Browsing by Subject "ADAPTIVE EVOLUTION"

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  • Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F.; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundstrom, Liselotte (2016)
    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene-and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee.
  • Verta, Jukka-Pekka; Debes, Paul; Piavchenko, Nikolai; Ruokolainen, Annukka; Ovaskainen, Outi Sinikka; Moustakas-Verho, Jacqueline; Tillanen, Seija Iiris; Parre, Noora; Aykanat, Tutku; Erkinaro, Jaakko; Primmer, Craig (2020)
    A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report acis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factorvestigial-like 3(vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show thatvgll3genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling ofvgll3expression in ten tissues across the first year of salmon development, we identify a pubertal transition invgll3expression where maturation coincided with a 66% reduction in testicularvgll3expression. Thelatematuration allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform ofvgll3pre-puberty. By comparing absolutevgll3mRNA copies in heterozygotes we show that the expression difference between theearlyandlatematurity alleles is largelycis-regulatory. We propose a model whereby expression of a rare isoform from thelateallele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits. Author summary Alternative life history strategies are an important source of diversity within populations and promote the maintenance of adaptive capacity and population resilience. However, in many cases the molecular basis of different life history strategies remains elusive. Age at maturity is a key adaptive life history trait in Atlantic salmon and has a relatively simple genetic basis. Using salmon age at maturity as a model, we report a mechanism whereby different transcript isoforms of the key age at maturity gene,vestigial-like 3(vgll3), associate with variation in the timing of male puberty. Our results show how gene regulatory differences in conjunction with variation in gene transcript structure can encode for complex alternative life histories.
  • Monzon-Argueello, Catalina; Consuegra, Sofia; Gajardo, Gonzalo; Marco-Rius, Francisco; Fowler, Daniel M.; De Faveri, Jacquelin; de Leaniz, Carlos Garcia (2014)
  • Pulkkinen, Katja; Pekkala, Nina; Ashrafi, Roghaieh; Hamalainen, Dorrit M.; Nkembeng, Aloysius N.; Lipponen, Anssi; Hiltunen, Teppo; Valkonen, Janne K.; Taskinen, Jouni (2018)
    Understanding ecological and epidemiological factors driving pathogen evolution in contemporary time scales is a major challenge in modern health management. Pathogens that replicate outside the hosts are subject to selection imposed by ambient environmental conditions. Increased nutrient levels could increase pathogen virulence by pre-adapting for efficient use of resources upon contact to a nutrient rich host or by favouring transmission of fast-growing virulent strains. We measured changes in virulence and competition in Flavobacterium columnare, a bacterial pathogen of freshwater fish, under high and low nutrient levels. To test competition between strains in genotype mixtures, we developed a quantitative real-time PCR assay. We found that a virulent strain maintained its virulence and outcompeted less virulent strains independent of the nutrient level and resource renewal rate while a less virulent strain further lost virulence in chemostats under low nutrient level and over long-term serial culture under high nutrient level. Our results suggest that increased outside-host nutrient levels might maintain virulence in less virulent strains and increase their contribution to epidemics in aquaculture. The results highlight a need to further explore the role of resource in the outside-host environment in maintaining strain diversity and driving evolution of virulence among environmentally growing pathogens.
  • O'Sullivan, Ronan James; Aykanat, Tutku; Johnston, Susan E.; Kane, Adam; Poole, Russell; Rogan, Ger; Prodöhl, Paulo A.; Primmer, Craig R.; McGinnity, Philip; Reed, Thomas Eric (2019)
    Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree-derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so-called "paradox of stasis." To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies-which have largely been limited to birds and mammals-to study evolutionary processes on contemporary timescales.
  • Shikano, Takahito; Laine, Veronika N.; Herczeg, Gabor; Vilkki, Johanna; Merilä, Juha (2013)
  • Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjørn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Wringe, Brendan; Fairweather, Robert; Bradbury, Ian R. (2020)
    Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
  • Yusuf, Leeban; Heatley, Matthew C.; Palmer, Joseph P. G.; Barton, Henry J.; Cooney, Christopher R.; Gossmann, Toni (2020)
    Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence, and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein-coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1434 protein-coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein-coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome-wide scale over macroevolutionary time is feasible. Although the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.
  • Teacher, Amber G. F.; Andre, Carl; Jonsson, Per R.; Merila, Juha (2013)
  • Wang, Yingnan; Zhao, Yongxin; Wang, Yu; Li, Zitong; Guo, Baocheng; Merilä, Juha (2020)
    Abstract The degree to which adaptation to similar selection pressures is underlain by parallel vs. non-parallel genetic changes is a topic of broad interest in contemporary evolutionary biology. Sticklebacks provide opportunities to characterize and compare the genetic underpinnings of repeated marine-freshwater divergences at both intra- and interspecific levels. While the degree of genetic parallelism in repeated marine-freshwater divergences has been frequently studied in the three-spined stickleback (Gasterosteus aculeatus), much less is known about this in other stickleback species. Using a population transcriptomic approach, we identified both genetic and gene expression variations associated with marine-freshwater divergence in the nine-spined stickleback (Pungitius pungitius). Specifically, we used a genome-wide association study approach, and found that ~1% of the total 173,491 identified SNPs showed marine-freshwater ecotypic differentiation. A total of 861 genes were identified to have SNPs associated with marine-freshwater divergence in nine-spined stickleback, but only 12 of these genes have also been reported as candidates associated with marine-freshwater divergence in the three-spined stickleback. Hence, our results indicate a low degree of interspecific genetic parallelism in marine-freshwater divergence. Moreover, 1,578 genes in the brain and 1,050 genes in the liver were differentially expressed between marine and freshwater nine-spined sticklebacks, ~5% of which have also been identified as candidates associated with marine-freshwater divergence in the three-spined stickleback. However, only few of these (e.g., CLDND1) appear to have been involved in repeated marine-freshwater divergence in nine-spined sticklebacks. Taken together, the results indicate a low degree of genetic parallelism in repeated marine-freshwater divergence both at intra- and interspecific levels.
  • Verta, Jukka-Pekka; Jones, Felicity (2019)
    Regulation of gene expression is thought to play a major role in adaptation but there are conflicting predictions for the relative importance of cis- and trans-regulatory mechanisms in the early stages adaptive divergence. Parallel evolution of marine and freshwater threespine stickleback fish provides an excellent opportunity to dissect whether the same molecular mechanisms underlie repeated adaptive divergence in gene expression. Using RNA-seq of four marine-freshwater ecotype pairs from Scotland and Canada, we first identified genes with parallel divergence in expression and show that these are found near previously reported adaptive loci and show a molecular signature of selection centered around the transcription start site. With allele-specific expression assays in F1 hybrids we next show that expression divergence is predominantly driven by cis-regulatory control in all four river systems, a pattern that is enriched in parallel divergently expressed genes. In particular, for genes whose expression is up-regulated in parallel among freshwater fish the quantitative degree of cis- and trans-regulation is also highly correlated, suggesting a shared genetic basis across populations. This stands in contrast to genes up-regulated in parallel in marine fish, whose degree of cis- and trans-regulation is less correlated and predictable. This observed asymmetry in parallelism in how genes are up-regulated in marine and freshwater fish can be explained by differences in the evolutionary contexts of the diverging ecotypes. Finally, we show that cis-regulation is predominantly additive and shows greater robustness to different in genetic backgrounds and environmental conditions. We argue that these features make cis-regulation well-poised for rapid adaptive divergence of gene expression under conditions of on-going gene flow. Combined our study highlights how natural selection on dispersed cis-regulatory elements can shape the adaptive landscape of the genome.
  • Morozov, Sergey; Leinonen, Tuomas; Merilä, Juha; McCairns, R. J. Scott (2018)
    Conspecifics inhabiting divergent environments frequently differ in morphology, physiology, and performance, but the interrelationships amongst traits and with Darwinian fitness remains poorly understood. We investigated population differentiation in morphology, metabolic rate, and swimming performance in three-spined sticklebacks (Gasterosteus aculeatus L.), contrasting a marine/ancestral population with two distinct freshwater morphotypes derived from it: the typical low-plated morph, and a unique small-plated morph. We test the hypothesis that similar to plate loss in other freshwater populations, reduction in lateral plate size also evolved in response to selection. Additionally, we test how morphology, physiology, and performance have evolved in concert as a response to differences in selection between marine and freshwater environments. We raised pure-bred second-generation fish originating from three populations and quantified their lateral plate coverage, burst- and critical swimming speeds, as well as standard and active metabolic rates. Using a multivariate Q(ST)-F-ST framework, we detected signals of directional selection on metabolic physiology and lateral plate coverage, notably demonstrating that selection is responsible for the reduction in lateral plate coverage in a small-plated stickleback population. We also uncovered signals of multivariate selection amongst all bivariate trait combinations except the two metrics of swimming performance. Divergence between the freshwater and marine populations exceeded neutral expectation in morphology and in most physiological and performance traits, indicating that adaptation to freshwater habitats has occurred, but through different combinations of traits in different populations. These results highlight both the complex interplay between morphology, physiology and performance in local adaptation, and a framework for their investigation.
  • Kerkkamp, Harald M. I.; Kini, R. Manjunatha; Pospelov, Alexey S.; Vonk, Freek J.; Henkel, Christiaan V.; Richardson, Michael K. (2016)
    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.