Search

The adaptive value of the Drosophila subobscura chromosomal inversion polymorphism with regard to environmental effects is well-known. However, the specific details of the inversion adaptations to the global warming scenario deserve to be analyzed. Toward this aim, polymorphism and karyotypes were studied in 574 individuals from Petnica (Serbia) in annual samples taken in June for the period 2019-2022. Comparing the results of Petnica (Cfa: humid subtropical climate) with those from Avala (Serbia: Cfb, temperate oceanic climate) and Font Groga (Barcelona, Spain; Csa: hot-summer Mediterranean climate), significant differences were observed for their chromosomal polymorphism. In Petnica, inversions from U and E chromosomes mainly reacted significantly with regard to temperature, humidity, and rainfall. Moreover, the inversion polymorphism from Petnica (2019-2022) was compared with that from 1995. In this period, a significant increase in mean and maximum temperature was observed. However, to properly explain the observed variations of inversions over time, it was necessary to carefully analyze annual seasonal changes and particular heat wave episodes. Interestingly, yearly fluctuations of U chromosome 'warm'-adapted inversions corresponded with opposite changes in 'non-thermal' inversions. Perhaps these types of inversions were not correctly defined with regard to thermal adaptation, or these fluctuations were also due to adaptations to other physical and/or biological variables. Finally, a joint study of chromosomal inversion polymorphism from many Balkan populations of D. subobscura indicated that different climatic regions presented distinct composition, including thermal-adapted inversions.

Evolutionary processes, including selection, can be indirectly inferred based on patterns of genomic variation among contemporary populations or species. However, this often requires unrealistic assumptions of ancestral demography and selective regimes. Sequencing ancient DNA from temporally spaced samples can inform about past selection processes, as time series data allow direct quantification of population parameters collected before, during, and after genetic changes driven by selection. In this Comment and Opinion, we advocate for the inclusion of temporal sampling and the generation of paleogenomic datasets in evolutionary biology, and highlight some of the recent advances that have yet to be broadly applied by evolutionary biologists. In doing so, we consider the expected signatures of balancing, purifying, and positive selection in time series data, and detail how this can advance our understanding of the chronology and tempo of genomic change driven by selection. However, we also recognize the limitations of such data, which can suffer from postmortem damage, fragmentation, low coverage, and typically low sample size. We therefore highlight the many assumptions and considerations associated with analyzing paleogenomic data and the assumptions associated with analytical methods. This work resulted from a synthesis and writing retreat as part of ADAPT (Ancient DNA studies of Adaptive Processes through Time) Special Topic Network generously funded by the European Society for Evolutionary Biology (ESEB). ADF was supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie grant agreement No. 663830. ASM was supported by a European Research Council (ERC) grant. LD and MD acknowledge fudning from the Swedish Research Coucil (VR grant 2017‐04647)

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase-separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can influence cell-to-cell variation in free protein abundance between individuals of a cell population (i.e., gene expression noise). This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase-separated assemblies and may influence cell fitness. This work was supported by the Medical Research Council (MC_U105185859; M.M.B., M.T., C.R., and N.S.G.), Marie Curie Actions (FP7-PEOPLE-2012- IEF-330352, to M.T.; and FP7-PEOPLE-2011-IEF299105, to N.S.G.), FEBS LongTerm Fellowships (N.S.G.), Beatriu de Pinos fellowships (M.T.), and the Ministerio de Economía y Competitividad (SAF2017-82158-R, SAF2015-72518-EXP, and RYC-2012-09999; M.T.). N.S.G. is a recipient of the MRC Centenary Award. M.M.B. is a Lister Institute Research Prize Fellow. We thank Gian Gaetano for supporting N.S.G. and Sean Munro for the gift of strain Y03157

It contains associated material.-- The 1000 Genomes Project Consortium, [Background] Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes., [Results] We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively., [Conclusions] We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research. © 2014 Colonna et al., This work was supported by The Wellcome Trust (098051), an Italian National Research Council (CNR) short-term mobility fellowship from the 2013 program to VC, and an EMBO Short Term Fellowship ASTF 324–2010 to VC.

A standard approach to model how selection shapes phenotypic traits is the analysis of capture–recapture data relating trait variation to survival. Divergent selection, however, has never been analyzed by the capture–recapture approach. Most reported examples of differences between urban and nonurban animals reflect behavioral plasticity rather than divergent selection. The aim of this paper was to use a capture–recapture approach to test the hypothesis that divergent selection can also drive local adaptation in urban habitats. We focused on the size of the black breast stripe (i.e., tie width) of the great tit (Parus major), a sexual ornament used in mate choice. Urban great tits display smaller tie sizes than forest birds. Because tie size is mostly genetically determined, it could potentially respond to selection. We analyzed capture/recapture data of male great tits in Barcelona city (N = 171) and in a nearby (7 km) forest (N = 324) from 1992 to 2008 using MARK. When modelling recapture rate, we found it to be strongly influenced by tie width, so that both for urban and forest habitats, birds with smaller ties were more trap-shy and more cautious than their larger tied counterparts. When modelling survival, we found that survival prospects in forest great tits increased the larger their tie width (i.e., directional positive selection), but the reverse was found for urban birds, with individuals displaying smaller ties showing higher survival (i.e., directional negative selection). As melanin-based tie size seems to be related to personality, and both are heritable, results may be explained by cautious personalities being favored in urban environments. More importantly, our results show that divergent selection can be an important mechanism in local adaptation to urban habitats and that capture–recapture is a powerful tool to test it.

T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) contains the canonical phosphoprotein phosphatase 1 (PPP1) binding motif, composed by the amino acid sequence RVSF. We identified and validated the binding of TCTEX1D4 to PPP1 and demonstrated that indeed this protein is a novel PPP1 interacting protein. Analyses of twenty-one mammalian species available in public databases and seven Lagomorpha sequences obtained in this work showed that the PPP1 binding motif 90RVSF93 is present in all of them and is flanked by a palindromic sequence, PLGS, except in three species of pikas (Ochotona princeps, O. dauurica and O. pusilla). Furthermore, for the Ochotona species an extra glycosylation site, motif 96NLS98, and the loss of the palindromic sequence were observed. Comparison with other lagomorphs suggests that this event happened before the Ochotona radiation. The dN/dS for the sequence region comprising the PPP1 binding motif and the flanking palindrome highly supports the hypothesis that for Ochotona species this region has been evolving under positive selection. In addition, mutational screening shows that the ability of pikas TCTEX1D4 to bind to PPP1 is maintained, although the PPP1 binding motif is disrupted, and the N- and C-terminal surrounding residues are also abrogated. These observations suggest pika as an ideal model to study novel PPP1 complexes regulatory mechanisms. published

Antisocial and criminal behaviors are multifactorial traits whose interpretation relies on multiple disciplines. Since these interpretations may have social, moral and legal implications, a constant review of the evidence is necessary before any scientific claim is considered as truth. A recent study proposed that men with wider faces relative to facial height (fWHR) are more likely to develop unethical behaviour mediated by a psychological sense of power. This research was based on reports suggesting that sexual dimorphism and selection would be responsible for a correlation between fWHR and aggression. Here we show that 4,960 individuals from 94 modern human populations belonging to a vast array of genetic and cultural contexts do not display significant amounts of fWHR sexual dimorphism. Further analyses using populations with associated ethnographical records as well as samples of male prisoners of the Mexico City Federal Penitentiary condemned by crimes of variable level of inter-personal aggression (homicide, robbery, and minor faults) did not show significant evidence, suggesting that populations/individuals with higher levels of bellicosity, aggressive behaviour, or power-mediated behaviour display greater fWHR. Finally, a regression analysis of fWHR on individual's fitness showed no significant correlation between this facial trait and reproductive success. Overall, our results suggest that facial attributes are poor predictors of aggressive behaviour, or at least, that sexual selection was weak enough to leave a signal on patterns of between- and within-sex and population facial variation., Facultad de Ciencias Naturales y Museo

Identification of signatures of positive selection has long been a major issue for understanding the unique features of any given species. However, only a fraction of human genes have been interrogated. Genes within segmental duplications are usually omitted due to the limitations of draft genome assemblies and the methodological reliance on accurate gene trees. In this work, we show the feasibility of a new method that does not need accurate gene trees or individual high-quality assemblies. We applied the concept to study exon evolution in the human genome, identifying 74 exons with evidence for rapid coding sequence evolution during human and Old World monkey evolution. Our results suggest abundant accelerated coding sequence evolution within duplicated regions of the genome and provide a more comprehensive view of the role of selection on the human genome., La identificación de señales debidas a la acción de la selección positiva es de gran relevancia para desvelar características únicas de las especies. A pesar de ello, solo una fracción de genes humanos han sido analizados. Los genes incluidos en duplicaciones segmentarias son normalmente ignorados debido a limitaciones impuestas por la naturaleza preliminar de los genomas distintos al humano, así como por la dependencia en adecuados árboles filogenéticos. En este proyecto, demostramos la viabilidad de un nuevo método que no necesita árboles filogenéticos correctos ni ensamblajes de genomas de alta calidad. Hemos aplicado el concepto al genoma humano y hemos identificado 74 exones que muestran evidencia de haber evolucionado más rápidamente desde la separación de los humanos y los monos del viejo mundo. Nuestros resultados sugieren que ha habido abundante evolución acelerada dentro de las regiones duplicadas y ofrece una visión más esclarecedora del rol de la selección en la evolución del genoma humano.

Natural selection has played an important role in shaping human genetic variation, thus, finding variants that have been targeted by positive selection can provide insights about which genes influence human phenotypic variability. In this work we conduct a genome-wide survey of protein-coding genes comparing humans, chimpanzees, and closely related species in order to detect the fraction of genes undergoing positive selection on the human lineage, and further investigate intraspecific variation in a subset of candidate genes in the search of recent selective events in worldwide human populations. Our results suggest that most of the genes implicated in selective events during early human evolution differ from those involved in recent human adaptations, implying distinct selective pressures during varying stages of human evolutionary history. We also found three genome regions with evidence of recent positive selection, which were dissected to propose targets of selection and discuss on the possible underlying selective pressures in each case., La selección natural ha moldeado de forma importante la variación genética humana, por lo que encontrar variantes que hayan sido seleccionadas positivamente puede dar indicios acerca de los genes que determinan la diversidad fenotípica humana. En este trabajo comparamos los genes del genoma humano, del chimpancé y de varias especies cercanamente emparentadas para detectar aquellos genes bajo selección positiva en el linaje humano, y posteriormente evaluar la variación intraespecífica en un subconjunto de genes con la intención de buscar eventos de selección reciente en poblaciones humanas de todo el mundo. Nuestros resultados sugieren que la mayoría de genes implicados en eventos selectivos durante la evolución temprana del hombre no son los mismos que aquellos involucrados en adaptaciones humanas recientes, lo que implica la existencia de diferentes presiones selectivas a lo largo de las distintas etapas de la historia evolutiva humana. También encontramos tres regiones genómicas con evidencias de selección positiva reciente, las cuales fueron analizadas en profundidad para proponer posibles dianas de selección y discutir las presiones selectivas subyacentes en cada caso.

El treball presentat en aquesta tesi és un estudi de la diversitat genètica en un conjunt de gens implicats en funcions neurològiques ("Gens cerebrals"). Hom ha examinat vint-i-dos gens implicats en els sistemes de neurotransmissió dopaminèrgic, serotoninèrgic i glutamatèrgic. L'objectiu de l'estudi té dos vessants: per una banda l'anàlisi de la diversitat genètica en un conjunt de gens implicats en malaltia humana, en aquest cas en malaltia psiquiàtrica, en poblacions humanes mundials, amb la intenció d'assentar les bases per propers esforços de mapatge genètic; i per altra banda analitzar la diversitat genètica en aquest conjunt de gens per tal de descobrir evidències d'esdeveniments històrics, incloent possibles evidències de selecció., The work presented in this thesis is a study of the genetic variation in a set of genes related to neurological function ('Brain genes'). Twenty two genes are examined, all of which are involved in either the Dopaminergic, Serotonergic or the Glutamatergic systems of neurotransmission.The objective of the study has two aspects: on the one hand the analysis of genetic variation in a set of genes which are implicated in human disease, in this case psychiatric disease, across global human populations, towards the end of providing some new insight for gene mapping efforts, and on the other hand the study of genetic variation in this set of genes may reveal traces of the population history events undergone, including possible evidence for selection.