|Id||Title||Authors||Abstract||Picture||Thematic fields||Recommender||Reviewers▲||Submission date|
31 Mar 2022
Gene network robustness as a multivariate characterArnaud Le Rouzic https://arxiv.org/abs/2101.01564
Genetic and environmental robustness are distinct yet correlated evolvable traits in a gene networkRecommended by Frédéric Guillaume based on reviews by Diogo Melo, Charles Mullon and Charles Rocabert
Organisms often show robustness to genetic or environmental perturbations. Whether these two components of robustness can evolve separately is the focus of the paper by Le Rouzic . Using theoretical analysis and individual-based computer simulations of a gene regulatory network model, he shows that multiple aspects of robustness can be investigated as a set of pleiotropically linked quantitative traits. While genetically correlated, various robustness components (e.g., mutational, developmental, homeostasis) of gene expression in the regulatory network evolved more or less independently from each other under directional selection. The quantitative approach of Le Rouzic could explain both how unselected robustness components can respond to selection on other components and why various robustness-related features seem to have their own evolutionary history. Moreover, he shows that all components were evolvable, but not all to the same extent. Robustness to environmental disturbances and gene expression stability showed the largest responses while increased robustness to genetic disturbances was slower. Interestingly, all components were positively correlated and remained so after selection for increased or decreased robustness.
This study is an important contribution to the discussion of the evolution of robustness in biological systems. While it has long been recognized that organisms possess the ability to buffer genetic and environmental perturbations to maintain homeostasis (e.g., canalization ), the genetic basis and evolutionary routes to robustness and canalization are still not well understood. Models of regulatory gene networks have often been used to address aspects of robustness evolution (e.g., ). Le Rouzic  used a gene regulatory network model derived from Wagner’s model . The model has as end product the expression level of a set of genes influenced by a set of regulatory elements (e.g., transcription factors). The level and stability of expression are a property of the regulatory interactions in the network.
Le Rouzic made an important contribution to the study of such gene regulation models by using a quantitative genetics approach to the evolution of robustness. He crafted a way to assess the mutational variability and selection response of the components of robustness he was interested in. Le Rouzic’s approach opens avenues to investigate further aspects of gene network evolutionary properties, for instance to understand the evolution of phenotypic plasticity.
Le Rouzic also discusses ways to measure his different robustness components in empirical studies. As the model is about gene expression levels at a set of protein-coding genes influenced by a set of regulatory elements, it naturally points to the possibility of using RNA sequencing to measure the variation of gene expression in know gene networks and assess their robustness. Robustness could then be studied as a multidimensional quantitative trait in an experimental setting.
 Le Rouzic, A (2022) Gene network robustness as a multivariate character. arXiv: 2101.01564, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://arxiv.org/abs/2101.01564
 Waddington CH (1942) Canalization of Development and the Inheritance of Acquired Characters. Nature, 150, 563–565. https://doi.org/10.1038/150563a0
 Draghi J, Whitlock M (2015) Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks. Evolution, 69, 2345–2358. https://doi.org/10.1111/evo.12732
 Wagner A (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proceedings of the National Academy of Sciences, 91, 4387–4391. https://doi.org/10.1073/pnas.91.10.4387
|Gene network robustness as a multivariate character||Arnaud Le Rouzic||<p style="text-align: justify;">Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic ar...||Bioinformatics & Computational Biology, Evolutionary Theory, Genotype-Phenotype, Quantitative Genetics||Frédéric Guillaume||Charles Mullon, Charles Rocabert, Diogo Melo||2021-01-11 17:48:20||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/10.1101/2020.07.17.209510
Making sense of vertebrate sirtuin genesRecommended by Frédéric Delsuc based on reviews by Filipe Castro, Nicolas Leurs and 1 anonymous reviewer
Sirtuin 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 . In mammals, the sirtuin gene family is composed of seven paralogs (SIRT1-7) grouped into four classes . Due to their involvement in maintaining cell cycle integrity, sirtuins have been studied as a way to understand fundamental mechanisms governing longevity . Indeed, the downregulation of sirtuin genes with aging seems to explain much of the pathophysiology that accumulates with aging . Biomedical studies have thus explored the potential therapeutic implications of sirtuins  but whether they can effectively be used as molecular targets for the treatment of human diseases remains to be demonstrated . 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  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  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  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  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.
 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
 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
 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
 Bordo D Structure and Evolution of Human Sirtuins. Current Drug Targets, 14, 662–665. http://dx.doi.org/10.2174/1389450111314060007
 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
 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|
30 Jun 2023
How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonalityChristoph Stritt, Sebastien Gagneux https://doi.org/10.32942/X2GW2P
How the tubercle bacillus got its genome: modernising, modelling, and making sense of the stories we tellRecommended by B. Jesse Shapiro based on reviews by 2 anonymous reviewers
In this instructive review, Stritt and Gagneux offer a balanced perspective on the evolutionary forces shaping Mycobacterium tuberculosis and make the case that our instinct for storytelling be balanced with quantitative models. M. tuberculosis is perhaps the best-known clonal bacterial pathogen – evolving largely in the absence of horizontal gene transfer. Its genome is full of puzzling patterns, including much higher GC content than most intracellular pathogens (which suggests efficient selection to resist AT-skewed mutational bias) but a very high ratio of nonsynonymous to synonymous substitution rates (dN/dS ~ 0.5, typically interpreted as weak selection against deleterious amino acid changes).
The authors offer alternative explanations for these patterns, framing the question: is M. tuberculosis evolution shaped mainly by drift or by efficient selection? They propose that this question can only be answered by accounting for the pathogen’s extreme clonality. A clonal lifestyle can have its advantages, for example when adaptations must arise in a particular order (Kondrashov and Kondrashov 2001). An important disadvantage highlighted by the authors are linkage effects: without recombination to shuffle them up, beneficial mutations are linked to deleterious mutations in the same genome (hitchhiking) and purging deleterious mutations also purges neutral diversity across the genome (background selection). The authors propose the latter – efficient purifying selection and strong linkage – as an explanation for the low genetic diversity observed in M. tuberculosis. This is of course not exclusive of other related explanations, such as clonal interference (Gerrish and Lenski 1998). They also champion the use of forward evolutionary simulations (Haller and Messer 2019) to model the interplay between selection, recombination, and demography as a powerful alternative to traditional backward coalescent models.
At times, Stritt and Gagneux are pessimistic about our existing methods – arguing that dN/dS and homoplasies “tell us little about the frequency and strength of selection.” Even though I favour a more optimistic view, I fully agree that our traditional population genetic metrics are sensitive to a slew of different deviations from a standard neutral evolution model and must be interpreted with caution. As I and others have argued, the extent of recombination (measured as the amount of linkage in a genome) is a key factor in determining how best to test for natural selection (Shapiro et al. 2009) and to conduct genotype-phenotype association studies (Chen and Shapiro 2021) in microbes. While this article is focused on the well-studied M. tuberculosis complex, there are many parallels with other clonal bacteria, including pathogens and symbionts. Whatever your favourite bug, we must all be careful to make sure the stories we tell about them are not “just so tales” but are supported, to the extent possible, by data and quantitative models.
Chen, Peter E., and B. Jesse Shapiro. 2021. "Classic Genome-Wide Association Methods Are Unlikely to Identify Causal Variants in Strongly Clonal Microbial Populations." bioRxiv.
Stritt, C., Gagneux, S. (2023). How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality. EcoEvoRxiv, ver.3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.32942/X2GW2P
|How do monomorphic bacteria evolve? The *Mycobacterium tuberculosis* complex and the awkward population genetics of extreme clonality||Christoph Stritt, Sebastien Gagneux||<p style="text-align: justify;">Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by <em>de novo</em> mutation are a group o...||Evolutionary Dynamics, Genome Evolution, Molecular Evolution, Population Genetics / Genomics, Reproduction and Sex||B. Jesse Shapiro||Gonçalo Themudo||2022-12-16 13:41:53||View|
23 Jan 2020
A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model systemGillingham, Mark A. F., Montero, B. Karina, Wilhelm, Kerstin, Grudzus, Kara, Sommer, Simone and Santos, Pablo S. C. https://doi.org/10.1101/638288
Improving the reliability of genotyping of multigene families in non-model organismsRecommended by François Rousset based on reviews by Sebastian Ernesto Ramos-Onsins, Helena Westerdahl and Thomas Bigot
The reliability of published scientific papers has been the topic of much recent discussion, notably in the biomedical sciences . Although small sample size is regularly pointed as one of the culprits, big data can also be a concern. The advent of high-throughput sequencing, and the processing of sequence data by opaque bioinformatics workflows, mean that sequences with often high error rates are produced, and that exact but slow analyses are not feasible.
 Ioannidis, J. P. A, Greenland, S., Hlatky, M. A., Khoury, M. J., Macleod, M. R., Moher, D., Schulz, K. F. and Tibshirani, R. (2014) Increasing value and reducing waste in research design, conduct, and analysis. The Lancet, 383, 166-175. doi: 10.1016/S0140-6736(13)62227-8
|A novel workflow to improve multi-locus genotyping of wildlife species: an experimental set-up with a known model system||Gillingham, Mark A. F., Montero, B. Karina, Wilhelm, Kerstin, Grudzus, Kara, Sommer, Simone and Santos, Pablo S. C.||<p>Genotyping novel complex multigene systems is particularly challenging in non-model organisms. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification...||Bioinformatics & Computational Biology, Evolutionary Ecology, Genome Evolution, Molecular Evolution||François Rousset||Helena Westerdahl, Sebastian Ernesto Ramos-Onsins, Arnaud Estoup, , Vincent Segura, , , , , , , , , , Thomas Bigot, ,||2019-05-15 17:30:44||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 10.1101/141127
Unravelling the history of Neotropical plant diversificationRecommended by Hervé Sauquet based on reviews by Thomas Couvreur and Hervé Sauquet
South 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.  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.
 Antonelli A, and Sanmartín I. 2011. Why are there so many plant species in the Neotropics? Taxon 60, 403–414.
 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
 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
 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
 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
 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|
15 Feb 2019
Architectural traits constrain the evolution of unisexual flowers and sexual segregation within inflorescences: an interspecific approachRubén Torices, Ana Afonso, Arne A. Anderberg, José M. Gómez and Marcos Méndez https://doi.org/10.1101/356147
Sometimes, sex is in the headRecommended by Juan Arroyo based on reviews by 3 anonymous reviewers
Plants display an amazing diversity of reproductive strategies with and without sex. This diversity is particularly remarkable in flowering plants, as highlighted by Charles Darwin, who wrote several botanical books scrutinizing plant reproduction. One particularly influential work concerned floral variation . Darwin recognized that flowers may present different forms within a single population, with or without sex specialization. The number of species concerned is small, but they display recurrent patterns, which made it possible for Darwin to invoke natural and sexual selection to explain them. Most of early evolutionary theory on the evolution of reproductive strategies was developed in the first half of the 20th century and was based on animals. However, the pioneering work by David Lloyd from the 1970s onwards excited interest in the diversity of plant sexual strategies as models for testing adaptive hypotheses and predicting reproductive outcomes . The sex specialization of individual flowers and plants has since become one of the favorite topics of evolutionary biologists. However, attention has focused mostly on cases related to sex differentiation (dioecy and associated conditions ). Separate unisexual flower types on the same plant (monoecy and related cases, rendering the plant functionally hermaphroditic) have been much less studied, apart from their possible role in the evolution of dioecy  or their association with particular modes of pollination .
 Darwin, C. (1877). The different forms of flowers on plants of the same species. John Murray.
|Architectural traits constrain the evolution of unisexual flowers and sexual segregation within inflorescences: an interspecific approach||Rubén Torices, Ana Afonso, Arne A. Anderberg, José M. Gómez and Marcos Méndez||<p>Male and female unisexual flowers have repeatedly evolved from the ancestral bisexual flowers in different lineages of flowering plants. This sex specialization in different flowers often occurs within inflorescences. We hypothesize that inflor...||Evolutionary Ecology, Morphological Evolution, Phenotypic Plasticity, Reproduction and Sex, Sexual Selection||Juan Arroyo||Jana Vamosi, Marcial Escudero, Anonymous||2018-06-27 10:49:52||View|
07 Sep 2018
Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineagesFlorentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pierre-Alexandre Gagnaire, Nicolas Bierne https://doi.org/10.1101/161786
Genomic parallelism in adaptation to orthogonal environments in sea horsesRecommended by Yaniv Brandvain based on reviews by 2 anonymous reviewers
Studies in speciation genomics have revealed that gene flow is quite common, and that despite this, species can maintain their distinct environmental adaptations. Although researchers are still elucidating the genomic mechanisms by which species maintain their adaptations in the face of gene flow, this often appears to involve few diverged genomic regions in otherwise largely undifferentiated genomes. In this preprint , Riquet and colleagues investigate the genetic structuring and patterns of parallel evolution in the long-snouted seahorse.
 Riquet, F., Liautard-Haag, C., Woodall, L., Bouza, C., Louisy, P., Hamer, B., Otero-Ferrer, F., Aublanc, P., Béduneau, V., Briard, O., El Ayari, T., Hochscheid, S. Belkhir, K., Arnaud-Haond, S., Gagnaire, P.-A., Bierne, N. (2018). Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. bioRxiv, 161786, ver. 4 recommended and peer-reviewed by PCI Evol Biol. doi: 10.1101/161786
|Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages||Florentine Riquet, Cathy Liautard-Haag, Lucy Woodall, Carmen Bouza, Patrick Louisy, Bojan Hamer, Francisco Otero-Ferrer, Philippe Aublanc, Vickie Béduneau, Olivier Briard, Tahani El Ayari, Sandra Hochscheid, Khalid Belkhir, Sophie Arnaud-Haond, Pi...||<p>Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the la...||Hybridization / Introgression, Molecular Evolution, Population Genetics / Genomics, Speciation||Yaniv Brandvain||Kathleen Lotterhos, Sarah Fitzpatrick||2017-07-11 13:12:40||View|
16 Mar 2023
Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersalLoïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Arranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André Crochet https://doi.org/10.1101/2022.09.30.510256
The difficult task of partitioning the effects of vicariance and isolation by distance in poor dispersersRecommended by Eric Pante based on reviews by Kevin Sánchez and Aglaia (Cilia) Antoniou
Partitioning the effects of vicariance and low dispersal has been a long-standing problem in historical biogeography and phylogeography. While the term “vicariance” refers to divergence in allopatry, caused by some physical (geological, geographical) or climatic barriers (e.g. Rosen 1978), isolation by distance refers to the genetic differentiation of remote populations due to the physical distance separating them, when the latter surpasses the scale of dispersal (Wright 1938, 1940, 1943).
Vicariance and dispersal have long been considered as separate forces leading to separate scenarii of speciation (e.g. reviewed in Hickerson and Meyer 2008). Nevertheless, these two processes are strongly linked, as, for example, vicariance theory relies on the assumption that ancestral lineages were once linked by dispersal prior to physical or climatic isolation (Rosen 1978). Low dispersal and vicariance are not mutually exclusive, and distinguishing these two processes in heterogeneous landscapes, especially for poor dispersers, remains therefore a severe challenge. For example, low dispersal (and/or small population size) can give rise to geographic patterns consistent with a phylogeographic break and be mistaken for geographic isolation (Irwin 2002, Kuo and Avise 2005).
The study of Rancilliac and colleagues (2023) is at the heart of this issue. It focuses on a nominal lizard species, the red-tailed spiny-footed lizard (Acanthodactylus erythrurus, Squamata: Lacertidae), which has a wide spatial distribution (from the Maghreb to the Iberian Peninsula), is found in a variety of different habitats, and has a wide range of morphological traits that do not always correlate with phylogeny. The main question is the following: have “the morphological and ecological diversification of this group been produced by vicariance and lineage diversification, or by local adaptation in the face of historical gene flow?” To tackle this question, the authors used sequence data from multiple mitochondrial and nuclear markers and a nested analysis workflow integrating phylogeography, multiple correspondence analyses and a relatively novel approach to IBD testing (Hausdorf & Henning, 2020). The latter is based on regression analysis and was shown to be less prone to error than the traditional (partial) Mantel test.
While this set of methods allowed the partitioning of the effect of isolation by distance and vicariance in shaping contemporary genetic diversity in red-tailed spiny-footed lizards, some of the evolutionary history of this species complex remains blurred by ongoing gene flow and admixture, retention of ancestral polymorphism, or selection. The lack of congruence between mitochondrial and nuclear gene trees once again warns us that proposing evolutionary scenarii based on individual gene trees is a risky business.
Hausdorf B, Hennig C (2020) Species delimitation and geography. Molecular Ecology Resources, 20, 950–960. https://doi.org/10.1111/1755-0998.13184
Hickerson MJ, Meyer CP (2008) Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. BMC Evolutionary Biology, 8, 322. https://doi.org/10.1186/1471-2148-8-322
Irwin DE (2002) Phylogeographic breaks without geographic barriers to gene flow. Evolution, 56, 2383–2394. https://doi.org/10.1111/j.0014-3820.2002.tb00164.x
Kuo C-H, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica, 124, 179–186. https://doi.org/10.1007/s10709-005-2095-y
Rancilhac L, Miralles A, Geniez P, Mendez-Aranda D, Beddek M, Brito JC, Leblois R, Crochet P-A (2023) Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal. bioRxiv, 2022.09.30.510256, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.09.30.510256
Rosen DE (1978) Vicariant Patterns and Historical Explanation in Biogeography. Systematic Biology, 27, 159–188. https://doi.org/10.2307/2412970
Wright, S (1938) Size of population and breeding structure in relation to evolution. Science 87:430-431.
Wright S (1940) Breeding Structure of Populations in Relation to Speciation. The American Naturalist, 74, 232–248. https://doi.org/10.1086/280891
Wright S (1943) Isolation by distance. Genetics, 28, 114–138. https://doi.org/10.1093/genetics/28.2.114
|Phylogeographic breaks and how to find them: Separating vicariance from isolation by distance in a lizard with restricted dispersal||Loïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Arranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, Pierre-André Crochet||<p>Aim</p> <p>Discontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise...||Phylogeography & Biogeography, Population Genetics / Genomics, Speciation, Systematics / Taxonomy||Eric Pante||Kevin Sánchez||2022-10-05 13:11:28||View|
06 Oct 2017
Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebratesFrancisco J. Novo https://doi.org/10.1101/150482
Combining molecular information on chromatin organisation with eQTLs and evolutionary conservation provides strong candidates for the evolution of gene regulation in mammalian brainsRecommended by Marc Robinson-Rechavi based on reviews by Marc Robinson-Rechavi and Charles Danko
In this manuscript , Francisco J. Novo proposes candidate non-coding genomic elements regulating neurodevelopmental genes.
What is very nice about this study is the way in which public molecular data, including physical interaction data, is used to leverage recent advances in our understanding to molecular mechanisms of gene regulation in an evolutionary context. More specifically, evolutionarily conserved non coding sequences are combined with enhancers from the FANTOM5 project, DNAse hypersensitive sites, chromatin segmentation, ChIP-seq of transcription factors and of p300, gene expression and eQTLs from GTEx, and physical interactions from several Hi-C datasets. The candidate regulatory regions thus identified are linked to candidate regulated genes, and the author shows their potential implication in brain development.
While the results are focused on a small number of genes, this allows to verify features of these candidates in great detail. This study shows how functional genomics is increasingly allowing us to fulfill the promises of Evo-Devo: understanding the molecular mechanisms of conservation and differences in morphology.
 Novo, FJ. 2017. Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebrates. bioRxiv, 150482, ver. 4 of Sept 29th, 2017. doi: 10.1101/150482
|Evolutionary analysis of candidate non-coding elements regulating neurodevelopmental genes in vertebrates||Francisco J. Novo||<p>Many non-coding regulatory elements conserved in vertebrates regulate the expression of genes involved in development and play an important role in the evolution of morphology through the rewiring of developmental gene networks. Available biolo...||Genome Evolution||Marc Robinson-Rechavi||Marc Robinson-Rechavi, Charles Danko||2017-06-29 08:55:41||View|
09 Dec 2019
Systematics and geographical distribution of Galba species, a group of cryptic and worldwide freshwater snailsPilar Alda, Manon Lounnas, Antonio Alejandro Vázquez, Rolando Ayaqui, Manuel Calvopina, Maritza Celi-Erazo, Robert Dillon, Luisa Carolina González Ramírez, Eric S. Loker, Jenny Muzzio-Aroca, Alberto Orlando Nárvaez, Oscar Noya, Andrés Esteban Pereira, Luiggi Martini Robles, Richar Rodríguez-Hidalgo, Nelson Uribe, Patrice David, Philippe Jarne, Jean-Pierre Pointier, Sylvie Hurtrez-Boussès https://doi.org/10.1101/647867
The challenge of delineating species when they are hiddenRecommended by Fabien Condamine based on reviews by Pavel Matos, Christelle Fraïsse and Niklas Wahlberg
The science of naming species (taxonomy) has been renewed with the developments of molecular sequencing, digitization of museum specimens, and novel analytical tools. However, naming species can be highly subjective, sometimes considered as an art , because it is based on human-based criteria that vary among taxonomists. Nonetheless, taxonomists often argue that species names are hypotheses, which are therefore testable and refutable as new evidence is provided. This challenge comes with a more and more recognized and critical need for rigorously delineated species not only for producing accurate species inventories, but more importantly many questions in evolutionary biology (e.g. speciation), ecology (e.g. ecosystem structure and functioning), conservation biology (e.g. targeting priorities) or biogeography (e.g. diversification processes) depend in part on those species inventories and our knowledge of species [2-3]. Inaccurate species boundaries or diversity estimates may lead us to deliver biased answers to those questions, exactly as phylogenetic trees must be reconstructed rigorously and analyzed critically because they are a first step toward discussing broader questions [2-3]. In this context, biological diversity needs to be studied from multiple and complementary perspectives requiring the collaboration of morphologists, molecular biologists, biogeographers, and modelers [4-5]. Integrative taxonomy has been proposed as a solution to tackle the challenge of delimiting species , especially in highly diverse and undocumented groups of organisms.
 Ohl, M. (2018). The art of naming. MIT Press.
|Systematics and geographical distribution of Galba species, a group of cryptic and worldwide freshwater snails||Pilar Alda, Manon Lounnas, Antonio Alejandro Vázquez, Rolando Ayaqui, Manuel Calvopina, Maritza Celi-Erazo, Robert Dillon, Luisa Carolina González Ramírez, Eric S. Loker, Jenny Muzzio-Aroca, Alberto Orlando Nárvaez, Oscar Noya, Andrés Esteban Pere...||<p>Cryptic species can present a significant challenge to the application of systematic and biogeographic principles, especially if they are invasive or transmit parasites or pathogens. Detecting cryptic species requires a pluralistic approach in ...||Phylogeography & Biogeography, Systematics / Taxonomy||Fabien Condamine||Pavel Matos, Christelle Fraïsse||2019-05-25 10:34:57||View|
Michael David Pirie
Alejandro Gonzalez Voyer