Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene

A Molecular Phylogeny And New Infrageneric Classification Of Mucuna Adans. (leguminosae-papilionoideae) Including Insights From Morphology And Hypotheses About Biogeography

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Premise of research. The genus Mucuna has a pantropical distribution and comprises approximately 105 species, many of which show great economic value for forage, ornament, and medicine. To date, phylogenetic relationships within Mucuna have not been investigated using molecular data. The aim of this study was to build a phylogenetic framework for Mucuna to address questions about its monophyly, infrageneric relationships, divergence times, and biogeography. Methodology. We sequenced plastid (trnL-F) and nuclear ribosomal (internal transcribed spacer) regions and applied Bayesian and maximum likelihood analyses. An ancestral area reconstruction coupled with a divergence time analysis was used to investigate the historical biogeography of the genus. Pivotal results. Our results show that Mucuna is a monophyletic genus and that subgenus Stizolobium is a monophyletic group within it. We present here the analyses and results that support the need to recircumscribe subgenus Mucuna and to segregate a small group of species with large fruits into a newly proposed subgenus (to be described formally elsewhere after additional investigations). Conclusions. On the basis of ancestral area reconstruction and divergence time analyses, we conclude that the genus Mucuna originated and first diversified in the Paleotropics around 29.2 Ma and achieved a pantropical distribution through multiple long-distance dispersal events, which were facilitated by the occurrence of seeds adapted to oceanic dispersal.17717689Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Science without Borders Program [245590/2012-9]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Shirley A. Graham Fellowship, Missouri Botanical GardenBiologia Vegetal postgraduate program at Universidade Estadual de Campinas (UNICAMP), BrazilRoyal Botanic Gardens, KewMissouri Botanical GardenCentro de Biologia Molecular e Engenharia Genetica (CBMEG) Laboratory, BrazilEnvironment Research and Technology Development Fund of the Ministry of the Environment, Japan [S-9]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum

To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32- 90%, with 2,839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization

Character Evolution and Microbial Community Structure in a Host-associated Grasshopper

The spotted bird grasshopper, Schistocerca lineata Scudder (Orthoptera: Acrididae), is a widely distributed species found throughout most of the continental United States and southern Canada. This species is known to be highly variable in morphology, with many distinct ecotypes across its native range. These ecotypes display high levels of association with type-specific host plants. Understanding the evolutionary relationships among different ecotypes is crucial groundwork for studying the process of ecological differentiation. I examine four ecotypes from morphological and phylogeographic perspectives, and look for evidence of distinct evolutionary lineages within the species. I also begin to explore the potential role of the microbial community of these grasshoppers in ecological divergence by using 454 pyrosequencing to see if the microbial community structure reflects the ecology of the grasshoppers. I find support for a distinct aposematic lineage when approaching the data from a phylogeographic perspective and also find that this ecotype tends to harbor a unique bacterial community, different from that of a single other ecotype

A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)

Chalcidoidea (Hymenoptera) are extremely diverse with more than 23,000 species described and over 500,000 species estimated to exist. This is the first comprehensive phylogenetic analysis of the superfamily based on a molecular analysis of 18S and 28S ribosomal gene regions for 19 families, 72 subfamilies, 343 genera and 649 species. The 56 outgroups are comprised of Ceraphronoidea and most proctotrupomorph families, including Mymarommatidae. Data alignment and the impact of ambiguous regions are explored using a secondary structure analysis and automated (MAFFT) alignments of the core and pairing regions and regions of ambiguous alignment. Both likelihood and parsimony approaches are used to analyze the data. Overall there is no impact of alignment method, and few but substantial differences between likelihood and parsimony approaches. Monophyly of Chalcidoidea and a sister group relationship between Mymaridae and the remaining Chalcidoidea is strongly supported in all analyses. Either Mymarommatoidea or Diaprioidea are the sister group of Chalcidoidea depending on the analysis. Likelihood analyses place Rotoitidae as the sister group of the remaining Chalcidoidea after Mymaridae, whereas parsimony nests them within Chalcidoidea. Some traditional family groups are supported as monophyletic (Agaonidae, Eucharitidae, Encyrtidae, Eulophidae, Leucospidae, Mymaridae, Ormyridae, Signiphoridae, Tanaostigmatidae and Trichogrammatidae). Several other families are paraphyletic (Perilampidae) or polyphyletic (Aphelinidae, Chalcididae, Eupelmidae, Eurytomidae, Pteromalidae, Tetracampidae and Torymidae). Evolutionary scenarios discussed for Chalcidoidea include the evolution of phytophagy, egg parasitism, sternorrhynchan parasitism, hypermetamorphic development and heteronomy

塩基組成の不均一な遺伝子配列データに基づく適切な進化系統樹推測法の探索：データリコーディング法および非一様モデルの有用性の検証

筑波大学 (University of Tsukuba)201

BIOGEOGRAPHY, INTERSPECIFIC INTROGRESSION, AND THE EVOLUTION OF HEMOGLOBIN GENES IN THE HIGH ANDES: THE EVOLUTIONARY HISTORY OF THE SOUTH AMERICAN SISKINS (Spinus)

Landscape features, interspecific introgression, and adaptation work in concert to shape the evolutionary history of a clade. Understanding the independent and cumulative consequences of these evolutionary processes on diversification is critical to revealing the origins of extant biodiversity. Studying these processes within rapid radiations, a significant contributor to global biodiversity, can provide powerful insight into the process of diversification. To assess how diversification is shaped by these evolutionary forces, I examined the biogeographic history, patterns of interspecific introgression and adaptation to high elevation in a recent, rapid radiation of finches, the South American siskins (Fringillidae: Spinus). I found that this continental radiation colonized South America from North America and subsequently diversified at an exceptional rate in the high Andes. Further, my results show that sympatric siskin species within the high Andes form a monophyletic clade. I hypothesized that the close proximity of near relatives at high elevation could challenge species limits in Spinus. I investigated this hypothesis using a genome-wide SNP dataset to construct phylogenetic trees and performed formal tests of introgression among high elevation species. I developed an approach for assessing introgression despite persistent phylogenetic uncertainty, and discovered evidence for multiple introgressive events among different high elevation Spinus species. Cold temperatures and decreased partial pressure of oxygen are chronic stressors on organisms living at high elevation. Finally, to understand the consequences of high elevation on adaptive divergence in Spinus , I sequenced all genes which encode the oxygen-transport protein hemoglobin across the Spinus clade and among several populations of a species with a wide elevational range. I identified multiple instances of non-synonymous mutations at the inter- and intra-specific level in both adult and embryonic hemoglobin proteins. These patterns of genetic variation within functionally significant loci across elevation suggest that hemoglobin genes have had a significant impact on adaptation and potentially diversification within the South American siskins