About

Stephen R. Downie leads a dynamic lab group focused on botanical research, particularly in the systematics of plant groups such as the basal Apioideae and Saniculoideae. His lab has a history of mentoring graduate students and hosting international postdoctoral researchers and visitors from various universities worldwide, including institutions in China, Turkey, South Africa, Poland, Korea, Russia, and more. The research in his lab includes detailed studies on genera such as Eryngium and Cymopterus, reflecting a strong emphasis on plant systematics and taxonomy. Downie encourages both graduate and undergraduate students to engage in independent research within his lab, supporting their academic and scientific development. The composition of his lab group is continually evolving, indicating an active and ongoing research environment.

Research topics

• Biology
• Evolutionary biology
• Genetics
• Botany
• Ecology
• Paleontology

Selected publications

• Resolving the tribal affiliation of the East Asia clade: phylogenomic evidence for its inclusion into Komarovieae (Apiaceae: Apioideae)

  Annals of Botany · 2025-11-07

  articleOpen accessSenior author

  BACKGROUND AND AIMS: The East Asia (or Physospermopsis) clade persists as one of the most taxonomically recalcitrant lineages in Apiaceae subfamily Apioideae. Despite previous delimitation efforts, myriad phylogenetic issues remain unsettled, spanning from chaotic interrelationships amongst constituent genera to affiliations with tribe Komarovieae. METHODS: In this study, we sampled 75 accessions from the East Asia clade, Komarovieae and nine other tribes/clades of Apioideae, and we leveraged integrated nuclear (262 genes) and plastid genomic data (81 loci) from genome skimming to further our understanding of this challenging group. Both coalescent-based and concatenation-based approaches were adopted. KEY RESULTS: Phylogenetic trees inferred from nuclear genes and chloroplast data yielded largely congruent topologies, with affiliations among previously recognized tribes and other major clades being well resolved. However, monophyly of the East Asia clade is robustly rejected; instead, analyses provide strong evidence that the East Asia clade is paraphyletic, with a monophyletic Komarovieae arising from within. Most genera within the East Asia clade are not resolved as monophyletic, with their members widely intermingled. By integrating these phylogenomic results with previously available morphological and phylogenetic evidence, we reinstate the genus Dactylaea to accommodate Sinocarum schizopetalum and discuss implications for taxonomic changes to problematic species previously recognized in Acronema, Hymenidium, Pimpinella and Tongoloa. Accordingly, we merge the East Asia clade into an expanded Komarovieae, which now comprises representatives of 21 genera. CONCLUSION: These results provide a robust phylogenetic framework for this systematically challenging group, while also highlighting the need for comprehensive taxonomic revision of the many non-monophyletic genera within the East Asia clade.

  PublisherOA PDFDOI

• Phylogenomics and the rise of the angiosperms

  Nature · 2024 · 369 citations

  • Biology
  • Evolutionary biology
  • Ecology

  provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

  PublisherOA PDFDOI

• Circumscription of the East Asia clade (Apiaceae subfamily Apioideae) and the taxonomic placements of several problematic genera

  Plant Diversity · 2023-11-29 · 5 citations

  articleOpen accessSenior author

  The East Asia (or Physospermopsis) clade was recognized in previous molecular phylogenetic investigations into the higher-level relationships of Apiaceae subfamily Apioideae. The composition of this clade, the phylogenetic relationships among its constituent taxa, and the placement of species previously determined to be problematic have yet to be resolved. Herein, nrDNA ITS sequences were obtained for 150 accessions of Apioideae, representing species whose distributions are in East Asia or genera having one or more species included within the East Asia clade. These data, along with published ITS sequences from other Apioideae (for 3,678 accessions altogether), were subjected to maximum likelihood and Bayesian inference analyses. The results show that the East Asia clade contains representatives of 11 currently recognized genera: Hansenia, Hymenolaena, Keraymonia, Sinolimprichtia, Acronema, Hymenidium, Physospermopsis, Pimpinella, Sinocarum, Tongoloa, and Trachydium. However, the latter seven genera have members falling outside of the East Asia clade, including the generic types of all except Tongoloa. Within the clade, the species comprising these seven genera are widely intermingled, greatly increasing confusion among relationships than previously realized. The problematic species Physospermopsis cuneata is confirmed as falling within the East Asia clade, whereas P. rubrinervis allies with the generic type in tribe Pleurospermeae. Physospermopsis kingdon-wardii is confirmed as a member of the genus Physospermopsis, whereas the generic attributions of P. cuneata and Tongoloa stewardii remain unclear. Two species of Sinocarum (S. filicinum and S. wolffianum) are transferred into the genus Meeboldia. This is the most comprehensive molecular phylogenetic investigation of the East Asia clade to date, and while the results increase systematic understanding of the clade, they also highlight the need for further studies of one of the most taxonomically intractable groups in Apioideae.

  PublisherDOI

• The chloroplast genomes of <i>Sanicula</i> (Apiaceae): plastome structure, comparative analyses and phylogenetic relationships

  Nordic Journal of Botany · 2022-06-05 · 9 citations

  article

  Sanicula (Apiaceae subfam. Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five Sanicula species ( S. flavovirens , S. giraldii , S. lamelligera , S. odorata and S. rubriflora ) were sequenced and compared to the previously published S. orthacantha plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein‐coding, 37 tRNA and 8 rRNA genes. The loci rpl2 , matK , psbA and ycf1 are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup Hydrocotyle (Araliaceae) suggest sectional relationships in Sanicula different from the traditional classification system, but support the monophyly of Apioideae and its sister group relationship to Saniculoideae and show concordant topologies to nrDNA ITS and other plastome‐based phylogenies. Sanicula orthacantha and S. chinensis form a sister group to S. lamelligera and S. odorata , consecutively. These four species comprise a sister group to the clade of S. rubriflora and S. flavovirens , with this entire group sister to S. giraldii . The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic and population‐level studies of Sanicula .

  PublisherDOI

• A higher-level nuclear phylogenomic study of the carrot family (Apiaceae)

  Zenodo (CERN European Organization for Nuclear Research) · 2022-06-10

  datasetOpen access

  Premise The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. Methods Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. Results We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (<em>Platysace</em>, <em>Klotzchia</em>, and <em>Hermas</em>); all three occupy isolated positions, with <em>Platysace</em>resolved as sister to all remaining Apiaceae. We placed nine genera (<em>Apodicarpum</em>, <em>Bonannia</em>, <em>Grafia</em>, <em>Haplosciadium</em>, <em>Microsciadium</em>, <em>Physotrichia</em>, <em>Ptychotis</em>, <em>Tricholaser</em>, <em>Xatardia</em>) that have never previously been included in any molecular phylogenetic study. Conclusions We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that <em>Hermas</em>, <em>Klotzschia</em>, and the <em>Platysace</em> clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus <em>Phlyctidocarpa</em> can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

  PublisherDOI

• A higher-level nuclear phylogenomic study of the carrot family (Apiaceae)

  Zenodo (CERN European Organization for Nuclear Research) · 2022-06-10

  datasetOpen access

  Premise The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. Methods Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. Results We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (<em>Platysace</em>, <em>Klotzchia</em>, and <em>Hermas</em>); all three occupy isolated positions, with <em>Platysace</em>resolved as sister to all remaining Apiaceae. We placed nine genera (<em>Apodicarpum</em>, <em>Bonannia</em>, <em>Grafia</em>, <em>Haplosciadium</em>, <em>Microsciadium</em>, <em>Physotrichia</em>, <em>Ptychotis</em>, <em>Tricholaser</em>, <em>Xatardia</em>) that have never previously been included in any molecular phylogenetic study. Conclusions We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that <em>Hermas</em>, <em>Klotzschia</em>, and the <em>Platysace</em> clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus <em>Phlyctidocarpa</em> can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

  PublisherDOI

• Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

  BIROn (Birkbeck, University of London) · 2021-06-08 · 1 citations

  articleOpen access

  PREMISE: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger- sequencing approaches, the <em>Lomatium packardiae/L. anomalum</em> subcomplex within the larger <em>Lomatium triternatum</em> complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS: The Angiosperms353 probe set was employed to resolve the ambiguity within <em>Lomatium triternatum</em> species complex using 48 accessions assigned to <em>L. packardiae, L. anomalum,</em> or <em>L. triternatum</em>. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent- based species tree analysis that takes incomplete lineage sorting into account; ASTRAL- III, another coalescent- based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS: The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS: The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent- based processes.

  OA PDFDOI

• A higher‐level nuclear phylogenomic study of the carrot family (Apiaceae)

  American Journal of Botany · 2021 · 56 citations

  • Biology
  • Botany
  • Evolutionary biology

  PREMISE: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. METHODS: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS: We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS: We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

  PublisherDOI

• Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the <i>Lomatium packardiae/L. anomalum</i> clade of the <i>L. triternatum</i> (Apiaceae) complex

  American Journal of Botany · 2021 · 24 citations

  • Biology
  • Evolutionary biology
  • Genetics

  PREMISE: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS: The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS: The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS: The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.

  PublisherOA PDFDOI

• Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

  Zenodo (CERN European Organization for Nuclear Research) · 2021-06-08

  articleOpen access

  PREMISE: Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger- sequencing approaches, the <em>Lomatium packardiae/L. anomalum</em> subcomplex within the larger <em>Lomatium triternatum</em> complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS: The Angiosperms353 probe set was employed to resolve the ambiguity within <em>Lomatium triternatum</em> species complex using 48 accessions assigned to <em>L. packardiae, L. anomalum,</em> or <em>L. triternatum</em>. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent- based species tree analysis that takes incomplete lineage sorting into account; ASTRAL- III, another coalescent- based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS: The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS: The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent- based processes.

  PublisherDOI

Recent grants

• A Phylogenetic Study of Apiaceae Tribe Oenantheae

  NSF · $231k · 2001–2005

• Molecular Phylogenetic Study of Apiaceae Subfamily Apioideae

  NSF · $240k · 1994–1998

Frequent coauthors

• Krzysztof Spalik

  University of Warsaw

  26 shared

• Deborah S. Katz‐Downie

  University of Illinois Urbana-Champaign

  26 shared

• Carolina I. Calviño

  Consejo Nacional de Investigaciones Científicas y Técnicas

  25 shared

• B.-E. Van Wyk

  University of Johannesburg

  24 shared

• A.R. Magee

  University of the Western Cape

  15 shared

• Gregory M. Plunkett

  13 shared

• Patricia M. Tilney

  University of Johannesburg

  13 shared

• Mary Ann Feist

  12 shared

Labs

• Stephen R. Downie LabPI

  The lab focuses on the systematics and evolution of flowering plants, particularly the family Apiaceae.