Yamama Naciri

Yamama Naciri
Conservatoire et Jardin botaniques de la Ville de Genève | CJB · Plant Systematics and Biodiversity Laboratory

PhD
Presently working on species delimitation

About

143
Publications
21,884
Reads
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Citations
Introduction
I am currently working on species delimitation in a highly diverse genus of Malagasy Sapotaceae Capurodendron using NGS data (gene capture). With my colleague, L. Gautier, and a post-doctoral fellow, C.G. Boluda, we aim at understanding the drivers of the radiation that occurred in that genus. With a PhD student A. Randririsoa, we also started a revision of all Sapotaceae of Madagascar.Besides, I am working on Hyphaene (Arecaceae), the invasion dynamics of Trachycarpus in Switzerland and Silene.
Additional affiliations
November 2015 - present
Conservatoire et Jardin botaniques de la Ville de Genève
Position
  • Head of Department
January 2010 - present
University of Geneva
Position
  • Lecturer
April 1999 - October 2015
Conservatoire et Jardin botaniques de la Ville de Genève
Position
  • Research officer, Head of the Molecular Laboratory
Education
January 1988 - January 1992
Université Paris-Sud 11
Field of study
  • Quantitative genetics & plant improvement
September 1984 - October 1987
Institut National Agronomique de Paris-Grignon
Field of study
  • Plant Improvement

Publications

Publications (143)
Article
Full-text available
An increasing number of studies using genetic data at the generic and species levels reveal complex patterns of relationships among populations and species. Incomplete lineage sorting and reticulation are, for instance, commonly observed in low-rank phylogenies. These two processes falsify the simplifying assumptions often used when reconstructing...
Article
Zelkova species, trees of the elm family (Ulmaceae), are part of the Cenozoic relict flora. In western Eurasia, the genus comprises three species that are restricted to disjunct areas (Z. sicula on Sicily, Z. abelicea on Crete and Z. carpinifolia in Transcaucasia). The situation is different in East Asia, where three species (Z. serrata, Z. schneid...
Article
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic st...
Book
Full-text available
This booklet is dedicated to teenagers ad has been issued in the context of the open-air exhibition 'The grand bazaar of evolution' that is presently installed in the Conservatoire & Jardin botanique de Genève (from May 20th to October 17th 2021)
Article
Full-text available
The Malagasy genus Capurodendron currently accommodates 26 described species and is the largest genus of the family Sapotaceae in Madagascar. These species are frequently logged because of their valued hardwood, which potentially puts them at risk of extinction. Species‐level identifications are often problematic, and this hinders both an accurate...
Article
Full-text available
Background Investigations of evolution knowledge and acceptance and their relation are central to evolution education research. Ambiguous results in this field of study demonstrate a variety of measuring issues, for instance differently theorized constructs, or a lack of standardized methods, especially for cross-country comparisons. In particular,...
Article
Full-text available
Capurodendron is the largest endemic genus of plants from Madagascar, with around 76% of its species threatened by deforestation and illegal logging. However, some species are not well circumscribed and many of them remain undescribed, impeding a confident evaluation of their conservation status. Here we focus on taxa delimitation and conservation...
Article
Large phylogeographic studies on lichens are scarce, and none involves a single species within which different lineages show fixed alternative dispersal strategies. We investigated Bryoria fuscescens (including B. capillaris) in Europe and western North Africa by phenotypically characterizing 1400 specimens from 64 populations and genotyping them w...
Article
Using molecular data to delimit species or reconstruct their evolutionary history is now widely used across all organisms. However, such analyses can suffer from poor or false specimen identifications leading to incorrect conclusions. Here we show that the use of misidentified specimens in a phylogenetic framework resulted in questionable conclusio...
Article
Full-text available
Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS....
Technical Report
Full-text available
This exploratory study aims to describe the learning opportunities in evolution across Europe in non-formal contexts. To better understand the current situation as well as to describe the landscape in evolution-themed, lifelong learning in Europe, we in the Working Group "Informal Educators" of the EU COST Action EuroScitizen have undertaken a lite...
Article
Full-text available
Randriarisoa, A., Y. Naciri & L. Gautier (2020). Labramia ambondrombeensis (Sapotaceae), a Critically Endangered new species from Madagascar. Candollea 75: 83–87. In English, English and French abstracts. Timber of the family Sapotaceae are appreciated for their physical properties internationally as well as locally, which often put a serious press...
Book
Full-text available
This is a booklet about evolution for teenagers
Book
Full-text available
Relict tree genus Zelkova: short presentation Zelkova is a small genus of relict trees belonging to the elm family (Ulmaceae). Species of Zelkova were important elements of the vast forests that prevailed throughout the Northern Hemisphere during much of the Cenozoic Era. The oldest fossils that are attributed to Zelkova date from the early Eocene...
Article
Biological processes such as hybridization, incomplete lineage sorting and gene flow can obscure the recognition of distinct evolutionary lineages, particularly in groups of organisms that have recently diverged. Therefore, compiling pieces of evidence from diverse data sources is critical to accurately assess species boundaries in such groups. The...
Article
Full-text available
Here we describe the origins, current advances and future perspectives of the “Hyphaene Project”, a multidisciplinary research effort aiming to expand our knowledge of the enigmatic genus Hyphaene (8 species), which ranks among the most economically important, yet extremely poorly known coryphoid palm genera. The genus was monographed about one cen...
Article
Full-text available
Gautier, L. & Y. Naciri (2018). Three Critically Endangered new species of Capurodendron (Sapotaceae) from Madagascar. Candollea 73: 121–129. In English, English and French abstracts. DOI: http://dx.doi.org/10.15553/c2018v731a13 Three new species in the Malagasy endemic genus Capurodendron Aubrév. (Sapotaceae) are described and illustrated. Their p...
Conference Paper
Full-text available
EUROPEAN BOTANIC GARDENS IN THE DECADE ON BIODIVERSITY CHALLENGES AND RESPONSABILITIES IN THE COUNT-DOWN TOWARDS 2020
Article
The Silene gigantea complex is characterized by a high degree of morphological variability that resulted in the description of three subspecies across its distribution range from the Balkan Peninsula to South-west Asia and Cyprus. In this work, we used nuclear and plastid markers in Bayesian phylogeographic analyses to investigate the taxonomy and...
Article
Full-text available
Silene sect. Siphonomorpha (Caryophyllaceae) has historically either been split into three different and homogeneous entities (sect. Italicae, sect. Paradoxae, sect. Siphonomorpha s.str.) or considered as a single group (sect. Siphonomorpha s.l.). In this study, we investigate the delimitation of sect. Siphonomorpha s.l. and the three subgroups, in...
Book
Full-text available
This booklet accompanies the exhibit The Many Lives of Herbaria opened to the public of Cabinet de Curiosités at the Conservatory and Botanical Garden of Geneva (March 2017-December 2018). It gives information about the history of the herbariumn of Geneva and its main collections as well as insights into its management as a dynamic research facilit...
Article
Full-text available
Background: Four plastid regions, rpoB, rpoC1, matK, and trnH-psbA, have been recommended as DNA barcodes for plants. Their success in delimiting species boundaries depends on the existence of a clear-cut difference between inter- and intraspecific variability. We tested the ability of these regions to discriminate among closely related species in...
Article
Full-text available
The Kuhl’s pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages....
Conference Paper
Full-text available
For good reasons, botanic gardens are often considered as infrastructures providing valuable services for researchers. Greenhouses allow growing species that could not survive under the local climates otherwise, therefore facilitating their observation and characterisation. Many other examples of such interactions exist and could be found in the nu...
Article
Full-text available
JEANMONOD, D., Y. NACIRI, A. SCHLÜSSEL & J. GAMISANS (2015). Floristic analyses of the Corsican flora : biogeographical origin and endemism. This article discusses various aspects of the biogeographical origin and endemism of the Corsican flora based on data retrieved from " Flora Corsica " project. It focuses on species richness, taxonomy, life fo...
Article
We investigated the morphology of the Silene gigantea complex across its distribution range in the Balkan Peninsula, south-western Turkey and Cyprus. We performed a factorial analysis for mixed quantitative and qualitative variables followed by k-means analyses to determine the most probable morphological clustering within the species. A linear dis...
Article
Full-text available
In the sixth paragraph of the Discussion section entitled “Regional Diversification in Manilkara,” in the sentence beginning “In Sapotaceae four lineages of Isonandreae have migrated… ” the citation of Swenson et al., 2008 should instead be: Swenson, U., Nylinder, S., and Munzinger, J. (2014). Sapotaceae biogeography supports New Caledonia being an...
Article
Full-text available
Species diversity is unequally distributed across the globe, with the greatest concentration occurring in the tropics. Even within the tropics, there are significant differences in the numbers of taxa found in each continental region. Manilkara is a pantropical genus of trees in the Sapotaceae comprising c. 78 species. Its distribution allows for b...
Conference Paper
Full-text available
A growing number of molecular surveys have shown that a single fragment of the mitochondrial genome can identify most species of vertebrates, including those that are elusive for direct observation, such as bats. One desirable property of such barcode approach to identify species is that interspecific genetic distances are larger than intraspecific...
Article
Full-text available
Botanic gardens and arboreta, particularly in regions where iconic relict trees naturally occur, play a vital role in the conservation of these species. Maintaining well-managed living ex situ collections of rare and threatened relict tree species provides an immediate insurance policy for the future species conservation. The aim of this research w...
Article
Aim To elucidate the phylogeographical patterns in three Cenozoic relict spe-cies: Zelkova sicula, Z. abelicea and Z. carpinifolia (Ulmaceae). Location Sicily, Crete and Transcaucasia. Methods Two chloroplast loci (trnH–psbA and trnL) and the nuclear ribo-somal markers ITS1 and ITS2 were sequenced for 154 samples collected from 14 populations of Z....
Article
We investigate the genetic diversity and demographic patterns of the Silene paradoxa group from section Siphonomorpha, which includes the three species S. paradoxa, S. fruticosa and S. aristidis. Eight additional taxa, belonging to the same section, were also included in this study for comparative purposes: S. nutans, S. viridiflora and six species...
Article
Aim To elucidate the phylogeographical patterns in three Cenozoic relict species: Zelkova sicula, Z. abelicea and Z. carpinifolia (Ulmaceae). Location Sicily, Crete and Transcaucasia. Methods Two chloroplast loci (trnH–psbA and trnL) and the nuclear ribo-somal markers ITS1 and ITS2 were sequenced for 154 samples collected from 14 populations of Z....
Article
Full-text available
Species diversity is unequally distributed across the globe, with the greatest concentration occurring in the tropics. Even within the tropics, there are significant differences in the numbers of taxa found in each continental region. Manilkara is a pantropical genus of trees in the Sapotaceae comprising c. 78 species. Its distribution allows for b...
Experiment Findings
Full-text available
Depuis deux ans, les interactions entre le Jardin et l’Unité de phylogénie et de génétique moléculaires se sont intensifiées. Sous l’impulsion du Jardin, plusieurs demandes ont été faites d’utiliser des marqueurs moléculaires pour identifier des plantes en culture ou des néophytes
Article
Full-text available
Phylogenetic relationships of the two Malagasy Sapotaceae endemic genera Capurodendron and Tsebona have been unclear until now. Recent collections from Madagascar as well as a better representation of the tribe Isonandreae, altogether 95 terminals, were used to estimate a phylogeny of subfamily Sapotoideae. We analysed sequences of nrDNA (ITS) and...
Conference Paper
Full-text available
Although a relatively small country, Switzerland contains multiple climatic zones and harbors remarkable levels of biodiversity (an estimated 50,000-70,000 species). DNA sequence data exist for very few groups and little is known about the genetic diversity that exists both within and among most species. To fill this gap, the Swiss Barcode of Life...
Article
This study puts together genetic data and an approximate bayesian computation (ABC) approach to infer the time at which the tree Geoffroea spinosa colonized the Galápagos Islands. The genetic diversity and differentiation between Peru and Galápagos population samples, estimated using three chloroplast spacers and six microsatellite loci, reveal sig...
Article
Success of species assignment using DNA barcodes has been shown to vary among plant lineages because of a wide range of different factors. In this study, we confirm the theoretical prediction that gene flow influences species assignment with simulations and a literature survey. We show that the genome experiencing the highest gene flow is, in the m...
Conference Paper
Full-text available
Background / Purpose: Paralogous fragments transferred from the chloroplast into the nucleus (NuCp) seem to be pervasive in plants, although their impact is usually overlooked. The different steps that led to the identification of such NuCps in Eryngium alpinum are presented here. A search in Genbank for similar artifacts was also carried out Ma...
Chapter
In the previous chapter much attention was given to the study of the present status of the seasonally dry tropical forest (SDTF) in the Neotropics. Nevertheless, a broader picture of this ecosystem requires consideration of the historical events governing it. Herein, we address the major biogeographical hypotheses concerning the colonization of the...
Article
The history and diversification of the genus Ilex (Aquifoliaceae), based on 108 different species (116 specimens), are inferred from the analysis of two nuclear (ITS and nepGS) and three plastid (rbcL, trnL-F and atpB-rbcL) sequences. Nuclear and plastid trees are highly incongruent and the nuclear tree is more compatible with current taxonomic cla...
Article
Very divergent psbA-trnH chloroplast sequences were, for some Eryngiun alpinum individuals, repeatedly obtained and could not be attributed to contaminations nor to casual intraspecific variation. The design of external primers allowed the amplification of two different sequences for the same individuals. The divergent sequences were found to be mo...
Article
Primers for four loci that amplify cpDNA regions have been designed for population genetic analyses in Dicranum scoparium Hedw. and compared with trnL(UAA)5'exon-trnF. All loci showed intraspecific variation with a number of haplotypes ranging between two and six. trnH-psbA(Dic) showed an intercontinental disjunction, but no variability within the...
Article
Based on morphological characters, the North African Silene patula has been divided into two subspecies, ssp. patula found North of Kabylies and Atlas Mountains, and ssp. amurensis found south of these regions. In order to test the hypothesis that S. patula could have derived from S. italica through the Sicilian Channel during the Messinian, we seq...
Conference Paper
Full-text available
The Gentiana group Ciminalis comprises seven species distributed in the mountains of central and southern Europe. In the present study the phylogenetic positions of four Gentiana species within the Ciminalis group are addressed: G.acaulis, G. angustifolia, G. alpina and G. clusii.
Article
Full-text available
This study investigates how anatomical characters can be used to differentiate two morphologically close species, Melanohalea olivacea (L.) O. Blanco et al. and M. septentrionalis (Lynge) O. Blanco et al. Although the two species are morphologically differentiated, mainly based on the position and shape of pseudocyphellae on the lobes, poorly-devel...
Article
The Afro-Asiatic and Nilo-Saharan language families come into contact in Western Ethiopia. Ethnic diversity is particularly high in the South, where the Nilo-Saharan Nyangatom and the Afro-Asiatic Daasanach dwell. Despite their linguistic differentiation, both populations rely on a similar agripastoralist mode of subsistence. Analysis of mitochondr...
Conference Paper
Full-text available
Eryngium alpinum is an Apiaceae found at the sub-alpine level (1000-2500m) of the European Alps. It grows on calcareous substrates, most often in mown meadows and avalanche corridors. It is a long-lived hemicryptophyte with limited primary dispersal abilities but possible secondary dispersal mediated by animals or birds. Because population sizes dr...
Article
Today, the Seasonally Dry Tropical Forests (SDTF) of eastern South America occur as large, well-defined nuclei (e.g. Caatinga in the northeast) and as smaller enclaves within other vegetations (e.g. Cerrado and Chaco). In order to infer the way the present SDTF distribution was attained, the genetic structure of Astronium urundeuva, a tree confined...
Article
Full-text available
Tree species belonging to genus Astronium Jacq. (Anacardiaceae R. Br.) can be sometimes difficult to identify on the sole basis of the morphological traits of the leaves. Individuals collected from Paraguay and Argentina were a priori identified in the field as Astronium urundeuva (Allemão) Engl., Astronium balansae Engl. and Astronium fraxinifoliu...