Browsing by Subject "EVOLUTION"

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  • Duggan, Ana T.; Perdomo, Maria F.; Piombino-Mascali, Dario; Marciniak, Stephanie; Poinar, Debi; Emery, Matthew V.; Buchmann, Jan P.; Duchene, Sebastian; Jankauskas, Rimantas; Humphreys, Margaret; Golding, G. Brian; Southon, John; Devault, Alison; Rouillard, Jean-Marie; Sahl, Jason W.; Dutour, Olivier; Hedman, Klaus; Sajantila, Antti; Smith, Geoffrey L.; Holmes, Edward C.; Poinar, Hendrik N. (2016)
    Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1-4], the timescale of emergence of the causative agent, variola virus (VARV), and how it evolved in the context of increasingly widespread immunization, have proven controversial [4-9]. In particular, some molecular-clock-based studies have suggested that key events in VARV evolution only occurred during the last two centuries [4-6] and hence in apparent conflict with anecdotal historical reports, although it is difficult to distinguish smallpox from other pustular rashes by description alone. To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. When compared to vaccinia virus, this archival strain contained the same pattern of gene degradation as 20th century VARVs, indicating that such loss of gene function had occurred before ca. 1650. Strikingly, the mummy sequence fell basal to all currently sequenced strains of VARV on phylogenetic trees. Molecular-clock analyses revealed a strong clock-like structure and that the timescale of smallpox evolution is more recent than often supposed, with the diversification of major viral lineages only occurring within the 18th and 19th centuries, concomitant with the development of modern vaccination.
  • Lutfullahoglu-Bal, Güleycan; Seferoglu, Ayse Bengisu; Keskin, Abdurrahman; Akdogan, Emel; Dunn, Cory D. (2018)
    Prokaryotes can provide new genetic information to eukaryotes by horizontal gene transfer (HGT), and such transfers are likely to have been particularly consequential in the era of eukaryogenesis. Since eukaryotes are highly compartmentalized, it is worthwhile to consider the mechanisms by which newly transferred proteins might reach diverse organellar destinations. Toward this goal, we have focused our attention upon the behavior of bacteria-derived tail anchors (TAs) expressed in the eukaryote Saccharomyces cerevisiae. In this study, we report that a predicted membrane-associated domain of the Escherichia coli YgiM protein is specifically trafficked to peroxisomes in budding yeast, can be found at a pre-peroxisomal compartment (PPC) upon disruption of peroxisomal biogenesis, and can functionally replace an endogenous, peroxisome-directed TA. Furthermore, the YgiM(TA) can localize to peroxisomes in mammalian cells. Since the YgiM(TA) plays no endogenous role in peroxisomal function or assembly, this domain is likely to serve as an excellent tool allowing further illumination of the mechanisms by which TAs can travel to peroxisomes. Moreover, our findings emphasize the ease with which bacteria-derived sequences might target to organelles in eukaryotic cells following HGT, and we discuss the importance of flexible recognition of organelle targeting information during and after eukaryogenesis.
  • Peris Tamayo, Ana-Maria; Devineau, Olivier; Praebel, Kim; Kahilainen, Kimmo K.; ostbye, Kjartan (2020)
    Adaptive radiation is the diversification of species to different ecological niches and has repeatedly occurred in different salmonid fish of postglacial lakes. In Lake Tinnsjoen, one of the largest and deepest lakes in Norway, the salmonid fish, Arctic charr (Salvelinus alpinus(L.)), has likely radiated within 9,700 years after deglaciation into ecologically and genetically segregated Piscivore, Planktivore, Dwarf, and Abyssal morphs in the pelagial, littoral, shallow-moderate profundal, and deep-profundal habitats. We compared trait variation in the size of the head, the eye and olfactory organs, as well as the volumes of five brain regions of these four Arctic charr morphs. We hypothesised that specific habitat characteristics have promoted divergent body, head, and brain sizes related to utilized depth differing in environmental constraints (e.g., light, oxygen, pressure, temperature, and food quality). The most important ecomorphological variables differentiating morphs were eye area, habitat, and number of lamellae. The Abyssal morph living in the deepest areas of the lake had the smallest brain region volumes, head, and eye size. Comparing the olfactory bulb with the optic tectum in size, it was larger in the Abyssal morph than in the Piscivore morph. The Piscivore and Planktivore morphs that use more illuminated habitats have the largest optic tectum volume, followed by the Dwarf. The observed differences in body size and sensory capacities in terms of vision and olfaction in shallow and deepwater morphs likely relates to foraging and mating habitats in Lake Tinnsjoen. Further seasonal and experimental studies of brain volume in polymorphic species are needed to test the role of plasticity and adaptive evolution behind the observed differences.
  • DREAM SMC-Het Participants; Salcedo, Adriana; Mustonen, Ville (2020)
    Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge. Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.
  • Novakovic, Bojan; Tsirvoulis, Georgios; Granvik, Mikael; Todovic, Ana (2017)
    We report the discovery of a new asteroid family among the dark asteroids residing in the Phocaea region the Tamara family. We make use of available physical data to separate asteroids in the region according to their surface reflectance properties, and establish the membership of the family. We determine the slope of the cumulative magnitude distribution of the family, and find it to be significantly steeper than the corresponding slope of all the asteroids in the Phocaea region. This implies that subkilometer dark Phocaeas are comparable in number to bright S-type objects, shedding light on an entirely new aspect of the composition of small Phocaea asteroids. We then use the Yarkovsky V-shape based method and estimate the age of the family to be 264 +/- 43Myr. Finally, we carry out numerical simulations of the dynamical evolution of the Tamara family. The results suggest that up to 50 Tamara members with absolute magnitude H <19.4 may currently be found in the near-Earth region. Despite their relatively small number in the near-Earth space, the rate of Earth impacts by small, dark Phocaeas is non-negligible.
  • Nichols, Hazel J.; Arbuckle, Kevin; Sanderson, Jennifer L.; Vitikainen, Emma I. K.; Marshall, Harry H.; Thompson, Faye J.; Cant, Michael A.; Wells, David A. (2021)
    Personality traits, such as the propensity to cooperate, are often inherited from parents to offspring, but the pathway of inheritance is unclear. Traits could be inherited via genetic or parental effects, or culturally via social learning from role models. However, these pathways are difficult to disentangle in natural systems as parents are usually the source of all of these effects. Here, we exploit natural 'cross fostering' in wild banded mongooses to investigate the inheritance of cooperative behaviour. Our analysis of 800 adult helpers over 21 years showed low but significant genetic heritability of cooperative personalities in males but not females. Cross fostering revealed little evidence of cultural heritability: offspring reared by particularly cooperative helpers did not become more cooperative themselves. Our results demonstrate that cooperative personalities are not always highly heritable in wild, and that the basis of behavioural traits can vary within a species (here, by sex).
  • Silva, Sofia Marques; Townsend Peterson, A.; Carneiro, Lincoln; Tortola Burlamaqui, Tiberio Cesar; Ribas, Camila C.; Sousa-Neves, Tiago; Miranda, Leonardo S.; Fernandes, Alexandre M.; d'Horta, Fernando M.; Araujo-Silva, Lucas Eduardo; Batista, Romina; Bandeira, Cinthia H. M. M.; Dantas, Sidnei M.; Ferreira, Mateus; Martins, Denise M.; Oliveira, Joiciane; Rocha, Taina C.; Sardelli, Carla H.; Thom, Gregory; Rego, Pericles Sena; Santos, Marcos Persio; Sequeira, Fernando; Vallinoto, Marcelo; Aleixo, Alexandre (2019)
    The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.
  • Cornetti, Luca; Fields, Peter D.; Van Damme, Kay; Ebert, Dieter (2019)
    In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system.
  • Webster, Mike M.; Chouinard-Thuly, Laura; Herczeg, Gabor; Kitano, Jun; Riley, Riva; Rogers, Sean; Shapiro, Michael D.; Shikano, Takahito; Laland, Kevin N. (2019)
    Whether learning primarily reflects general processes or species-specific challenges is a long-standing matter of dispute. Here, we present a comprehensive analysis of public information use (PI-use) in sticklebacks (Gasterosteidae). PI-use is a form of social learning by which animals are able to assess the relative quality of resources, here prey patches, by observing the behaviour of others. PI-use was highly specific with only Pungitius and their closest relative Culaea inconstans showing evidence of PI-use. We saw no effects of ontogenetic experience upon PI-use in Pungitius pungitius. Experiments with live demonstrators and animated fish revealed that heightened activity and feeding strikes by foraging conspecifics are important cues in the transmission of PI. Finally, PI-use was the only form of learning in which P. pungitius and another stickleback, Gasterosteus aculeatus differed. PI-use in sticklebacks is species-specific and may represent an 'ecological specialization' for social foraging. Whether this reflects selection on perception, attentional or cognitive processes remains to be determined.
  • Marin-Gomez, Oscar H.; MacGregor-Fors, Ian (2021)
    Urbanization drives changes in acoustic communication systems in some animal species. Noise and light pollution are among the main urban factors known to disrupt the timing and structure of avian singing behaviour. Despite our understanding of the ways in which urbanization can drive variations in avian acoustic communication, our ability to generalize the underlying causes of such variation and its consequences is still limited. Here, we reviewed the literature focused on the study of avian dawn choruses in urban settings at a global scale. Our findings reveal that avian dawn chorus research has focused on the impact of anthropogenic noise on dawn chorus traits (i.e. timing, peak, song output, song frequencies); relationships between light pollution and chorus timing; the effects of temperature, cloudiness, moonlight and natural light on chorus timing; relationships between nocturnal noise and light, and dawn chorus timing; the effects of chemical pollution and supplementary feeding on dawn chorus activity; and ecological patterns of dawn choruses in soundscapes across urban-non-urban gradients. We identified important knowledge gaps in the study of avian dawn choruses in urban settings and thus suggest future research directions, including frameworks (e.g. the urbanization intensity gradient) and consideration of a wider array of urban conditions and variables. Given the complexity of urban settings, we encourage further studies to address the role that all sources of pollution can have on avian acoustic communication at dawn. Additionally, a central question to resolve is whether the function of avian dawn choruses in urban areas differs, and if so how, from non-urban counterparts. Given that most research has been performed across Holarctic cities and towns, studies from tropical and subtropical regions are needed if we aim to understand the phenomenon globally. Finally, studies at the community- and soundscape-level across cities could advance understanding of the way in which urban birds use the acoustic space during the most critical singing time period, dawn.
  • Sirviö, Anu; Johnston, J. Spencer; Wenseleers, Tom; Pamilo, Pekka (2011)
  • Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F.; Guo, Baocheng; Nederbragt, Alexander J.; Jakobsen, Kjetill S.; Merilä, Juha (2019)
    The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
  • Oksanen, Otto; Zliobaite, Indre; Saarinen, Juha; Lawing, A. Michelle; Fortelius, Mikael (2019)
    Aim The links between geo- and biodiversity, postulated by Humboldt, can now be made quantitative. Species are adapted to their environments and interact with their environments by having pertinent functional traits. We aim to improve global ecometric models using functional traits for estimating palaeoclimate and apply models to Pleistocene fauna for palaeoclimate interpretation. Location Global at present day, Pleistocene of Europe for fossil data analysis. Taxa Artiodactyla, Perissodactyla, Proboscidea and Primates. Methods We quantify functional traits of large mammal communities and develop statistical models linking trait distributions to local climate at present day. We apply these models to the fossil record, survey functional traits, and quantitatively estimate climates of the past. This approach to analysing functional relationships between faunal communities and their environments is called ecometrics. Results and main conclusions Here, we present new global ecometric models for estimating mean annual and minimum temperature from dental traits of present day mammalian communities. We also present refined models for predicting net primary productivity. Using dental ecometric models, we produce palaeoclimate estimates for 50 Pleistocene fossil localities in Europe and show that the estimates are consistent with trends derived from other proxies, especially for minimum temperatures, which we hypothesize to be ecologically limiting. Our new temperature models allow us to trace the distribution of freezing and non-freezing ecosystems in the recent past, opening new perspectives on the evolution of cold-adaptive biota as the Pleistocene cooling progressed.
  • Roikonen, Petri Juhani; Heikkinen, Sakari (2020)
    This study presents the new Gini coefficient and top income share series for Finland in the years 1865–1934 by utilizing Finnish tax statistics, which provide data on a poor country on the threshold of modern economic growth. Income inequality was relatively moderate in 1865, while famine (1867–1868) decreased it further. Income inequality increased substantially during the late nineteenth century, then declined during WWI and its aftermath, followed by another increase in inequality in the late 1920s that was halted by the Great Depression. The rising level of inequality before WWI fits well with the ideas of the Kuznets curve and maximum inequality, whereas the decline in inequality was due to shocks (e.g., civil war).
  • Lumby, Casper K.; Zhao, Lei; Breuer, Judith; Illingworth, Christopher J. R. (2020)
    Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection N-e for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an N-e of 2.5 x 10(7) (95% confidence range 1.0 x 10(7) to 9.0 x 10(7)) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
  • Fountain, Toby; Ravinet, Mark; Naylor, Richard; Reinhardt, Klaus; Butlin, Roger K. (2016)
    The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F-2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species.
  • Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjorn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Regular, Paul; Fairweather, Robert; Bradbury, Ian R. (2019)
    Chromosome structural variation may underpin ecologically important intraspecific diversity by reducing recombination within supergenes containing linked, coadapted alleles. Here, we confirm that an ancient chromosomal rearrangement is strongly associated with migratory phenotype and individual genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. We reconstruct trends in effective population size over the last century and reveal declines in effective population size matching onset of industrialized harvest (after 1950). We find different demographic trajectories between individuals homozygous for the chromosomal rearrangement relative to heterozygous or homozygous individuals for the noninverted haplotype, suggesting different selective histories across the past 150 years. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic, phenotypic, and demographic variation in a highly connected marine species and show how overfishing may have led to loss of biocomplexity within Northern cod stock.
  • Darragh, Kathy; Orteu, Anna; Black, Daniella; Byers, Kelsey J. R. P.; Szczerbowski, Daiane; Warren, Ian A.; Rastas, Pasi; Pinharanda, Ana; Davey, John W.; Fernanda Garza, Sylvia; Abondano Almeida, Diana; Merrill, Richard M.; McMillan, W. Owen; Schulz, Stefan; Jiggins, Chris D. (2021)
    Plants and insects often use the same compounds for chemical communication, but not much is known about the genetics of convergent evolution of chemical signals. The terpene (E)-beta-ocimene is a common component of floral scent and is also used by the butterfly Heliconius melpomene as an anti-aphrodisiac pheromone. While the biosynthesis of terpenes has been described in plants and microorganisms, few terpene synthases (TPSs) have been identified in insects. Here, we study the recent divergence of 2 species, H. melpomene and Heliconius cydno, which differ in the presence of (E)-beta-ocimene; combining linkage mapping, gene expression, and functional analyses, we identify 2 novel TPSs. Furthermore, we demonstrate that one, HmelOS, is able to synthesise (E)-beta-ocimene in vitro. We find no evidence for TPS activity in HcydOS (HmelOS ortholog of H. cydno), suggesting that the loss of (E)-beta-ocimene in this species is the result of coding, not regulatory, differences. The TPS enzymes we discovered are unrelated to previously described plant and insect TPSs, demonstrating that chemical convergence has independent evolutionary origins.
  • Ala-Kurikka, Tommi; Pospelov, Alexey; Summanen, Milla; Alafuzoff, Aleksander; Kurki, Samu; Voipio, Juha; Kaila, Kai (2021)
    Objective Birth asphyxia (BA) is often associated with seizures that may exacerbate the ensuing hypoxic-ischemic encephalopathy. In rodent models of BA, exposure to hypoxia is used to evoke seizures, that commence already during the insult. This is in stark contrast to clinical BA, in which seizures are typically seen upon recovery. Here, we introduce a term-equivalent rat model of BA, in which seizures are triggered after exposure to asphyxia. Methods Postnatal day 11-12 male rat pups were exposed to steady asphyxia (15 min; air containing 5% O-2 + 20% CO2) or to intermittent asphyxia (30 min; three 5 + 5-min cycles of 9% and 5% O-2 at 20% CO2). Cortical activity and electrographic seizures were recorded in freely behaving animals. Simultaneous electrode measurements of intracortical pH, Po-2, and local field potentials (LFPs) were made under urethane anesthesia. Results Both protocols decreased blood pH to Significance The rate of brain pH recovery has a strong influence on post-asphyxia seizure propensity. The recurring hypoxic episodes during intermittent asphyxia promote neuronal excitability, which leads to seizures only after the suppressing effect of the hypercapnic acidosis is relieved. The present rodent model of BA is to our best knowledge the first one in which, consistent with clinical BA, behavioral and electrographic seizures are triggered after and not during the BA-mimicking insult.