across the maize genome, the local meiotic recombination rate limits the resolving power of quantitative trait mapping and the precision of favorable allele introgression. The consequences of low recombination also theoretically extend to the species-wide scale by decreasing the power of selection relative to genetic drift, and thereby hindering the purging of deleterious mutations. In this study, we used genotyping-by-sequencing (GBS) to identify 136,000 recombination breakpoints at high resolution within US and Chinese maize nested association mapping populations. We find that the pattern of cross-overs is highly predictable on the broad scale, following the distribution of gene density and CpG methylation. Several large inversions also suppress recombination in distinct regions of several families. We also identify recombination hotspots ranging in size from 1 kb to 30 kb. We find these hotspots to be historically stable and, compared with similar regions with low recombination, to have strongly differentiated patterns of DNA methylation and GC content. We also provide evidence for the historical action of GC-biased gene conversion in recombination hotspots. Finally, using genomic evolutionary rate profiling (GERP) to identify putative deleterious polymorphisms, we find evidence for reduced genetic load in hotspot regions, a phenomenon that may have considerable practical importance for breeding programs worldwide.

scholarly journals PHENOLOGICAL SENSITIVITIES TO CLIMATE ARE SIMILAR IN TWO CLARKIA CONGENERS: INDIRECT EVIDENCE FOR FACILITATION, CONVERGENCE, NICHE CONSERVATISM, OR GENETIC CONSTRAINTS

Madroño ◽  
2021 ◽  
Vol 68 (4) ◽  
Author(s):  
Susan J. Mazer ◽  
Natalie L. R. Love ◽  
Isaac W. Park ◽  
Tadeo Ramirez-Parada ◽  
Elizabeth R. Matthews
Keyword(s):  
Indirect Evidence ◽  
Niche Conservatism ◽  
Genetic Constraints

scholarly journals Domestication Reshaped the Genetic Basis of Inbreeding Depression in a Maize Landrace Compared to its Wild Relative, Teosinte

2021 ◽  
Author(s):  
James B. Holland ◽  
L.F. Samayoa ◽  
B.A. Olukolu ◽  
C.J. Yang ◽  
Q. Chen ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Rare Variants ◽  
Sequence Data ◽  
Genetic Load ◽  
Population History ◽  
Additional Contribution ◽  
Wild Relative ◽  
Small Individual ◽  
Maize Population ◽  
Close Relatives

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to rare large-effect variation versus potentially more common variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load predicted from sequence data in the maize population. For many traits - and more commonly in maize - genetic variation among self-fertilized families was less than expected based on additive and dominance variance estimated in outcrossed families, suggesting that a negative covariance between additive and homozygous dominance effects limits the variation available to selection under partial inbreeding. We identified quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect recessive variation underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following to the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against large effect variants, but polygenic load is harder to purge and segregating mutational burden increased in maize compared to teosinte.

scholarly journals Evolution of parasitism and mutualism between filamentous phage M13 andEscherichia coli

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2060 ◽  
Author(s):  
Jason W. Shapiro ◽  
Elizabeth S.C.P. Williams ◽  
Paul E. Turner
Keyword(s):  
Pathogenic Bacteria ◽  
Horizontal Transmission ◽  
Recent Theory ◽  
Negative Effects ◽  
Growth Environment ◽  
E Coli ◽  
Positive Effects ◽  
Physiological Constraints ◽  
Bacteriophage M13 ◽  
Bacterial Fitness

Background.How host-symbiont interactions coevolve between mutualism and parasitism depends on the ecology of the system and on the genetic and physiological constraints of the organisms involved. Theory often predicts that greater reliance on horizontal transmission favors increased costs of infection and may result in more virulent parasites or less beneficial mutualists. We set out to understand transitions between parasitism and mutualism by evolving the filamentous bacteriophage M13 and its hostEscherichia coli.Results.The effect of phage M13 on bacterial fitness depends on the growth environment, and initial assays revealed that infected bacteria reproduce faster and to higher density than uninfected bacteria in 96-well microplates. These data suggested that M13 is, in fact, a facultative mutualist ofE. coli. We then allowedE. coliand M13 to evolve in replicated environments, which varied in the relative opportunity for horizontal and vertical transmission of phage in order to assess the evolutionary stability of this mutualism. After 20 experimental passages, infected bacteria from treatments with both vertical and horizontal transmission of phage had evolved the fastest growth rates. At the same time, phage from these treatments no longer benefited the ancestral bacteria.Conclusions.These data suggest a positive correlation between the positive effects of M13 onE. colihosts from the same culture and the negative effects of the same phage toward the ancestral bacterial genotype. The results also expose flaws in applying concepts from the virulence-transmission tradeoff hypothesis to mutualism evolution. We discuss the data in the context of more recent theory on how horizontal transmission affects mutualisms and explore how these effects influence phages encoding virulence factors in pathogenic bacteria.

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