BACKGROUND:Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used / however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.RESULTS:Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.CONCLUSIONS:The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.

In this thesis I have connected different evolutionary studies of Lioalemus lizards. In Chapter 1, I followed an integrative approach to delimit species in the Liolaemus walkeri complex. Using mitochondrial markers, morphological data, bioclimatic information and methods appropriate for each data type, we found that the name L. walkeri was covering three new lineages. Three new species were described and one of them (L. chavin) is now categorized as Near Threatened in the IUCN red list. In Chapter 2, I change the subject from species boundaries to the study of viviparity and placentation. In this paper we employed scanning electron and confocal microscopy to compare the placental ultra-structure and pattern of blood vessels in two Liolaemus species. One of the most remarkable traits found is the complete reduction of the eggshell in both placentae, a possible adaptation to improve gas exchange in the hypoxic environments of the high Andes. In chapter 3, I returned to the issue of species delimitation and employed two integrative approaches: a hypothetical deductive framework and a model-based procedure. I applied both approaches in lowland and highland Liolaemus species of the montanus group. I found that in only one case (of four) an unnamed lowland lineage ("Nazca") was delimited concordantly by both procedures. In Chapter 4, I focus on a study of convergent evolution of desert phenotype in Liolaemus species and Ctenoblepharys adspersa. I performed a Bayesian time calibrated and maximum likelihood tree based on 55 taxa and seven molecular markers. We employed quantitative and categorical traits based on 400 specimens and non-metric multidimensional scaling to obtain new quantitative variables. I used three phylogenetic comparative methods to identify and measure the strength of convergence. My results found a strong case of convergent traits in C. adspersa, L. lentus, L. manueli, L. poconchilensis and L. stolzmanni that are probably related to predator avoidance in the Peruvian-Atacama and Monte deserts. In addition, my time calibrated tree resolves the origin of these traits first in C. adspersa at about 80 million years (My) and later independently in Liolaemus species at about 25 My suggesting the present of evolutionary constraints.

No description available.

Yes / There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. / This study was supported by the Research Foundation Flanders (grant 11A0618N), the Flanders Innovation and Entrepreneurship Agency (grants IWT-SB 141198 and IWT/50052), and the University of Antwerp (grant FFB150344).

I highlight two squamate lineages endemic to Southeast Asia, the Asian water monitors (Varanus salvator Complex) and the Angle-headed lizards (Agamidae: Gonocephalus), and elucidate their systematic affinities and historical biogeography. My results represent novel phylogenetic inferences, with biogeographic histories and diversification events corresponding to major climatic fluctuations over the past 30 million years. Additionally, I solidify the taxonomy and systematics of the Varanus salvator Complex, and enumerate more than a dozen Gonocephalus lineages as candidate species in need of taxonomic scrutiny. Lastly, I investigate contemporary and historical patterns of dispersal throughout Sundaland, and between Sundaland and the Philippines.

The inference of species boundaries and phylogenetic relationships are fundamental for evolutionary, ecological, and conservation studies. The resolution of species boundaries and the inference of phylogenetic relationships among species are required to define the units of analysis and to find the most closely related units for evaluating alternative models of speciation. I highlight lizards as model organisms for ecological and evolutionary studies, emphasizing their contributions to advances in understanding linkages between phylogeography and speciation. In this dissertation, I focus on the phylogenetic relationships of the lizards in the Liolaemus darwinii group, and the species boundaries of a nested clade within the group, the L. darwinii complex, because of several advantages that make these taxa ideal for phylogeographic studies of speciation. I infer a phylogeny for the L. darwinii group based on DNA sequences of 20 loci (19 nuclear and 1 mitochondrial) using species trees methods that take into account the incongruence among gene trees. I found the minimum number of loci, number of sequences per species, and number of base pairs per locus that should be included in an analysis for an accurate and precise estimate of the species tree. The species tree based on all available data support a clade of closely related species (L. darwinii, L. grosseorum, and L. laurenti) known as the L. darwinii complex. A new method for species delimitation using Approximate Bayesian Computation is introduced and is shown to accurately delimit species given that limited or no gene flow has occurred after divergence and despite biased estimates of demographic parameters. ABC analyses supported the distinctness of two lineages within L. darwinii under a model of speciation with gene flow. Based on the species tree and the species limits obtained in this dissertation, phylogenetic comparative methods can be carried out to address the morphological and ecological evolution in the L. darwinii group and several sister species can be used for testing the alternative speciation models via correlation analyses of genetic, morphological, and ecological datasets. Future studies should assess the role speciation due to adaptive processes and its association the species' ecological niches and life histories.

Les écosystèmes des eaux souterraines sont de plus en plus reconnus pour leur faune endémique, phylogénétiquement ancienne et écologiquement spécialisée. Avec plus de 425 espèces décrites, les amphipodes niphargidés constituent la famille des eaux souterraines la plus riche en espèces au monde et un système modèle intéressant pour la biologie de l'évolution. Cependant, les scientifiques doivent faire face à des données incomplètes et biaisées en raison de trois déficits majeurs: le déficit Linnéen pour la taxonomie, le déficit Darwinien pour la phylogénie, et le déficit Wallacien pour la biogéographie. La présente thèse vise à évaluer l'importance de ces déficits chez les niphargidés, ouvrant ainsi la voie pour y remédier. Le premier chapitre est une évaluation des effets de la découverte d'espèces cryptiques (une des causes du déficit Linnéen) sur notre compréhension des modèles de distribution à grande échelle de la diversité des niphargidés. Contrairement à ce que l'on attendait, les espèces cryptiques putatives sont réparties de manière homogène le long des gradients environnementaux, et leur découverte ne modifie donc pas notre compréhension des modèles de distribution. Le deuxième chapitre analyse l'importance de l'application des techniques moléculaires à la taxonomie des niphargidés. En étudiant le genre Microniphargus, la morphologie seule s'est avérée peu informative en raison de la pédomorphose et de l'homoplasie. L'utilisation de marqueurs ADN a permis d'attribuer le genre à une famille différente (Pseudoniphargidae), venant éclaircir les relations phylogénétiques au sein des Niphargidae (et contribuant ainsi à remédier au déficit Darwinien). Le troisième chapitre traite du rôle des régressions et transgressions marines sur la distribution des niphargidés en utilisant la biogéographie moléculaire et une modélisation biogéographique innovante (afin de remédier au déficit Wallacien). Les résultats soutiennent l'idée que la dispersion a joué un rôle essentiel dans la biogéographie historique des niphargidés, en montrant que leurs voies de dispersion sont corrélées à des événements paléogéographiques anciens. Enfin, le quatrième chapitre traite de la taxonomie, de la phylogénie et de la biogéographie d'un clade de niphargidés distribué dans la région des Alpes et des Carpates, et illustre un cas de discordance mitonucléaire dans la délimitation d'espèces vivant dans des zones affectées par les glaciations quaternaires. Une histoire complexe de divergence de lignées évolutives et de contacts secondaires pendant les fluctuations climatiques du Pléistocène explique la plus grande variabilité de l'ADN mitochondrial par rapport aux marqueurs nucléaires. Dans une telle situation, la description formelle d'espèces cryptiques basée sur le seul barcodage de l'ADN mitochondrial, comme dans certains articles récents sur les niphargidés, n'est pas recommandée. Cette thèse ouvre plusieurs perspectives pour des recherches futures basées sur la taxonomie intégrative et la modélisation biogéographique, permettant aux niphargidés très diversifiés de jouer un rôle majeur dans la surveillance des écosystèmes des eaux souterraines. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

The cosmopolitan echiniscid genus Hypechiniscus contains exclusively rare species. In this contribution, by combining statistical morphometry and molecular phylogeny, we present qualitative and quantitative aspects of Hypechiniscus diversity, which remained hidden under the two purportedly cosmopolitan species: H. gladiator and H. exarmatus. A neotype is designated for H. gladiator from Creag Meagaidh (Scotland), and an informal re-description is provided for H. exarmatus based on animals from Creag Meagaidh and the Isle of Skye (Inner Hebrides). Subspecies/forms of H. gladiator are suppressed due to the high developmental variability of the cirrus dorsalis. At the same time, four species of the genus are described: H. daedalus sp. nov. from Roan Mountain and the Great Smoky Mountains (Southern Appalachian Mountains, USA), H. flavus sp. nov. and H. geminus sp. nov. from the Yatsugatake Mountains (Honshu, Japan), and H. cataractus sp. nov. from the Malay Archipelago (Borneo and the Moluccas). Dorsal and ventral sculpturing, together with morphometric traits, are shown to be the key characters that allow for the phenotypic discrimination of species within the genus. Furthermore, the morphology of Hypechiniscus is discussed and compared to that of the most similar genera, Pseudechiniscus and Stellariscus. Finally, a diagnostic key to all recognized Hypechiniscus species is provided.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24457号 / 理博第4956号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 中野 隆文, 教授 本川 雅治, 教授 森 哲 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple species within the widespread Heteromys desmarestianus. I found several well-supported lineages within the H.desmarestianus complex, including H. goldmani and H. oresterus. Incorporating karyotype and allozyme data from earlier studies, I found sufficient supporting evidence to justify maintaining H. goldmani and H. oresterus as species as well as identifying four lineages as candidate species. I present a revised taxonomic arrangement within the genus; the subgenus Heteromys should be divided into three species groups: anomalus (H. anomalus and H. australis), gaumeri (H. gaumeri), and desmarestianus (H. desmarestianus, H. goldmani, H. oresterus, and the four candidate species).