Selected Publications

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids—a clade of ~25% of all angiosperm species—to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species’ temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.
In Nat. Commun., 2020

Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. We used a supermatrix for rosids and one well‐sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
In AJB, 2020

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.
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
In Nature, 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.
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.
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.
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.
In JSE, 2010

Publications

More Publications

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a …

Recent advances in generating large‐scale phylogenies enable broad‐scale estimation of species diversification. These now common …

Catnip or catmint ( Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This …

The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit …

A major goal of phylogenetic systematics is to understand both the patterns of diversification and the processes by which these …

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a …

High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of …

Recent studies have detected strong phylogenetic signals in tree–fungus associations for diseased leaves and mycorrhizal symbioses. …

Recently Ulloa Ulloa et al.(2017) published a 2600-page online checklist of the New World vascular plants (the Checklist hereafter) …

Projects

*

Dimensions

Biodiversity is multidimensional, composed of genetic, phenotypic, ecological, and geographic variation within and among species. The forests of eastern Asia and eastern North America were anciently connected, offering an excellent opportunity to study the drivers of its biodiversity. This is a US-China collaboration project. See Project Homepage

Rosid Phylogeny and Diversification

Rosids, among the largest clades of angiosperms (90,000–120,000 species, ca. 25% of all angiosperms), exhibit tremendous overall diversity in morphology, chemistry, habit, reproductive strategy, and life history. However, our knowledge of this clade is remarkably limited along any sampling metric, hampering efforts to better understand its incredible species diversity.

Posts

博客

More Posts

Explained the importance of understanding the underlying conflict among gene trees. List all the steps required to reach the final …

Research talk to introduce my 5-year post-doc research to students, and researchers at Institute of Botany, Chinese Academy of Sciences

5-min lightning talk to introduce my research to researchers at Florida Museum of Natural History

I have visited a lot places in south part of China. These places are genreally hostspots of biodiversity of China. Especially I love …

Those outreach activities always make me wondering how could I deliver the knowledge I learned to the public and also make me realized …

Teaching

I am Certified Instructor of The Carpentries (a non-profit organization, aiming to teach foundational coding and data science skills to researchers worldwide). I’m aslo an ex-board member of UF Carpentries Club. Here are some workshop stats that summerize the numbers of workshops we organized and the numbers of people that we trained.

2018

2017

Experience

 
 
 
 
 
March 2020 – August 2020
Ann Arbor, Michigan, USA

Visiting Scholar on PhyloSynth Project

Ecology and Evolutionary Biology (EEB)

 
 
 
 
 
October 2019 – Present
Aarhus, Denmark

Postdoc on PhyloSynth Project

Department of Bioscience

  • Evaluate data avaiblity of molecular and taxonomic data
  • Collaborate with Dr. Stephen Smith
  • Design the best strategy in integrating all data
  • Reconstruct a global plant tree of life
  • Apply this large-scale tree in Macro-evolution and -ecology
  • Publication (papers, and posters)
 
 
 
 
 
January 2016 – August 2019
Gainesville, FL, USA

Postdoc on Dimensions Project

Florida Museum of Nature History

  • Served as a main communicating point between US and China
  • Data assemblage (field work and sampling, DNA extraction, evaluation, and sample preparation, molecuar marker design, and molecular data generation)
  • Analyses (phylogeny)
  • Publication (paper, and posters)
 
 
 
 
 
January 2015 – January 2016
Gainesville, FL, USA

Postdoc on Tree of Life Project

Department of Biology, University of Florida

  • Bridging US and China research teams
  • Assembling data
  • Building the China Tree of Plant Life (rosids)
  • Publishing results
 
 
 
 
 
September 2014 – January 2015
Beijing, China

Research Assistant

Institute of Botany, Chinese Academy of Sciences

  • Chinese vasular plant phylogeny reconstruction

Contact

  • +45 9one 97 63 1o
  • Ny Munkegade 116, Building 1535, Room 227, 8000 Aarhus C, Denmark

Curriculum Vitae

Miao Sun

Contact Information

Plant Evolution and Biodiversity (PEB) Group
Department of Bioscience – Ecoinformatics and Biodiversity, Aarhus University
Ny Munkegade 116, Building 1535, Room 227, 8000 Aarhus C, Denmark

Email: cactusresponsible@gmail.com; miaosun@bios.au.dk

Homepage: https://www.sunmiao.name

Twitter: \@Miao_the_Sun

Positions

Research Interests

A phylogenetic tree is a pivotal framework for solving fundamental issues in biology. My long-term research goal is to use a robust phylogeny to elucidate patterns of evolutionary radiations in angiosperms and to address the causes of plant diversification using the tools of comparative biology.

Education

  • 2009 ~ 2014, PhD in Botany, Institute of Botany, Chinese Academy of Sciences
  • 2006 ~ 2009, Master of Botany, Institute of Botany, Chinese Academy of Sciences
  • 2002 ~ 2006, Bachelor of Environmental Science, College of Resources and Environment, Beijing Forestry University

Research Skills

  • Taxonomic skills:

    Able to identify most seed plants at genera level or at least family level and expert in Elaeagnus (Elaeagnaceae), familiar with International Code of Botanical Nomenclature and mastering the process of compressing specimens

  • Molecular biology skills:

    DNA extraction, clone, PCR, sequencing, genome assembling, and genome size measurement
    Experienced in Target Enrichment data analyses using aTRAM and HybPiper, and gene tree congruence visulizaion using Phyparts and Pycharts.

  • Bioinformatical skills:

    • Experienced with standard biological software and genome dataset analysis (e.g., probe design, genome assembly)
    • Proficient in Shell, R, git, Perl, and Python programming languages, familiar with SQL, version control (git), experienced in applied programming for biological data analysis and reproducible data science.

  • Language skills:

    Fluent spoken and written Chinese and English

Honors & Awards

  • 2017: Certified Instructor of Software Carpentry, and qualified to teach Software Carpentry’s core curriculum.
  • 2006 ~ 2014: First-class Scholarship for Graduate Student of Chinese Academy of Sciences
  • 2008: Honored as a science popularization volunteer
  • 2004 ~ 2005: Second Scholarships for Excellent Academic Score BFU and National Grants.
  • 2003: Third Scholarships for Excellent Academic Score and National second-class scholarship.
  • 2002: Chinese scholarship.

Publications

*equally contributing author; 26 publications, h-index 9; 452 total citations according to Google Scholar

Papers:

  1. Shimai H, Setoguchi P, Roberts D, Sun M. (In prep.) Phylogeny and biogeography of the genus Pinguicula L. (Lentibulariaceae) based on nuclear ribosomal DNA and chloroplast DNA.

  2. Sun M, Folk FA, Gitzendanner MA, Smith SA, Germain-Aubrey C, Guralnick RP, Soltis PS, Chen ZD, Soltis DE. Exploring the phylogeny and diversification of rosids with a five-locus supermatrix. bioRxiv 694950. doi: 10.1101694950.

  3. Sun M, Folk FA, Gitzendanner MA, Soltis PS, Chen ZD, Soltis DE, Guralnick RP. (2020). Recent, accelerated diversification in rosids occurred outside the tropics. Nature Communications 11: 3333. doi: 10.1038/s41467-020-17116-5.

  4. Sun M, Folk FA, Gitzendanner MA, Soltis PS, Chen ZD, Soltis DE, Guralnick RP. (2020). Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids. American Journal of Botany 107(6): 1–15. doi: 10.1002/ajb2.1479 (also see bioRxiv 749325).

  5. Lichman BR, Godden GT, Hamilton JP, Lira Palmer L, Kamileen MO, Zhao D, Vaillancourt B, Wood J, Sun M, Henry LK, Lopez CR, Dudareva N, Soltis DE, Soltis PS, Buell CR, O’Connor SE. (2020). The evolutionary origins of the cat attractant nepetalactone in catnip. Science Advances 6: eaba0721. doi: 10.1126/sciadv.aba0721.

  6. Mu XY, Tong L, Sun M, Zhu YX, Wen J, Lin QW, Liu B. (2020). Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data. Molecular Phylogenetics and Evolution 147: 106802. doi: 10.1016/j.ympev.2020.106802.

  7. Xue B, Guo X, Landis JB, Sun M, Tang CC, Soltis PS, Soltis DE, R.M.K. Saunders RMK. (2019). Accelerated diversification correlated with functional traits shapes extant diversity of the early divergent angiosperm family Annonaceae. Molecular Phylogenetics and Evolution 142: 106659. doi: 10.1016/j.ympev.2019.106659.

  8. Li DJ, Lauren Trotta L, Marx HE, Allen JM, Sun M, Soltis DE, Soltis PS, Guralnick RP, Baiser BH. (2019). For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies. Ecology. doi: 10.1002/ecy.2788.

  9. Yang T, Tedersoo L, Soltis PS, Soltis DE, Gilbert JA, Sun M, Shi Y, Wang HF, Li YT, Zhang J, Chen ZD, Lin HY, Zhao YP, Fu CX, Chu HY. (2018). Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China. The ISME Journal 13: 686–697.

  10. Marodiev EV, Sun M, Schroder L, Steadman DW, Ebach MC. (2018). Moving from modern toward post-modern science: comment on “An integrated assessment of the vascular plants of the Americas.” Phytotaxa 351: 96–98.

  11. Folk RA, Sun M, Soltis PS, Smith SA, Soltis DE, and Robert P. Guralnick. (2018). Challenges of comprehensive taxon sampling in comparative biology: Wrestling with Rosids. American Journal of Botany 105(3): 433–445.

  12. Lu LM, Mao L, Yang T, Ye JF, Liu B, Li HL, Sun M*, Miller JT, Mathews S, Hu HH, Niu YT, Peng DX, Chen YH, Smith SA, Chen M, Xiang KL, Le CT, Dang VC, Lu AM, Soltis PS, Soltis DE, Li JH, Chen ZD. (2018). Evolutionary history of the angiosperm flora of China. Nature 554: 234–238. doi: 10.1038/nature25485.

  13. Mu XY, Sun M, Yang PF, Lin QW. (2017). Unveiling the identity of Wenwan walnuts and phylogenetic relationships of Asian Juglans species using restriction site-associated DNA-sequencing. Frontiers in Plant Science (8): 1708. doi: 10.3389/fpls.2017.01708

  14. Hodel RG, Gitzendanner MA, Germain-Aubrey CC, Liu X, Crowl AA, Sun M, Landis JB, Segovia-Salcedo MC, Douglas NA, Chen SC, Soltis DE, Soltis PS. (2016). A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes. Applications in Plant Sciences 4(6): 1600024.

  15. Hodel RG, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu XX, Gitzendanner MA, Douglas NA, Germain-Aubrey CC, Chen SC, Soltis DE, Soltis PS. (2016). The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. Applications in Plant Sciences 4(6): 1600025.

  16. Chen ZD, Yang T, Li Lin, Lu LM, Li HL, Sun M, Liu B, Chen M, Niu YT, Ye JF, Cao ZY, Liu HM, Wang XM, Wang W, Zhang JB, Meng Z, Cao W, Li JH, Wu SD, Zhao HL, Liu ZJ, Du ZY, Wang QF, Guo J, Tan XX, Su JX, Zhang LJ, Yang LL, Liao YY, Li MH, Zhang GQ, Chung SW, Zhang J, Xiang KL, Li RQ, Soltis DE, Soltis PS, Zhou SL, Ran JH, Wang XQ, Jin XH, Chen YS, Gao TG, Li JH, Zhang SZ, Lu AM. (2016). Tree of life for the genera of Chinese vascular plants. Journal of Systematics and Evolution 54(4): 227-306.

  17. Li HL, Wang W, Li RQ, Zhang JB, Sun M, Naeem R, Su JX, Xiang XG, Mortimer PE, Li DZ, Hyde KD, Xu JC, Soltis DE, Soltis PS, Li JH, Zhang SZ, Wu H, Chen ZD, Lu AM. (2016). Global versus Chinese perspectives on the phylogeny of the N-fixing clade. Journal of Systematics and Evolution 54(4): 392-399.

  18. Sun M, Naeem R, Su JX, Burleigh GJ, Solits DE, Soltis PS, Chen ZD. (2016). Phylogeny of the Rosidae: A dense taxon sampling analysis. Journal of Systematics and Evolution 54(4): 363-391.

  19. Sun M, Solits DE, Soltis PS, Zhu XY, Burleigh GJ, Chen ZD. (2015). Deep phylogenetic incongruence in the angiosperm clade Rosidae. Molecular Phylogenetics and Evolution 83: 156-166.

  20. Wang B, Zhang Y, Wei P, Sun M, Ma X, Zhu X. (2015). Identification of nuclear low-copy genes and their phylogenetic utility in rosids. Genome 57(10): 150203143525007.

  21. Lu LM, Sun M, Zhang JB, Li HL, Lin L, Yang T, Chen M, Chen ZD. (2014). Tree of life and its applications. Biodiversity Science 22: 3-20.

  22. Sun M, Lin Q. (2010). A revision of Elaeagnus L. (Elaeagnaceae) in mainland China. Journal of Systematics and Evolution 48(5): 356-390.

  23. Sun M, Lin Q, Sun Q, Bei SQ, Li HL, Yang ZR. (2008). Validation of eight names of Chinese taxa in Ranunculaceae, Rosaceae and Scrophulariaceae. Kew Bulletin 64: 573-575.

  24. Sun M, Lin Q. (2008). Lectotypification of five scientific names in Rosaceae. Guihaia 28: 295-297. (In Chinese)

  25. Lin Q, Bei SQ, Li HL, Cao ZY, Sun Q, Sun M, Yang ZR. (2008). Lectotypification of twenty names of Chinese taxa in Angiospermae. Bulletin of Botanical Research 5: 534-539.

  26. Lin Q, Sun Q, Sun M, Bei SQ, Li HL. (2007). Lectotypification of twenty-eight names of Chinese taxa in Angiospermae. Acta Botanica Boreali-occidentalia Sinica, 27: 1247-1255.

Book chapters:

  1. Sun M et al. (2018). Malvaceae, Malpighiaceae, Celastraceae. In: Li DZ, Chen ZD, Wnag H, Lu AM eds. Flora of Genera and Families of China Vascular Plants, Science Press, Beijing
  2. Sun M et al. (2018). Malvaceae, Malpighiaceae, Celastraceae. In: Li DZ, Chen ZD, Wnag H, Lu AM eds. Dictionary of Genera and Families of China Vascular Plants, Science Press, Beijing
  3. Sun M, Peng H. (2016). Elaeagnaceae. In: Liu B, Lin QW eds. Higher Plants of China in Color, Volume 5, Angiosperms: Euphorbiaceae — Cornaceae, Science Press, Beijing, China
  4. Sun M et al. (2015). In: Lin Q, Yang ZR eds. Types Specimens in China National Herbarium (PE), Volume 6, Angiospermae, Henan Science and Technology Press, Henan, China
  5. Sun M et al. (2015). In: Lin Q, Yang Y, Yang ZR eds. Types Specimens in China National Herbarium (PE), Volume 7, Angiospermae, Henan Science and Technology Press, Henan, China
  6. Sun M et al. (2015). In: Lin Q, Yang ZR, Lin Y eds. Types Specimens in China National Herbarium (PE), Volume 10, Angiospermae, Henan Science and Technology Press, Henan, China
  7. Sun M. (2014). Exploring deep phylogenetic incongruence of the COM clade in Rosidae: Phylogenomics approach. [PhD dissertation], Institute of Botany, the Chinese Academy of Sciences, Beijing, China
  8. Simpson M. (2012). Plant Systematics (2nd Edition) (Chen ZD, Lu AM, Sun M Trans.), Science Press, Beijing, China (Original publisher Academic Press)
  9. Sun M. (2009). Primary Taxonomic Study of Elaeagnus (Elaeagnaceae) in Mainland China. [Master thesis], Institute of Botany, the Chinese Academy of Sciences, Beijing, China

Conference Presentations/Posters:

  1. Sun M, Folk RA, Gitzendanner M, Smith AS, Chen ZD, Solits P, Soltis D. (2020). Phylogenetic and diversification analyses of rosids. Botany Conference. (Presentation)
  2. Abair A, Godden G, Sun M, El-Bahawy A, Soltis D, Soltis P. (2020). Assembling and Dating a Near-Comprehensive Phylogeny of Lamiaceae. Botany Conference. (Presentation)
  3. Sun M. (2019). Build and use large-scale phylogenetic trees. IBCAS Youth Forum. (Presentation)
  4. Sun M. (2018). Building, Using, and Tending the Tree of Life. Chinese Genomics Meet-up. (Presentation)
  5. Sun M, Germain-Aubrey CC, Smith SA, Soltis PS, Chen ZD, Soltis DE. (2018). Exploring the phylogeny and diversification of rosids with a five-locus supermatrix. The 1st AsiaEvo Conference 2018 (Shenzhen, China). Abstract ID: S38. (Poster)
  6. Millar J, Collins M, Picardi S, Riemer K, Stucky B, Sun M, Ye H. (2018). A Carpentries Culture at the University of Florida. CarpentryCon 2018 (Dublin, Ireland), Abstract ID: 13. (Poster)
  7. Sun M, Whitten WM, Gitzendanner MA, Soltis DE, Soltis PS. (2017). Exploring the Applicability of Fluidigm Amplification and NGS Sequencing Using Samples From Multiple Families. The XIX International Botanical Congress 2017 (Shenzhen, China), Abstract ID: T2-12-19. (Poster)
  8. Sun M, Germain-Aubrey CC, Smith SA, Soltis PS, Chen ZD, Soltis DE. (2017). Exploring the phylogeny and diversification of rosids through a five-gene supermatrix approach. The XIX International Botanical Congress 2017 (Shenzhen, China), Abstract ID: T2-44-15. (Poster)
  9. Zhang T, Lichstein JW, Sun M. (2017). Functional traits and population dynamics of North American tree species in a phylogenetic and biogeographic context. Annual Meeting of Ecological Society of America (ESA), August 10, 2017 (Portland, USA). Abstract ID: COS135-5. (Poster)
  10. Lichstein J, Zhang T, Sun M, Mack M, Graves S, Whitten M, Jantzen J, Park J, Bohlman S, Gitzendanner M, Soltis D, Soltis P. (2017). Ecological traits and recent populationdynamics of eastern Asian-eastern North American disjunct tree species in North America. The XIX International Botanical Congress 2017 (Shenzhen, China), Abstract ID: T2-12-05. (Presentation)
  11. Sun M, Germain-Aubrey CC, Gitzendanner MA, Smith SA, Soltis PS, Chen ZD, Soltis DE. (2016). Wrestling with the Rosids I: progress and challenges for phylogenetics of a large, hyper-diverse angiosperm clade. Botany Conference 2016 (Savannah, Georgia), Abstract ID: 404. (Presentation)

Classes Audited

  • 2018

    • RSSIG - R Social Sciences Interest Group
    • Phylogenetics Systematics ( BOT6935/ZOO6927 )
    • Computational Tools for Research ( ZOO6927/ZOO4926 )
    • the Origin of Species Reading Group ( BOT6935/ZOO6927 )
  • 2017

    • Grant Writing Seminar ( ZOO6927/BOT6935 )
    • Principles of Systematic Biology ( BOT6726/ZOO6927 )
    • Niche Modelling ( ZOO6927 )
  • 2016

    • Data & Analysis in Natural Sciences ( ZOO6927/ZOO4926||GLY6932/GLY4930 )
    • Phylogenomics ( BOT6935/ZOO6927 )
    • Practical Computational Biology ( ZOO4926/ZOO6927 )
  • 2015

    • Taxonomy of Vascular Plants ( BOT5725C )
    • Principles of Systematic Biology ( BOT6726/ZOO6927 )

Fieldwork Experience

  • 2015
    • Worked in Mountain Lake Biological Station (Virginia State) with Jeremy Lichstein (Department of Biology, University of Florida) and other ecologists collecting DNA, metabolites, RNA materials from canopy trees and understory communities, soil samples, and other microbial materials for Dimensions US-China Project ( Collaborative Research: How historical constraints, local adaptation, and species interactions shape biodiversity across an ancient floristic disjunction Dimensions).
    • Participated in Talladega National Forest (Alabama State) with Doug Soltis and Pam Soltis (Florida Museum of Natural History, University of Florida) and other ecologists for material collection and first hand data generation for Dimensions US-China Project.
    • Worked in Ordway Biological Station (Florida State) with Mark Whitten, Eric Tripplets, and other ecologists for material collection and first hand data generation for Dimensions US-China Project.
  • 2012
    • Trip to southern Yunnan along Myanmar border with Pam S. Soltis and Doug E. Soltis, collecting materials for Tree of life — China Project.
    • Trip to Hainan tropical rain forest with Doug E. Soltis, collecting materials of Tree for life — China Project.
  • 2006 ~ 2011
    • Joined in the expedition team of national herbarium (PE) for collection many times, successively visited a series of biodiversity hotspots, such as Hubei, Chongqing, Guangxi, Sichuan, Xizang, etc.

Academic Activities

  • 2020

  • 2019

  • 2018

    • Co-organizer and co-translator of The Great Tree of Life
    • Co-organizer of Research Bazaar event
    • Instructor and Helper of a serial of “Software and Data Carpentry Workshops” events
    • Instructor for Precollegiate Education and Training event
    • co-translated TreeTender movie into Chinese languague for public education
    • Digital outreach with 4th and 5th graders from Bunker Hill Elementary School in D.C
  • 2017

    • Board member of UF Carpentries Club
    • Organizer of several Tree of Life pop-up tent events (UF campus, FLMNH public museum, local brew-pub)
    • Helper of Research Computing Training at UF Information Technology, Research Computing (University of Florida)
    • Coordinated with the 100-year anniversary exhibit celebration of FLMNH
    • Organizer of One Tree one Planet Encore
    • Judge for Graduate Student Research Day
    • Instructor and Helper in several “Software Carpentry Workshop” events
    • Instructor for the 54th Florida Regional Junior Science, Engineering, and Humanities Symposium
  • 2016

    • Volunteer Tree of Life Pop-Up Science! Florida Museum of Natural History
    • Member of Botanical Society of America
    • Oral Talk “Wrestling with the Rosids I: progress and challenges for phylogenetics of a large, hyper-diverse angiosperm clade.” in the annual Botany Conference (Savannah, Georgia)
    • Table volunteer for iDigBio at BSA meeting
    • Organizing volunteer, iDigBio workshop: Using Digitized Herbarium Data in Research: A Crash Course
  • 2015 ~ 2010

    • Training college students for taxonomic skills
    • Speaker of the conference about dioecious plants in Angiosperm in Peking University
    • Participate in the evaluation of “Red List of China Higher Plants” as a taxonomy expert
    • Contributed to develop a “Molecular Data and Application Environment” website and a winner for the best of website name and domain name, “Darwin Tree” and “http://www.darwintree.cn/”, respectively

Service

  • Peer reviews for: South African Journal of Botany, Evolutionary Bioinformatics, Journal of Systematics and Evolution, International Journal of Tropical Biology and Conservation, Plant Physiology and Biochemistry, Taxon, Scientific Reports, Botany, PeerJ, Journal of Agriculture and Rural Development in the Tropics and Subtropics, and Phytotaxa.
  • Certified Instructor of Software Carpentry (The Carpentries; taught classes of >400 students)
  • Board member of UF Carpentries Club (a workshop series to teach informatics skills)
  • Judge for Graduate Student Research Day at University of Florida
  • Judge Graduate Student Research Grant proposals for American Society of Plant Taxonomists
  • Educator Summer Science Institute Tree of Life for high school teacher
  • Volunteer Tree of Life Pop-Up Science
  • Member of Botanical Society of America
  • Table volunteer for iDigBio events
  • Taxonomic instructor for training college students
  • Board member of “Red List of China Higher Plants” evaluation committee

References contact information

Pamela S. Soltis (Postdoc advisor)
Florida Museum of Natural History
University of Florida
Gainesville, FL 32611, USA
Email: psoltis@flmnh.ufl.edu
Phone: +1 (352) 273-1964

Douglas E. Soltis (Postdoc advisor)
Department of Biology
University of Florida
Gainesville, FL 32611, USA
Email: dsoltis@ufl.edu
Phone: +1 (352) 273-1963

Wolf Eiserhardt (Postdoc advisor)
Department of Bioscience
Ny Munkegade 116
building 1535, 225
8000 Aarhus C, Denmark
Email: wolf.eiserhardt@bios.au.dk
Phone: +4587156136

Zhiduan Chen (PhD advisor)
State Key Laboratory of Systematic and Evolutionary Botany
Institute of Botany
Chinese Academy of Sciences
Email: zhiduan@ibcas.ac.cn
Phone: +86 010-62836434

Matthew A. Gitzendanner (Bioinformatics Mentor)
Scientist, Department of Biology
Collection Manager, Florida Museum of Natural History
Training Coordinator and Bioinformatics Specialist, UF Research Computing
Email: magitz@ufl.edu
Tel.: +1 (352) 273-1960
FAX: +1 (352) 846-2154

Last modification: 2020-07-03

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