Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.
Daijiang Li, Lauren Trotta, Hannah E Marx, Julie M Allen, Miao Sun, Douglas E Soltis, Pamela S Soltis, Robert P Guralnick, Benjamin H Baiser
In Ecology,
2019
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau and the development of the monsoon—provided new habitats that promoted remarkable radiation. However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04–25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29–18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and provide a foundation on which to build conservation efforts in China
Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T Miller, Sarah Mathews, Hai-Hua Hu, others
In Nature,
2018
Ryan A Folk, Miao Sun, Pamela S Soltis, Stephen A Smith, Douglas E Soltis, Robert P Guralnick
In AJB,
2018
Premise of the study: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. Methods and Results: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross‐amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. Conclusions: We believe microsatellites still have a place in the genomic age—they remain effective and cost‐efficient markers. The loci presented here are a valuable resource for researchers.
Richard GJ Hodel, Matthew A Gitzendanner, Charlotte C Germain-Aubrey, Xiaoxian Liu, Andrew A Crowl, Miao Sun, Jacob B Landis, M Claudia Segovia-Salcedo, Norman A Douglas, Shichao Chen, others
In APPS,
2016
Rosidae, a clade of approximately 90,000 species of angiosperms, exhibits remarkable morphological diversity and extraordinary heterogeneity in habitats and life forms. Resolving phylogenetic relationships within Rosidae has been difficult, in large part due to nested radiations and the enormous size of the clade. Current estimates of phylogeny contain areas of poor resolution and/or support, and there have been few attempts to synthesize the available data into a comprehensive view of Rosidae phylogeny. We aim to improve understanding of the phylogeny of Rosidae with a dense sampling scheme using both newly generated sequences and data from GenBank of the chloroplast rbcL, atpB, and matK genes and the mitochondrial matR gene. We combined sequences from 9,300 species, representing 2,775 genera, 138 families, and 17 orders into a supermatrix. Although 59.26% of the cells in the supermatrix have no data, our results generally agree with previous estimates of Rosidae phylogeny and provide greater resolution and support in several areas of the topology. Several noteworthy phylogenetic relationships are recovered, including some novel relationships. Two families (Euphorbiaceae and Salvadoraceae) and 467 genera are recovered as non‐monophyletic in our sampling, suggesting the need for future systematic studies of these groups. Our study shows the value of a botanically informed bioinformatics approach and dense taxonomic sampling for resolving rosid relationships. The resulting tree provides a starting point for large‐scale analyses of the evolutionary patterns within Rosidae.
Miao Sun, Rehan Naeem, Jun-Xia Su, Zhi-Yong Cao, J Gordon Burleigh, Pamela S Soltis, Douglas E Soltis, Zhi-Duan Chen
In JSE,
2016
Analysis of large data sets can help resolve difficult nodes in the tree of life and also reveal complex evolutionary histories. The placement of the Celastrales–Oxalidales–Malpighiales (COM) clade within Rosidae remains one of the most confounding phylogenetic questions in angiosperms, with previous analyses placing it with either Fabidae or Malvidae. To elucidate the position of COM, we assembled multi-gene matrices of chloroplast, mitochondrial, and nuclear sequences, as well as large single- and multi-copy nuclear gene data sets. Analyses of multi-gene data sets demonstrate conflict between the chloroplast and both nuclear and mitochondrial data sets, and the results are robust to various character-coding and data-exclusion treatments. Analyses of single- and multi-copy nuclear loci indicate that most loci support the placement of COM with Malvidae, fewer loci support COM with Fabidae, and almost no loci support COM outside a clade of Fabidae and Malvidae. Although incomplete lineage sorting and ancient introgressive hybridization remain as plausible explanations for the conflict among loci, more complete sampling is necessary to evaluate these hypotheses fully. Our results emphasize the importance of genomic data sets for revealing deep incongruence and complex patterns of evolution.
Miao Sun, Douglas E Soltis, Pamela S Soltis, Xinyu Zhu, J Gordon Burleigh, Zhiduan Chen
In MPE,
2015
A revision of Elaeagnus L. for mainland China is provided based on field observations and herbarium studies. Forty‐two morphological characters are selected and coded, then the matrix is prepared following cluster analysis. Morphological characters and species delimitation are re‐evaluated resulting in the recognition of 36 species, one subspecies and five varieties in mainland China. Thirteen species names and three variety names are regarded as new synonyms. Species information covers full synonyms, type information, description, taxonomic remarks, distribution range, occupied habitats, examined specimens, relevant illustrations, and references to selected published illustrations and reports. A key for whole species determination is provided. The lectotypification of Elaeagnus magna (Serv.) Rehd. has been designated.
Miao Sun, Qi Lin
In JSE,
2010
