Phylogenomics Yields New Insight Into Relationships Within Vernonieae (Asteraceae)

Abstract

Asteraceae, or the sunflower family, is the largest family of flowering plants and is usually considered difficult to work with, not only due to its size, but also because of the abundant cases of polyploidy and ancient whole-genome duplications. Traditional molecular systematics studies were often impaired by the low levels of variation found in chloroplast markers and the high paralogy of traditional nuclear markers like ITS. Next-generation sequencing and novel phylogenomics methods, such as target capture and Hyb-Seq, have provided new ways of studying the phylogeny of the family with great success. While the resolution of the backbone of the family is in progress with some results already published, smaller studies focusing on internal clades of the phylogeny are important to increase sampling and allow morphological, biogeography, and diversification analyses, as well as serving as basis to test the current infrafamilial classification. Vernonieae is one of the largest tribes in the family, accounting for approximately 1,500 species. From the 1970s to the 1990s, the tribe went through several reappraisals, mainly due to the splitting of the mega genus Vernonia into several smaller segregates. Only three phylogenetic studies focusing on the Vernonieae have been published to date, both using a few molecular markers, overall presenting low resolution and support in deepest nodes, and presenting conflicting topologies when compared. In this study, we present the first attempt at studying the phylogeny of Vernonieae using phylogenomics. Even though our sampling includes only around 4% of the diversity of the tribe, we achieved complete resolution of the phylogeny with high support recovering approximately 700 nuclear markers obtained through target capture. We also analyzed the effect of missing data using two different matrices with different number of markers and the difference between concatenated and gene tree analysis.

Phylogenomics of the hyperdiverse daisy tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae

“…In addition, the conservative pipeline phyluce (Faircloth, 2016) is regularly employed for these markers, because it minimizes paralogy by removing a locus from the data set for a taxon if two or more contigs from that taxon match a targeted locus. This phylogenomic approach has been extensively tested for the Asteraceae and has yielded excellent phylogenetic accuracy and resolution at different taxonomic levels (Mandel et al, 2014, 2015, 2017, 2019; Herrando‐Moraira et al, 2018, 2019; Jones et al, 2019; Siniscalchi et al, 2019; Lichter‐Marck et al, 2020; Thapa et al, 2020). Nonetheless, we recognize that conflicting support may result for some lineages due to noisy data caused by paralogy of nuclear markers in a polyploid background in the family and in these tribes specifically.…”

Using genomic data to develop SSR markers for species of Chresta (Vernonieae, Asteraceae) from the Caatinga

“…Despite the limitations of our study, with a low number of individuals per species, we found that most of our newly described loci are polymorphic, although with relatively low number of alleles (Table 5). Given how readily the nuclear and plastid markers were successfully amplified and genotyped across three species, even with the considerable phylogenetic distance among them (Siniscalchi et al 2019b), our results show that the use of comparative genomic data for the development of microsatellite markers is promising. Complementary studies focusing on genetic diversity and structure of the three species presented here and other related taxa are being developed in order to elucidate the microevolutionary processes that drive diversification in these taxa and possibly in other endemic taxa from the Caatinga.…”

“…Although these seven species share many morphological similarities and environmental preferences, they do not form a monophyletic group, with C. martii actually being the sister taxa to the rest of the genus. The other six Caatinga species form a clade which is further subdivided into two clades (Siniscalchi et al 2019b).…”

“…The natural isolation of the populations of Chresta in the Caatinga and the presence of morphological variability throughout a geographic gradient raise interesting questions about the evolutionary processes that act on these species, as the gene flow between different populations is likely limited. Aiming to facilitate future studies of the genetic variation in Chresta species, we developed microsatellite markers using previously obtained genomic data from a phylogenetic study of Vernonieae (Siniscalchi et al 2019b), comprising both nuclear and chloroplast sequences.…”

Generic boundaries in subtribe Saussureinae (Compositae: Cardueae): Insights from Hyb‐Seq data

“…In recent years, most phylogenomic studies conducted on Compositae have succesfully employed the Hyb‐Seq technique based on 1061 COS loci, at family (Mandel & al., 2014, 2015, 2017, 2019; Jones & al., 2019), tribe (Herrando‐Moraira & al., 2019; Siniscalchi & al., 2019), and genus level (Herrando‐Moraira & al., 2018; Thapa & al., 2019). For Saussureinae, this method also allowed to recover a well‐supported phylogeny.…”