Systematic Biology最新文献

Birth-death models are widely used to describe the diversification process which leads to the observed species and phylogenies. When integrated into Bayesian phylogenetic inference, birth-death models allow the joint inference of the phylogeny and the diversification parameters from molecular information. Two major classes of extensions of the birth-death process are considered in this article. The first extends the phylogenetic tree to include fossil samples alongside extant species, allowing the inference to integrate information about the past diversity. This type of inference uses either morphological or taxonomic information to place fossils in the phylogeny. The second extension models diversification rates which can vary between lineages, and is thus able to infer patterns of variation in speciation or extinction rates. In this work, we combine these two types of extension into a multi-type fossilized birth-death (MTFBD) process, which can perform the joint inference of a phylogeny including extinct and extant samples, and lineage-specific diversification and fossil sampling rates in a Bayesian framework. The MTFBD model is implemented as part of the phylogenetic inference framework BEAST2. Using simulated and empirical datasets, we demonstrate the performance and accuracy of the new model compared to a model with rate heterogeneity but using only extant samples, and compared to a model without rate variation including fossils. We demonstrate that including fossils improves the accuracy of the phylogeny and diversification rates, especially extinction rates, provided that the inference includes detailed morphological information to accurately place the fossil samples. When this information is not available however, MTFBD estimates are strongly driven by the priors and are thus no better or even worse than estimates obtained only with extant samples. With informative fossil characters, the MTFBD model provides accurate phylogenies, and precisely characterizes how speciation, extinction and fossil sampling rates vary as diversification proceeds.

The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversification dynamics of Triticeae species remain uncertain. Here, we infer the phylogenetic and diversification patterns of Triticeae using 1,546 nuclear genes from 164 transcriptomes/genomes that represent ∼83% of the recognized genera. Our phylogeny provides robust and well-supported estimates of the relationships among diploids and polyploids, which will be indispensable for studying biodiversity and breeding innovative germplasms. Diversification dynamic analysis suggests that Triticeae has undergone continuous evolutionary diversification to varying degrees since its origin during the Miocene, with acceleration in the St-ortholog lineages, indicating asymmetric diversification patterns among the homoeologous lineages in the St-genome-containing polyploid radiation. Multiple factors, including extinct donors and nonreciprocal recombination, complicated the origin of the B and G genomes of wheat and the Y and Xm genomes of wheatgrass. Asymmetric polyploidization and mixed-ploidy introgression might have constituted an evolutionary impetus driving rapid radiation and hyperdiversity of the St-genome-containing polyploid species in Triticeae. Our results provide new insights into the evolutionary origins of Triticeae that could promote the study of other rapidly radiated lineages in terms of polyploid origin and diversification processes.

Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.