Latest recommendations
Id | Title | Authors | Abstract | Picture | Thematic fields▼ | Recommender | Reviewers | Submission date | |
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23 Feb 2024
Exploring the effects of ecological parameters on the spatial structure of genetic tree sequencesMariadaria K. Ianni-Ravn, Martin Petr, Fernando Racimo https://doi.org/10.1101/2023.03.27.534388Disentangling the impact of mating and competition on dispersal patternsRecommended by Diego Ortega-Del Vecchyo based on reviews by Anthony Wilder Wohns, Christian Huber and 2 anonymous reviewersSpatial population genetics is a field that studies how different evolutionary processes shape geographical patterns of genetic variation. This field is currently hampered by the lack of a deep understanding of the impact of different evolutionary processes shaping the genetic diversity observed across a continuous space (Bradburd and Ralph 2019). Luckily, the recent development of slendr (Petr et al. 2023), which uses the simulator SLiM (Haller and Messer 2023), provides a powerful tool to perform simulations to analyze the impact of different evolutionary parameters on spatial patterns of genetic variation. Here, Ianni-Ravn, Petr, and Racimo 2023 present a series of well-designed simulations to study how three evolutionary factors (dispersal distance, competition distance, and mate choice distance) shape the geographical structure of genealogies. The authors model the dispersal distance between parents and their offspring using five different distributions. Then, the authors perform simulations and they contrast the correspondence between the distribution of observed parent-offspring distances (called DD in the paper) and the distribution used in the simulations (called DF). The authors observe a reasonable correspondence between DF and DD. The authors then show that the competition distance, which decreases the fitness of individuals due to competition for resources if the individuals are close to each other, has small effects on the differences between DD and DF. In contrast, the mate choice distance (which specifies how far away can a parent go to choose a mate) causes discrepancies between DD and DF. When the mate choice distance is small, the individuals tend to cluster close to each other. Overall, these results show that the observed distances between parents and offspring are dependent on the three parameters inspected (dispersal distance, competition distance, and mate choice distance) and make the case that further ecological knowledge of each of these parameters is important to determine the processes driving the dispersal of individuals across geographical space. Based on these results, the authors argue that an “effective dispersal distance” parameter, which takes into account the impact of mate choice distance and dispersal distance, is more prone to be inferred from genetic data. The authors also assess our ability to estimate the dispersal distance using genealogical data in a scenario where the mating distance has small effects on the dispersal distance. Interestingly, the authors show that accurate estimates of the dispersal distance can be obtained when using information from all the parents and offspring going from the present back to the coalescence of all the individuals to the most recent common ancestor. On the other hand, the estimates of the dispersal distance are underestimated when less information from the parent-offspring relationships is used to estimate the dispersal distance. This paper shows the importance of considering mating patterns and the competition for resources when analyzing the dispersal of individuals. The analysis performed by the authors backs up this claim with carefully designed simulations. I recommend this preprint because it makes a strong case for the consideration of ecological factors when analyzing the structure of genealogies and the dispersal of individuals. Hopefully more studies in the future will continue to use simulations and to develop analytical theory to understand the importance of various ecological processes driving spatial genetic variation changes. Bradburd, Gideon S., and Peter L. Ralph. 2019. “Spatial Population Genetics: It’s About Time.” Annual Review of Ecology, Evolution, and Systematics 50 (1): 427–49. https://doi.org/10.1146/annurev-ecolsys-110316-022659. Haller, Benjamin C., and Philipp W. Messer. 2023. “SLiM 4: Multispecies Eco-Evolutionary Modeling.” The American Naturalist 201 (5): E127–39. https://doi.org/10.1086/723601. Ianni-Ravn, Mariadaria K., Martin Petr, and Fernando Racimo. 2023. “Exploring the Effects of Ecological Parameters on the Spatial Structure of Genealogies.” bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.03.27.534388. Petr, Martin, Benjamin C. Haller, Peter L. Ralph, and Fernando Racimo. 2023. “Slendr: A Framework for Spatio-Temporal Population Genomic Simulations on Geographic Landscapes.” Peer Community Journal 3 (e121). https://doi.org/10.24072/pcjournal.354. | Exploring the effects of ecological parameters on the spatial structure of genetic tree sequences | Mariadaria K. Ianni-Ravn, Martin Petr, Fernando Racimo | <p>Geographic space is a fundamental dimension of evolutionary change, determining how individuals disperse and interact with each other. Consequently, space has an important influence on the structure of genealogies and the distribution of geneti... | Phylogeography & Biogeography, Population Genetics / Genomics | Diego Ortega-Del Vecchyo | 2023-03-31 18:21:02 | View | ||
05 Jun 2018
Pleistocene climate change and the formation of regional species poolsJoaquín Calatayud, Miguel Á. Rodríguez, Rafael Molina-Venegas, María Leo, José Luís Hórreo, Joaquín Hortal https://doi.org/10.1101/149617Recent assembly of European biogeographic species poolRecommended by Fabien Condamine based on reviews by 3 anonymous reviewersBiodiversity is unevenly distributed over time, space and the tree of life [1]. The fact that regions are richer than others as exemplified by the latitudinal diversity gradient has fascinated biologists as early as the first explorers travelled around the world [2]. Provincialism was one of the first general features of land biotic distributions noted by famous nineteenth century biologists like the phytogeographers J.D. Hooker and A. de Candolle, and the zoogeographers P.L. Sclater and A.R. Wallace [3]. When these explorers travelled among different places, they were struck by the differences in their biotas (e.g. [4]). The limited distributions of distinctive endemic forms suggested a history of local origin and constrained dispersal. Much biogeographic research has been devoted to identifying areas where groups of organisms originated and began their initial diversification [3]. Complementary efforts found evidence of both historical barriers that blocked the exchange of organisms between adjacent regions and historical corridors that allowed dispersal between currently isolated regions. The result has been a division of the Earth into a hierarchy of regions reflecting patterns of faunal and floral similarities (e.g. regions, subregions, provinces). Therefore a first ensuing question is: “how regional species pools have been assembled through time and space?”, which can be followed by a second question: “what are the ecological and evolutionary processes leading to differences in species richness among species pools?”. To address these questions, the study of Calatayud et al. [5] developed and performed an interesting approach relying on phylogenetic data to identify regional and sub-regional pools of European beetles (using the iconic ground beetle genus Carabus). Specifically, they analysed the processes responsible for the assembly of species pools, by comparing the effects of dispersal barriers, niche similarities and phylogenetic history. They found that Europe could be divided in seven modules that group zoogeographically distinct regions with their associated faunas, and identified a transition zone matching the limit of the ice sheets at Last Glacial Maximum (19k years ago). Deviance of species co-occurrences across regions, across sub-regions and within each region was significantly explained, primarily by environmental niche similarity, and secondarily by spatial connectivity, except for northern regions. Interestingly, southern species pools are mostly separated by dispersal barriers, whereas northern species pools are mainly sorted by their environmental niches. Another important finding of Calatayud et al. [5] is that most phylogenetic structuration occurred during the Pleistocene, and they show how extreme recent historical events (Quaternary glaciations) can profoundly modify the composition and structure of geographic species pools, as opposed to studies showing the role of deep-time evolutionary processes. The study of biogeographic assembly of species pools using phylogenies has never been more exciting and promising than today. Catalayud et al. [5] brings a nice study on the importance of Pleistocene glaciations along with geographical barriers and niche-based processes in structuring the regional faunas of European beetles. The successful development of powerful analytical tools in recent years, in conjunction with the rapid and massive increase in the availability of biological data (including molecular phylogenies, fossils, georeferrenced occurrences and ecological traits), will allow us to disentangle complex evolutionary histories. Although we still face important limitations in data availability and methodological shortcomings, the last decade has witnessed an improvement of our understanding of how historical and biotic triggers are intertwined on shaping the Earth’s stupendous biological diversity. I hope that the Catalayud et al.’s approach (and analytical framework) will help movement in that direction, and that it will provide interesting perspectives for future investigations of other regions. Applied to a European beetle radiation, they were able to tease apart the relative contributions of biotic (niche-based processes) versus abiotic (geographic barriers and climate change) factors. References [1] Rosenzweig ML. 1995. Species diversity in space and time. Cambridge: Cambridge University Press. | Pleistocene climate change and the formation of regional species pools | Joaquín Calatayud, Miguel Á. Rodríguez, Rafael Molina-Venegas, María Leo, José Luís Hórreo, Joaquín Hortal | <p>Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring... | Phylogeography & Biogeography | Fabien Condamine | 2017-06-14 07:30:32 | View | ||
02 Jan 2019
Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by EricaMichael D. Pirie, Martha Kandziora, Nicolai M. Nuerk, Nicholas C. Le Maitre, Ana Laura Mugrabi de Kuppler, Berit Gehrke, Edward G.H. Oliver, and Dirk U. Bellstedt https://doi.org/10.1101/290791The colonization history of largely isolated habitatsRecommended by Andrea S. Meseguer based on reviews by Simon Joly, Florian Boucher and 2 anonymous reviewersThe build-up of biodiversity is the result of in situ speciation and immigration, with the interplay between geographical distance and ecological suitability determining the probability of an organism to establish in a new area. The relative contribution of these factors have long interested biogeographers, in particular to explain the distribution of organisms adapted to habitats that remained largely isolated, such as the colonization of oceanic islands or land waters. The focus of this study is the formation of the afrotemperate flora; patches of temperate vegetation separated by thousands of kilometers in Africa, with high levels of endemism described in the Cape region, the Drakensberg range and the high mountains of tropical east Africa [1]. The floristic affinities between these centers of endemism have frequently been explored but the origin of many afrotemperate lineages remains enigmatic [2]. References [1] Linder, H.P. 1990. On the relationship between the vegetation and floras of the Afromontane and the Cape regions of Africa. Mitteilungen aus dem Institut für Allgemeine Botanik Hamburg 23b:777–790. | Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica | Michael D. Pirie, Martha Kandziora, Nicolai M. Nuerk, Nicholas C. Le Maitre, Ana Laura Mugrabi de Kuppler, Berit Gehrke, Edward G.H. Oliver, and Dirk U. Bellstedt | <p>The coincidence of long distance dispersal and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors o... | Phylogeography & Biogeography | Andrea S. Meseguer | 2018-04-09 10:10:04 | View | ||
13 Dec 2016
POSTPRINT
Repeated replacements of an intrabacterial symbiont in the tripartite nested mealybug symbiosisHusnik F, McCutcheon JP doi: 10.1073/pnas.1603910113Obligate dependence does not preclude changing partners in a Russian dolls symbiotic systemRecommended by Emmanuelle Jousselin and Fabrice VavreSymbiotic associations with bacterial partners have facilitated important evolutionary transitions in the life histories of eukaryotes. For instance, many insects have established long-term interactions with intracellular bacteria that provide them with essential nutrients lacking in their diet. However, despite the high level of interdependency among organisms involved in endosymbiotic systems, examples of symbiont replacements along the evolutionary history of insect hosts are numerous.
In their paper, Husnik and McCutcheon [1] test the stability of symbiotic systems in a particularly imbricated Russian-doll type interaction, where one bacterium lives insides another bacterium, which itself lives inside insect cells. For their study, they chose representative species of mealybugs (Pseudococcidae), a species rich group of sap-feeding insects that hosts diverse and complex symbiotic systems. In species of the subfamily Pseudococcinae, data published so far suggest that the primary symbiont, a ß-proteobacterium named Tremblaya princeps, is supplemented by a second bacterial symbiont (a ϒ-proteobaterium) that lives within its cytoplasm; both participate to the metabolic pathways that provide essential amino acids and vitamins to their hosts. Here, Husnik and McCutcheon generate host and endosymbiont genome data for five phylogenetically divergent species of Pseudococcinae in order to better understand: 1) the evolutionary history of the symbiotic associations; 2) the metabolic roles of each partner, 3) the timing and origin of Horizontal Gene Transfers (HGT) between the hosts and their symbionts. Reference [1] Husnik F., McCutcheon JP. 2016. Repeated replacements of an intrabacterial symbiont in the tripartite nested mealybug symbiosis. PNAS 113: E5416-E5424. doi: 10.1073/pnas.1603910113 | Repeated replacements of an intrabacterial symbiont in the tripartite nested mealybug symbiosis | Husnik F, McCutcheon JP | Stable endosymbiosis of a bacterium into a host cell promotes cellular and genomic complexity. The mealybug *Planococcus citri* has two bacterial endosymbionts with an unusual nested arrangement: the γ-proteobacterium *Moranella endobia* lives in ... | Phylogenetics / Phylogenomics, Species interactions | Emmanuelle Jousselin | 2016-12-13 14:27:09 | View | ||
29 Sep 2017
Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continentMichael D. Pirie, Paul J. M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou 10.1101/141127Unravelling the history of Neotropical plant diversificationRecommended by Hervé Sauquet based on reviews by Thomas Couvreur and Hervé SauquetSouth American rainforests, particularly the Tropical Andes, have been recognized as the hottest spot of plant biodiversity on Earth, while facing unprecedented threats from human impact [1,2]. Considerable research efforts have recently focused on unravelling the complex geological, bioclimatic, and biogeographic history of the region [3,4]. While many studies have addressed the question of Neotropical plant diversification using parametric methods to reconstruct ancestral areas and patterns of dispersal, Pirie et al. [5] take a distinct, complementary approach. Based on a new, near-complete molecular phylogeny of two Neotropical genera of the flowering plant family Annonaceae, the authors modelled the ecological niche of each species and reconstructed the history of niche differentiation across the region. The main conclusion is that, despite similar current distributions and close phylogenetic distance, the two genera experienced rather distinct processes of diversification, responding differently to the major geological events marking the history of the region in the last 20 million years (Andean uplift, drainage of Lake Pebas, and closure of the Panama Isthmus). As a researcher who has not personally worked on Neotropical biogeography, I found this paper captivating and especially enjoyed very much reading the Introduction, which sets out the questions very clearly. The strength of this paper is the near-complete diversity of species the authors were able to sample in each clade and the high-quality data compiled for the niche models. I would recommend this paper as a nice example of a phylogenetic study aimed at unravelling the detailed history of Neotropical plant diversification. While large, synthetic meta-analyses of many clades should continue to seek general patterns [4,6], careful studies restricted on smaller, but well controlled and sampled datasets such as this one are essential to really understand tropical plant diversification in all its complexity. References [1] Antonelli A, and Sanmartín I. 2011. Why are there so many plant species in the Neotropics? Taxon 60, 403–414. [2] Mittermeier RA, Robles-Gil P, Hoffmann M, Pilgrim JD, Brooks TB, Mittermeier CG, Lamoreux JL and Fonseca GAB. 2004. Hotspots revisited: Earths biologically richest and most endangered ecoregions. CEMEX, Mexico City, Mexico 390pp [3] Antonelli A, Nylander JAA, Persson C and Sanmartín I. 2009. Tracing the impact of the Andean uplift on Neotropical plant evolution. Proceedings of the National Academy of Science of the USA 106, 9749–9754. doi: 10.1073/pnas.0811421106 [4] Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, Sanmartín I, Sanchez-Meseguer A, Anderson CL, Figueiredo JP, Jaramillo C, Riff D, Negri FR, Hooghiemstra H, Lundberg J, Stadler T, Särkinen T and Antonelli A. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330, 927–931. doi: 10.1126/science.1194585 [5] Pirie MD, Maas PJM, Wilschut R, Melchers-Sharrott H and Chatrou L. 2017. Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent. bioRxiv, 141127, ver. 3 of 28th Sept 2017. doi: 10.1101/141127 [6] Bacon CD, Silvestro D, Jaramillo C, Tilston Smith B, Chakrabartye P and Antonelli A. 2015. Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proceedings of the National Academy of Science of the USA 112, 6110–6115. doi: 10.1073/pnas.1423853112 | Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent | Michael D. Pirie, Paul J. M. Maas, Rutger A. Wilschut, Heleen Melchers-Sharrott & Lars W. Chatrou | Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Peba... | Phylogenetics / Phylogenomics, Phylogeography & Biogeography | Hervé Sauquet | Hervé Sauquet, Thomas Couvreur | 2017-06-03 21:25:48 | View | |
09 Feb 2018
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreakSimon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey https://doi.org/10.1101/163691Simulating the effect of public health interventions using dated virus sequences and geographical dataRecommended by Samuel Alizon based on reviews by Christian Althaus, Chris Wymant and 1 anonymous reviewerPerhaps because of its deadliness, the 2013-2016 Ebola Virus (EBOV) epidemics in West-Africa has led to unprecedented publication and sharing of full virus genome sequences. This was both rapid (90 full genomes were shared within weeks [1]) and important (more than 1500 full genomes have been released overall [2]). Furthermore, the availability of the metadata (especially GPS location) has led to depth analyses of the geographical spread of the epidemics [3]. References [1] Gire et al. 2014. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345: 1369–1372. doi: 10.1126/science.1259657. | Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak | Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey | <p>This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100046). The recent Ebola virus (EBOV) outbreak in West Africa witnessed considerable efforts to obtain viral genom... | Phylogenetics / Phylogenomics, Phylogeography & Biogeography | Samuel Alizon | 2017-09-30 13:49:57 | View | ||
18 Jan 2021
Trait plasticity and covariance along a continuous soil moisture gradientJ Grey Monroe, Haoran Cai, David L Des Marais https://doi.org/10.1101/2020.02.17.952853Another step towards grasping the complexity of the environmental response of traitsRecommended by Benoit Pujol based on reviews by 2 anonymous reviewersOne can only hope that one day, we will be able to evaluate how the ecological complexity surrounding natural populations affects their ability to adapt. This is more like a long term quest than a simple scientific aim. Many steps are heading in the right direction. This paper by Monroe and colleagues (2021) is one of them. References Gienapp P. & J.E. Brommer. 2014. Evolutionary dynamics in response to climate change. In: Charmentier A, Garant D, Kruuk LEB, editors. Quantitative genetics in the wild. Oxford: Oxford University Press, Oxford. pp. 254–273. doi: https://doi.org/10.1093/acprof:oso/9780199674237.003.0015 | Trait plasticity and covariance along a continuous soil moisture gradient | J Grey Monroe, Haoran Cai, David L Des Marais | <p>Water availability is perhaps the greatest environmental determinant of plant yield and fitness. However, our understanding of plant-water relations is limited because it is primarily informed by experiments considering soil moisture variabilit... | Phenotypic Plasticity | Benoit Pujol | 2020-02-20 16:34:40 | View | ||
11 Jun 2019
A bird’s white-eye view on neosex chromosome evolutionThibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Sèverine Bérard, Laura Csukonyi, Maëva Gabrielli, Céline Scornavacca, Borja Milá, Christophe Thébaud, Benoit Nabholz https://doi.org/10.1101/505610Young sex chromosomes discovered in white-eye birdsRecommended by Kateryna Makova based on reviews by Gabriel Marais, Melissa Wilson and 1 anonymous reviewerRecent advances in next-generation sequencing are allowing us to uncover the evolution of sex chromosomes in non-model organisms. This study [1] represents an example of this application to birds of two Sylvioidea species from the genus Zosterops (commonly known as white-eyes). The study is exemplary in the amount and types of data generated and in the thoroughness of the analysis applied. Both male and female genomes were sequenced to allow the authors to identify sex-chromosome specific scaffolds. These data were augmented by generating the transcriptome (RNA-seq) data set. The findings after the analysis of these extensive data are intriguing: neoZ and neoW chromosome scaffolds and their breakpoints were identified. Novel sex chromosome formation appears to be accompanied by translocation events. The timing of formation of novel sex chromosomes was identified using molecular dating and appears to be relatively recent. Yet first signatures of distinct evolutionary patterns of sex chromosomes vs. autosomes could be already identified. These include the accumulation of transposable elements and changes in GC content. The changes in GC content could be explained by biased gene conversion and altered recombination landscape of the neo sex chromosomes. The authors also study divergence and diversity of genes located on the neo sex chromosomes. Here their findings appear to be surprising and need further exploration. The neoW chromosome already shows unique patterns of divergence and diversity at protein-coding genes as compared with genes on either neoZ or autosomes. In contrast, the genes on the neoZ chromosome do not display divergence or diversity patterns different from those for autosomes. This last observation is puzzling and I believe should be explored in further studies. Overall, this study significantly advances our knowledge of the early stages of sex chromosome evolution in vertebrates, provides an example of how such a study could be conducted in other non-model organisms, and provides several avenues for future work. References [1] Leroy T., Anselmetti A., Tilak M.K., Bérard S., Csukonyi L., Gabrielli M., Scornavacca C., Milá B., Thébaud C. and Nabholz B. (2019). A bird’s white-eye view on neo-sex chromosome evolution. bioRxiv, 505610, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/505610 | A bird’s white-eye view on neosex chromosome evolution | Thibault Leroy, Yoann Anselmetti, Marie-Ka Tilak, Sèverine Bérard, Laura Csukonyi, Maëva Gabrielli, Céline Scornavacca, Borja Milá, Christophe Thébaud, Benoit Nabholz | <p>Chromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a p... | Molecular Evolution, Population Genetics / Genomics | Kateryna Makova | 2019-01-24 14:17:15 | View | ||
27 Jul 2020
Evolution of the DAN gene family in vertebratesJuan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott V. Edwards https://doi.org/10.1101/794404An evolutionary view of a biomedically important gene familyRecommended by Kateryna Makova based on reviews by 2 anonymous reviewersThis manuscript [1] investigates the evolutionary history of the DAN gene family—a group of genes important for embryonic development of limbs, kidneys, and left-right axis speciation. This gene family has also been implicated in a number of diseases, including cancer and nephropathies. DAN genes have been associated with the inhibition of the bone morphogenetic protein (BMP) signaling pathway. Despite this detailed biochemical and functional knowledge and clear importance for development and disease, evolution of this gene family has remained understudied. The diversification of this gene family was investigated in all major groups of vertebrates. The monophyly of the gene members belonging to this gene family was confirmed. A total of five clades were delineated, and two novel lineages were discovered. The first lineage was only retained in cephalochordates (amphioxus), whereas the second one (GREM3) was retained by cartilaginous fish, holostean fish, and coelanth. Moreover, the patterns of chromosomal synteny in the chromosomal regions harboring DAN genes were investigated. Additionally, the authors reconstructed the ancestral gene repertoires and studied the differential retention/loss of individual gene members across the phylogeny. They concluded that the ancestor of gnathostome vertebrates possessed eight DAN genes that underwent differential retention during the evolutionary history of this group. During radiation of vertebrates, GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major vertebrate groups. At the same time, GREM3, CER1, and DAND5 were differentially lost in some vertebrate lineages. At least two DAN genes were present in the common ancestor of vertebrates, and at least three DAN genes were present in the common ancestor of chordates. Therefore the patterns of retention and diversification in this gene family appear to be complex. Evolutionary slowdown for the DAN gene family was observed in mammals, suggesting selective constraints. Overall, this article puts the biomedical importance of the DAN family in the evolutionary perspective. References [1] Opazo JC, Hoffmann FG, Zavala K, Edwards SV (2020) Evolution of the DAN gene family in vertebrates. bioRxiv, 794404, ver. 3 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/794404 | Evolution of the DAN gene family in vertebrates | Juan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott V. Edwards | <p>The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogene... | Molecular Evolution | Kateryna Makova | 2019-10-15 16:43:13 | View | ||
29 Sep 2022
How many sirtuin genes are out there? evolution of sirtuin genes in vertebrates with a description of a new family memberJuan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Meléndez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia V. Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones https://doi.org/10.1101/2020.07.17.209510Making sense of vertebrate sirtuin genesRecommended by Frédéric Delsuc based on reviews by Filipe Castro, Nicolas Leurs and 1 anonymous reviewerSirtuin proteins are class III histone deacetylases that are involved in a variety of fundamental biological functions mostly related to aging. These proteins are located in different subcellular compartments and are associated with different biological functions such as metabolic regulation, stress response, and cell cycle control [1]. In mammals, the sirtuin gene family is composed of seven paralogs (SIRT1-7) grouped into four classes [2]. Due to their involvement in maintaining cell cycle integrity, sirtuins have been studied as a way to understand fundamental mechanisms governing longevity [1]. Indeed, the downregulation of sirtuin genes with aging seems to explain much of the pathophysiology that accumulates with aging [3]. Biomedical studies have thus explored the potential therapeutic implications of sirtuins [4] but whether they can effectively be used as molecular targets for the treatment of human diseases remains to be demonstrated [1]. Despite this biomedical interest and some phylogenetic analyses of sirtuin paralogs mostly conducted in mammals, a comprehensive evolutionary analysis of the sirtuin gene family at the scale of vertebrates was still lacking. In this preprint, Opazo and collaborators [5] took advantage of the increasing availability of whole-genome sequences for species representing all main groups of vertebrates to unravel the evolution of the sirtuin gene family. To do so, they undertook a phylogenomic approach in its original sense aimed at improving functional predictions by evolutionary analysis [6] in order to inventory the full vertebrate sirtuin gene repertoire and reconstruct its precise duplication history. Harvesting genomic databases, they extracted all predicted sirtuin proteins and performed phylogenetic analyses based on probabilistic inference methods. Maximum likelihood and Bayesian analyses resulted in well-resolved and congruent phylogenetic trees dividing vertebrate sirtuin genes into three major clades. These analyses also revealed an additional eighth paralog that was previously overlooked because of its restricted phyletic distribution. This newly identified sirtuin family member (named SIRT8) was recovered with unambiguous statistical support as a sister-group to the SIRT3 clade. Comparative genomic analyses based on conserved gene synteny confirmed that SIRT8 was present in all sampled non-amniote vertebrate genomes (cartilaginous fish, bony fish, coelacanth, lungfish, and amphibians) except cyclostomes. SIRT8 has thus most likely been lost in the last common ancestor of amniotes (mammals, reptiles, and birds). Discovery of such previously unknown genes in vertebrates is not completely surprising given the plethora of high-quality genomes now available. However, this study highlights the importance of considering a broad taxonomic sampling to infer evolutionary patterns of gene families that have been mostly studied in mammals because of their potential importance for human biology. Based on its phylogenetic position as closely related to SIRT3 within class I, it could be predicted that the newly identified SIRT8 paralog likely has a deacetylase activity and is probably located in mitochondria. To test these evolutionary predictions, Opazo and collaborators [5] conducted further bioinformatics analyses and functional experiments using the elephant shark (Callorhinchus milii) as a model species. RNAseq expression data were analyzed to determine tissue-specific transcription of sirtuin genes in vertebrates, including SIRT8 found to be mainly expressed in the ovary, which suggests a potential role in biological processes associated with reproduction. The elephant shark SIRT8 protein sequence was used with other vertebrates for comparative analyses of protein structure modeling and subcellular localization prediction both pointing to a probable mitochondrial localization. The protein localization and its function were further characterized by immunolocalization in transfected cells, and enzymatic and functional assays, which all confirmed the prediction that SIRT8 proteins are targeted to the mitochondria and have deacetylase activity. The extensive experimental efforts made in this study to shed light on the function of this newly discovered gene are both rare and highly commendable. Overall, this work by Opazo and collaborators [5] provides a comprehensive phylogenomic study of the sirtuin gene family in vertebrates based on detailed evolutionary analyses using state-of-the-art phylogenetic reconstruction methods. It also illustrates the power of adopting an integrative comparative approach supplementing the reconstruction of the duplication history of the gene family with complementary functional experiments in order to elucidate the function of the newly discovered SIRT8 family member. These results provide a reference phylogenetic framework for the evolution of sirtuin genes and the further functional characterization of the eight vertebrate paralogs with potential relevance for understanding the cellular biology of aging and its associated diseases in human. References [1] Vassilopoulos A, Fritz KS, Petersen DR, Gius D (2011) The human sirtuin family: Evolutionary divergences and functions. Human Genomics, 5, 485. https://doi.org/10.1186/1479-7364-5-5-485 [2] Yamamoto H, Schoonjans K, Auwerx J (2007) Sirtuin Functions in Health and Disease. Molecular Endocrinology, 21, 1745–1755. https://doi.org/10.1210/me.2007-0079 [3] Morris BJ (2013) Seven sirtuins for seven deadly diseases ofaging. Free Radical Biology and Medicine, 56, 133–171. https://doi.org/10.1016/j.freeradbiomed.2012.10.525 [4] Bordo D Structure and Evolution of Human Sirtuins. Current Drug Targets, 14, 662–665. http://dx.doi.org/10.2174/1389450111314060007 [5] Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA (2022) How many sirtuin genes are out there? evolution of sirtuin genes in vertebrates with a description of a new family member. bioRxiv, 2020.07.17.209510, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.07.17.209510 [6] Eisen JA (1998) Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Research, 8, 163–167. https://doi.org/10.1101/gr.8.3.163 | How many sirtuin genes are out there? evolution of sirtuin genes in vertebrates with a description of a new family member | Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Meléndez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia V. Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones | <p style="text-align: justify;">Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disent... | Molecular Evolution | Frédéric Delsuc | Filipe Castro, Anonymous, Nicolas Leurs | 2022-05-12 16:06:04 | View |
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