About

A. Jonathan Shaw is a Professor of Biology at Duke University, holding this position since 2001. His research centers on the evolution and diversity of bryophytes, with a particular focus on the genus Sphagnum (peatmosses). His work involves molecular phylogenetic analyses at various levels of biological organization, utilizing DNA sequence data from nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. Shaw's research explores geographic patterns in phylogenetic diversity within peatmosses, emphasizing biogeographic relationships between boreal, tropical, and Southern Hemisphere taxa, as well as between New and Old World taxa. He is especially interested in the genetic structure of both rare and widespread species and employs morphological and molecular information to understand these patterns. Shaw serves as the Curator of the Bryophyte Herbarium at Duke, which includes approximately 230,000 collections of mosses, liverworts, and hornworts, making it a central resource for bryological research. His laboratory collaborates with institutions such as the New York Botanical Garden, the University of Connecticut, the Missouri Botanical Garden, and the University of Alberta. His recent publications address eco-evolutionary aspects of Sphagnum moss, the use of artificial intelligence for herbarium specimen identification, and the role of microbiomes in Sphagnum moss growth and ecosystem function. His ongoing projects include studying microbial controls on peatland nutrient cycling, curating the Sphagnum collection, and building a global bryophyte and lichen consortium. Shaw's academic background includes a Ph.D. from the University of Michigan, an M.S. from the University of Alberta, and a B.S. from Cornell University.

Research topics

• Biology
• Genetics
• Ecology
• Evolutionary biology
• Paleontology
• Astrobiology

Selected publications

• A new propaguliferous species of Pohlia (Mielichhoferiaceae, Bryopsida) from Tibet, China

  The Catalogue of Life · 2026-02-16

  datasetOpen access
  PublisherDOI

• Data from: Climate niches structure a regional hybrid zone in <em>Sphagnum</em> (peatmoss, Bryophyta)

  Open MIND · 2025-12-16

  dataset

  Premise: Hybridization is an important evolutionary process across all groups of embryophyte land plants, but relatively little is known about hybridization and introgression in spore producing plants with a dominant gametophyte life cycle stage (i.e., bryophytes). The Sphagnum magellanicum complex, with four North American species, is proving to be a valuable system for studying population genomics, speciation, and climate adaptation. This paper focuses on hybridization between the four species, with focus on a regional zone where virtually all plants in the two most recently diverged species (S. diabolicum, S. magniae) show genetic admixture. Methods: Analyses of population genetics and introgression utilized three types of molecular data: RADseq, “RADseq-like” data derived from in silico digestion of genome sequences, and species-specific barcode markers developed previously for this group. 582 gametophytes were sampled from 79 collecting sites representing 23 U.S. states and five Canadian provinces, from 27 o to 56o N. A range of analytical methods were employed: phylogeny reconstruction, STRUCTURE to assess individual genetic admixture, demographic modeling to estimate the timing and extent of interspecific gene flow, and comparative genomics to evaluate the occurrence and locations of introgressed SNPs. Results: Low but significant gene flow was detected among all pairwise combinations of extant species as well as between ancestral lineages and those species. Greater genetic similarities among species where they occur sympatrically within peatlands suggests that hybridization is on-going. Hybridization between S. diabolicum and S. magniae is especially pronounced and plants in a regional zone from North Carolina to New Jersey are genetically admixed. Demographic analyses all indicate that this admixture reflects hybridization, not just incomplete lineage sorting. Introgressed SNPs were detected across all chromosomes but introgressed SNPs fixed in genetically pure samples of the two species were concentrated on four autosomes: 2, 7, 14, and 19. Introgression block sizes and numbers were positively correlated with the level of genetic admixture. Patterns of genomic admixture/introgression were significantly correlated with climate variation across collection sites within the hybrid zone. Conclusions: Previous analyses indicated that climate adaptation has played an important role in speciation within this group, especially the divergence of warm-temperate to subtropical S. magniae from cold-temperate to boreal S. diabolicum. This work shows that the genomic structure of plants in a regional hybrid zone between S. magniae and S. diabolicum is also structured by climate adaptation and strengthens the value of this group for learning more about both speciation and climate adaptation.

  DOI

• Host Species–Microbiome Interactions Contribute to <i>Sphagnum</i> Moss Growth Acclimation to Warming

  Global Change Biology · 2025-02-01 · 5 citations

  articleOpen access

  Sphagnum moss is the dominant plant genus in northern peatlands responsible for long-term carbon accumulation. Sphagnum hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome + environment) plays a key role in nutrient acquisition along with carbon cycling. Climate change can modify the Sphagnum-associated microbiome, resulting in enhanced host growth and thermal acclimation as previously shown in warming experiments. However, the extent of microbiome benefits to the host and the influence of host-microbe specificity on Sphagnum thermal acclimation remain unclear. Here, we extracted Sphagnum microbiomes from five donor species of four peatland warming experiments across a latitudinal gradient and applied those microbiomes to three germ-free Sphagnum species grown across a range of temperatures in the laboratory. Using this experimental system, we test if Sphagnum's growth response to warming depends on the donor and/or recipient host species, and we determine how the microbiome's growth conditions in the field affect Sphagnum host growth across a range of temperatures in the laboratory. After 4 weeks, we found that the highest growth rate of recipient Sphagnum was observed in treatments of matched host-microbiome pairs, with rates approximately 50% and 250% higher in comparison to maximum growth rates of non-matched host-microbiome pairs and germ-free Sphagnum, respectively. We also found that the maximum growth rate of host-microbiome pairs was reached when treatment temperatures were close to the microbiome's native temperatures. Our study shows that Sphagnum's growth acclimation to temperature is partially controlled by its constituent microbiome. Strong Sphagnum host-microbiome species specificity indicates the existence of underlying, unknown physiological mechanisms that may drive Sphagnum's ability to acclimatize to elevated temperatures. Together with rapid acclimation of the microbiome to warming, these specific microbiome-plant associations have the potential to enhance peatland resilience in the face of climate change.

  PublisherOA PDFDOI

• Data from: Genetic structure of the Sphagnum magellanicum (Sphagnaceae) complex in Europe

  Open MIND · 2025-01-01

  dataset

  Sphagnum magellanicum has historically been interpreted as a widespread species across both the Northern and Southern Hemispheres. Recent research, however, indicates that it comprises at least seven phylogenetic species, and that S. magellanicum s.str. It is restricted to southern Argentina and Chile. Four species are recorded from North America, and two of them, S. divinum and S. medium, are known to occur in Europe (and are typified by European collections). Here, we assess European plants of this complex to test if two apparent North American endemics, S. diabolicum and S. magniae, occur in Europe, and document the genetic structure of European species of the complex, including gametophyte sex ratios and patterns of genetic diversity. We further assess evidence for gene flow between the species in Europe and between North American and European plants of species that occur on both continents. Molecular data, especially RADseq, were used to assess genetic and phylogenetic patterns, and additional plants were identified with barcode markers to document European geographic distributions. The results indicate that S. diabolicum and S. magniae are endemic to North America. In Europe, S. divinum is more genetically diverse than S. medium. Sex ratios in both species did not depart from 50:50. Low levels of interspecific gene flow between the two species occur in Europe, as well as higher levels of gene flow between North American and European plants within S. divinum and S. medium. Overall, our results corroborate evidence that S. divinum and S. medium are phylogenetically distinct species and represent separate gene pools despite low levels of introgression.

• <scp>AI</scp> for difficult herbarium specimens: identification of peat mosses (subgenus <i>Sphagnum</i>) without dissection

  New Phytologist · 2025-08-16 · 2 citations

  articleOpen access

  Summary Artificial intelligence (AI) for image‐based herbarium specimen identification has thus far focused on plants that can be identified by eye. Here, we develop the first AI focused on identifying herbarium specimens of a bryophyte group, peat mosses in Sphagnum subgenus Sphagnum . These plants have substantial morphological plasticity, and confident identifications require time‐consuming dissections and microscopy. We hypothesized that AI, using unmagnified low‐resolution images, can (H 1 ) identify species and (H 2 ) discover novel morphological characters. We collected 4386 publicly available herbarium specimen images of all 10 North American species and imaged an additional 105 specimens with determinations verified by DNA and morphology. AI identification was generally successful with our newly formulated FireNetSEz model (68% AUCPR (area under the curve: precision recall)). We produced a reduced dataset (the five most imaged species) that we, the authors, could attempt. Our identifications took hours and were all lower‐scoring than the AI. These H 1 results show that AI can learn hard‐to‐identify botanical species without microscopy and outperform both generalist botanists and Sphagnum experts. Regarding H 2 , we found the AI focuses on edges of organs that humans often ignore. AI holds promise for hard botanical identifications and the potential to rapidly identify Sphagnum , which is important for studying peatlands that strongly impact climate.

  PublisherOA PDFDOI

• Climate niches structure a regional hybrid zone in <i>Sphagnum</i> (peatmoss, Bryophyta)

  American Journal of Botany · 2025-12-22 · 1 citations

  article1st authorCorresponding

  PREMISE: Hybridization is an important evolutionary process across all groups of embryophyte land plants, but relatively little is known about hybridization and introgression in plants with a dominant gametophyte life cycle stage. This paper focuses on hybridization between four closely related species of the moss genus Sphagnum. METHODS: Analyses utilized three types of molecular data: restriction-site-associated DNA sequencing (RADseq), RADseq-like data derived from in silico digestion of genome sequences, and species-specific barcode markers developed previously for this group. Sampling included 582 gametophytes from 79 collecting sites from 27° to 56°N. A range of analytical methods were employed: phylogeny reconstruction, genetic analyses using the program structure, demographic modeling, and comparative genomics. RESULTS: Gene flow was detected among all pairwise combinations of extant species and between ancestral lineages and those species. Hybridization between S. diabolicum and S. magniae was especially pronounced and plants in a regional zone from North Carolina to New Jersey were genetically admixed. Demographic analyses indicated that this admixture reflects hybridization. Introgressed SNPs were detected across all chromosomes, but introgressed SNPs fixed in genetically pure samples of the two species were concentrated on four autosomes: 2, 7, 14, and 19. Patterns of genomic admixture/introgression were significantly correlated with climate variation across collection sites within the hybrid zone. CONCLUSIONS: The genomic structure of plants in a regional hybrid zone between S. magniae and S. diabolicum was structured by climate adaptation and strengthens the value of this group for learning more about speciation and climate adaptation.

  PublisherDOI

• Genetic structure of the Sphagnum magellanicum (Sphagnaceae) complex in Europe

  The Bryologist · 2025-07-16 · 1 citations

  article1st authorCorresponding

  Contains fulltext : 324044.pdf (Publisher’s version ) (Open Access)

  PublisherDOI

• The challenging but unique eco‐evolutionary aspects of <i>Sphagnum</i> moss

  New Phytologist · 2025-06-01 · 9 citations

  reviewOpen accessSenior author

  Sphagnum is emerging as a useful system for advancing knowledge at the interface between ecology and evolutionary biology. Here, we explore: the importance of the Sphagnum microbiome to ecosystem structure and function; the value of naturally occurring genetic variation within Sphagnum populations; and the ongoing process of speciation and ecological divergence in the genus. Recent advances in understanding the molecular genetics underpinning cyanobacteria associations with Sphagnum's living and hyaline cells make this a rich area for future research, including implications for carbon and nitrogen exchange. We review niche differentiation in Sphagnum, underlying functional traits, and phylogenetic conservation. More knowledge is needed about naturally occurring variation within Sphagnum species, including trait plasticity and variation between sexes, to explore broader issues such as the mechanisms underpinning metabolism and its consequences for microbiomes as well as how we can most effectively use Sphagnum in restoration and other ecological problem solving. We use newly resolved phylogenetic relationships within the S. magellanicum complex to illustrate its potential for studying ecologically driven speciation. Our review focuses on the unique challenges in using Sphagnum as an eco-evolutionary system but also offers insights into emerging questions across genetics, physiological traits, ecological function, and biogeochemical cycling.

  PublisherOA PDFDOI

• Ecological differentiation and sympatry of cryptic species in the <i>Sphagnum magellanicum</i> complex (Bryophyta)

  American Journal of Botany · 2024-09-01 · 9 citations

  articleOpen accessSenior author

  PREMISE: Sphagnum magellanicum (Sphagnaceae, Bryophyta) has been considered to be a single semi-cosmopolitan species, but recent molecular analyses have shown that it comprises a complex of at least seven reciprocally monophyletic groups, that are difficult or impossible to distinguish morphologically. METHODS: Newly developed barcode markers and RADseq analyses were used to identify species among 808 samples from 119 sites. Molecular approaches were used to assess the geographic ranges of four North American species, the frequency at which they occur sympatrically, and ecological differentiation among them. Microhabitats were classified with regard to hydrology and shade. Hierarchical modelling of species communities was used to assess climate variation among the species. Climate niches were projected back to 22,000 years BP to assess the likelihood that the North American species had sympatric ranges during the late Pleistocene. RESULTS: The species exhibited parallel morphological variation, making them extremely difficult to distinguish phenotypically. Two to three species frequently co-occurred within peatlands. They had broadly overlapping microhabitat and climate niches. Barcode- versus RADseq-based identifications were in conflict for 6% of the samples and always involved S. diabolicum vs. S. magniae. CONCLUSIONS: These species co-occur within peatlands at scales that could permit interbreeding, yet they remain largely distinct genetically and phylogenetically. The four cryptic species exhibited distinct geographic and ecological patterns. Conflicting identifications from barcode vs. RADseq analyses for S. diabolicum versus S. magniae could reflect incomplete speciation or hybridization. They comprise a valuable study system for additional work on climate adaptation.

  PublisherOA PDFDOI

• Metal Tolerance In Bryophytes

  2024-10-04 · 3 citations

  book-chapter1st authorCorresponding

  Bryophytes hold special promise for studies of the evolution of metal tolerance. Their characteristics include the haploid condition of free-living plants, a tendency to accumulate metals and develop a high degree of tolerance, and the occurrence of species or complexes of species showing an ecological association with metal-enriched habitats.

  PublisherDOI

Recent grants

• Collaborative Research: AToL: Assembling the Pleurocarp Tree of Life: Resolving the rapid radiation using genomics and transcriptomics

  NSF · $451k · 2013–2017

• Phylogeny and Speciation in Sphagnum Section Subsecunda

  NSF · $472k · 2005–2010

• ATOL: Collaborative Research - Assembling the Liverwort Tree of Life: A Window into the Evolution and Diversification of Early Land Plants

  NSF · $870k · 2006–2011

• Linking evolutionary processes and taxonomy in the peatmoss group Sphagnum subg. Cuspidata

  NSF · $851k · 2020–2024

• Dimensions: Collaborative Research: Genome structure and adaptive evolution in peatmosses (Sphagnum): ecosystem engineers

  NSF · $1.2M · 2017–2023

Frequent coauthors

• Blanka Shaw

  Duke University

  36 shared

• Sandra B. Boles

  Duke University

  27 shared

• Bernard Goffinet

  University of Connecticut

  26 shared

• Jeremy Schmutz

  HudsonAlpha Institute for Biotechnology

  25 shared

• David J. Weston

  Oak Ridge National Laboratory

  24 shared

• Péter Szövényi

  University of Zurich

  23 shared

• Cymon J. Cox

  Centro de Ciências do Mar do Algarve

  22 shared

• Matthew G. Johnson

  Texas Tech University

  22 shared

Labs

• Duke Bryology LaboratoryPI

  The lab focuses on the evolution and diversity of bryophytes.

Education

• Ph.D, Biology

  University of Michigan

  1983