Estudos filogenéticos e genômicos no gênero Anathallis (Orchidaceae)

Orientador: Eric de Camargo SmidtCoorientadora: Leila do Nascimento VieiraCoorientador: Antônio Luiz Vieira Toscano de BritoDissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em botânica. Defesa : Curitiba, 31/10/2018Inclui referênciasResumo: riqueza da família Orchidaceae com mais de 5 mil espécies, todas restritas à região neotropical. Apesar de seu monofiletismo estar bem estabelecido, a circunscrição de seus gêneros ainda é muito debatida, como ocorre com Anathallis. Porém, os trabalhos filogenéticos desenvolvidos até então utilizaram uma amostragem ineficiente e exploraram poucos conjuntos de dados, basicamente o sequenciamento da região nrITS, estabelecendo relações taxonômicas duvidosas entre as espécies de Anathallis e os demais gêneros do grupo. Além disso, não foram realizados estudos genômicos focados na subtribo, indicando uma profunda lacuna de conhecimento acerca da biologia molecular desse grupo de orquídeas. Este trabalho foi desenvolvido em dois capítulos, sendo que no primeiro foram realizadas análises filogenéticas e de datação molecular utilizando uma amostragem mais robusta do gênero Anathallis e valendo-se do sequenciamento de seis regiões moleculares, incluindo a nrITS. Também foram codificados caracteres morfológicos, incorporados em análises filogenéticas conjuntas e de reconstrução de caracteres morfológicos. No segundo capítulo é apresentada a sequência completa do genoma cloroplastidial de Anathallis obovata, espécie-tipo do gênero, que foi comparada com sequências genômicas de táxons próximos das subtribos Pleurothallidinae e Laeliinae. Palavras-chave: Pleurothallidinae; genoma cloroplastidial; orquídeas neotropicais; datação molecular; filogenia de evidência total.Abstract: The subtribe Pleurothallidinae (Epidendroideae: Epidendrae) represents 20% of the species richness of Orchidaceae with more than 5 thousand species, all restricted to the neotropical region. Although its monophyletism is well established, the circumscription of its genera is still much debated, as is the case of Anathallis. Previous phylogenetic studies used inefficient sampling and explored few data sets, basically the sequencing of the nrITS region, establishing dubious taxonomic relationships between Anathallis species and the other genera of Pleurothallidinae. In addition, there are no Pleurothallidinae-focused genomic studies, indicating a lack of knowledge about the molecular biology of this orchid group. This work was developed in two chapters. In the first one, phylogenetic and molecular dating analyses were performed using a larger sample of the genus Anathallis and using the sequencing of six molecular regions, including the nrITS. Morphological characters were also coded, used in concatenated phylogenetic and morphological characters reconstruction analysis. In the second chapter we present the complete sequence of the chloroplast genome of Anathallis obovata, the type-species of the genus, which was compared with genomic sequences of closely-related taxa of the subtribe Pleurothallidinae and also of subtribe Laeliinae. Keywords: Pleurothallidinae; chloroplast genome; neotropic orchids; molecular dating; total evidence phylogeny

The origin and speciation of orchids

SummaryOrchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis.We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants.The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica.These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation

Madisonia Luer 2004

Madisonia Luer (2004: 258). TYPE:— Madisonia kerrii (Braga) Luer (2004: 258). Fig. 2, 3. Basionym: Pleurothallis kerrii Braga (1981: 172). Etymology:—Named in honour of Michael Madison, co-collector of the type specimen. Plants small, epiphytic or rupicolous, long-repent; rhizome slender, segmented between the ramicauls, nodes with ribbed, slightly ciliate sheaths. Ramicaul shorter than the leaf, enclosed by 1–2 ribbed, more or less ciliate sheaths. Leaf decumbent to erect, cuneate below a short petiole, broadly elliptical to lanceolate, minutely tridenticulate to apiculate, thick to coriaceous. Inflorescence a successively few-flowered raceme, shorter or longer than the leaf. Flower resupinate or not, dark-red to purple, glabrous; dorsal sepal lanceolate to oblong, lateral sepals connate at least to the middle, adnate to the column-foot, sometimes forming a mentum; petals linear to oblong; lip oblong to ovate, trilobed, disc generally smooth, with or without callosities, lateral lobes erect, apical lobe acute to rounded, smooth, pilose or irregular; column semiterete usually bidentate at the apex, anther subapical, stigma ventral. Distribution:—Know to occur in Trinidad and Tobago and Jamaica in the Caribbean, the Amazon from Bolivia, Brazil, Colombia, Ecuador, French Guiana, Guyana, Peru, Suriname and Venezuela, and the Brazilian Atlantic Rainforest.Published as part of Smidt, Eric De Camargo, Toscano De Brito, A. L. V., Mauad, Anna Victoria Silvério R. & Morales, Nicolás Gutiérrez, 2021, An expanded concept of Madisonia including miscellaneous species of Pleurothallidinae (Orchidaceae): evidence from molecular analysis, pp. 71-84 in Phytotaxa 505 (1) on page 77, DOI: 10.11646/phytotaxa.505.1.5, http://zenodo.org/record/542525

Lurking in the depth: Pond depth predicts microhabitat selection by Rhinella icterica (Anura: Bufonidae) tadpoles at two different sampling scales

Habitat selection has long been a central theme in ecology and has historically considered both physiological responses and ecological factors affecting species establishment. Investigating habitat selection patterns at different scales can provide important information on the relative roles of the environmental factors influencing the organisms’ abilities to use their surrounding habitat. This work aimed at investigating which environmental factors determine habitat selection by Rhinella icterica tadpoles, and also took the opportunity to investigate how the scale in which tadpoles and environmental data are sampled might influence the habitat selection results. A total of 2.240 tadpoles were counted in the whole sampling area, and while substrate cover and depth were the variables that better explained the abundance of tadpoles at the larger scale (plot level), depth and water turbidity better explained tadpoles’ abundance at the smaller scale (subplot level). The results suggest that avoiding predation by matching the background color is a likely process explaining tadpoles’ occupancy at both scales. Depth is known to influence tadpole habitat use in the tropics, and although its combination with turbidity and substrate cover varied between scales, our study suggests that sampling at different scales might not affect the inferred ecological processes driving habitat selection. This information might also be useful to predict tadpoles’ responses to micro-environmental perturbations and help in guiding the choice of parameters that should be taken into account when analyzing the effects of habitat degradation in Atlantic Forest amphibian populations

Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data.

We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the genes. The independent loss of genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics