Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships

We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole

Sistematics of MIkania Willd. (Eupatorieae - Asteraceae)

Nesta tese foi realizado um estudo sistemático de Mikania Willd., o maior gênero de plantas escandentes em Asteraceae, com mais de 400 espécies conhecidas. O foco principal do trabalho foi a realização de um estudo filogenético do gênero visando a reavaliar a organização dos grupos infragenéricos previamente publicados e prover uma nova classificação filogenética. Adicionalmente, foi compilado um Nomenclator do gênero. No primeiro capítulo, é apresentada a construção da hipótese filogenética sobre Mikania, baseada em dados de quatro marcadores moleculares (dois plastidiais e dois nucleares), obtidos de 128 terminais do gênero e mais quatro grupos-externos. A topologia resultante da análise bayesiana apresentou boa resolução, com clados bem sustentados (destacando-se a divergência em duas grandes linhagens na base da árvore), permitindo a reconstrução da evolução de nove caracteres que foram utilizados anteriormente para a classificação infragenérica de Mikania. Uma das hipóteses centrais desenvolvidas com a filogenia é a de aquisição de hábito lianescente no ancestral de Mikania, o qual pode ter facilitado a grande irradiação do gênero ao explorar a orla de florestas, com alguns eventos mais recentes de reversão ao hábito ereto, aparentemente ligados à ocupação de habitats abertos em diferentes linhagens do grupo. Os padrões de evolução das sinflorescências também revelaram ter forte sinal filogenético, assim como a posição da bráctea subinvolucral, o número de cerdas do pappus e alguns outros caracteres, embora sempre com homoplasias. No segundo capítulo, é apresentada uma revisão cronológica das classificações infragenéricas de Mikania, e em seguida uma proposta de um novo sistema de classificação infragenérico baseado na filogenia molecular desenvolvida no primeiro capítulo, além de um Nomenclator do gênero contendo todos os 426 nomes corretos, citação de protólogos e tipos nomenclaturais, e a distribuição geográfica e a posição de cada espécie na classificação. Foram feitas oito lectotipificações, quatro mudanças de status e quatro novas seções descritas. Mikania está agora organizado em dois subgêneros, M. subg. Mikania (com 182 espécies e distribuição no Novo e Velho Mundos, dividido em duas seções e duas subseções), e M. subg. Cylindrolepis (com 218 espécies, restritas ao continente americano, distribuídas em seis seções). O terceiro capítulo apresenta a descrição de uma nova espécie do gênero, ocorrente no estado de Minas Gerais, que foi encontrada durante os estudos realizados para o desenvolvimento da tese. Almeja-se que os resultados gerados neste trabalho possam contribuir para o entendimento da evolução e diversificação de Mikania, e que o sistema de classificação infragenérico produzido, na medida em que contém apenas grupos monofiléticos, permita direcionar futuros estudos, sobretudo morfológicos e taxonômicos em clados particulares desse gênero megadiversoThis work performed a systematic study of Mikania Willd., the greatest genus of vines plants in Asteraceae, accounting for more than 400 known species. This work\'s main focus was the phylogenetic study of the genus, aiming to reevaluate the organization of previously published infrageneric groups and to provide a new phylogenetic classification. Additionally, a Nomenclator of the genus was compiled. In the first chapter, a construction of the phylogenetic hypothesis for Mikania is presented based in data from four molecular markers (two plastids and two nuclear) obtained from 128 terminals of the genus and four external groups. The resulting topology of the Bayesian analysis showed satisfactory resolution, with well supported clades (highlighting the divergence between the two greatest lineages in the base of the tree), allowing the reconstruction of the evolution of nine characters previously used for the infrageneric classification of Mikania. One of the central hypothesis developed from the phylogeny is the gain of climbing habits in Mikania\'s ancestral, which may have facilitated its great irradiation exploring the forests\' edges, with some recent events of erect habit reversion, apparently linked to the occupation of open habitats in different lineages of the group. The patterns of sinflorescence evolution also revealed a strong phylogenetic signal, as well as the position of the subinvolucral bracts, number of pappus bristels and some other characters, although always homoplasic. In the second chapter, a chronological review of the infrageneric classifications of Mikania is presented, following a proposal for a new classification system based in the molecular phylogeny developed in the first chapter, besides a genus Nomenclator containg all correct 426 names, protologue citation and nomenclatural types, and the geographic distribution and position of each species in the classification. Eight lectotypifications were done, four status changes and four new sections were described. Mikania is now organized in two subgenus, M. subg. Mikania (with 182 species distributed in the New and Old Worlds, divided in two sections and two subsections), and M. subg. Cylindrolepis (with 218 species, restricted to the American continent, distributed in six sections). The third chapter presents the description of a new species of the genus occurring in Minas Gerais federal state, which was found during the studies for the development of the thesis. It is intended that the results generated by this work may contribute for the knowledge of the evolution and diversification of Mikania, and may the proposed infrageneric classification system, to the extent of containing only monophyletic groups, allow the direction of future studies, especially morphologic and taxonomic studies in particular clades of this megadiverse genu

Flora do Ceará, Brasil: Mikania (Asteraceae: Eupatorieae)

Resumo Dentre os gêneros de Asteraceae destaca-se Mikania que compreende ca. 450 espécies de distribuição principalmente neotropical. Mikania é considerado monofilético e pode ser facilmente reconhecido pelos capítulos com quatro flores e quatro brácteas involucrais subentendidos por uma bráctea subinvolucral. Este estudo objetivou realizar o levantamento florístico do gênero Mikania no Ceará, nordeste do Brasil. Foram analisadas amostras dos herbários ALCB, EAC, HCDAL, HUEFS, HVASF, IPA, K, P, NY e R, consultadas bibliografias especializadas e imagens disponíveis nas bases SpeciesLink, JSTOR e Herbário Virtual Reflora, além de coletas obtidas atraves de expedições a campo. Para o Ceará foram listadas oito espécies de Mikania, das quais três são novos registros. Mikania biformis é também nova ocorrência para a Região Nordeste. Mikania elliptica e M. ternata foram coletadas em ambientes de mata úmida; a primeira possuía registros apenas para a Bahia e Minas Gerais, em áreas de Caatinga e Cerrado, e a segunda, para a Bahia e regiões Sudeste e Sul do Brasil nos domínios do Cerrado e Mata Atlântica. As demais espécies (M. congesta, M. cordifolia, M. micrantha, M. psilostachya e M. vitifolia) são amplamente distribuídas no Brasil

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions forecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosys-tem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts withdomestic dogs, these species have been threatened locally, regionally, or even across their fulldistribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths.Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae(3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data onDasypus pilo-sus(Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized,but new genetic studies have revealed that the group is represented by seven species. In thisdata paper, we compiled a total of 42,528 records of 31 species, represented by occurrence andquantitative data, totaling 24,847 unique georeferenced records. The geographic range is fromthe southern United States, Mexico, and Caribbean countries at the northern portion of theNeotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regardinganteaters,Myrmecophaga tridactylahas the most records (n=5,941), andCyclopessp. havethe fewest (n=240). The armadillo species with the most data isDasypus novemcinctus(n=11,588), and the fewest data are recorded forCalyptophractus retusus(n=33). Withregard to sloth species,Bradypus variegatushas the most records (n=962), andBradypus pyg-maeushas the fewest (n=12). Our main objective with Neotropical Xenarthrans is to makeoccurrence and quantitative data available to facilitate more ecological research, particularly ifwe integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, andNeotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure,habitat loss, fragmentation effects, species invasion, and climate change effects will be possiblewith the Neotropical Xenarthrans data set. Please cite this data paper when using its data inpublications. We also request that researchers and teachers inform us of how they are usingthese data

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics

Xenarthrans—anteaters, sloths, and armadillos—have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data