With contributions by: Abreu, Maria C.; Acevedo-Rodríguez, Pedro; Agra, Maria F.; Almeida Jr., Eduardo B.; Almeida, Gracineide S.S.; Almeida, Rafael F.; Alves, Flávio M.; Alves, Marccus; Alves-Araujo, Anderson; Amaral, Maria C.E.; Amorim, André M.; Amorim, Bruno; Andrade, Ivanilza M.; Andreata, Regina H.P.; Andrino, Caroline O.; Anunciação, Elisete A.; Aona, Lidyanne Y.S.; Aranguren, Yani; Aranha Filho, João L.M.; Araújo, Andrea O.; Araújo, Ariclenes A.M.; Araújo, Diogo; Arbo, María M.; Assis, Leandro; Assis, Marta C.; Assunção, Vivian A.; Athiê-Souza, Sarah M.; Azevedo, Cecilia O.; Baitello, João B.; Barberena, Felipe F.V.A.; Barbosa, Maria R.V.; Barros, Fábio; Barros, Lucas A.V.; Barros, Michel J.F.; Baumgratz, José F.A.; Bernacci, Luis C.; Berry, Paul E.; Bigio, Narcísio C.; Biral, Leonardo; Bittrich, Volker; Borges, Rafael A.X.; Bortoluzzi, Roseli L.C.; Bove, Cláudia P.; Bovini, Massimo G.; Braga, João M.A.; Braz, Denise M.; Bringel Jr., João B.A.; Bruniera, Carla P.; Buturi, Camila V.; Cabral, Elza; Cabral, Fernanda N.; Caddah, Mayara K.; Caires, Claudenir S.; Calazans, Luana S.B.; Calió, Maria F.; Camargo, Rodrigo A.; Campbell, Lisa; Canto-Dorow, Thais S.; Carauta, Jorge P.P. †; Cardiel, José M.; Cardoso, Domingos B.O.S.; Cardoso, Leandro J.T.; Carneiro, Camila R.; Carneiro, Cláudia E.; Carneiro-Torres, Daniela S.; Carrijo, Tatiana T.; Caruzo, Maria B.R.; Carvalho, Maria L.S.; Carvalho-Silva, Micheline; Castello, Ana C.D.; Cavalheiro, Larissa; Cervi, Armando C. †; Chacon, Roberta G.; Chautems, Alain; Chiavegatto, Berenice; Chukr, Nádia S.; Coelho, Alexa A.O.P.; Coelho, Marcus A.N.; Coelho, Rubens L.G.; Cordeiro, Inês; Cordula, Elizabeth; Cornejo, Xavier; Côrtes, Ana L.A.; Costa, Andrea F.; Costa, Fabiane N.; Costa, Jorge A.S.; Costa, Leila C.; Costa-e-Silva, Maria B.; Costa-Lima, James L.; Cota, Maria R.C.; Couto, Ricardo S.; Daly, Douglas C.; De Stefano, Rodrigo D.; De Toni, Karen; Dematteis, Massimiliano; Dettke, Greta A.; Di Maio, Fernando R.; Dórea, Marcos C.; Duarte, Marília C.; Dutilh, Julie H.A.; Dutra, Valquíria F.; Echternacht, Lívia; Eggers, Lilian; Esteves, Gerleni; Ezcurra, Cecilia; Falcão Junior, Marcus J.A.; Feres, Fabíola; Fernandes, José M.; Ferreira, D.M.C.; Ferreira, Fabrício M.; Ferreira, Gabriel E.; Ferreira, Priscila P.A.; Ferreira, Silvana C.; Ferrucci, Maria S.; Fiaschi, Pedro; Filgueiras, Tarciso S.; Firens, Marcela; Flores, Andreia S.; Forero, Enrique; Forster, Wellington; Fortuna-Perez, Ana P.; Fortunato, Reneé H.; Fraga, Cláudio N.; França, Flávio; Francener, Augusto; Freitas, Joelcio; Freitas, Maria F.; Fritsch, Peter W.; Furtado, Samyra G.; Gaglioti, André L.; Garcia, Flávia C.P.; Germano Filho, Pedro; Giacomin, Leandro; Gil, André S.B.; Giulietti, Ana M.; Godoy, Silvana A.P. ; Goldenberg, Renato; Gomes da Costa, Géssica A.; Gomes, Mário; Gomes-Klein, Vera L.; Gonçalves, Eduardo Gomes; Graham, Shirley; Groppo, Milton; Guedes. Juliana S.; Guimarães, Leonardo R.S.; Guimarães, Paulo J.F.; Guimarães, Elsie F.; Gutierrez, Raul; Harley, Raymond; Hassemer, Gus...

No abstract

Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum . We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium , showing significant differences in length (155,262–164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD , or within petB ). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum . The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.

Premise Lantana and Lippia (Verbenaceae) are two large Linnean genera whose classification has been based on associated fruit traits: fleshy vs. dry fruits and one vs. two seed‐bearing units. We reconstruct evolutionary relationships and the evolution of the two fruit traits to test the validity of these traits for classification. Methods Previous studies of plastid DNA sequences provided limited resolution for this group. Consequently, seven nuclear loci, including ITS, ETS, and five PPR loci, were sequenced for 88 accessions of the Lantana/Lippia clade and three outgroups. Results Neither Lantana nor Lippia is monophyletic. Burroughsia, Nashia, Phyla, and several Aloysia species are included within the clade comprising Lantana and Lippia. We provide a hypothesis for fruit evolution and biogeographic history in the group and their relevance for classification. Conclusions Fleshy fruits evolved multiple times in the Lantana/Lippia clade and thus are not suitable taxonomic characters. Several sections of Lantana and Lippia and the small genera are monophyletic, but Lippia section Zappania is broadly paraphyletic, making circumscription of genera difficult. Lippia sect. Rhodolippia is a polyphyletic group characterized by convergence in showy bracts. Species of Lantana sect. Sarcolippia, previously transferred to Lippia, are not monophyletic. The clade originated and diversified in South America, with at least four expansions into both Central America and the Caribbean and two to Africa. The types species of Lantana and Lippia occur in small sister clades, rendering any taxonomy that retains either genus similar to its current circumscription impossible.

The accurate analyses of massive amounts of data obtained through next-generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate "supergene" approach. The effects of molecular evolutionary models and character partition strategies on plastome-based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well-supported conflicting topologies). We compared different datasets (e.g., non-coding regions, exons, and codon-aligned and translated amino acids) using concatenated approaches under siteheterogeneous and site-homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

Background and aims – The last comprehensive study that estimated the number of Verbenaceae genera and species was published in 2004, and included 34 genera and around 1200 species. Since then, several publications based on morphology and/or molecular data have proposed important changes within the family. Due to the lack of updated literature to cite when referring to the number of Verbenaceae taxa, a review of these estimates is necessary.Key results and conclusion – We present a detailed list of genera currently accepted in Verbenaceae with the number of species contained in each and compare our numbers with the previous estimate. In addition, we indicate the geographic distribution and the most recent important taxonomic or phylogenetic works for each genus. Our compilation shows that Verbenaceae have 32 genera and 800 species currently accepted.This work provides up-to-date numbers and brings a holistic view of the family.

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176, 332–348.

The shortage of reliable primary taxonomic data limits the description of biological taxa and the understanding of biodiversity patterns and processes, complicating biogeographical, ecological, and evolutionary studies. This deficit creates a significant taxonomic impediment to biodiversity research and conservation planning. The taxonomic impediment and the biodiversity crisis are widely recognized, highlighting the urgent need for reliable taxonomic data. Over the past decade, numerous countries worldwide have devoted considerable effort to Target 1 of the Global Strategy for Plant Conservation (GSPC), which called for the preparation of a working list of all known plant species by 2010 and an online world Flora by 2020. Brazil is a megadiverse country, home to more of the world's known plant species than any other country. Despite that, Flora Brasiliensis, concluded in 1906, was the last comprehensive treatment of the Brazilian flora. The lack of accurate estimates of the number of species of algae, fungi, and plants occurring in Brazil contributes to the prevailing taxonomic impediment and delays progress towards the GSPC targets. Over the past 12 years, a legion of taxonomists motivated to meet Target 1 of the GSPC, worked together to gather and integrate knowledge on the algal, plant, and fungal diversity of Brazil. Overall, a team of about 980 taxonomists joined efforts in a highly collaborative project that used cybertaxonomy to prepare an updated Flora of Brazil, showing the power of scientific collaboration to reach ambitious goals. This paper presents an overview of the Brazilian Flora 2020 and provides taxonomic and spatial updates on the algae, fungi, and plants found in one of the world's most biodiverse countries. We further identify collection gaps and summarize future goals that extend beyond 2020. Our results show that Brazil is home to 46,975 native species of algae, fungi, and plants, of which 19,669 are endemic to the country. The data compiled to date suggests that the Atlantic Rainforest might be the most diverse Brazilian domain for all plant groups except gymnosperms, which are most diverse in the Amazon. However, scientific knowledge of Brazilian diversity is still unequally distributed, with the Atlantic Rainforest and the Cerrado being the most intensively sampled and studied biomes in the country. In times of “scientific reductionism”, with botanical and mycological sciences suffering pervasive depreciation in recent decades, the first online Flora of Brazil 2020 significantly enhanced the quality and quantity of taxonomic data available for algae, fungi, and plants from Brazil. This project also made all the information freely available online, providing a firm foundation for future research and for the management, conservation, and sustainable use of the Brazilian funga and flora.