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Abstract In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Abstract Aim Phylogenetic diversification is a precursor to speciation, but the underlying patterns and processes are not well‐studied in lichens. Here we investigate what factors drive diversification in two tropical, morphologically similar macrolichens that occupy a similar range but differ in altitudinal and habitat preferences, testing for isolation by distance (IBD), environment (IBE), and fragmentation (IBF).
Location Neotropics, Hawaii, Macaronesia.
Taxon Sticta andina ,S. scabrosa (Peltigeraceae).Methods We analysed 395 specimens from 135 localities, using the fungal ITS barcoding marker to assess phylogenetic diversification, through maximum likelihood tree reconstruction, TCS haplotype networks, and Tajima's D. Mantel tests were employed to detect structure in genetic vs. geographic, environmental, and fragmentation distances. Habitat preferences were quantitatively assessed by statistical analysis of locality‐based BIOclim variables.
Results Sticta andina exhibited high phenotypic variation and reticulate phylogenetic diversity across its range, whereas the phenotypically uniformS. scabrosa contained two main haplotypes, one unique to Hawaii.Sticta andina is restricted to well‐preserved andine forests and paramos, naturally fragmented habitats due to disruptive topology, whereasS. scabrosa thrives in lowland to lower montane zones in exposed or disturbed microsites, representing a continuous habitat.Sticta scabrosa showed IBD only across its full range (separating the Hawaiian population) but not within continental Central and South America, there exhibiting a negative Tajima's D.Sticta andina did not exhibit IBD but IBE at continental level and IBF in the northern Andes.Main conclusions Autecology, particularly preference for either low or high altitudes, indirectly drives phylogenetic diversification. Low diversification in the low altitude species,
S. scabrosa , can be attributed to rapid expansion and effective gene flow across a more or less continuous niche due to disturbance tolerance. In contract, high diversification in the high altitude species,S. andina , can be explained by niche differentiation (IBE) and fragmentation (IBF) caused by the Andean uplift.
