Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments

Abstract

27Survival in harsh environments is associated with several adaptations in plants. Species in the 28 Portulacineae (Caryophyllales) have adapted to some of the most extreme terrestrial conditions on 29 Earth, including extreme heat, cold, and salinity. Here, we generated 52 new transcriptomes and 30 combined these with 30 previously generated transcriptomes, forming a dataset containing 68 species 31 of Portulacinaeae, seven from its sister clade Molluginaceae, and seven outgroups. We performed a 32 phylotranscriptomic analysis to examine patterns of molecular evolution within the Portulacineae. Our 33 inferred species tree topology was largely congruent with previous analyses. We also identified several 34 nodes that were characterized by excessive gene tree conflict and examined the potential influence of 35 outlying genes. We identified gene duplications throughout the Portulacineae, and found corroborating 36 evidence for previously identified paleopolyploidy events along with one newly identified event 37

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

“…Multispecies K s values (i.e., ortholog divergence K s values) for selected combinations of taxa were generated according to the methods of Wang et al. (). The effect of evolutionary rate‐heterogeneity among ericalean species was investigated by conducting a multispecies K s analysis of each non‐balsaminoid ericalean taxon against Impatiens balsamifera , because all evidence suggests each of these species pairs have the same MCRA (i.e., the deepest node in the Ericales phylogeny).…”

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

“…Further studies of Molluginaceae would also be valuable for their insight into C 4 evolution, as would more targeted studies of its sister clade the Portulacineae. More specific analyses using transcriptome data have helped uncover adaptive gene family expansions in Portulacineae (Wang et al., ), multiple paleopolyploidy events in the carnivorous Caryophyllales (Walker et al., ) and are warranted to explore the convergent evolution of the many other extreme adaptations across Caryophyllales. Some of these include the evolution of cold tolerance across Caryophyllaceae and Polygonaceae, multiple origins of C 4 photosynthesis in Amaranthaceae s.l., and the evolution of drought tolerance in Nyctaginaceae, Polygonaceae, Aizoaceae, and Portulacineae.…”

“…Many Caryophyllales (most famously, many cacti) are noted for their extreme drought tolerance, but the clade also contains species that exhibit extreme cold tolerance (Cavieres et al., ), halophytism (Flowers and Colmer, ; White et al., ), heavy metal hyper‐accumulation (Moray et al., ), carnivory (e.g. Venus flytrap, sundews, and Nepenthes pitcher plants) (Albert et al., ; Givnish, ), betalain pigmentation (Brockington et al., ), C 4 and CAM photosynthesis (Wang et al., ; Sage et al., ; Moore et al., ; Sage, ), and succulence (Sajeva and Mauseth, ; Eggli and Nyffeler, ). Most of these adaptations are known to have arisen multiple times throughout the clade, making Caryophyllales a key natural laboratory for understanding trait evolution in angiosperms.…”

An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

“…Alternatively, the following approaches do not require genomic location information: guenomu, a Bayesian hierarchical model that estimates species trees from unrooted gene trees from multiple gene families (de Oliveira Martins and Posada, ), and a recent model within PhyloNet that incorporates incomplete lineage sorting and gene duplication and loss (Du et al., ). Conflict analyses allow further investigation into discordance between gene and species trees and detection of outlier gene trees for large genomic data sets, for example, using the software phyparts (Smith et al., ), which has been used for conflict analyses in a number of lineages, including Pleurothallidinae (Orchidaceae; Bogarín et al., ), Portulacineae (Wang et al., ), Caryophyllales (Walker et al., ), and Metazoa (Shen et al., ). At lower taxonomic levels, network approaches might supersede tree‐based approaches due to the large extent of reticulation in such data sets.…”