scholarly journals Gene flow influences the genomic architecture of local adaptation in six riverine fish species

2021 ◽  
Author(s):  
Yue Shi ◽  
Kristen L. Bouska ◽  
Garrett J. McKinney ◽  
William Dokai ◽  
Andrew Bartels ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Fish Species ◽  
Genomic Architecture ◽  
Riverine Fish

scholarly journals Gene flow influences the genomic architecture of local adaptation in six riverine fish species

2021 ◽  
Author(s):  
Yue Shi ◽  
Kristen L Bouska ◽  
Garrett J McKinney ◽  
William Dokai ◽  
Andrew Bartels ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Fish Species ◽  
Mississippi River ◽  
Life Histories ◽  
River System ◽  
Genomic Islands ◽  
Adaptive Divergence ◽  
Adaptive Responses ◽  
Large Gradient

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from among-population recombination and thus be selected for, but few studies have tested this hypothesis with empirical data. Here, we used RADseq to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We then conducted genome scans for genomic islands of divergence to examine the distribution of adaptive loci and investigated whether these loci were found in inversions. We found that gene flow varied among species, and adaptive loci were clustered more tightly in species with higher gene flow. For example, the two species with the highest overall FST (0.03 - 0.07) and therefore lowest gene flow showed little evidence of clusters of adaptive loci, with adaptive loci spread uniformly across the genome. In contrast, nearly all adaptive loci in the species with the lowest FST (0.0004) were found in a single large putative inversion. Two other species with intermediate gene flow (FST ~ 0.004) also showed clustered genomic architectures, with most islands of divergence clustered on a few chromosomes. These results provide important empirical evidence to support the hypothesis that increasingly clustered architectures of local adaptation are associated with high gene flow. Our study utilized a unique system with species spanning a large gradient of life histories to highlight the importance of gene flow in shaping adaptive divergence.

scholarly journals Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Katherine Cure ◽  
Luke Thomas ◽  
Jean-Paul A. Hobbs ◽  
David V. Fairclough ◽  
W. Jason Kennington
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Fish Species ◽  
Genomic Signatures ◽  
High Gene Flow ◽  
High Gene ◽  
Source Sink

scholarly journals A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish

2021 ◽  
Author(s):  
Matt J. Thorstensen ◽  
Peter T. Euclide ◽  
Jennifer D. Jeffrey ◽  
Yue Shi ◽  
Jason R. Treberg ◽  
...  
Keyword(s):  
Gene Flow ◽  
Freshwater Fish ◽  
Local Adaptation ◽  
Evolutionary Dynamics ◽  
Chromosomal Inversion ◽  
Reduced Representation ◽  
Chromosomal Inversions ◽  
Genomic Architecture ◽  
Periodic Gene ◽  
Reduced Representation Sequencing

AbstractGenomic architecture, such as chromosomal inversions, may play an important role in facilitating adaptation despite opportunities for gene flow. One system where chromosomal inversions may be important for eco-evolutionary dynamics are in freshwater fish, which often live in heterogenous environments characterized by varying levels of connectivity and varying opportunities for gene flow. In the present study, reduced representation sequencing was used to study possible adaptation in n=345 walleye (Sander vitreus) from three North American waterbodies: Cedar Bluff Reservoir (Kansas, USA), Lake Manitoba (Manitoba, Canada), and Lake Winnipeg (Manitoba, Canada). Haplotype and outlier-based tests revealed a putative chromosomal inversion that contained three expressed genes and was nearly fixed for alternate genotypes in each Canadian lake. These patterns exist despite several opportunities for gene flow between these proximate Canadian lakes, suggesting that the inversion may be important for facilitating adaptative divergence between the two lakes despite gene flow. Our study illuminates the importance of genomic architecture for facilitating local adaptation in freshwater fish and provides additional evidence that inversions may facilitate local adaptation in many organisms that inhabit connected but heterogenous environments.

Gene flow favours local adaptation under habitat choice in ciliate microcosms

2017 ◽  
Vol 1 (9) ◽  
pp. 1407-1410 ◽  
Author(s):  
Staffan Jacob ◽  
Delphine Legrand ◽  
Alexis S. Chaine ◽  
Dries Bonte ◽  
Nicolas Schtickzelle ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Habitat Choice

Gene Flow, Spatial Structure, Local Adaptation, and Assisted Migration in Trees

2012 ◽  
pp. 71-116 ◽  
Author(s):  
Konstantin V. Krutovsky ◽  
Jaroslaw Burczyk ◽  
Igor Chybicki ◽  
Reiner Finkeldey ◽  
Tanja Pyhäjärvi ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Structure ◽  
Local Adaptation ◽  
Assisted Migration

Local adaptation along a sharp rainfall gradient occurs in a native Patagonian grass, Festuca pallescens, regardless of extensive gene flow

2020 ◽  
Vol 171 ◽  
pp. 103933
Author(s):  
Aldana S. López ◽  
Dardo R. López ◽  
Gonzalo Caballé ◽  
Guillermo L. Siffredi ◽  
Paula Marchelli
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Rainfall Gradient ◽  
Festuca Pallescens

scholarly journals The limits to parapatric speciation 3: evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190532 ◽  
Author(s):  
Alexandre Blanckaert ◽  
Claudia Bank ◽  
Joachim Hermisson
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Local Adaptation ◽  
Theme Issue ◽  
Genetic Barrier ◽  
Incipient Species ◽  
Postzygotic Reproductive Isolation ◽  
Minimal Configuration ◽  
Parapatric Speciation ◽  
Two Populations

Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky–Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that many incipient species may initially face. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

2019 ◽  
Vol 36 (11) ◽  
pp. 2557-2571 ◽  
Author(s):  
Tuomas Hämälä ◽  
Outi Savolainen
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Demographic History ◽  
Rate Variation ◽  
Arabidopsis Lyrata ◽  
Trade Offs ◽  
Northern Latitudes ◽  
Local Selection ◽  
Empirical Level ◽  
Selected Traits

AbstractShort-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged <2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

Watershed-level sampling effort requirements for determining riverine fish species composition

2005 ◽  
Vol 62 (7) ◽  
pp. 1580-1588 ◽  
Author(s):  
Katherine L Smith ◽  
Michael L Jones
Keyword(s):  
Species Richness ◽  
Species Composition ◽  
Fish Species ◽  
Correlation Coefficients ◽  
Sampling Effort ◽  
Species Accumulation Curves ◽  
Targeted Sampling ◽  
Weak Negative Correlation ◽  
Fish Species Composition ◽  
Riverine Fish

Accurate assessments of watershed-level species composition are necessary for comparative ecological studies, ecosystem health assessments, monitoring, and aquatic conservation prioritization. Several studies have addressed sampling effort requirements for characterizing fish species composition at a section of stream, but none have examined watershed-level requirements. In the spring and summer of 2002, we extensively sampled nine Great Lakes watersheds to assess sampling-effort requirements. Sampling requirements increased with the targeted percentage of estimated species richness. Sampling 15–119 randomly selected reaches of stream, stratified by stream order, was on average sufficient to detect 80%–100% of estimated species richness. Watershed size (km2) and estimated species richness each showed a weak, negative correlation with sampling-effort requirements in our study streams, with Pearson's correlation coefficients of –5.06 and –0.590, respectively. Because of among-watershed variability in sampling effort requirements, field crews should plot species accumulation curves onsite to determine adequate inventory completion. Based on the difficulty of detecting the last 10% of species, random sampling should be conducted in conjunction with targeted sampling of rare species.

Management and monitoring of the return of riverine fish species following rehabilitation of Dutch rivers.

Large Rivers ◽  
2003 ◽  
Vol 15 (1-4) ◽  
pp. 391-411 ◽  
Author(s):  
J. J. De Leeuw ◽  
A. D. Buijse ◽  
R. E. Grift ◽  
H. V. Winter
Keyword(s):  
Fish Species ◽  
Riverine Fish
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