Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient

2015 ◽  
Vol 29 (2) ◽  
pp. 241-252 ◽  
Author(s):  
W. C. Funk ◽  
M. A. Murphy ◽  
K. L. Hoke ◽  
E. Muths ◽  
S. M. Amburgey ◽  
...  
Keyword(s):  
Gene Flow ◽  
Altitudinal Gradient ◽  
Adaptive Divergence ◽  
Restricted Gene Flow

scholarly journals Adaptive divergence in resistance to herbivores inDatura stramonium

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1411 ◽  
Author(s):  
Guillermo Castillo ◽  
Pedro L. Valverde ◽  
Laura L. Cruz ◽  
Johnattan Hernández-Cumplido ◽  
Guadalupe Andraca-Gómez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Drift ◽  
Datura Stramonium ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Trichome Density ◽  
Phenotypic Differentiation ◽  
Phenotypic Resistance ◽  
Resistance Traits

Defensive traits exhibited by plants vary widely across populations. Heritable phenotypic differentiation is likely to be produced by genetic drift and spatially restricted gene flow between populations. However, spatially variable selection exerted by herbivores may also give rise to differences among populations. To explore to what extent these factors promote the among-population differentiation of plant resistance of 13 populations ofDatura stramonium, we compared the degree of phenotypic differentiation (PST) of leaf resistance traits (trichome density, atropine and scopolamine concentration) against neutral genetic differentiation (FST) at microsatellite loci. Results showed that phenotypic differentiation in defensive traits among-population is not consistent with divergence promoted by genetic drift and restricted gene flow alone. Phenotypic differentiation in scopolamine concentration was significantly higher thanFSTacross the range of trait heritability values. In contrast, genetic differentiation in trichome density was different fromFSTonly when heritability was very low. On the other hand, differentiation in atropine concentration differed from the neutral expectation when heritability was less than or equal to 0.3. In addition, we did not find a significant correlation between pair-wise neutral genetic distances and distances of phenotypic resistance traits. Our findings reinforce previous evidence that divergent natural selection exerted by herbivores has promoted the among-population phenotypic differentiation of defensive traits inD. stramonium.

scholarly journals Does selection occur at the intermediate zone of two insufficiently isolated populations? A whole-genome analysis along an altitudinal gradient

2021 ◽  
Author(s):  
Naofumi Yoshida ◽  
Shin-Ichi Morinaga ◽  
Takeshi Wakamiya ◽  
Yuu Ishii ◽  
Shosei Kubota ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Altitudinal Gradient ◽  
Intermediate Zone ◽  
Adaptive Divergence ◽  
Population Divergence ◽  
Whole Genome ◽  
Isolated Populations ◽  
Whole Genome Analysis ◽  
Single Nucleotide

Abstract Adaptive divergence would occur even between the insufficiently isolated populations when there is a great difference in the environments of their habitats. The individuals present in the intermediate zone of the two divergent populations are expected to have an admixed genetic structure due to gene flow. A selective pressure that acts on the genetically admixed individuals may limit the gene flow and promote the adaptive divergence. Here, we addressed a question whether the selection occurs in the genetically admixed individuals between the divergent populations and assessed its effects on the population divergence. We obtained the whole-genome sequences of a perennial montane plant, Arabidopsis halleri, which has clear phenotypic dimorphisms between altitudes, along an altitudinal gradient of 359–1,317 m with a high spatial resolution (mean altitudinal interval of 20 m). We found the zone where the highland and lowland genes were mixing. Using the FST approach, we found that 35 and 13 genes in the admixed zone had a high frequency of alleles that are accumulated in highland and lowland subpopulations, respectively, suggesting that these genes have been selected in the admixed zone. This selection might limit the gene flow and contribute to the adaptive divergence along the altitudes. In the single-nucleotide polymorphism (SNP)-based analysis, 3,000 out of 27,792 Altitude-Dependent SNPs had extremely high homozygosity in the admixed zone. In 84.7% of these SNPs, the frequency of homozygotes of highland alleles was comparable to that of lowland alleles, suggesting that these alleles are neutral but the heterozygotes were selectively eliminated. The distribution of highland and lowland alleles of these SNPs was not clearly separated between altitudes, implying that such selection did not impede the gene flow. We conclude that the selection occurring at the intermediate altitude affects the genetic structure in the admixed zone and adaptive divergence along the altitudes.

scholarly journals Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment

2020 ◽  
Author(s):  
Di Cui ◽  
Cuifeng Tang ◽  
Hongfeng Lu ◽  
Jinmei Li ◽  
Xiaoding Ma ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Target Genes ◽  
Isolation By Distance ◽  
Local Environment ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Geographical Isolation ◽  
Rice Landraces ◽  
Isolation By Environment

Abstract Background Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. Results The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Conclusion Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.

scholarly journals Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Di Cui ◽  
Cuifeng Tang ◽  
Hongfeng Lu ◽  
Jinmei Li ◽  
Xiaoding Ma ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Target Genes ◽  
Isolation By Distance ◽  
Local Environment ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Geographical Isolation ◽  
Rice Landraces ◽  
Isolation By Environment

Abstract Background Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. Results The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Conclusions Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.

scholarly journals Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax

2016 ◽  
Vol 113 (27) ◽  
pp. 7584-7589 ◽  
Author(s):  
Kexin Li ◽  
Liuyang Wang ◽  
Binyamin A. Knisbacher ◽  
Qinqin Xu ◽  
Erez Y. Levanon ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Divergence ◽  
Nuclear Dna ◽  
Gc Content ◽  
Sympatric Speciation ◽  
Adaptive Divergence ◽  
Restricted Gene Flow ◽  
Mole Rat ◽  
New Evidence ◽  
Two Populations

Incipient sympatric speciation in blind mole rat, Spalax galili, in Israel, caused by sharp ecological divergence of abutting chalk–basalt ecologies, has been proposed previously based on mitochondrial and whole-genome nuclear DNA. Here, we present new evidence, including transcriptome, DNA editing, microRNA, and codon usage, substantiating earlier evidence for adaptive divergence in the abutting chalk and basalt populations. Genetic divergence, based on the previous and new evidence, is ongoing despite restricted gene flow between the two populations. The principal component analysis, neighbor-joining tree, and genetic structure analysis of the transcriptome clearly show the clustered divergent two mole rat populations. Gene-expression level analysis indicates that the population transcriptome divergence is displayed not only by soil divergence but also by sex. Gene ontology enrichment of the differentially expressed genes from the two abutting soil populations highlights reproductive isolation. Alternative splicing variation of the two abutting soil populations displays two distinct splicing patterns. L-shaped FST distribution indicates that the two populations have undergone divergence with gene flow. Transcriptome divergent genes highlight neurogenetics and nutrition characterizing the chalk population, and energetics, metabolism, musculature, and sensory perception characterizing the abutting basalt population. Remarkably, microRNAs also display divergence between the two populations. The GC content is significantly higher in chalk than in basalt, and stress-response genes mostly prefer nonoptimal codons. The multiple lines of evidence of ecological–genomic and genetic divergence highlight that natural selection overrules the gene flow between the two abutting populations, substantiating the sharp ecological chalk–basalt divergence driving sympatric speciation.

scholarly journals Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 435
Author(s):  
Thijs M. P. Bal ◽  
Alejandro Llanos-Garrido ◽  
Anurag Chaturvedi ◽  
Io Verdonck ◽  
Bart Hellemans ◽  
...  
Keyword(s):  
Gene Flow ◽  
Brackish Water ◽  
Environmental Gradient ◽  
Spatial Scales ◽  
Morphological Differentiation ◽  
Genotyping By Sequencing ◽  
Adaptive Divergence ◽  
Linkage Groups ◽  
Closely Related Species ◽  
Genomic Patterns

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.

Restricted gene flow in fragmented populations of a wind-pollinated tree

2007 ◽  
Vol 9 (6) ◽  
pp. 1521-1532 ◽  
Author(s):  
Jim Provan ◽  
Gemma E. Beatty ◽  
Andrea M. Hunter ◽  
Robbie A. McDonald ◽  
Emma McLaughlin ◽  
...  
Keyword(s):  
Gene Flow ◽  
Restricted Gene Flow ◽  
Fragmented Populations
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