Cryptic species and Miocene diversification of Palaearctic naked-toed geckos (Squamata: Gekkonidae) in the Indian dry zone

We sampled Palaearctic naked-toed geckos from across their range in India and used two mitochondrial and two nuclear genes to reconstruct relationships within a global phylogeny. Published sequences of Peninsular Indian Hemidactylus allow us to contrast these two groups in dating analyses - providing insights into the history of the Indian dry zone. Palaearctic naked-toed geckos first moved onto the Indian Plate in the Oligocene, with higher-level diversification probably linked to collision of the Indian and Eurasian plates, and subsequent dispersal into-India and diversification with increasing Miocene aridity. An independent gekkonid radiation with species in the dry zone, Hemidactylus diversified during the same period in Peninsular India. Our results demonstrate that dry zone taxa across India may date back to at least the Miocene, with a potential historical climatic barrier between the Indus and Peninsular Indian Divisions. `Cyrtopodion' aravallense is revealed to be a complex with seven genetically and environmentally divergent lineages that began diversifying in the late Miocene, congruent with increased aridity in north-western India. This discovery of cryptic diversity in the Indian dry zone represents the first terrestrial vertebrate radiation from north-western central India and highlights how little we understand of the regions' biodiversity, emphasizing the need for systematic geographic sampling and multiline evidence to reveal true patterns of diversity. The ancestor of `Cyrtopodion' aravallense came into the nascent Indian dry zone in the Miocene and has since diversified, potentially in the absence of any sympatric scansorial rupicolous geckos. Cyrtopodion scabrum represents a unique case of commensalism and shows phylogeographic structure in its presumed native range. The taxonomic implications of our study include a number of undescribed species, recognition of `Cyrtopodion' as a distinct lineage and the non-monophyly of Altiphylax.

Sun skink diversification across the Indian-Southeast Asian biogeographical interface

Aim Widespread, transcontinental vertebrate groups represent ideal systems for biogeographical studies, because they can shed light on a wide range of questions relating to species diversification across the geographical template. We combined extensive geographical and genetic sampling from across multiple biogeographical realms to examine the timing and location of diversification in Asian sun skinks, a clade characterized by problematic species boundaries and a particularly enigmatic evolutionary history. Location Indian subcontinent, the Philippines, Southeast Asia and Sundaland. Methods We sequenced one mitochondrial and nine nuclear genes for most species in the genus Eutropis, and estimated phylogenetic relationships and divergence times using coalescent methods. To investigate the location of diversification events, we also estimated ancestral geographical ranges using several methods. Finally, we explored patterns of genetic diversity within several poorly understood, but widely distributed species. Results Divergence-time estimates indicate that Eutropis began to diversify during the Eocene. Biogeographical reconstructions show that species diversification was associated with dispersal into three biogeographical realms: India, Sundaland and the Philippines. Main conclusions The results of this study clarify several questions related to the evolutionary history of Eutropis, and place them in the context of classic Southeast Asian biogeography. Our study represents one of the first to compile a heavily sampled multilocus dataset ranging across international boundaries in southern Asia that have historically prevented a unified understanding of biogeographical and evolutionary processes involving the Indian subcontinent, mainland southern Asia and the island archipelagos of Southeast Asia.

O Complexo Cliona celata Grant, 1826 (Porifera, Demospongiae) na América do Sul: uma abordagem molecular e morfológica

Este trabalho visou a averiguação do status taxonômico das esponjas bioerosivas do complexo Cliona celata da América do Sul por meio de técnicas moleculares, utilizando como marcadores a subunidade I da Citocromo c oxidase (cox1) e os Espaçadores Internos Transcritos do RNAr nuclear (ITS1 e ITS2), além de testar outros marcadores. Igualmente, avaliou o grau de variabilidade morfológica encontrado nessas espécies, principalmente por meio da morfometria dos tilóstilos, a fim de estabelecer uma diagnose para elas. Ainda, tentou determinar as relações filogenéticas dessas espécies com as demais esponjas bioerosivas utilizando o gene 28S do RNAr nuclear. Foi possível determinar a existência de cinco clados de esponjas bioerosivas do complexo Cliona celata para a América do Sul, e dois outros clados não-sulamericanos, por meio dos marcadores moleculares utilizados. Embora seja discutida a validade desses clados como espécies distintas, continua impossível, por meio de caracteres morfológicos, distingui-los, e dessa forma, a proposição formal de novas espécies é evitada. Através da reconstrução filogenética do grupo, é possível verificar que as esponjas bioerosivas analisadas se apresentaram como um grupo monofilético, e se separa em três principais clados: Pione, Spirastrellidae, e Clionaidae. Por meio desta, é sugerida a alocação das espécies do complexo C. viridis e C. schimidti dentro de Spirastrella, além de ser necessária a criação de um novo gênero para alocar as espécies do novo complexo identificado aqui, o complexo C. delitrix.

Diversidade genética em um grupo de anuros em miniatura endêmico da Mata Atlântica brasileira (Euparkerella Griffiths 1959).

A Mata Atlântica (MA) está entre as regiões com maior biodiversidade e mais ameaçadas do planeta. Esforços em diversas áreas do conhecimento têm sido feitos para que se tenha uma estimativa mais refinada da diversidade existente e sua organização ao longo do bioma. O crescente número de estudos que buscam reconstituir a história da diversificação da MA apontam para um cenário espacial e temporal complexo, havendo ainda uma lacuna no conhecimento dos processos em pequena escala. Vertebrados em miniatura têm se mostrado uma boa ferramenta para estudos de processos evolutivos em pequena escala. Assim, o gênero Euparkerella, endêmico de uma pequena região da MA dos Estados do Rio de Janeiro (RJ) e Espírito Santo (ES), foi escolhido como modelo para este estudo. No primeiro capítulo buscou-se descrever a diversidade existente dentro do gênero a partir de uma filogenia molecular. Para isso, utilizaram-se métodos bayesianos para gerar genealogias de genes e de espécies a partir de um fragmento de gene mitocondrial e quatro fragmentos de genes nucleares. Os resultados obtidos apontaram para uma grande diversidade críptica no gênero. Foram identificadas seis unidades evolutivas significativamente divergentes para o RJ: duas em Euparkerella cochranae, três em Euparkerella brasiliensis, e Euparkerella sp.. A espécie mais basal recuperada foi Euparkerella robusta, do ES, e estimou-se o início da diversificação do gênero para o final do Mioceno. O segundo capítulo descreve onze marcadores de microssatélites desenvolvidos para Euparkerella brasiliensis através do método de pirosequenciamento de nova geração 454. No terceiro capítulo estudou-se apenas uma unidade evolutiva, Euparkerella brasiliensis da área dos Três Picos/ RJ. A partir de marcadores de evolução rápida (microssatélites) e lenta (sequências de DNA) buscou-se compreender a estrutura e a dinâmica populacional desta unidade evolutiva em uma área bastante pequena (aprox. 20 km) sob influência de um gradiente ambiental altitudinal (40 m 1000 m). Foram identificadas, a partir dos microssatélites, duas subpopulações geneticamente distintas nas bordas do gradiente. O fluxo gênico se deu predominantemente das bordas para a zona de contato, onde foi observado o maior efetivo populacional. Tais resultados indicam que pequenas variações ambientais podem atuar no isolamento populacional em Euparkerella e corroboram o padrão de formas microendêmicas identificadas na filogenia. Futuros estudos devem ser feitos no sentido de buscar caracterizar morfologicamente as unidades evolutivas aqui identificadas; preencher as lacunas amostrais, especialmente no ES; e descrever os processos que atuam em pequena escala nas zonas de contato entre as unidades evolutivas e fatores limitantes a distribuição das mesmas.

稻属A基因组的分子系统发育--兼论亚洲栽培稻的起源

稻属Oryza隶属禾本科Poaceae，包括20多个野生种和2个栽培种(亚洲栽培稻O. sativa L和非洲栽培稻O. glaberrima Steud) ，广泛分布于全球热带和亚热带。稻属物种可划分为10个基因组(又称染色体组)类型：A, B, C, BC, CD, E, F, G, HJ 和 HK。栽培稻所属的A基因组是稻属中物种数目最多、地理分布最广的基因组类型，由8个种组成。由于栽培稻属于A基因组，故A基因组物种是栽培稻遗传改良的巨大基因源。数十年来，国际上许多学者对A基因组类群开展了大量涉及形态、细胞、同工酶和分子标记方面的研究，但由于A基因组物种间遗传关系十分接近，形态上差异小且地理分布重叠，使得A基因组物种的系统发育、物种起源和生物地理学等方面存在诸多悬而未决的问题，是稻属中分类和鉴定困难较多的类群。本文利用核基因内含子序列，结合转座子插入分析，重建了A基因组的系统发育，估测了各类群的分化时间;与此同时，基于多克隆测序和基因谱系分析，探讨了O. rufipogon和O. nivara遗传关系以及亚洲栽培稻起源。主要研究结果如下： 1. A基因组的系统发育 在水稻全基因组数据库搜索的基础上，测定了4个单拷贝核基因（Adh1 及3个未注释基因）的内含子序列，构建了稻属A基因组8个种的系统发育关系。基于最大简约法和贝叶斯法的系统发育分析表明：1）澳大利亚的O. meridionalis为A基因组的基部类群;2）亚洲栽培稻两个亚种O. sativa ssp. japonica 和 O. sativa ssp. indica分别和不同的野生类群聚为独立的两个分支，支持japonica 和 indica为多次起源;3）O. rufipogon和O. nivara在系统发育树上完全混在一起，显示出二者间不存在遗传分化;4）非洲一年生野生种O. barthii是非洲栽培稻O. glaberrima的祖先，而非洲多年生野生种O. longistaminata与O. glaberrima/O. barthii.亲缘关系较远;5）分子钟方法估测A基因组类群约在2百万年前（2.0MYA）开始分化，亚洲栽培稻和非洲栽培稻，以及亚洲栽培稻的两个亚种则分别在0.7和 0.4 MYA左右开始分化。此外，通过核基因内含子序列与其它常用片段如ITS，matK等对比分析表明，进化速率相对较快的核基因内含子序列可以有效地用于近缘类群的系统发育研究。 2. Oryza rufipogon 和O. nivara群体遗传研究及亚洲栽培稻起源 对于亚洲野生类群O. rufipogon和O. nivara是合并为一个种还是处理为两个独立的种一直存在争议。在系统发育研究基础上，我们选取4个核基因内含子或5’-UTR区（Waxy, LHS，CatA和1个未注释基因），对采自整个分布区的群体样品进行了多克隆测序，结果表明：1）检测到O. rufipogon和O. nivara均有较高的核苷酸多态性，4个位点上π值和θw值平均分别为0.011和0.014;2）且二者在遗传上没有明显分化，两个类群在4个核基因位点上均检测到大量共享多态（shared polymorphism），未发现固有差异(fixed difference)，表明它们历史上可能属于一个大群体，支持将二者作为种内不同生态型或亚种处理;3）基因谱系树表明亚洲栽培稻的两个亚种indica和japonica分别和不同的O. rufipogon (包括O. nivara)群体聚在一起，进一步从基因谱系角度支持亚洲栽培稻多次起源假说。 3．转座子在群体遗传与系统发育研究中的应用 鉴于目前植物谱系地理学研究中缺乏具有足够信息量的分子标记用于检测种内遗传变异，我们选取3个核基因中的转座子，通过对取自O. rufipogon和O. nivara整个分布区的37份样品的克隆测序，探讨了进化速率快、信息含量丰富的转座子序列在群体遗传上的应用。结果表明：1）无论在物种水平还是群体水平，转座子能检测到比包括内含子在内的其它DNA区域高得多的遗传变异;2）在物种水平上，异交多年生的O. rufipogon和自交一年生的O. nivara多样性均较高，且2个种间相差很小，二者在3个位点上平均核苷酸多样性π值均为0.013，差别主要表现在O. rufipogon杂合位点比例（46.1%）明显高于O. nivara（9.1%），说明交配系统不同并不一定和物种多样性水平相关;3）是否发生转座子序列插入是有价值的系统发育信息，发生在不同染色体上3个基因中的转座子插入进一步证实A基因组基部类群是O. meridionalis;通过叶绿体中3个转座子的插入现象推断了稻族一些四倍体物种，如稻属BC基因组的一些类群的母本来源。

食肉目哺乳动物的系统发育学研究概述

Carnivora; Caniformia; Feliformia; Phylogenetic tree; Mitochondrial DNA; Nuclear genes; 【摘要】 追溯生物界不同生物类型的起源及进化关系,即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容。食肉目哺乳动物位于食物链顶端,很多成员不仅在我国野生动物保护工作中占有重要地位,而且还是研究动物适应性进化遗传机制的重要模式生物。因而,食肉目物种作为物种资源中的一个重要类群,其系统发育学一直是国内外研究的热门课题。构建可靠的食肉目分子系统树,无疑将具有重要的进化理论意义和保护生物学价值。鉴于目前食肉目各科间系统发育关系仍然处于“广泛争论”的状态,本文将针对食肉目科水平上的系统发育学研究进展,包括来自于形态学特征、细胞学及分子生物学方面的证据,做简要概述,并提出目前研究中存在的问题。这对今后食肉目系统发育方面的进一步研究工作具有指导意义,并为以该类群作为模式生物开展适应性进化研究奠定基础

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

核基因在鸟类分子系统发育学研究中的应用

核基因作为一种新的遗传标记,近年来被广泛应用于鸟类分子系统发育研究中.核基因与线粒体基因位于不同的遗传载体上,因此被引入到系统发育学研究中为物种树的重建提供独立的证据.常用的外显子标记为重组激活基因1(RAG-1),重组激活基因2(RAG-2),癌基因c-myc,原癌基因c-mos,它们由于缓慢的进化速率而被用于鸟类高级分类阶元的系统学研究中.常用的内含子标记是β纤维蛋白原基因内含子7(β-fibrinogen intron7,β-fibint7),肌红蛋白基因内含子Ⅱ(myoglobin intionⅡ).内含子标记通常与线粒体序列联合使用,形成具有互补系统发育信号的数据集,应用于各种分类阶元的系统学研究中.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages

The four species of "river dolphins" are associated with six separate great river systems on three subcontinents and have been grouped for more than a century into a single taxon based on their similar appearance. However, several morphologists recently questioned the monophyly of that group. By using phylogenetic analyses of nucleotide sequences from three mitochondrial and two nuclear genes, we demonstrate with statistical significance that extant river dolphins are not monophyletic and suggest that they are relict species whose adaptation to riverine habitats incidentally insured their survival against major environmental changes in the marine ecosystem or the emergence of Delphinidae.

A new species of Pareledone (Cephalopoda : Octopodidae) from Antarctic Peninsula Waters

During recent cruises aboard RV Polarstern in the Antarctic Peninsula region, a new species of benthic octopodid was discovered whose generic affinities based on morphological characteristics were uncertain. Molecular sequence analysis of six mitochondrial and nuclear genes allows this species to be placed with confidence within the genus Pareledone. The species is described herein and morphological diagnostic characters are provided for its identification.

Genetic diversity of liver flukes (Fasciola hepatica) from Eastern Europe.

The genetic diversity of liver fluke populations in three different countries from Eastern Europe (Greece, Bulgaria, and Poland) in comparison with available data from other countries was determined. Specifically, SNPs from regions of two nuclear genes, 28S rDNA, ß-tubulin 3 and an informative region of the mitochondrial genome were examined. Two major lineages for the 28S rDNA gene based on the highly polymorphic 105th nucleotide position were found. These lineages were widely and almost equally spread not only through the countries studied but also in other investigated geographical areas. Two basic lineages and additional haplotypes were defined for the mtDNA gene region, consisting of the cytochrome c oxidase subunit III gene, transfer RNA histidine gene and cytochome b gene. The basic lineages were observed within Greek, Bulgarian, and Polish Fasciola hepatica populations but the distribution of additional haplotypes differed between the populations from the three countries. For the ß-tubulin 3 gene multiple polymorphic sites were revealed but no explicit clades. The SNPs were spread unequally in all studied geographical regions with an evident distinction between the Greek and Polish specimens. Additional genotypes for the 28S rDNA region as well as haplotypes of the mtDNA region that were typical for the Greek or Polish populations were observed. Significant polymorphisms for ß-tubulin 3 gene were displayed with decreasing percentage of presence within populations from Greece to Poland. There was an amino acid substitution in ß-tubulin 3 protein found only among Polish specimens. It is hypothesized that genotypic differences between Greek, Bulgarian, and Polish liver fluke populations are due to territorial division and genetic drift in past epochs.

Genetic risk factors affecting mitochondrial function are associated with kidney disease in people with Type 1 diabetes

AIM: To evaluate the association with diabetic kidney disease of single nucleotide polymorphisms (SNPs) that may contribute to mitochondrial dysfunction.

METHODS: The mitochondrial genome and 1039 nuclear genes that are integral to mitochondrial function were investigated using a case (n=823 individuals with diabetic kidney disease) vs. control (n=903 individuals with diabetes and no renal disease) approach. All people included in the analysis were of white European origin and were diagnosed with Type 1 diabetes before the age of 31 years. Replication was conducted in 5093 people with similar phenotypes to those of the discovery collection. Association analyses were performed using the plink genetic analysis toolset, with adjustment for relevant covariates.

RESULTS: A total of 25 SNPs were evaluated in the mitochondrial genome, but none were significantly associated with diabetic kidney disease or end-stage renal disease. A total of 38 SNPs in nuclear genes influencing mitochondrial function were nominally associated with diabetic kidney disease and 16 SNPS were associated with end-stage renal disease, secondary to diabetic kidney disease, with meta-analyses confirming the same direction of effect. Three independent signals (seven SNPs) were common to the replication data for both phenotypes with Type 1 diabetes and persistent proteinuria or end-stage renal disease.

CONCLUSIONS: Our results suggest that SNPs in nuclear genes that influence mitochondrial function are significantly associated with diabetic kidney disease in a white European population

A phylogenomics approach to resolving fungal evolution, and phylogenetic method development

Bien que les champignons soient régulièrement utilisés comme modèle d'étude des systèmes eucaryotes, leurs relations phylogénétiques soulèvent encore des questions controversées. Parmi celles-ci, la classification des zygomycètes reste inconsistante. Ils sont potentiellement paraphylétiques, i.e. regroupent de lignées fongiques non directement affiliées. La position phylogénétique du genre Schizosaccharomyces est aussi controversée: appartient-il aux Taphrinomycotina (précédemment connus comme archiascomycetes) comme prédit par l'analyse de gènes nucléaires, ou est-il plutôt relié aux Saccharomycotina (levures bourgeonnantes) tel que le suggère la phylogénie mitochondriale? Une autre question concerne la position phylogénétique des nucléariides, un groupe d'eucaryotes amiboïdes que l'on suppose étroitement relié aux champignons. Des analyses multi-gènes réalisées antérieurement n'ont pu conclure, étant donné le choix d'un nombre réduit de taxons et l'utilisation de six gènes nucléaires seulement. Nous avons abordé ces questions par le biais d'inférences phylogénétiques et tests statistiques appliqués à des assemblages de données phylogénomiques nucléaires et mitochondriales. D'après nos résultats, les zygomycètes sont paraphylétiques (Chapitre 2) bien que le signal phylogénétique issu du jeu de données mitochondriales disponibles est insuffisant pour résoudre l'ordre de cet embranchement avec une confiance statistique significative. Dans le Chapitre 3, nous montrons à l'aide d'un jeu de données nucléaires important (plus de cent protéines) et avec supports statistiques concluants, que le genre Schizosaccharomyces appartient aux Taphrinomycotina. De plus, nous démontrons que le regroupement conflictuel des Schizosaccharomyces avec les Saccharomycotina, venant des données mitochondriales, est le résultat d'un type d'erreur phylogénétique connu: l'attraction des longues branches (ALB), un artéfact menant au regroupement d'espèces dont le taux d'évolution rapide n'est pas représentatif de leur véritable position dans l'arbre phylogénétique. Dans le Chapitre 4, en utilisant encore un important jeu de données nucléaires, nous démontrons avec support statistique significatif que les nucleariides constituent le groupe lié de plus près aux champignons. Nous confirmons aussi la paraphylie des zygomycètes traditionnels tel que suggéré précédemment, avec support statistique significatif, bien que ne pouvant placer tous les membres du groupe avec confiance. Nos résultats remettent en cause des aspects d'une récente reclassification taxonomique des zygomycètes et de leurs voisins, les chytridiomycètes. Contrer ou minimiser les artéfacts phylogénétiques telle l'attraction des longues branches (ALB) constitue une question récurrente majeure. Dans ce sens, nous avons développé une nouvelle méthode (Chapitre 5) qui identifie et élimine dans une séquence les sites présentant une grande variation du taux d'évolution (sites fortement hétérotaches - sites HH); ces sites sont connus comme contribuant significativement au phénomène d'ALB. Notre méthode est basée sur un test de rapport de vraisemblance (likelihood ratio test, LRT). Deux jeux de données publiés précédemment sont utilisés pour démontrer que le retrait graduel des sites HH chez les espèces à évolution accélérée (sensibles à l'ALB) augmente significativement le support pour la topologie « vraie » attendue, et ce, de façon plus efficace comparée à d'autres méthodes publiées de retrait de sites de séquences. Néanmoins, et de façon générale, la manipulation de données préalable à l'analyse est loin d’être idéale. Les développements futurs devront viser l'intégration de l'identification et la pondération des sites HH au processus d'inférence phylogénétique lui-même.

Systématique moléculaire et biogéographie de trois genres malgaches menacés d'extinction Delonix, Colvillea et Lemuropisum (Caesalpinioideae: Leguminosae)

Ce mémoire porte sur les relations phylogénétiques, géographiques et historiques du genre afro-malgache Delonix qui contient onze espèces et des genres monospécifiques et endémiques Colvillea et Lemuropisum. Les relations intergénériques et interspécifiques entre les espèces de ces trois genres ne sont pas résolues ce qui limite la vérification d’hypothèses taxonomiques, mais également biogéographiques concernant la dispersion de plantes depuis ou vers Madagascar. Une meilleure compréhension des relations évolutives et biogéographiques entre ces espèces menacées d’extinction permettrait une plus grande efficacité quant à leur conservation. L’objectif de ce mémoire est de reconstruire la phylogénie des espèces à l’aide de régions moléculaires des génomes chloroplastique et nucléaire, d’identifier les temps de divergences entre les espèces et de reconstruire l’aire géographique ancestrale pour chacun des groupes. Ce projet démontre que le genre Delonix n’est pas soutenu comme étant monophylétique et qu’une révision taxonomique s’impose. Les relations intergénériques demeurent floues quant à la position phylogénétique de Colvillea et nos résultats suggèrent de l’hybridation ou un assortiment incomplet de cette lignée. Les espèces sont apparues et se sont diversifiées au Miocène à partir d’un ancêtre commun du sud de Madagascar. La phylogénie montre deux clades associés aux aires géographiques de répartition des espèces opposant les espèces largement répandues à celles majoritairement restreintes au fourré aride. Différentes hypothèses afin d’expliquer la dispersion des Delonix africains au Miocène à partir de Madagascar sont discutées. Un point de mire sur les interactions biotiques et abiotiques, passées et présentes, dans le fourré aride de Madagascar est recommandé en terme de conservation.