Une phylogénie du grade des Caesalpinieae inférée à partir de marqueurs nucléaires et chloroplastiques

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Historical, archaeological and linguistic evidence test the phylogenetic inference of Viking-Age plant use

In this paper, past plant knowledge serves as a case study to highlight the promise and challenges of interdisciplinary data collection and interpretation in cultural evolution. Plants are central to human life and yet, apart from the role of major crops, people–plant relations have been marginal to the study of culture. Archaeological, linguistic, and historical evidence are often limited when it comes to studying the past role of plants. This is the case in the Nordic countries, where extensive collections of various plant use records are absent until the 1700s. Here, we test if relatively recent ethnobotanical data can be used to trace back ancient plant knowledge in the Nordic countries. Phylogenetic inferences of ancestral states are evaluated against historical, linguistic, and archaeobotanical evidence. The exercise allows us to discuss the opportunities and shortcomings of using phylogenetic comparative methods to study past botanical knowledge. We propose a ‘triangulation method’ that not only combines multiple lines of evidence, but also quantitative and qualitative approaches. This article is part of the theme issue ‘Foundations of cultural evolution’

Giải mã hệ gen ở thực vật và các loài thuộc chi Nhân sâm (Panax L.)

Advances in genome sequencing technologies have created a new genomic era of life sciences research worldwide in which a number of modern and sophisticated techniques and tools have been developed and employed. Many countries have invested in plant genome sequencing as part of a sustainable development strategy. Each year, the number of plant genomes and transcriptomes sequenced has increased. The results obtained offer opportunities for fundamental and applied research, provide valuable data for identification of genes or molecular markers linked to traits that are important for selection, cultivation, and/or production. In Vietnam, partial or complete genome sequencing of crops has been recently conducted, primarily as part of international collaborative projects. The genus Panax L. (Araliaceae family) is comprised of several species of commercial value with narrow distributions such as P. bipinnatifidus Seem., P. stipuleanatus H.T.Tsai K.M.Feng, and Panax vietnamensis Ha et Grushv. Despite their very important roles in traditional medicine, understanding of their genetic characteristics is still limited. Molecular studies on the genus have, so far, only evaluated limited markers for phylogenetic analysis. Therefore, genome sequencing of these important herbal plants is needed to understand their genetic characteristics, their evolutionary history and the genes and biochemical pathways contributing to medicinally important metabolites. This review summarizes all related genome sequencing technologies including the most recent advances in the last decade and their applications in genome and transcriptome sequencing of plants in general and in the genus Panax L. in particular.Thành công trong việc phát triển các công nghệ giải trình tự gen đã mở ra thời kỳ phát triển mới trong nghiên cứu về khoa học sự sống với rất nhiều kỹ thuật phức tạp và hiện đại đã được phát triển và ứng dụng. Với chiến lược phát triển bền vững, nhiều nước trên thế giới đã đầu tư mạnh cho nghiên cứu giải mã và phân tích hệ gen ở các đối tượng thực vật. Hàng năm, số lượng các loài được giải mã hệ gen tăng lên nhanh chóng. Kết quả đạt được mở ra nhiều cơ hội cho các nghiên cứu cơ bản và ứng dụng, cung cấp dữ liệu cho việc tìm kiếm các chỉ thị phân tử liên quan đến các tính trạng quan trọng và xác định nguồn gen. Ở Việt Nam, nghiên cứu giải mã toàn bộ hoặc một phần hệ gen các loài cây trồng có giá trị chỉ được bắt đầu trong thời gian gần đây trong khuôn khổ các chương trình hợp tác quốc tế. Chi Nhân sâm bao gồm các loài cây rất có giá trị kinh tế với khu vực phân bố hẹp như Sâm vũ diệp (P. bipinnatifidus Seem.), Tam thất hoang (P. stipuleanatus H.T.Tsai K.M.Feng) và Sâm Ngọc linh hay còn gọi là Sâm việt nam (P. vietnamensis Ha et Grushv.)…Mặc dù là các loài dược liệu quý nhưng những hiểu biết về di truyền phân tử của các loài này còn rất hạn chế. Hiện nay, các nghiên cứu chỉ sử dụng một số chỉ thị phân tử để nhận dạng hay đánh giá đa dạng di truyền nguồn gen. Vì vậy, các nghiên cứu liên quan đến giải mã hệ gen, phát triển bộ mã vạch phân tử góp phần hiểu biết sâu hơn về các đặc tính di truyền phân tử và tiến hóa của loài. Bài viết này sẽ tổng quan một số công trình nghiên cứu về các công nghệ giải trình tự DNA/hệ gen trên thế giới và những ứng dụng trong giải mã hệ gen, hệ gen biểu hiện ở thực vật nói chung và các loài thuộc chi Nhân sâm nói riêng

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.publishedVersio

Travel Tales of a Worldwide Weed: Genomic Signatures of Plantago major L. Reveal Distinct Genotypic Groups With Links to Colonial Trade Routes

Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers and early colonists making transoceanic journeys; however, records are scarce to document this. We use genotyping-by-sequencing and genotype-likelihood methods on the selfing, global weed, Plantago major, collected from 50 populations worldwide to investigate how patterns of genomic diversity are distributed among populations of this global weed. Although genomic differentiation among populations is found to be low, we identify six unique genotype groups showing very little sign of admixture and low degree of outcrossing among them. We show that genotype groups are latitudinally restricted, and that more than one successful genotype colonized and spread into the introduced ranges. With the exception of New Zealand, only one genotype group is present in the Southern Hemisphere. Three of the most prevalent genotypes present in the native Eurasian range gave rise to introduced populations in the Americas, Africa, Australia, and New Zealand, which could lend support to the hypothesis that P. major was unknowlingly dispersed by early European colonists. Dispersal of multiple successful genotypes is a likely reason for success. Genomic signatures and phylogeographic methods can provide new perspectives on the drivers behind the historic introductions and the successful colonization of introduced species, contributing to our understanding of the role of genomic variation for successful establishment of introduced taxa.info:eu-repo/semantics/publishedVersio

Raising the bar - Molecular identification of plants

Up to a third of biodiversity is threatened due to the global economy and its international supply chains. The lack of global assessments of international supply chains and appropriate methods for the tractability of the traded products complicate the evaluation of the international trade’s impact on biodiversity loss. The goal of this thesis is, first, to explore new tech- nologies for traditional barcoding and metabarcoding, and then to develop alternative approaches to achieve better resolu- tion for the identification of species. Paper I shows illegal plant trade of orchids using standard barcoding markers and distance-based methods to identify traded species. These tools are also used in Paper II, which aims to identify adulteration and substitution of Hypericum perforatum L. herbal supplements. Paper III focuses on ginseng. This paper uses species delimitation approaches based on the phylogenomics of plastid genomes for the identification of ginseng species. Paper IV presents the evolution of Anacyclus and tests for hybridization using hundreds of nuclear genes. Then, in Paper V, traded market samples are used to understand the supply chain of Anacyclus pyrethrum