scholarly journals Local adaptation fuels cryptic speciation in terrestrial annelids

2019 ◽  
Author(s):  
Daniel Fernández Marchán ◽  
Marta Novo ◽  
Nuria Sánchez ◽  
Jorge Domínguez ◽  
Darío J. Díaz Cosín ◽  
...  
Keyword(s):  
Geometric Morphometrics ◽  
Cryptic Species ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Regulation Of Transcription ◽  
Cryptic Speciation ◽  
Evolutionary Forces ◽  
Genome Wide

AbstractUncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

scholarly journals The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants ◽  
2016 ◽  
Vol 2 (11) ◽  
Author(s):  
Xiangchao Gan ◽  
Angela Hay ◽  
Michiel Kwantes ◽  
Georg Haberer ◽  
Asis Hallab ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Human Genetics ◽  
Morphological Evolution ◽  
Morphological Diversity ◽  
Close Relative ◽  
Gene Duplications ◽  
Tandem Gene Duplication ◽  
Genome Wide ◽  
Differential Gene

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.

scholarly journals Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

2020 ◽  
Author(s):  
Nicholas Price ◽  
Jack L. Mullen ◽  
Junjiang Lin ◽  
Christina Boucher ◽  
John K. McKay
Keyword(s):  
Cold Acclimation ◽  
Local Adaptation ◽  
Freezing Tolerance ◽  
Evolutionary Biology ◽  
Species Conservation ◽  
Selective Constraint ◽  
Expression Variation ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Signatures Of Selection

AbstractUnderstanding how genomic and expression variation is linked to adaptation of plants to local environments is fundamental to the fields of evolutionary biology and species conservation. Using locally adapted Arabidopsis thaliana Italy and Sweden populations, we examine how variation in gene expression under control and cold acclimation conditions, is linked to allele frequency differentiation (AFD); linkage disequilibrium (LD); selective constraint at nonsynonymous sites; and genetic-tradeoff quantitative trait loci (GT-QTL). Our results indicate that contrary to genes showing a main effect in environment (E), expression genotype by environment interactions (GxE) show significantly higher AFD along cis-regulatory and nonsynonymous sites than the neutral expectation; and interestingly, highly differentiated GxE genes show higher expression and inter-species selective constraint than the rest of the genes. When examining the association between genomic signatures of selection along GxE/E genes and GT-QTL, we find that GxE genes showing a high AFD and LD, display a significant and much higher enrichment along GT-QTL than the genome-wide/E set of genes. Nonetheless, E genes show a higher enrichment than the genome-wide control. In summary, our results suggest, that these highly expressed and selectively constrained GxE genes, may have been part of a cold-responsive regulon of E genes that experienced recent selection when migrating to new environments. Candidate GxE genes underlying GT-QTL reveal interesting biological processes that may underlie local adaptation to temperature, including flowering time, light-dependent cold acclimation, freezing tolerance, and response to hypoxia. Finally, we find no evidence linking lower expression of the CBF-dependent freezing tolerance pathway to genetic-tradeoffs and adaptation to warmer climates.

scholarly journals The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci

2019 ◽  
Vol 110 (4) ◽  
pp. 494-513 ◽  
Author(s):  
Adam G Jones ◽  
Stevan J Arnold ◽  
Reinhard Bürger
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Quantitative Traits ◽  
Trait Divergence ◽  
Genome Wide ◽  
Outlier Loci ◽  
Wide Range ◽  
Marker Loci ◽  
Neutral Marker ◽  
Fst Outlier

Abstract With the advent of next-generation sequencing approaches, the search for individual loci underlying local adaptation has become a major enterprise in evolutionary biology. One promising method to identify such loci is to examine genome-wide patterns of differentiation, using an FST-outlier approach. The effects of pleiotropy and epistasis on this approach are not yet known. Here, we model 2 populations of a sexually reproducing, diploid organism with 2 quantitative traits, one of which is involved in local adaptation. We consider genetic architectures with and without pleiotropy and epistasis. We also model neutral marker loci on an explicit genetic map as the 2 populations diverge and apply FST outlier approaches to determine the extent to which quantitative trait loci (QTL) are detectable. Our results show, under a wide range of conditions, that only a small number of QTL are typically responsible for most of the trait divergence between populations, even when inheritance is highly polygenic. We find that the loci making the largest contributions to trait divergence tend to be detectable outliers. These loci also make the largest contributions to within-population genetic variance. The addition of pleiotropy reduces the extent to which quantitative traits can evolve independently but does not reduce the efficacy of outlier scans. The addition of epistasis, however, reduces the mean FST values for causative QTL, making these loci more difficult, but not impossible, to detect in outlier scans.

scholarly journals Phylogenetic tree inference from local gene content

2015 ◽  
Author(s):  
Galina Glazko ◽  
Michael Gensheimer ◽  
Arcady Mushegian
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Gene Content ◽  
Orthologous Genes ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Tree Inference ◽  
Gene Order Conservation ◽  
Systematic Biases ◽  
Horizontal Transfers

Abstract Background: Complete genome sequences provide many new characters suitable for studying phylogenetic relationships. The limitations of the single sequence-based phylogenetic reconstruction prompted the efforts to build trees based on genome-wide properties, such as the fraction of shared orthologous genes or conservation of adjoining gene pairs. Gene content-based phylogenies, however, have their own biases: most notably, differential losses and horizontal transfers of genes interfere with phylogenetic signal, each in their own way, and special measures need to be taken to eliminate these types of noise. Results: We expand the repertoire of genome-wide traits available for phylogeny building, by developing a practical approach for measuring local gene conservation in two genomes. We counted the number of orthologous genes shared by chromosomal neighborhoods (“bins”), and built the phylogeny of 63 prokaryotic genomes on this basis. The tree correctly resolved all well-established clades, and also suggested the monophyly of firmicutes, which tend to be split in other genome-based trees. Conclusions: Our measure of local gene order conservation extracts strong phylogenetic signal. This new measure appears to be substantially resistant to the observed instances of gene loss and horizontal transfer, two evolutionary forces which can cause systematic biases in the genome-based phylogenies.

scholarly journals Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in theOctopus vulgarisspecies complex

2019 ◽  
Author(s):  
Michael D. Amor ◽  
Stephen R. Doyle ◽  
Mark D. Norman ◽  
Alvaro Roura ◽  
Nathan E. Hall ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Octopus Vulgaris ◽  
Nuclear Markers ◽  
Divergence Time Estimates ◽  
Mitochondrial Markers ◽  
Species Complexes ◽  
Genome Wide ◽  
Mitochondrial And Nuclear Markers

ABSTRACTMany marine species once considered to be cosmopolitan are now recognised as cryptic species complexes. Mitochondrial markers are ubiquitously used to address phylogeographic questions, and have been used to identify some cryptic species complexes; however, their efficacy in inference of evolutionary processes in the nuclear genome has not been thoroughly investigated. We used double digest restriction site-associated DNA sequencing (ddRADseq) markers to quantify species boundaries in the widely distributed and high value common octopus,Octopus vulgaris, comparing genome-wide phylogenetic signal to that obtained from mitochondrial markers. Phylogenetic analyses, genome-wide concordance and species tree estimation based on 604 genome-wide ddRADseq loci revealed six species within theO. vulgarisgroup. Divergence time estimates suggested modern-day species evolved over the last 2.5 ma, during a period of global cooling. Importantly, our study identified significant phylogenetic discordance between mitochondrial and nuclear markers; genome-wide nuclear loci supportedO. vulgarissensu stricto and Type III (South Africa) as distinct species, which mtDNA failed to recognise. Our finding of conflicting phylogenetic signal between mitochondrial and nuclear markers has broad implications for many taxa. Improved phylogenetic resolution ofO. vulgarishas significant implications for appropriate management of the group and will allow greater accuracy in global fisheries catch statistics.

scholarly journals Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

2014 ◽  
Author(s):  
Alan O. Bergland ◽  
Ray Tobler ◽  
Josefa Gonzalez ◽  
Paul Schmidt ◽  
Dmitri Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
North America ◽  
Local Adaptation ◽  
Latitudinal Gradients ◽  
Secondary Contact ◽  
Clinal Variation ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Spatially Varying ◽  
Spatially Varying Selection

Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations ofDrosophila melanogastersampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation inD. melanogasterand provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.

scholarly journals Phylogenetic paleoecology: macroecology within an evolutionary framework

Paleobiology ◽  
2021 ◽  
Vol 47 (2) ◽  
pp. 171-177
Author(s):  
James C. Lamsdell ◽  
Curtis R. Congreve
Keyword(s):  
Species Diversity ◽  
Spatial Variation ◽  
Geographic Distribution ◽  
Evolutionary Biology ◽  
Phylogenetic Signal ◽  
Evolutionary Rates ◽  
The Other ◽  
Ecological Data ◽  
Temporal And Spatial Variation ◽  
Temporal And Spatial

The burgeoning field of phylogenetic paleoecology (Lamsdell et al. 2017) represents a synthesis of the related but differently focused fields of macroecology (Brown 1995) and macroevolution (Stanley 1975). Through a combination of the data and methods of both disciplines, phylogenetic paleoecology leverages phylogenetic theory and quantitative paleoecology to explain the temporal and spatial variation in species diversity, distribution, and disparity. Phylogenetic paleoecology is ideally situated to elucidate many fundamental issues in evolutionary biology, including the generation of new phenotypes and occupation of previously unexploited environments; the nature of relationships among character change, ecology, and evolutionary rates; determinants of the geographic distribution of species and clades; and the underlying phylogenetic signal of ecological selectivity in extinctions and radiations. This is because phylogenetic paleoecology explicitly recognizes and incorporates the quasi-independent nature of evolutionary and ecological data as expressed in the dual biological hierarchies (Eldredge and Salthe 1984; Congreve et al. 2018; Fig. 1), incorporating both as covarying factors rather than focusing on one and treating the other as error within the dataset.

scholarly journals Genomic basis of striking fin shapes and colours in the fighting fish

2021 ◽  
Author(s):  
Le Wang ◽  
Fei Sun ◽  
Zi Yi Wan ◽  
Baoqing Ye ◽  
Yanfei Wen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Association Studies ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Major Effect ◽  
Betta Splendens ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Phenotypic Variations ◽  
Genomic Basis

Abstract Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole genome sequencing, QTL mapping, genome-wide association studies and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double tail mutant was suggested to be caused by a deletion in a zic1/zic4 co-enhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

scholarly journals Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Camilla A Santos ◽  
Gabriel G Sonoda ◽  
Thainá Cortez ◽  
Luiz L Coutinho ◽  
Sónia C S Andrade
Keyword(s):  
Local Adaptation ◽  
Differentially Expressed Genes ◽  
Evolutionary Biology ◽  
Rocky Shore ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Marine Species ◽  
Differentially Expressed ◽  
Planktonic Larva ◽  
Structure Changes

Abstract Understanding how selection shapes population differentiation and local adaptation in marine species remains one of the greatest challenges in the field of evolutionary biology. The selection of genes in response to environment-specific factors and microenvironmental variation often results in chaotic genetic patchiness, which is commonly observed in rocky shore organisms. To identify these genes, the expression profile of the marine gastropod Littoraria flava collected from four Southeast Brazilian locations in ten rocky shore sites was analyzed. In this first L. flava transcriptome, 250,641 unigenes were generated, and 24% returned hits after functional annotation. Independent paired comparisons between 1) transects, 2) sites within transects, and 3) sites from different transects were performed for differential expression, detecting 8,622 unique differentially expressed genes. Araçá (AR) and São João (SJ) transect comparisons showed the most divergent gene products. For local adaptation, fitness-related differentially expressed genes were chosen for selection tests. Nine and 24 genes under adaptative and purifying selection, respectively, were most related to biomineralization in AR and chaperones in SJ. The biomineralization-genes perlucin and gigasin-6 were positively selected exclusively in the site toward the open ocean in AR, with sequence variants leading to pronounced protein structure changes. Despite an intense gene flow among L. flava populations due to its planktonic larva, gene expression patterns within transects may be the result of selective pressures. Our findings represent the first step in understanding how microenvironmental genetic variation is maintained in rocky shore populations and the mechanisms underlying local adaptation in marine species.

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