Publications by authors named "François-Joseph Lapointe"

40 Publications

Corrigendum: Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome.

Front Microbiol 2020 26;11:588889. Epub 2020 Oct 26.

Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada.

[This corrects the article DOI: 10.3389/fmicb.2020.01776.].
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http://dx.doi.org/10.3389/fmicb.2020.588889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649613PMC
October 2020

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats () Infected With the Causal Agent of White-Nose Syndrome.

Front Microbiol 2020 23;11:1776. Epub 2020 Jul 23.

Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada.

Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus (), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of in the context of has not been done. In January 2017, we captured hibernating , sampled their skin microbiota, and inoculated them with or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) infection would not disrupt the skin microbiota of -resistant ; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with . Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of -inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, and are known for antifungal potential against and other fungi. Thus, in contrast to hypothesis 1, infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of , suggesting potential associations between the bat skin microbiota and resistance to the infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.
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http://dx.doi.org/10.3389/fmicb.2020.01776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390961PMC
July 2020

Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data.

Genome Biol Evol 2019 09;11(9):2653-2665

Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.

Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks.
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http://dx.doi.org/10.1093/gbe/evz182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761957PMC
September 2019

Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.

Genome Biol 2018 06 7;19(1):75. Epub 2018 Jun 7.

Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7138 Evolution Paris Seine, 75005, Paris, France.

Background: Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group.

Results: We report the creation of 320 novel composite genes, both early in the evolution of Haloarchaea during haloarchaeal genesis and later in diverged haloarchaeal groups. One hundred and twenty-six of these novel composite genes derived from genetic material from bacterial genomes. These latter genes, largely involved in metabolic functions but also in oxygenic lifestyle, constitute a different gene pool from the laterally acquired bacterial genes formerly identified. These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points.

Conclusions: Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes.
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http://dx.doi.org/10.1186/s13059-018-1454-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992828PMC
June 2018

Paternity Analysis of Wood Turtles (Glyptemys insculpta) Reveals Complex Mating Patterns.

J Hered 2018 05;109(4):405-415

Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

Mating system characteristics are of great importance as they may influence male and female reproductive success and reproductive isolation. The wood turtle (Glyptemys insculpta) is a terrestrial freshwater species listed as endangered by the International Union for Conservation of Nature. Considering its conservation status and the paucity of information currently available on parentage relationship for the species, we performed a microsatellite analysis to study the mating system of wood turtles in the Shawinigan River (Québec). We sampled 38 clutches over 2 years (14 in 2006 and 24 in 2007), for a total of 248 offspring genotyped with 7 microsatellite loci. The reconstructed genotypes of the fathers revealed that reproductive success in the sampled clutches varied greatly between males and are positively correlated with the number of mates and clutches sired. Frequency of multiple paternity was estimated at 37% through a consensus of 3 different estimation methods. Positive correlation was observed between the genetic diversity of clutches and the number of fathers. Repeat paternity, however, was observed in 88% of the clutches by the same female in successive years, which suggests either a frequent use of sperm storage, or remating with the same partner in successive years.
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http://dx.doi.org/10.1093/jhered/esx103DOI Listing
May 2018

The Inuit gut microbiome is dynamic over time and shaped by traditional foods.

Microbiome 2017 11 16;5(1):151. Epub 2017 Nov 16.

Département de sciences biologiques, Université de Montréal, 90 Vincent-d'Indy, Montréal, Qc, H2V2S9, Canada.

Background: The human gut microbiome represents a diverse microbial community that varies across individuals and populations, and is influenced by factors such as host genetics and lifestyle. Diet is a major force shaping the gut microbiome, and the effects of dietary choices on microbiome composition are well documented. However, it remains poorly known how natural temporal variation in diet can affect the microbiome. The traditional Inuit diet is primarily based on animal products, which are thought to vary seasonally according to prey availability. We previously investigated the Inuit gut microbiome sampled at a single time point, and found no detectable differences in overall microbiome community composition attributable to the traditional Inuit diet.

Results: To determine whether seasonal changes in the Inuit diet might induce more pronounced changes in the microbiome, we collected stool and toilet paper samples, and dietary information from Inuit volunteers living in Resolute Bay (Nunavut, Canada), and compared them to individuals of European descent living in Montréal (Québec, Canada) consuming a typical Western diet. We sequenced the V4 region of the 16S rRNA gene to characterize microbiome diversity and composition, and compared samples collected with toilet paper or from stool. Our results show that these sampling methods provide similar, but non-identical portraits of the microbiome. Based on toilet paper samples, we found that much of the variation in microbiome community composition could be explained by individual identity (45-61% of variation explained, depending on the beta diversity metric used), with small but significant variation (3-5%) explained by sex or geography (Nunavut or Montréal). In contrast with our previous study at one time point, sampling over the course of a year revealed that diet explains 11% of variation in community composition across all participants, and 17% of variation specifically among Nunavut participants. However, we observed no clear seasonal shifts in the microbiomes of participants from either Nunavut or Montréal. Within-individual microbial diversity fluctuated more over time in Nunavut than in Montréal, consistent with a more variable and highly individualized diet in Nunavut.

Conclusions: Together, these results shows that the traditional Inuit diet and lifestyle has an impact on the composition, diversity and stability of the Inuit gut microbiome, even if the seasonality of the diet is less pronounced than expected, perhaps due to an increasingly westernized diet.
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http://dx.doi.org/10.1186/s40168-017-0370-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5689144PMC
November 2017

CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection.

Mol Biol Evol 2018 01;35(1):252-255

Institut de Biologie Paris-Seine (IBPS), UPMC Université Paris 06, Sorbonne Universités, Paris, France.

Genes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast, and scalable method to detect composite gene families in large data sets (typically in the range of several million sequences). CompositeSearch generalizes the use of similarity networks to detect composite and component gene families with a greater recall, accuracy, and precision than recent programs (FusedTriplets and MosaicFinder). Moreover, CompositeSearch provides user-friendly quality descriptions regarding the distribution and primary sequence conservation of these gene families allowing critical biological analyses of these data.
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http://dx.doi.org/10.1093/molbev/msx283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850286PMC
January 2018

Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome.

Microbiome 2017 09 5;5(1):115. Epub 2017 Sep 5.

Département de Sciences Biologiques, Université de Montréal, CP 6182, Succursale Centre-ville, Montréal, Québec, H2V 2S9, Canada.

Background: Infectious diseases of wildlife are increasing worldwide with implications for conservation and human public health. The microbiota (i.e. microbial community living on or in a host) could influence wildlife disease resistance or tolerance. White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), has killed millions of hibernating North American bats since 2007. We characterized the skin microbiota of naïve, pre-WNS little brown bats (Myotis lucifugus) from three WNS-negative hibernation sites and persisting, previously exposed bats from three WNS-positive sites to test the hypothesis that the skin microbiota of bats shifts following WNS invasion.

Results: Using high-throughput 16S rRNA gene sequencing on 66 bats and 11 environmental samples, we found that hibernation site strongly influenced the composition and diversity of the skin microbiota. Bats from WNS-positive and WNS-negative sites differed in alpha and beta diversity, as well as in microbiota composition. Alpha diversity was reduced in persisting, WNS-positive bats, and the microbiota profile was enriched with particular taxa such Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia, and Rhodococcus. Some of these taxa are recognized for their antifungal activity, and specific strains of Rhodococcus and Pseudomonas are known to inhibit Pd growth. Composition of the microbial community in the hibernaculum environment and the community on bat skin was superficially similar but differed in relative abundance of some bacterial taxa.

Conclusions: Our results are consistent with the hypothesis that Pd invasion leads to a shift in the skin microbiota of surviving bats and suggest the possibility that the microbiota plays a protective role for bats facing WNS. The detection of what appears to be enrichment of beneficial bacteria in the skin microbiota of persisting bats is a promising discovery for species re-establishment. Our findings highlight not only the potential value of management actions that might encourage transmission, growth, and establishment of beneficial bacteria on bats, and within hibernacula, but also the potential risks of such management actions.
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http://dx.doi.org/10.1186/s40168-017-0334-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584028PMC
September 2017

Environment and host species shape the skin microbiome of captive neotropical bats.

PeerJ 2016 20;4:e2430. Epub 2016 Sep 20.

Département de Sciences Biologiques, Université de Montréal , Montréal , Canada.

Background: A wide range of microorganisms inhabit animal skin. This microbial community (microbiome) plays an important role in host defense against pathogens and disease. Bats (Chiroptera: Mammalia) are an ecologically and evolutionarily diversified group with a relatively unexplored skin microbiome. The bat skin microbiome could play a role in disease resistance, for example, to white nose syndrome (WNS), an infection which has been devastating North American bat populations. However, fundamental knowledge of the bat skin microbiome is needed before understanding its role in health and disease resistance. Captive neotropical frugivorous bats Artibeus jamaicensis and Carollia perspicillataprovide a simple controlled system in which to characterize the factors shaping the bat microbiome. Here, we aimed to determine the relative importance of habitat and host species on the bat skin microbiome.

Methods: We performed high-throughput 16S rRNA gene sequencing of the skin microbiome of two different bat species living in captivity in two different habitats. In the first habitat, A. jamaicensis and C. perspicillata lived together, while the second habitat contained only A. jamaicensis.

Results: We found that both habitat and host species shape the composition and diversity of the skin microbiome, with habitat having the strongest influence. Cohabitating A. jamaicensis and C. perspicillata shared more similar skin microbiomes than members of the same species (A. jamaicensis) across two habitats.

Discussion: These results suggest that in captivity, the skin microbial community is homogenised by the shared environments and individual proximities of bats living together in the same habitat, at the expense of the innate host species factors. The predominant influence of habitat suggests that environmental microorganisms or pathogens might colonize bat skin. We also propose that bat populations could differ in pathogen susceptibility depending on their immediate environment and habitat.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036103PMC
http://dx.doi.org/10.7717/peerj.2430DOI Listing
October 2016

Using hybridization networks to retrace the evolution of Indo-European languages.

BMC Evol Biol 2016 09 6;16:180. Epub 2016 Sep 6.

Department of Computer Science, Université du Québec à Montréal, Case postale 8888, succursale Centre-ville, Montréal, Québec, H3C 3P8, Canada.

Background: Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics.

Results: Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods.

Conclusion: We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.
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http://dx.doi.org/10.1186/s12862-016-0745-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012036PMC
September 2016

BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts.

PLoS One 2016 31;11(8):e0161474. Epub 2016 Aug 31.

Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

Various types of genome and gene similarity networks along with their characteristics have been increasingly used for retracing different kinds of evolutionary and ecological relationships. Here, we present a new polynomial time algorithm and the corresponding software (BRIDES) to provide characterization of different types of paths existing in evolving (or augmented) similarity networks under the constraint that such paths contain at least one node that was not present in the original network. These different paths are denoted as Breakthroughs, Roadblocks, Impasses, Detours, Equal paths, and Shortcuts. The analysis of their distribution can allow discriminating among different evolutionary hypotheses concerning genomes or genes at hand. Our approach is based on an original application of the popular shortest path Dijkstra's and Yen's algorithms. The C++ and R versions of the BRIDES program are freely available at: https://github.com/etiennelord/BRIDES.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161474PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007014PMC
July 2017

Self-tracking the microbiome: where do we go from here?

Microbiome 2015 Dec 12;3:70. Epub 2015 Dec 12.

Département de sciences biologiques, Université de Montréal, CP. 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada.

The quantified self community brings together enthusiasts who are using technological devices to monitor their health and social media to share their personal data with others online. In light of the growing popularity of this movement, self-trackers are challenging the health-care system by raising important questions about data ownership and risk-taking. As we enter a new era of consumer genomics, a significant number of quantified self (QS) individuals are now interested in the monitoring of their microbiome and performing personal interventions. In this paper, we discuss the scientific validity of experiments involving serial observations of a single individual as opposed to randomized clinical trials. We look at self-tracking from an ethical standpoint by questioning the risks and assessing the potential benefits for personalized medicine in general and for microbiome research in particular.
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http://dx.doi.org/10.1186/s40168-015-0138-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676868PMC
December 2015

Phylogeographic Structure of the White-Footed Mouse and the Deer Mouse, Two Lyme Disease Reservoir Hosts in Québec.

PLoS One 2015 3;10(12):e0144112. Epub 2015 Dec 3.

Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

Modification of a species range is one of many consequences of climate change and is driving the emergence of Lyme disease in eastern Canada. The primary reservoir host of the bacteria responsible for Lyme disease, Borrelia burgdorferi, is the white-footed mouse (Peromyscus leucopus), whose range is rapidly shifting north into southern Québec. The deer mouse, P. maniculatus, is occurring over most Québec province and is a less competent host for B. burgdorferi. Here, we compared the phylogeographic structure of both Peromyscus species in Québec. Using a combination of multiple mitochondrial DNA markers and phylogeographic methods, we detected an ongoing and rapid expansion of P. leucopus, while P. maniculatus appears more stable. Haplotype and populations networks indicated that populations of P. maniculatus exhibit more genetic structure than P. leucopus across the study area. Furthermore, significant and consistent genetic divergences between populations of the two species on both sides of the St. Lawrence River suggest that distinct lineages of P. leucopus and P. maniculatus with different ancestral origins colonized Southern Québec following the Last Glacial Maximum. The phylogeographic structure of pathogens is expected to mirror the structure observed in their reservoir hosts. As different strains of Borrelia burgdorferi may be associated with different levels of pathogenicity and immune responses of their hosts, our results are helpful at better understanding the pattern of spread of Lyme disease in a zone of emergence, and associated risk for human populations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144112PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669108PMC
June 2016

Being human is a gut feeling.

Microbiome 2015 13;3. Epub 2015 Mar 13.

Département de sciences biologiques, Université de Montréal, P. O. Box 6128, Station Centre-ville, Montréal, QC H3C 3J7 Canada.

Some metagenomic studies have suggested that less than 10% of the cells that comprise our bodies are Homo sapiens cells. The remaining 90% are bacterial cells. The description of this so-called human microbiome is of great interest and importance for several reasons. For one, it helps us redefine what a biological individual is. We suggest that a human individual is now best described as a super-individual in which a large number of different species (including Homo sapiens) coexist. New concepts of biological individuality must extend beyond the traditional limitations of our own skin to include our resident microbes. Besides its important contributions to science, microbiome research raises philosophical questions that strike close to home. What is left of Homo sapiens? If most of our cells are not Homo sapiens cells, what does it mean to be an individual human being? In this paper, we argue that the biological individual is determined by the amount of functional integration among its constitutive parts, a definition that applies perfectly to Homo sapiens and its microbiome.
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http://dx.doi.org/10.1186/s40168-015-0076-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359430PMC
March 2015

Climate change and habitat fragmentation drive the occurrence of Borrelia burgdorferi, the agent of Lyme disease, at the northeastern limit of its distribution.

Evol Appl 2014 Aug 7;7(7):750-64. Epub 2014 May 7.

Redpath Museum, McGill University Montreal, QC, Canada.

Lyme borreliosis is rapidly emerging in Canada, and climate change is likely a key driver of the northern spread of the disease in North America. We used field and modeling approaches to predict the risk of occurrence of Borrelia burgdorferi, the bacteria causing Lyme disease in North America. We combined climatic and landscape variables to model the current and future (2050) potential distribution of the black-legged tick and the white-footed mouse at the northeastern range limit of Lyme disease and estimated a risk index for B. burgdorferi from these distributions. The risk index was mostly constrained by the distribution of the white-footed mouse, driven by winter climatic conditions. The next factor contributing to the risk index was the distribution of the black-legged tick, estimated from the temperature. Landscape variables such as forest habitat and connectivity contributed little to the risk index. We predict a further northern expansion of B. burgdorferi of approximately 250-500 km by 2050 - a rate of 3.5-11 km per year - and identify areas of rapid rise in the risk of occurrence of B. burgdorferi. Our results will improve understanding of the spread of Lyme disease and inform management strategies at the most northern limit of its distribution.
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http://dx.doi.org/10.1111/eva.12165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227856PMC
August 2014

Genetic structure of the white-footed mouse in the context of the emergence of Lyme disease in southern Québec.

Ecol Evol 2013 Jul 3;3(7):2075-88. Epub 2013 Jun 3.

Redpath Museum, McGill University 859 Sherbrooke Street W., Montréal, Québec, H3A 0C4, Canada.

The white-footed mouse (Peromyscus leucopus) has expanded its northern limit into southern Québec over the last few decades. P. leucopus is a great disperser and colonizer and is of particular interest because it is considered a primary reservoir for the spirochete bacterium that causes Lyme disease. There is no current information on the gene flow between mouse populations on the mountains and forest fragments found scattered throughout the Montérégie region in southern Québec, and whether various landscape barriers have an effect on their dispersal. We conducted a population genetics analysis on eleven P. leucopus populations using eleven microsatellite markers and showed that isolation by distance was weak, yet barriers were effective. The agricultural matrix had the least effect on gene flow, whereas highways and main rivers were effective barriers. The abundance of ticks collected from mice varied within the study area. Both ticks and mice were screened for the presence of the spirochete bacterium Borrelia burgdorferi, and we predicted areas of greater risk for Lyme disease. Merging our results with ongoing Lyme disease surveillance programs will help determine the future threat of this disease in Québec, and will contribute toward disease prevention and management strategies throughout fragmented landscapes in southern Canada.
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http://dx.doi.org/10.1002/ece3.620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728948PMC
July 2013

Canid hybridization: contemporary evolution in human-modified landscapes.

Ecol Evol 2012 Sep 25;2(9):2128-40. Epub 2012 Jul 25.

Département de sciences biologiques, Université de Montréal Montréal, Québec, H3C 3J7, Canada.

Contemporary evolution through human-induced hybridization occurs throughout the taxonomic range. Formerly allopatric species appear especially susceptible to hybridization. Consequently, hybridization is expected to be more common in regions with recent sympatry owing to human activity than in areas of historical range overlap. Coyotes (Canis latrans) and gray wolves (C. lupus) are historically sympatric in western North America. Following European settlement gray wolf range contracted, whereas coyote range expanded to include eastern North America. Furthermore, wolves with New World (NW) mitochondrial DNA (mtDNA) haplotypes now extend from Manitoba to Québec in Canada and hybridize with gray wolves and coyotes. Using mtDNA and 12 microsatellite markers, we evaluated levels of wolf-coyote hybridization in regions where coyotes were present (the Canadian Prairies, n = 109 samples) and absent historically (Québec, n = 154). Wolves with NW mtDNA extended from central Saskatchewan (51°N, 69°W) to northeastern Québec (54°N, 108°W). On the Prairies, 6.3% of coyotes and 9.2% of wolves had genetic profiles suggesting wolf-coyote hybridization. In contrast, 12.6% of coyotes and 37.4% of wolves in Québec had profiles indicating hybrid origin. Wolves with NW and Old World (C. lupus) mtDNA appear to form integrated populations in both regions. Our results suggest that hybridization is more frequent in historically allopatric populations. Range shifts, now expected across taxa following climate change and other human influence on the environment, might therefore promote contemporary evolution by hybridization.
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http://dx.doi.org/10.1002/ece3.335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488665PMC
September 2012

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

Biol Direct 2011 Jul 20;6:39; discussion 39. Epub 2011 Jul 20.

Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

Background: We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches.

Results: We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements.

Conclusions: Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.
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http://dx.doi.org/10.1186/1745-6150-6-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160433PMC
July 2011

Evaluating phylogenetic congruence in the post-genomic era.

Genome Biol Evol 2011 28;3:571-87. Epub 2011 Jun 28.

Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.
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http://dx.doi.org/10.1093/gbe/evr050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156567PMC
November 2011

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis.

BMC Evol Biol 2011 Mar 9;11:64. Epub 2011 Mar 9.

Département de Sciences biologiques, Université de Montréal, C.P. 6128, Succ, Centre-ville, Montréal, Québec H3C3J7, Canada.

Background: CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions.

Results: Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices.

Conclusions: Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.
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http://dx.doi.org/10.1186/1471-2148-11-64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065422PMC
March 2011

Harvesting evolutionary signals in a forest of prokaryotic gene trees.

Mol Biol Evol 2011 Apr 20;28(4):1393-405. Epub 2010 Dec 20.

UMR CNRS 7138 Systématique, Adaptation, Evolution, Muséum National d'Histoire Naturelle, Paris, France.

Phylogenomic studies produce increasingly large phylogenetic forests of trees with patchy taxonomical sampling. Typically, prokaryotic data generate thousands of gene trees of all sizes that are difficult, if not impossible, to root. Their topologies do not match the genealogy of lineages, as they are influenced not only by duplication, losses, and vertical descent but also by lateral gene transfer (LGT) and recombination. Because this complexity in part reflects the diversity of evolutionary processes, the study of phylogenetic forests is thus a great opportunity to improve our understanding of prokaryotic evolution. Here, we show how the rich evolutionary content of such novel phylogenetic objects can be exploited through the development of new approaches designed specifically for extracting the multiple evolutionary signals present in the forest of life, that is, by slicing up trees into remarkable bits and pieces: clans, slices, and clips. We harvested a forest of 6,901 unrooted gene trees comprising up to 100 prokaryotic genomes (41 archaea and 59 bacteria) to search for evolutionary events that a species tree would not account for. We identified 1) trees and partitions of trees that reflected the lifestyle of organisms rather than their taxonomy, 2) candidate lifestyle-specific genetic modules, used by distinct unrelated organisms to adapt to the same environment, 3) gene families, nonrandomly distributed in the functional space, that were frequently exchanged between archaea and bacteria, sometimes without major changes in their sequences. Finally, 4) we reconstructed polarized networks of genetic partnerships between archaea and bacteria to describe some of the rules affecting LGT between these two Domains.
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http://dx.doi.org/10.1093/molbev/msq323DOI Listing
April 2011

Retrieving a mitogenomic mammal tree using composite taxa.

Mol Phylogenet Evol 2011 Feb 4;58(2):149-56. Epub 2010 Dec 4.

Département de Sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

Supermatrices are often characterized by a large amount of missing data. One possible approach to minimize such missing data is to create composite taxa. These taxa are formed by sampling sequences from different species in order to obtain a composite sequence that includes a maximum number of genes. Although this approach is increasingly used, its accuracy has rarely been tested and some authors prefer to analyze incomplete supermatrices by coding unavailable sequences as missing. To further validate the composite taxon approach, it was applied to complete mitochondrial matrices of 102 mammal species representing 93 families with varying amount of missing data. On average, missing data and composite matrices showed similar congruence to model trees obtained from the complete sequence matrix. As expected, the level of congruence to model trees decreased as missing data increased, with both approaches. We conclude that the composite taxon approach is worth considering in a phylogenomic context since it performs well and reduces computing time when compared to missing data matrices.
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http://dx.doi.org/10.1016/j.ympev.2010.11.017DOI Listing
February 2011

Weighted bootstrapping: a correction method for assessing the robustness of phylogenetic trees.

BMC Evol Biol 2010 Aug 17;10:250. Epub 2010 Aug 17.

Département d'informatique, Université du Québec à Montréal, CP 8888 succ, Centre-Ville, Montreal, QC H3C 3P8, Canada.

Background: Non-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data 1 and, as such, it has become a common method for assessing tree confidence in phylogenetics 2. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.

Results: In this article, we discuss the idea of applying weighted bootstrapping to phylogenetic reconstruction by weighting each phylogeny inferred from resampled sequences. Tree weights can be based either on the least-squares (LS) tree estimate or on the average secondary bootstrap score (SBS) associated with each resampled tree. Secondary bootstrapping consists of the estimation of bootstrap scores of the trees inferred from resampled data. The LS and SBS-based bootstrapping procedures were designed to take into account the quality of each "pseudo-replicated" phylogeny in the final tree estimation. A simulation study was carried out to evaluate the performances of the five weighting strategies which are as follows: LS and SBS-based bootstrapping, LS and SBS-based bootstrapping with data normalization and the traditional unweighted bootstrapping.

Conclusions: The simulations conducted with two real data sets and the five weighting strategies suggest that the SBS-based bootstrapping with the data normalization usually exhibits larger bootstrap scores and a higher robustness compared to the four other competing strategies, including the traditional bootstrapping. The high robustness of the normalized SBS could be particularly useful in situations where observed sequences have been affected by noise or have undergone massive insertion or deletion events. The results provided by the four other strategies were very similar regardless the noise level, thus also demonstrating the stability of the traditional bootstrapping method.
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http://dx.doi.org/10.1186/1471-2148-10-250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939571PMC
August 2010

Clanistics: a multi-level perspective for harvesting unrooted gene trees.

Trends Microbiol 2010 Aug 31;18(8):341-7. Epub 2010 May 31.

Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada.

Prokaryotic evolution takes place within and between genomes, when significant amounts of genes are transferred and recombined between interacting genetic partners. These non-tree-like evolutionary processes, intertwined with events of vertical descent, lead to a massive production of unrooted trees in which branches, nodes and groupings have different biological meanings than for the rooted trees usually studied by phylogenetics. Such unrooted gene trees can not only inform us about organismal phylogeny, but also about the variety of evolutionary, genetic, functional and ecological relationships affecting a plurality of evolutionary units, at multiple levels - from genes, groups of genes, organisms and consortia, to communities. Here we introduce new notions designed to analyze unrooted trees with more depth and accuracy. We demonstrate how a clanistic perspective can significantly improve our knowledge of evolutionary processes and relationships for most evolving systems, whether they are mobile genetic elements or cellular genomes.
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http://dx.doi.org/10.1016/j.tim.2010.03.009DOI Listing
August 2010

An application of supertree methods to Mammalian mitogenomic sequences.

Evol Bioinform Online 2010 May 12;6:57-71. Epub 2010 May 12.

Université de Montréal, Département de Sciences Biologiques, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada.

TWO DIFFERENT APPROACHES CAN BE USED IN PHYLOGENOMICS: combined or separate analysis. In the first approach, different datasets are combined in a concatenated supermatrix. In the second, datasets are analyzed separately and the phylogenetic trees are then combined in a supertree. The supertree method is an interesting alternative to avoid missing data, since datasets that are analyzed separately do not need to represent identical taxa. However, the supertree approach and the corresponding consensus methods have been highly criticized for not providing valid phylogenetic hypotheses. In this study, congruence of trees estimated by consensus and supertree approaches were compared to model trees obtained from a combined analysis of complete mitochondrial sequences of 102 species representing 93 mammal families. The consensus methods produced poorly resolved consensus trees and did not perform well, except for the majority rule consensus with compatible groupings. The weighted supertree and matrix representation with parsimony methods performed equally well and were highly congruent with the model trees. The most similar supertree method was the least congruent with the model trees. We conclude that some of the methods tested are worth considering in a phylogenomic context.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880846PMC
http://dx.doi.org/10.4137/ebo.s4527DOI Listing
May 2010

The use and validity of composite taxa in phylogenetic analysis.

Syst Biol 2009 Dec 21;58(6):560-72. Epub 2009 Sep 21.

Département de sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec H3C 3J7, Canada.

In phylogenetic analysis, one possible approach to minimize missing data in DNA supermatrices consists in sampling sequences from different species to obtain a complete sequence for all genes included in the study. We refer to those complete sequences as composite taxa because DNA sequences that are combined belong to different species. An alternative approach is to analyze incomplete supermatrices by coding unavailable DNA sequences as missing. The accuracy of phylogenetic trees estimated using matrices that include composite taxa has recently been questioned, and the best approach for analyzing incomplete supermatrices is highly debated. Through computer simulations, we compared the phylogenetic accuracy of the 2 competing approaches. We explored the effect of composite taxa when inferring higher level relationships, that is, relationships between monophyletic groups. DNA sequences were simulated on a 42-taxon model tree and incomplete supermatrices containing different percentages of missing data were generated. These incomplete supermatrices were analyzed either by coding the missing data with "?" or by reducing the amount of missing data through the combination of 2 or more taxa to generate composite taxa. Of 180 comparisons (18 simulation cases with 2 different inference methods and 5 levels of incompleteness), we observed significantly higher phylogenetic accuracies for composite matrices in 46 comparisons, whereas missing data matrices outperformed composites in 8 comparisons. In all other cases, the phylogenetic accuracy obtained with composite matrices was not significantly different from that of missing data matrices. This study demonstrates that composite taxa represent an interesting approach to minimize the amount of missing data in supermatrices and we suggest that it is the optimal approach to use in phylogenomic studies to reduce computing time.
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http://dx.doi.org/10.1093/sysbio/syp056DOI Listing
December 2009

Microsatellite analyses provide evidence of male-biased dispersal in the radiated tortoise Astrochelys radiata (Chelonia: Testudinidae).

J Hered 2010 Jul-Aug;101(4):403-12. Epub 2010 Mar 22.

Allan Wilson Centre for Molecular Ecology and School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.

Dispersal is a major force in shaping the genetic structure and dynamics of species; thus, its understanding is critical in formulating appropriate conservation strategies. In many species, sexes do not face the same evolutionary pressures, and consequently dispersal is often asymmetrical between males and females. This is well documented in birds and mammals but has seldom been investigated in other taxa, including reptiles and, more specifically, nonmarine chelonians. In these species, nest-site fidelity observations are frequent but still remain to be associated with natal homing. Here, we tested for sex-biased dispersal in the radiated tortoise (Astrochelys radiata) from southern Madagascar. Using data from 13 microsatellite markers, we investigated patterns of relatedness between sexes in 2 populations. All Mantel tests indicated significant isolation by distance at the individual level in females but not in males. Furthermore, spatial autocorrelation analyses and 2 analytical approaches designed to assess general trends in sex-specific dispersal also supported male-biased dispersal. On the other hand, comparisons of overall genetic structure among sampling sites did not provide conclusive support for greater philopatry in females, but these tests may have low statistical power because of methodological and biological constraints. Radiated tortoises appear to be both polyandrous and polygynous, and evolutionary processes that may lead to a sex bias in dispersal are discussed with respect to tortoise breeding biology. Female natal homing is hypothesized as a key trait explaining greater female philopatry in A. radiata. These findings highlight the necessity of additional research on natal homing in tortoises, a behavioral trait with direct implications for conservation.
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http://dx.doi.org/10.1093/jhered/esq020DOI Listing
October 2010

A statistical procedure to assess the significance level of barriers to gene flow.

J Genet Genomics 2009 Nov;36(11):685-93

Allan Wilson Centre for Molecular Ecology & School of Biological Sciences, Victoria University of Wellington, PO Box 600 Wellington 6140, New Zealand.

Although several methods are available to study the extent of isolation by distance (IBD) among natural populations, comparatively few exist to detect the presence of sharp genetic breaks in genetic distance datasets. In recent years, Monmonier's maximum-difference algorithm has been increasingly used by population geneticists. However, this method does not provide means to measure the statistical significance of such barriers, nor to determine their relative contribution to population differentiation with respect to IBD. Here, we propose an approach to assess the significance of genetic boundaries. The method is based on the calculation of a multiple regression from distance matrices, where binary matrices represent putative genetic barriers to test, in addition to geographic and genetic distances. Simulation results suggest that this method reliably detects the presence of genetic barriers, even in situations where IBD is also significant. We also illustrate the methodology by analyzing previously published datasets. Conclusions about the importance of genetic barriers can be misleading if one does not take into consideration their relative contribution to the overall genetic structure of species.
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http://dx.doi.org/10.1016/S1673-8527(08)60161-7DOI Listing
November 2009

Prokaryotic evolution and the tree of life are two different things.

Biol Direct 2009 Sep 29;4:34. Epub 2009 Sep 29.

UPMC, UMR CNRS 7138, 75005 Paris, France.

Background: The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.

Results: It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.

Conclusion: Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.

Reviewers: This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.
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http://dx.doi.org/10.1186/1745-6150-4-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761302PMC
September 2009

Seeing the trees for the network: consensus, information content, and superphylogenies.

Syst Biol 2007 Apr;56(2):345-55

Département de sciences biologiques, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal (Québec), H3C 3J7, Canada.

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http://dx.doi.org/10.1080/10635150701286549DOI Listing
April 2007