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1.
Life (Basel) ; 14(7)2024 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-39063667

RESUMO

Many of the fundamental molecules of life share extraordinary pigment-like optical properties in the long-wavelength UV-C spectral region. These include strong photon absorption and rapid (sub-pico-second) dissipation of the induced electronic excitation energy into heat through peaked conical intersections. These properties have been attributed to a "natural selection" of molecules resistant to the dangerous UV-C light incident on Earth's surface during the Archean. In contrast, the "thermodynamic dissipation theory for the origin of life" argues that, far from being detrimental, UV-C light was, in fact, the thermodynamic potential driving the dissipative structuring of life at its origin. The optical properties were thus the thermodynamic "design goals" of microscopic dissipative structuring of organic UV-C pigments, today known as the "fundamental molecules of life", from common precursors under this light. This "UV-C Pigment World" evolved towards greater solar photon dissipation through more complex dissipative structuring pathways, eventually producing visible pigments to dissipate less energetic, but higher intensity, visible photons up to wavelengths of the "red edge". The propagation and dispersal of organic pigments, catalyzed by animals, and their coupling with abiotic dissipative processes, such as the water cycle, culminated in the apex photon dissipative structure, today's biosphere.

2.
J Evol Biol ; 37(8): 862-876, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-38822575

RESUMO

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.


Assuntos
Evolução Molecular , Genoma Viral , Filogenia , Seleção Genética , RNA Viral/genética , Conformação de Ácido Nucleico , Vírus de RNA/genética
3.
J Exp Bot ; 75(13): 3993-4004, 2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-38634646

RESUMO

Hypoallometric (slope<1) scaling between metabolic rate and body mass is often regarded as near-universal across organisms. However, there are compelling reasons to question hypoallometric scaling in woody plants, where metabolic rate is directly proportional to leaf area. This leaf area must provide carbon to the volume of the metabolically active sapwood (VMASW). Within populations of a species, variants in which VMASW increases per unit leaf area with height growth (e.g. ⅔ or ¾ scaling) would have proportionally less carbon for growth and reproduction as they grow taller. Therefore, selection should favor individuals in which, as they grow taller, leaf area scales isometrically with shoot VMASW (slope=1). Using tetrazolium staining, we measured total VMASW and total leaf area (LAtot) across 22 individuals of Ricinus communis and confirmed that leaf area scales isometrically with VMASW, and that VMASW is much smaller than total sapwood volume. With the potential of the LAtot-VMASW relationship to shape factors as diverse as the crown area-stem diameter relationship, conduit diameter scaling, reproductive output, and drought-induced mortality, our work indicates that the notion that sapwood increases per unit leaf area with height growth requires revision.


Assuntos
Biomassa , Folhas de Planta , Árvores , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/metabolismo , Folhas de Planta/anatomia & histologia , Árvores/crescimento & desenvolvimento , Árvores/metabolismo , Ricinus/crescimento & desenvolvimento , Ricinus/metabolismo , Madeira/crescimento & desenvolvimento , Madeira/metabolismo
5.
Mol Immunol ; 163: 86-103, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37769577

RESUMO

Plasmodium vivax's biological complexity has restricted in vitro culture development for characterising antigens involved in erythrocyte invasion and their immunological relevance. The murine model is proposed as a suitable alternative in the search for therapeutic candidates since Plasmodium yoelii uses homologous proteins for its invasion. The AMA-1 protein is essential for parasite invasion of erythrocytes as it is considered an important target for infection control. This study has focused on functional PyAMA-1 peptides involved in host-pathogen interaction; the protein is located in regions under negative selection as determined by bioinformatics analysis. It was found that pyama1 has two highly conserved regions amongst species (>70%) under negative selection. Fourteen synthetic peptides spanning both conserved regions were evaluated; 5 PyAMA-1 peptides having high specific binding (HABP) to murine erythrocytes were identified. The parasite's invasion inhibition capability was analysed through in vitro assays, suggesting that peptides 42681 (43-ENTERSIKLINPWDKYMEKY-62), 42903 (206-RYSSNDANNENQPFSFTPEK-225) and 42904 (221-FTPEKIENYKDLSYLTKNLR-240) had greater than 50% inhibition profile and restricted P. yoelii intra-erythrocyte development. This work proposes that the screening of conserved HABPs under negative selective pressure might be good candidates for developing a synthetic anti-malarial vaccine since they share functionally-relevant characteristics, such as interspecies conservation, specific RBC binding profile, invasion and parasite development inhibition capability, and the predicted B-epitopes within were recognised by sera obtained from experimentally-infected mice.


Assuntos
Antimaláricos , Animais , Camundongos , Antimaláricos/farmacologia , Antimaláricos/metabolismo , Sequência de Aminoácidos , Plasmodium falciparum , Proteínas de Protozoários , Peptídeos , Eritrócitos/metabolismo , Antígenos de Protozoários
6.
BMC Ecol Evol ; 23(1): 58, 2023 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-37770825

RESUMO

BACKGROUND: Dengue is a mosquito-borne viral disease posing a significant threat to public health. Dengue virus (DENV) evolution is often characterized by lineage turnover, which, along with ecological and immunological factors, has been linked to changes in dengue phenotype affecting epidemic dynamics. Utilizing epidemiologic and virologic data from long-term population-based studies (the Nicaraguan Pediatric Dengue Cohort Study and Nicaraguan Dengue Hospital-based Study), we describe a lineage turnover of DENV serotype 2 (DENV-2) prior to a large dengue epidemic in 2019. Prior to this epidemic, Nicaragua had experienced relatively low levels of DENV transmission from 2014 to 2019, a period dominated by chikungunya in 2014/15 and Zika in 2016. RESULTS: Our phylogenetic analyses confirmed that all Nicaraguan DENV-2 isolates from 2018 to 2019 formed their own clade within the Nicaraguan lineage of the Asian/American genotype. The emergence of the new DENV-2 lineage reflects a replacement of the formerly dominant clade presiding from 2005 to 2009, a lineage turnover marked by several shared derived amino acid substitutions throughout the genome. To elucidate evolutionary drivers of lineage turnover, we performed selection pressure analysis and reconstructed the demographic history of DENV-2. We found evidence of adaptive evolution by natural selection at the codon level as well as in branch formation. CONCLUSIONS: The timing of its emergence, along with a statistical signal of adaptive evolution and distinctive amino acid substitutions, the latest in the NS5 gene, suggest that this lineage may have increased fitness relative to the prior dominant DENV-2 strains. This may have contributed to the intensity of the 2019 DENV-2 epidemic, in addition to previously identified immunological factors associated with pre-existing Zika virus immunity.


Assuntos
Vírus da Dengue , Dengue , Infecção por Zika virus , Zika virus , Humanos , Criança , Animais , Vírus da Dengue/genética , Dengue/epidemiologia , Nicarágua/epidemiologia , Filogenia , Estudos de Coortes
7.
Genome Biol Evol ; 15(9)2023 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-37625795

RESUMO

A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.


Assuntos
Abelhas , Quimera , Animais , Masculino , Aclimatação/genética , Aclimatação/fisiologia , África , Altitude , Abelhas/genética , Abelhas/fisiologia , Quimera/genética , Quimera/fisiologia , Clima , Europa (Continente) , Genômica , Sêmen , América do Sul , Colômbia
8.
Malar J ; 22(1): 225, 2023 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-37537581

RESUMO

BACKGROUND: Knowledge of the diversity of invasion ligands in malaria parasites in endemic regions is essential to understand how natural selection influences genetic diversity of these ligands and their feasibility as possible targets for future vaccine development. In this study the diversity of four genes for merozoite invasion ligands was studied in Ecuadorian isolates of Plasmodium vivax. METHODS: Eighty-eight samples from P. vivax infected individuals from the Coast and Amazon region of Ecuador were obtained between 2012 and 2015. The merozoite invasion genes pvmsp-1-19, pvdbpII, pvrbp1a-2 and pvama1 were amplified, sequenced, and compared to the Sal-1 strain. Polymorphisms were mapped and genetic relationships between haplotypes were determined. RESULTS: Only one nonsynonymous polymorphism was detected in pvmsp-1-19, while 44 nonsynonymous polymorphisms were detected in pvdbpII, 56 in pvrbp1a-2 and 33 in pvama1. While haplotypes appeared to be more related within each area of study and there was less relationship between parasites of the coastal and Amazon regions of the country, diversification processes were observed in the two Amazon regions. The highest haplotypic diversity for most genes occurred in the East Amazon of the country. The high diversity observed in Ecuadorian samples is closer to Brazilian and Venezuelan isolates, but lower than reported in other endemic regions. In addition, departure from neutrality was observed in Ecuadorian pvama1. Polymorphisms for pvdbpII and pvama1 were associated to B-cell epitopes. CONCLUSIONS: pvdbpII and pvama1 genetic diversity found in Ecuadorian P. vivax was very similar to that encountered in other malaria endemic countries with varying transmission levels and segregated by geographic region. The highest diversity of P. vivax invasion genes in Ecuador was found in the Amazonian region. Although selection appeared to have small effect on pvdbpII and pvrbp1a-2, pvama1 was influenced by significant balancing selection.


Assuntos
Malária Vivax , Plasmodium vivax , Humanos , Equador , Antígenos de Protozoários/genética , Proteínas de Protozoários/genética , Reticulócitos , Ligantes , Malária Vivax/epidemiologia , Polimorfismo Genético , Seleção Genética , Variação Genética
9.
Entropy (Basel) ; 25(7)2023 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-37510006

RESUMO

Evolutionary theory suggests that the origin, persistence, and evolution of biology is driven by the "natural selection" of characteristics improving the differential reproductive success of the organism in the given environment. The theory, however, lacks physical foundation, and, therefore, at best, can only be considered a heuristic narrative, of some utility for assimilating the biological and paleontological data at the level of the organism. On deeper analysis, it becomes apparent that this narrative is plagued with problems and paradoxes. Alternatively, non-equilibrium thermodynamic theory, derived from physical law, provides a physical foundation for describing material interaction with its environment at all scales. Here we describe a "natural thermodynamic selection" of characteristics of structures (or processes), based stochastically on increases in the global rate of dissipation of the prevailing solar spectrum. Different mechanisms of thermodynamic selection are delineated for the different biotic-abiotic levels, from the molecular level at the origin of life, up to the level of the present biosphere with non-linear coupling of biotic and abiotic processes. At the levels of the organism and the biosphere, the non-equilibrium thermodynamic description of evolution resembles, respectively, the Darwinian and Gaia descriptions, although the underlying mechanisms and the objective function of selection are fundamentally very different.

10.
Evolution ; 77(8): 1769-1779, 2023 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-37128948

RESUMO

Urbanization is currently one of the trademarks of the Anthropocene, accelerating evolutionary processes and reshaping ecological interactions over short time scales. Species interactions represent a fundamental pillar of diversity that is being altered globally by anthropogenic change. Urban environments, despite their potential impact, have seldom been studied in relation to how they shape natural selection of phenotypic traits in multispecies interactions. Using a seed-dispersal mutualism as a study system, we estimated the regime and magnitude of phenotypic selection exerted by frugivores on fruit and seed traits across three plant populations with different degrees of urbanization (urban, semiurban, and rural). Urbanization weakened phenotypic selection via an indirect positive impact on fruit production and fitness and, to a lesser extent, through a direct positive effect on species visitation rates. Our results show that urban ecosystems may affect multifarious selection of traits in the short term and highlight the role of humans in shaping eco-evolutionary dynamics of multispecies interactions.


Assuntos
Frutas , Dispersão de Sementes , Humanos , Ecossistema , Urbanização , Simbiose , Sementes
11.
Genome Biol Evol ; 15(3)2023 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-36726304

RESUMO

To characterize host risk factors for infectious disease in Mesoamerican populations, we interrogated 857,481 SNPs assayed using the Affymetrix 6.0 genotyping array for signatures of natural selection in immune response genes. We applied three statistical tests to identify signatures of natural selection: locus-specific branch length (LSBL), the cross-population extended haplotype homozygosity (XP-EHH), and the integrated haplotype score (iHS). Each of the haplotype tests (XP-EHH and iHS) were paired with LSBL and significance was determined at the 1% level. For the paired analyses, we identified 95 statistically significant windows for XP-EHH/LSBL and 63 statistically significant windows for iHS/LSBL. Among our top immune response loci, we found evidence of recent directional selection associated with the major histocompatibility complex (MHC) and the peroxisome proliferator-activated receptor gamma (PPAR-γ) signaling pathway. These findings illustrate that Mesoamerican populations' immunity has been shaped by exposure to infectious disease. As targets of selection, these variants are likely to encode phenotypes that manifest themselves physiologically and therefore may contribute to population-level variation in immune response. Our results shed light on past selective events influencing the host response to modern diseases, both pathogenic infection as well as autoimmune disorders.


Assuntos
Doenças Transmissíveis , Genômica , Humanos , Genoma , Seleção Genética , Doenças Transmissíveis/genética
12.
Ecol Evol ; 13(1): e9768, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36713487

RESUMO

Color polymorphism can be maintained in natural populations by natural selection or sexual selection. In this study, we use two different approaches to test which of these evolutionary mechanisms may explain the presence of color polymorphism in the Cuban Limia (Limia vittata), an endemic livebearing fish from Cuba. First, we investigate the role of sexual selection using traditional binary choice tests looking at both female and male preferences relative to varying degrees of black spotting in stimulus mates. Second, we assess the role of natural selection by analyzing the frequency and geographic distribution of black-spotted and nonspotted morphs of L. vittata in natural populations from Cuba. The frequency of black-spotted morphs is significantly higher in brackish and saltwater environments compared with freshwater habitats, which could be related to higher predation pressure in coastal ecosystems compared with purely freshwater environments. Our results suggest that habitat variation is the most important factor in maintaining color polymorphism in L. vittata. Salinity levels could be indirectly responsible for maintaining different color morphs in this species, likely due to the regulatory effect of saline gradients on predation regimes.

13.
Am J Bot ; 110(3): 1-12, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36706269

RESUMO

PREMISE: In fleshy-fruited plants, fruit removal is widely used as a proxy for plant reproductive success. Nevertheless, this proxy may not accurately reflect the number of seeds dispersed, an assumed better proxy for total fitness (fruit removal × mean number of seeds dispersed per fruit). METHODS: We examined under what circumstances fruit removal can be reliable as a proxy for total fitness when assessing bird-mediated selection on fruit traits. In three populations of the Blue Passionflower (Passiflora caerulea), we used the number of fruits pecked per plant as a surrogate for fruit removal to estimate phenotypic selection on fruit and seed traits, and simulations of the effect of the fruit-seed number trade-off on the number of fruits removed. RESULTS: Fruit removal was a good indicator of fitness, accounting for 55 to 68% of the variability in total fitness, measured as total number of seeds removed. Moreover, multivariate selection analyses on fruit crop size, mean fruit diameter and mean seed number using fruit removal as a fitness proxy yielded similar selection regimes to those using total fitness. Simulations showed that producing more fruits, a lower number of seeds per fruit, and a higher variability in seed number can result in a negative relationship between fruit removal and total fitness. CONCLUSIONS: Our results suggest that fruit removal can be reliably used as a proxy for total fitness when (1) there is a weak fruit number-seed number trade-off, (2) fruit crop size and fruit removal correlate positively, and (3) seed number variability does not largely exceed fruit number variability.


Assuntos
Frutas , Dispersão de Sementes , Animais , Sementes , Aves
14.
Proc Natl Acad Sci U S A ; 120(1): e2207544120, 2023 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-36574663

RESUMO

A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.


Assuntos
Genética Populacional , Nível de Saúde , Humanos , Biomarcadores , Bolívia , Genômica , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único , Seleção Genética , Genoma Humano
15.
Conserv Biol ; 37(3): e14033, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36349503

RESUMO

Given the speed at which humans are changing the climate, species with high degrees of endemism may not have time to avoid extinction through adaptation. We investigated through teleconnection analysis the origin of rainfall that determines the phylogenetic diversity of rainforest frogs and the effects of microclimate differences in shaping the morphological traits of isolated populations (which contribute to greater phylogenetic diversity and speciation). We also investigated through teleconnection analysis how deforestation in Amazonia can affect ecosystem services that are fundamental to maintaining the climate of the Atlantic rainforest biodiversity hotspot. Seasonal winds known as flying rivers carry water vapor from Amazonia to the Atlantic Forest, and the breaking of this ecosystem service could lead Atlantic Forest species to population decline and extinction in the short term. Our results suggest that the selection of morphological traits that shape Atlantic Forest frog diversity and their population dynamics are influenced by the Amazonian flying rivers. Our results also suggest that the increases of temperature anomalies in the Atlantic Ocean due to global warming and in the Amazon forest due to deforestation are already breaking this cycle and threaten the biodiversity of the Atlantic Forest hotspot.


Efectos de los ríos voladores de la Amazonía sobre la diversidad y las poblaciones de ranas en la Mata Atlántica Resumen Con la velocidad a la que la humanidad está alterando el clima, puede que las especies con un nivel elevado de endemismo no cuenten con tiempo suficiente para adaptarse y evitar la extinción. Usamos un análisis de teleconexión para investigar el origen de las precipitaciones que determinan la diversidad filogenética de las ranas selváticas y los efectos de las diferencias microclimáticas sobre la determinación de las características morfológicas de las poblaciones aisladas, las cuales contribuyen a una mayor especiación y diversidad filogenética. También utilizamos este análisis para investigar cómo la deforestación en la Amazonía puede afectar los servicios ambientales que son fundamentales para mantener el punto caliente de biodiversidad que es la Mata Atlántica. Los ríos voladores son vientos estacionales que transportan vapor de agua desde la Amazonía hasta la Mata Atlántica; la interrupción de este servicio ambiental podría derivar en la declinación poblacional y la extinción a corto plazo de las especies en este ecosistema. Nuestros resultados sugieren que los ríos voladores de la Amazonía influyen sobre la selección de las características morfológicas que determinan la diversidad de ranas y sus dinámicas poblacionales en la Mata Atlántica. Nuestros resultados también sugieren que el incremento de anomalías térmicas en el Océano Atlántico, causadas por el calentamiento global, y en la Amazonía, causadas por la deforestación, ya están interrumpiendo este ciclo y son una amenaza para la biodiversidad del punto caliente que es la Mata Atlántica.


Assuntos
Ecossistema , Floresta Úmida , Humanos , Animais , Filogenia , Conservação dos Recursos Naturais , Biodiversidade , Brasil , Anuros
16.
Virus Evol ; 8(2): veac109, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36582501

RESUMO

A new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization by South African health authorities on 24 November 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicron's presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility has had on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of the circulation of Omicron. We inferred 160 introduction events of Omicron in Mexico since its first detection in South Africa; subsequently, after the first introductions there was an evident increase in the prevalence of SARS-CoV-2 during January. This higher prevalence of the novel variant resulted in a peak of reported cases; on average 6 weeks after, a higher mobility trend was reported. During the peak of cases in the country from January to February 2022, the Omicron BA.1.1 sub-lineage dominated, followed by the BA.1 and BA.15 sub-lineages. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found six non-synonymous mutations in the receptor binding domain of the spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved; however, we identified homoplasic mutations in non-structural proteins, indicating a parallel evolution.

17.
Front Genet ; 13: 954015, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36246591

RESUMO

Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures through in silico modeling to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure are under positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

18.
Mol Biol Evol ; 39(10)2022 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-36026493

RESUMO

The alcohol dehydrogenase (ADH) family of genes encodes enzymes that catalyze the metabolism of ethanol into acetaldehyde. Nucleotide variation in ADH genes can affect the catalytic properties of these enzymes and is associated with a variety of traits, including alcoholism and cancer. Some ADH variants, including the ADH1B*48His (rs1229984) mutation in the ADH1B gene, reduce the risk of alcoholism and are under positive selection in multiple human populations. The advent of Neolithic agriculture and associated increase in fermented foods and beverages is hypothesized to have been a selective force acting on such variants. However, this hypothesis has not been tested in populations outside of Asia. Here, we use genome-wide selection scans to show that the ADH gene region is enriched for variants showing strong signals of positive selection in multiple Afroasiatic-speaking, agriculturalist populations from Ethiopia, and that this signal is unique among sub-Saharan Africans. We also observe strong selection signals at putatively functional variants in nearby lipid metabolism genes, which may influence evolutionary dynamics at the ADH region. Finally, we show that haplotypes carrying these selected variants were introduced into Northeast Africa from a West-Eurasian source within the last ∼2,000 years and experienced positive selection following admixture. These selection signals are not evident in nearby, genetically similar populations that practice hunting/gathering or pastoralist subsistence lifestyles, supporting the hypothesis that the emergence of agriculture shapes patterns of selection at ADH genes. Together, these results enhance our understanding of how adaptations to diverse environments and diets have influenced the African genomic landscape.


Assuntos
Álcool Desidrogenase , Alcoolismo , Acetaldeído , Agricultura , Álcool Desidrogenase/genética , Álcool Desidrogenase/metabolismo , Alcoolismo/genética , Etanol/metabolismo , Etiópia , Humanos , Nucleotídeos , Seleção Genética
19.
HLA ; 100(4): 325-348, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35754199

RESUMO

Leukocyte immunoglobulin (Ig)-like receptors (LILR) LILRB1 and LILRB2 may play a pivotal role in maintaining self-tolerance and modulating the immune response through interaction with classical and nonclassical HLA molecules. Although both diversity and natural selection patterns over HLA genes have been extensively evaluated, little information is available concerning the genetic diversity and selection signatures on the LILRB1/2 regions. Therefore, we identified the LILRB1/2 genetic diversity using next-generation sequencing in a population sample from São Paulo State, Brazil. We identified 58 LILRB1 Single Nucleotide Variants (SNVs), which gave rise to 13 haplotypes, and 41 LILRB2 SNVs arranged into 11 haplotypes. Although we may not exclude as a possible effect of population structure, we found evidence of either positive or purifying selection on LILRB1/2 coding regions. Some residues in both proteins showed to be under the effect of positive selection, suggesting that amino acid replacements in these proteins resulted in beneficial functional changes. Finally, we have revealed that allelic variation (six and five amino acid exchanges in LILRB1 and LILRB2, respectively) affects the structure and/or stability of both molecules. Nonetheless, LILRB2 has shown higher average stability, with no D1/D2 residue affecting protein structure. Overall, our findings demonstrate that LILRB1 and LILRB2 are as polymorphic as HLA class Ib genes and provide strong evidence supporting the directional selection regime hypothesis.


Assuntos
Antígenos CD , Receptor B1 de Leucócitos Semelhante a Imunoglobulina , Glicoproteínas de Membrana , Receptores Imunológicos , Alelos , Aminoácidos , Antígenos CD/genética , Brasil , Variação Genética , Humanos , Receptor B1 de Leucócitos Semelhante a Imunoglobulina/genética , Glicoproteínas de Membrana/genética , Receptores Imunológicos/genética , Receptores Imunológicos/metabolismo
20.
Proc Natl Acad Sci U S A ; 118(42)2021 10 19.
Artigo em Inglês | MEDLINE | ID: mdl-34654747

RESUMO

Hybridization is among the evolutionary mechanisms most frequently hypothesized to drive the success of invasive species, in part because hybrids are common in invasive populations. One explanation for this pattern is that biological invasions coincide with a change in selection pressures that limit hybridization in the native range. To investigate this possibility, we studied the introduction of the brown anole (Anolis sagrei) in the southeastern United States. We find that native populations are highly genetically structured. In contrast, all invasive populations show evidence of hybridization among native-range lineages. Temporal sampling in the invasive range spanning 15 y showed that invasive genetic structure has stabilized, indicating that large-scale contemporary gene flow is limited among invasive populations and that hybrid ancestry is maintained. Additionally, our results are consistent with hybrid persistence in invasive populations resulting from changes in natural selection that occurred during invasion. Specifically, we identify a large-effect X chromosome locus associated with variation in limb length, a well-known adaptive trait in anoles, and show that this locus is often under selection in the native range, but rarely so in the invasive range. Moreover, we find that the effect size of alleles at this locus on limb length is much reduced in hybrids among divergent lineages, consistent with epistatic interactions. Thus, in the native range, epistasis manifested in hybrids can strengthen extrinsic postmating isolation. Together, our findings show how a change in natural selection can contribute to an increase in hybridization in invasive populations.


Assuntos
Lagartos/genética , Seleção Genética , Animais , Variação Genética , Espécies Introduzidas , Hibridização de Ácido Nucleico
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