Philippe Henry - Academia.edu (original) (raw)

Papers by Philippe Henry

Research paper thumbnail of Title: Single nucleotide polymorphisms shed light on correlations between environmental vairalbe and adaptive genetic divergence in Chum salmon (Oncorhynchus keta)

Identifying the genetic and ecological basis of adaptation is of immense importance in evolutiona... more Identifying the genetic and ecological basis of adaptation is of immense importance in evolutionary biology. In our study, we applied a panel of 58 biallelic single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus keta. Samples included 4164 individuals from 43 populations ranging from Coastal Western Alaska to southern British Colombia and northern Washington. Signatures of natural selection were detected by identifying seven outlier loci using two independent approaches: one based on outlier detection and another based on environmental correlations. Evidence of divergent selection at two candidate SNP loci, Oke_RFC2-168 and Oke_MARCKS-362, indicates significant environmental correlations, particularly with the number of frost-free days (NFFD). Important associations found between environmental variables and outlier loci indicate that those environmental variables could be the major driving forces of allele frequency divergence at the candidate loci. NFFD, in particular, may play an important adaptive role in shaping genetic variation in O. keta. Correlations between divergent selection and local environmental variables will help shed light on processes of natural selection and molecular adaptation to local environmental conditions.

Research paper thumbnail of Identification of Chemotypic Markers in Three Chemotype Categories of Cannabis Using Secondary Metabolites Profiled in Inflorescences, Leaves, Stem Bark, and Roots

Frontiers in Plant Science, 2021

Previous chemotaxonomic studies of cannabis only focused on tetrahydrocannabinol (THC) dominant s... more Previous chemotaxonomic studies of cannabis only focused on tetrahydrocannabinol (THC) dominant strains while excluded the cannabidiol (CBD) dominant strains and intermediate strains (THC ≈ CBD). This study investigated the utility of the full spectrum of secondary metabolites in different plant parts in three cannabis chemotypes (THC dominant, intermediate, and CBD dominant) for chemotaxonomic discrimination. Hierarchical clustering, principal component analysis (PCA), and canonical correlation analysis assigned 21 cannabis varieties into three chemotypes using the content and ratio of cannabinoids, terpenoids, flavonoids, sterols, and triterpenoids across inflorescences, leaves, stem bark, and roots. The same clustering results were obtained using secondary metabolites, omitting THC and CBD. Significant chemical differences were identified in these three chemotypes. Cannabinoids, terpenoids, flavonoids had differentiation power while sterols and triterpenoids had none. CBD dominan...

Research paper thumbnail of HMNinv_gen.txt

Genotype data (Genepop format) for 8 microsatellite loci for 49 invasive populations of Heracleum... more Genotype data (Genepop format) for 8 microsatellite loci for 49 invasive populations of Heracleum mantegazzianum from the western Swiss Alps

Research paper thumbnail of Data from: Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps

The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as we... more The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analyzed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, ten clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum

Research paper thumbnail of Cannabis chemovar classification: terpenes hyper-classes and targeted genetic markers for accurate discrimination of flavours and effects

The classification of Cannabis varieties has been increasingly discussed in the past years, parti... more The classification of Cannabis varieties has been increasingly discussed in the past years, particularly in the wake of emerging legal markets, with implications for intellectual property development, marketing and improvement of the scientific understanding of this contentious plant. While the concept of chemovars has been proposed and has gained popularity of late, the lack of guidance in introducing this concept and the fact that chemovars are based on indirectly assessed traits with a heritable basis has likely impeded the implementation of the concept to a broader audience. Here I propose a simplified version of terpene hyper-classes based on three dominant terpenes that is shown to outperformed the classic indica-sativa-hybrid scheme of classification as well as a recently proposed terpene super-class scheme. This information was used to identify the most informative genetic markers for chemovar classification based on the terpene hyper-classes. I demonstrate the ability of cl...

Research paper thumbnail of Genome-wide triallelic single nucleotide polymorphisms as genetic markers to separate three chemotypes of cannabis strains

The whole-genomes of 23 cannabis strains marketed in Canada were sequenced, aligned to a referenc... more The whole-genomes of 23 cannabis strains marketed in Canada were sequenced, aligned to a reference genome assembly ASM23057v4 of a drug type strain Purple Kush (PK) in the NCBI BioProject database under accession number PRJNA73819. Here we deposited the SNP files for these 23 strains, which were used to study the genetic structure and identify genetic markers to differentiate three chemotypes strains.

Research paper thumbnail of HMNnative_gen.txt

Research paper thumbnail of The Cannabis-Human relationship

Presentation given at Womens Grow signature event in Kelowna BC on July 16 2016.

Research paper thumbnail of Two Single Nucleotide Polymorphisms Tease Apart Hemp, CBDA and THCA Expressing Cannabis

Research paper thumbnail of Neighbour joining tree of ITS sequences available on NCBI. Powdery mildew from cannabis cluster closer to Golovinomyces spadiceus, also known to cause PM in sunflower

Research paper thumbnail of Multivariate chemical analyses of common Cannabis cultivars

Research paper thumbnail of Henry et al., cannabis genetic data (VCF and CSV) for 1409 SNP and 38 highly informative SNPs along with Neighbour joining tree (Supplentarry Figure 1), as well as chemotypic data for the same accessions (Supplementary Table 1)

Two VCF (and CSV) files containing 1409 SNPs and 38 highly informative SNPs to predict terpenoid ... more Two VCF (and CSV) files containing 1409 SNPs and 38 highly informative SNPs to predict terpenoid expression and inform individual identification in vegetative cannabis accessions.<br>Supplementary Table 1. Chemotypic data for 70 accessions used in this study. RSPID numbers can be entered into http://kannapedia.net to retrieve original submission and individual VCF files from MGC.<br>Supplementray Figure 1. NJ-tree of the 70 accessions demonstrating lack of confidence in strain names vs clustering of accessions.

Research paper thumbnail of Discordant signals of genetic differentiation in the Cannabis genus based on SNP and SSR data

Recently published studies have identified contrasting patterns of clustering in the Cannabis gen... more Recently published studies have identified contrasting patterns of clustering in the Cannabis genus based on Single Nulceotide Polymorphism (SNPs) and microsatellite (SSR) markers. Here we review the differences of previously identified population structure with particular focus on the affinity of NLD, BLD and NLH Cannabis varieties.

Research paper thumbnail of Applying Genomic tools to Cannabis Breeding

Research paper thumbnail of Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

PLoS ONE, 2021

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strain... more The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a refe...

Research paper thumbnail of On Domestication and Feralization: re-rethinking invasive species from a genetic perspective

A photograph of the author during his MSc work on invasive giant hogweeds, undertaken at the Univ... more A photograph of the author during his MSc work on invasive giant hogweeds, undertaken at the University of Lausanne, Switzerland. The thesis, like many others assumes that invasive are aggressive species that will displace natives and result in the loss of biodiversity. The new wild and the concepts that emanate from it extends our static understanding of invasive species and their genes to provide alternative ways in which any species may cope with the drastic and unprecedented pace of climate change. Had the author had the clairvoyance afforded by experience, he may have come up with this theory on his own. Luckily, humanity has one large connected network of brains that operate through open access to knowledge and data and we influence each other in better our understanding of the world that surrounds us. Paradigm shifts are open for all, you may be next in line!

Research paper thumbnail of The cannabis-human relationship

Research paper thumbnail of Identification of Phenotypic Characteristics in Three Chemotype Categories in the Genus Cannabis

HortScience

Modern Cannabis cultivars are morphologically distinguished by their leaflet shapes (wide for “In... more Modern Cannabis cultivars are morphologically distinguished by their leaflet shapes (wide for “Indica” and narrow for “Sativa”) by users and breeders. However, there are no scientific bases or references for determining the shape of these leaflets. In addition, these two categories contained mostly THC dominant (high THC) cultivars while excluded CBD dominant (high CBD) and intermediate (intermediate level of both THC and CBD) cultivars. This study investigated the phenotypic variation in 21 Cannabis cultivars covering three chemical phenotypes, referred to as chemotypes, grown in a commercial greenhouse. Thirty morphological traits were measured in the vegetative, flowering, and harvest stages on live plants and harvested inflorescences. The collected data were subjected to correlation analysis, hierarchical clustering, principal component analysis, and canonical correlation analysis with preassigned chemotypes. Canonical correlation analysis assigned individual plants to their che...

Research paper thumbnail of A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife pop... more Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife populations. A number of studies have reported using noninvasive sampling techniques to investigate population genetics and demography of wild populations 1. This approach has proven to be especially useful when dealing with rare or elusive species 2

Research paper thumbnail of A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

Molecular Ecology Resources, 2008

This study reports the isolation and polymorphism characterization of four plastid indels and six... more This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.

Research paper thumbnail of Title: Single nucleotide polymorphisms shed light on correlations between environmental vairalbe and adaptive genetic divergence in Chum salmon (Oncorhynchus keta)

Identifying the genetic and ecological basis of adaptation is of immense importance in evolutiona... more Identifying the genetic and ecological basis of adaptation is of immense importance in evolutionary biology. In our study, we applied a panel of 58 biallelic single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus keta. Samples included 4164 individuals from 43 populations ranging from Coastal Western Alaska to southern British Colombia and northern Washington. Signatures of natural selection were detected by identifying seven outlier loci using two independent approaches: one based on outlier detection and another based on environmental correlations. Evidence of divergent selection at two candidate SNP loci, Oke_RFC2-168 and Oke_MARCKS-362, indicates significant environmental correlations, particularly with the number of frost-free days (NFFD). Important associations found between environmental variables and outlier loci indicate that those environmental variables could be the major driving forces of allele frequency divergence at the candidate loci. NFFD, in particular, may play an important adaptive role in shaping genetic variation in O. keta. Correlations between divergent selection and local environmental variables will help shed light on processes of natural selection and molecular adaptation to local environmental conditions.

Research paper thumbnail of Identification of Chemotypic Markers in Three Chemotype Categories of Cannabis Using Secondary Metabolites Profiled in Inflorescences, Leaves, Stem Bark, and Roots

Frontiers in Plant Science, 2021

Previous chemotaxonomic studies of cannabis only focused on tetrahydrocannabinol (THC) dominant s... more Previous chemotaxonomic studies of cannabis only focused on tetrahydrocannabinol (THC) dominant strains while excluded the cannabidiol (CBD) dominant strains and intermediate strains (THC ≈ CBD). This study investigated the utility of the full spectrum of secondary metabolites in different plant parts in three cannabis chemotypes (THC dominant, intermediate, and CBD dominant) for chemotaxonomic discrimination. Hierarchical clustering, principal component analysis (PCA), and canonical correlation analysis assigned 21 cannabis varieties into three chemotypes using the content and ratio of cannabinoids, terpenoids, flavonoids, sterols, and triterpenoids across inflorescences, leaves, stem bark, and roots. The same clustering results were obtained using secondary metabolites, omitting THC and CBD. Significant chemical differences were identified in these three chemotypes. Cannabinoids, terpenoids, flavonoids had differentiation power while sterols and triterpenoids had none. CBD dominan...

Research paper thumbnail of HMNinv_gen.txt

Genotype data (Genepop format) for 8 microsatellite loci for 49 invasive populations of Heracleum... more Genotype data (Genepop format) for 8 microsatellite loci for 49 invasive populations of Heracleum mantegazzianum from the western Swiss Alps

Research paper thumbnail of Data from: Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps

The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as we... more The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analyzed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, ten clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum

Research paper thumbnail of Cannabis chemovar classification: terpenes hyper-classes and targeted genetic markers for accurate discrimination of flavours and effects

The classification of Cannabis varieties has been increasingly discussed in the past years, parti... more The classification of Cannabis varieties has been increasingly discussed in the past years, particularly in the wake of emerging legal markets, with implications for intellectual property development, marketing and improvement of the scientific understanding of this contentious plant. While the concept of chemovars has been proposed and has gained popularity of late, the lack of guidance in introducing this concept and the fact that chemovars are based on indirectly assessed traits with a heritable basis has likely impeded the implementation of the concept to a broader audience. Here I propose a simplified version of terpene hyper-classes based on three dominant terpenes that is shown to outperformed the classic indica-sativa-hybrid scheme of classification as well as a recently proposed terpene super-class scheme. This information was used to identify the most informative genetic markers for chemovar classification based on the terpene hyper-classes. I demonstrate the ability of cl...

Research paper thumbnail of Genome-wide triallelic single nucleotide polymorphisms as genetic markers to separate three chemotypes of cannabis strains

The whole-genomes of 23 cannabis strains marketed in Canada were sequenced, aligned to a referenc... more The whole-genomes of 23 cannabis strains marketed in Canada were sequenced, aligned to a reference genome assembly ASM23057v4 of a drug type strain Purple Kush (PK) in the NCBI BioProject database under accession number PRJNA73819. Here we deposited the SNP files for these 23 strains, which were used to study the genetic structure and identify genetic markers to differentiate three chemotypes strains.

Research paper thumbnail of HMNnative_gen.txt

Research paper thumbnail of The Cannabis-Human relationship

Presentation given at Womens Grow signature event in Kelowna BC on July 16 2016.

Research paper thumbnail of Two Single Nucleotide Polymorphisms Tease Apart Hemp, CBDA and THCA Expressing Cannabis

Research paper thumbnail of Neighbour joining tree of ITS sequences available on NCBI. Powdery mildew from cannabis cluster closer to Golovinomyces spadiceus, also known to cause PM in sunflower

Research paper thumbnail of Multivariate chemical analyses of common Cannabis cultivars

Research paper thumbnail of Henry et al., cannabis genetic data (VCF and CSV) for 1409 SNP and 38 highly informative SNPs along with Neighbour joining tree (Supplentarry Figure 1), as well as chemotypic data for the same accessions (Supplementary Table 1)

Two VCF (and CSV) files containing 1409 SNPs and 38 highly informative SNPs to predict terpenoid ... more Two VCF (and CSV) files containing 1409 SNPs and 38 highly informative SNPs to predict terpenoid expression and inform individual identification in vegetative cannabis accessions.<br>Supplementary Table 1. Chemotypic data for 70 accessions used in this study. RSPID numbers can be entered into http://kannapedia.net to retrieve original submission and individual VCF files from MGC.<br>Supplementray Figure 1. NJ-tree of the 70 accessions demonstrating lack of confidence in strain names vs clustering of accessions.

Research paper thumbnail of Discordant signals of genetic differentiation in the Cannabis genus based on SNP and SSR data

Recently published studies have identified contrasting patterns of clustering in the Cannabis gen... more Recently published studies have identified contrasting patterns of clustering in the Cannabis genus based on Single Nulceotide Polymorphism (SNPs) and microsatellite (SSR) markers. Here we review the differences of previously identified population structure with particular focus on the affinity of NLD, BLD and NLH Cannabis varieties.

Research paper thumbnail of Applying Genomic tools to Cannabis Breeding

Research paper thumbnail of Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

PLoS ONE, 2021

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strain... more The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a refe...

Research paper thumbnail of On Domestication and Feralization: re-rethinking invasive species from a genetic perspective

A photograph of the author during his MSc work on invasive giant hogweeds, undertaken at the Univ... more A photograph of the author during his MSc work on invasive giant hogweeds, undertaken at the University of Lausanne, Switzerland. The thesis, like many others assumes that invasive are aggressive species that will displace natives and result in the loss of biodiversity. The new wild and the concepts that emanate from it extends our static understanding of invasive species and their genes to provide alternative ways in which any species may cope with the drastic and unprecedented pace of climate change. Had the author had the clairvoyance afforded by experience, he may have come up with this theory on his own. Luckily, humanity has one large connected network of brains that operate through open access to knowledge and data and we influence each other in better our understanding of the world that surrounds us. Paradigm shifts are open for all, you may be next in line!

Research paper thumbnail of The cannabis-human relationship

Research paper thumbnail of Identification of Phenotypic Characteristics in Three Chemotype Categories in the Genus Cannabis

HortScience

Modern Cannabis cultivars are morphologically distinguished by their leaflet shapes (wide for “In... more Modern Cannabis cultivars are morphologically distinguished by their leaflet shapes (wide for “Indica” and narrow for “Sativa”) by users and breeders. However, there are no scientific bases or references for determining the shape of these leaflets. In addition, these two categories contained mostly THC dominant (high THC) cultivars while excluded CBD dominant (high CBD) and intermediate (intermediate level of both THC and CBD) cultivars. This study investigated the phenotypic variation in 21 Cannabis cultivars covering three chemical phenotypes, referred to as chemotypes, grown in a commercial greenhouse. Thirty morphological traits were measured in the vegetative, flowering, and harvest stages on live plants and harvested inflorescences. The collected data were subjected to correlation analysis, hierarchical clustering, principal component analysis, and canonical correlation analysis with preassigned chemotypes. Canonical correlation analysis assigned individual plants to their che...

Research paper thumbnail of A Noninvasive Hair Sampling Technique to Obtain High Quality DNA from Elusive Small Mammals

Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife pop... more Noninvasive genetic sampling approaches are becoming increasingly important to study wildlife populations. A number of studies have reported using noninvasive sampling techniques to investigate population genetics and demography of wild populations 1. This approach has proven to be especially useful when dealing with rare or elusive species 2

Research paper thumbnail of A set of primers for plastid indels and nuclear microsatellites in the invasive plant Heracleum mantegazzianum (Apiaceae) and their transferability to Heracleum sphondylium

Molecular Ecology Resources, 2008

This study reports the isolation and polymorphism characterization of four plastid indels and six... more This study reports the isolation and polymorphism characterization of four plastid indels and six nuclear microsatellite loci in the invasive plant Heracleum mantegazzianum. These markers were tested in 27 individuals from two distant H. mantegazzianum populations. Plastid indels revealed the presence of five chlorotypes while five nuclear microsatellite loci rendered polymorphism. Applications of these markers include population genetics and phylogeography of H. mantegazzianum. A very good transferability of markers to Heracleum sphondylium was demonstrated.