Multiplexed‐shotgun‐genotyping data resolve phylogeny within a very recently derived insular lineage

Abstract

The current study illustrates the utility of MSG data for resolving relationships in lineages that have undergone recent, rapid diversification resulting in extensive ecological and morphological diversity. We suggest that a similar approach may prove generally useful for other rapid plant radiations where resolving phylogeny has been difficult.

RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs

“…RAD sequencing generates thousands of informative characters distributed over the whole genome that provide enough information to resolve interspecific relationships. Thus, many studies have used RAD sequencing methods to resolve phylogenetic relationships in groups where Sanger sequence‐based data have failed due to insufficient variation, gene tree discordance, or both (e.g., Eaton & Ree, ; Ebel et al., ; Escudero, Eaton, Hahn, & Hipp, ; Jones et al., ; Herrera & Shank, ; Hipp et al., ; Mort et al., ; Vargas et al., ; Wagner et al., ; Wang et al., ). When investigating more divergent taxa with restriction digestion methods, the high amount of loci drop out and subsequently missing data may create difficulties (e.g., Cariou, Duret, & Charlat, ; Lemmon & Lemmon, ; Leaché, Banbury, Felsenstein, Nieto‐Montes de Oca, & Stamatakis, ; Ree & Hipp, ; Andrews et al., ; Huang & Knowles, ).…”

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high‐Andean diversification (Asteraceae: Astereae:Diplostephium)

“…Poorly resolved relationships within Andean taxa confirm the prediction that phylogenies resulting from rapid radiations are difficult to estimate because of low and conflicting signal caused by short internodes (Whitfield & Lockhart, ). High‐throughput sequencing, a technology capable of producing orders of magnitude more data than obtained by Sanger sequencing, has created new opportunities for overcoming the difficulties of working with recently diversified taxa (Bock et al ., ; Ma et al ., ; Mort et al ., ). Here, we implement genome skimming (Straub et al ., ) and double‐digest restriction site‐associated DNA sequencing (ddRAD; Peterson et al ., ) to infer the phylogenetic patterns of one of the most species‐rich genera of Andean plants and its relatives.…”

Phylogenetic relationships and phylogeography of relevant lineages within the complex Campanulaceae family in Macaronesia

“…Although most of the phylogenetic studies have been focused on single lineages with emphasis on Canaries, which displays ca. one‐third of the endemic plant diversity of Macaronesia, some studies include two or more Macaronesian archipelagos (Carine, Francisco‐Ortega, Santos‐Guerra, & Russell, ; Mort et al., ; Moura, Carine, Malékot, et al., ; Moura, Carine, & Sequeira, ; Romeiras et al., ). Nonetheless, broad‐scale studies focused on a plant family covering native and endemics and comparing distinct patterns of phylogenetic structure among the five archipelagos was not yet addressed for this hotspot region.…”