Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

O projeto Flora Fanerogâmica do Estado de São Paulo tem se dedicado a inventariar a flora paulistana há quase 20 anos. Conta com a atuação de mais de 200 colaboradores, a maioria do próprio estado, além de pesquisadores de outros estados e do exterior. Desde 2001, foram publicados sete volumes com as monografias de 151 famílias, contendo 3.237 espécies em 722 gêneros. Este projeto foi o ponto de partida para o conhecimento da diversidade das espécies de espermatófitas do estado de São Paulo. A apresentação do checklist neste momento é oportuna por constituir a produção de uma listagem das espécies com identificações certificadas pelos especialistas, além de conter a referência de uma coleção de herbário para a maior parte dos táxons (material-testemunho) ou referência à bibliografia em que a espécie é citada como ocorrente, de forma nativa ou subespontânea, no estado. Dessa forma, é aqui apresentada a listagem das espermatófitas do estado de São Paulo, com 7.305 espécies, distribuídas em 1.776 gêneros e em 197 famílias (segundo Cronquist 1981) ou então 195 (segundo o APG III). Em relação à flora do Brasil, com 31.728 espécies de espermatófitas, o estado São Paulo compartilha de 23% dessas espécies. As famílias mais representativas são Orchidaceae (797 espécies), Asteraceae (676 espécies), Fabaceae (513 espécies), Poaceae (500 espécies), Myrtaceae (304), Rubiaceae (265 espécies) e Melastomataceae (253 espécies) que, juntas, somam 3.308 espécies e constituem mais de 45% do total de espécies de espermatófitas do estado. Considerando a grande diversidade vegetal brasileira, parcialmente expressa em um estado, depreende-se a grande importância da continuidade dos estudos florísticos no Brasil, país provavelmente detentor da maior diversidade vegetal do planeta.

-(distribution of the community of vascular epiphytes in sites under different degrees of disturbance in the ipanema national Forest, são Paulo, Brazil). despite the importance of vascular epiphytes to indicate the degree of local conservation, there is little research on this subject. the present research was performed in the ipanema national Forest, iperó, são Paulo, Brazil, aiming to characterize the vascular epiphytic community, to analyze their vertical distribution and to analyze the correlation among different sites. Three sites were considered: RIA -remnant isolated/modified, FAB -advanced forest/border, and Fai -advanced forest/inside. on each site 90 assorted trees (dBh ≥ 20 cm) were sampled. Frequency, abundance and diversity parameters based on the occurrence of epiphytes in the strata and in the assorted trees were estimated. in the present survey 21 species belonging to 14 genera and six families were found. the shannon index of diversity (H') for the whole epiphytic community was 2.272, the equability (J) = 0.713 and Margalef's richness (d) = 2.467. the richness and diversity of sites were: 18 species, H' = 2.159, J = 0.747 and d = 2.180 for the Ria site, seven species, H' = 1.270, J = 0.652 and d = 1.017 for the FaB site, and 13 species, H' = 1.587, J = 0.618 and d = 1.919 for the Fai site. although there are significant differences among RIA to FAB and FAI, there is no difference between FAB and FAI. This research highlights the influence of environmental changes over epiphytic communities and the importance of disturbed forest remnants or even isolated trees to sustain the vascular epiphytes.Key words -atlantic Forest, environmental change, phytosociology of epiphytes RESUMO -(Distribuição da comunidade de epífitas vasculares em sítios sob diferentes graus de perturbação na Floresta Nacional de Ipanema, São Paulo, Brasil). Apesar da importância de epífitas vasculares em refletir o grau de preservação local, existem poucas pesquisas sobre o tema. esta pesquisa foi desenvolvida na Floresta nacional de ipanema, iperó, sP, e teve por objetivo caracterizar e analisar a comunidade epifítica vascular em sítios sob diferentes graus de perturbação. Foram determinados três sítios: RIA -remanescente isolado/alterado, FAB -floresta avançada/borda e FAI -floresta avançada/interior e, em cada sítio, foram amostrados 90 forófitos com DAP ≥ 20 cm. Foram estimamos os parâmetros de freqüência, dominância e diversidade com base na ocorrência das epífitas nos estratos e nos forófitos. No levantamento foram encontradas 21 espécies, 14 gêneros e seis famílias. o índice de diversidade shannon (H') para toda a comunidade epifítica foi de 2,172, a equabilidade (J) = 0,713 e a riqueza de Margalef (d) = 2,467. A riqueza e a diversidade dos sítios foram de: 18 espécies, H' = 2,159, J = 0,747 e d = 2,180 para o Sítio RIA; sete espécies, H' = 1,270, J = 0,652 e d = 1,017 para o Sítio FAB; e 13 espécies, H' = 1,587, J = 0,618 e d = 1,919 para o Sítio FAI. Embora existam diferenças significativas entre os sítios RIA ...

24 Recent phylogenomic analyses have solved evolutionary relationships between most of the 25 Orchidaceae subfamilies and tribes, yet phylogenetic relationships remain unclear within the 26 42 43 45 46 47 100, PP = 0.77-1.0), and only a few positions remained unresolved. Here, the relationship between 128 Codonorchidae+Orchideae was moderately supported (LBS = 86) together with that of 129 Cymbidiinae and the remaining Cymbidieae (LBS = 62). The monophyly of Nervilieae and 130 Triphoreae was moderately supported (LBS = 79), as well as the phylogenetic relationships of 131 Nervilieae+Triphoreae and the remainder of Epidendroideae (LBS = 75), and Epidendreae and 132 Coelia + Eria (LBS = 52) (Fig. 2). 133 134 2.3 Molecular characterisation of plastid genomes 135 Whole plastome sequences belonging to 97 species (11 sequenced here and 86 reported in 136 NCBI) were annotated for 75 protein-coding genes. Five additional genes were recovered when 137 concatenating this data matrix with the protein coding regions matrix used by Givnish 2 , giving a 138 6

Epiphytes are hyper‐diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non‐vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer‐reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non‐vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non‐vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

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