Subtopic Deep Dive
Cyperus Phylogenetic Relationships
Research Guide
What is Cyperus Phylogenetic Relationships?
Cyperus phylogenetic relationships reconstruct evolutionary history within the genus Cyperus (Cyperaceae) using molecular markers like rbcL, ETS1f, and plastid DNA alongside morphological traits to resolve sectional boundaries and paraphyly.
Studies employ maximum likelihood, Bayesian inference, and parsimony analyses on nuclear ribosomal (ETS1f) and plastid (rpl32-trnL, trnH-psbA, rbcL) sequences. Key works include Larridon et al. (2013, 112 citations) on C4 Cyperus and Muasya et al. (2002, 70 citations) using plastid data. Over 10 papers from 2002-2021 address generic delimitation and hybridization.
Why It Matters
Accurate Cyperus phylogenies guide taxonomy for invasive species control, such as Cyperus rotundus, and conservation of endemic taxa. Larridon et al. (2013) redefined C4 Cyperus boundaries, aiding ecological management. Muasya et al. (2002) clarified Cyperus s.s. circumscription, supporting biodiversity inventories; Simpson et al. (2007) enhanced family-wide systematics for habitat restoration.
Key Research Challenges
Paraphyly Resolution
Cyperus s.l. forms a giant paraphyletic grade requiring generic recircumscription. Larridon et al. (2013) used ETS1f and plastid markers to delimit C4 Cyperus but sectional conflicts persist. Hybridization obscures boundaries (Muasya et al., 2008).
Molecular Marker Conflicts
Plastid vs. nuclear data yield incongruent trees in Cypereae. Simpson et al. (2007) rbcL analysis conflicted with Muasya et al. (2002) plastid results. Hybrid introgression demands multi-locus approaches (Bauters et al., 2014).
Morphology Integration
Floral ontogeny and embryography support molecular clades but homology assessment challenges generic limits. Larridon et al. (2011) combined data for C3 Cyperus changes. Muasya et al. (2011) described Dracoscirpoides using ontogeny.
Essential Papers
Towards a new classification of the giant paraphyletic genus<i>Cyperus</i>(Cyperaceae): phylogenetic relationships and generic delimitation in C<sub>4</sub><i>Cyperus</i>
Isabel Larridon, Kenneth Bauters, Marc Reynders et al. · 2013 · Botanical Journal of the Linnean Society · 112 citations
Maximum likelihood and Bayesian inference analyses of nuclear ribosomal DNA (ETS1f) and plastid DNA (rpl32-trnL, trnH-psbA) sequence data are presented for 'C4Cyperus' (Cyperaceae). The term 'C4Cyp...
Phylogeny of Cyperaceae Based on DNA Sequence Data–a New rbcL Analysis
David Simpson, A. Muthama Muasya, Marccus Alves et al. · 2007 · Aliso · 110 citations
Since the Monocots II meeting in 1998, significant new data have been published that enhance our systematic knowledge of Cyperaceae. Phylogenetic studies in the family have also progressed steadily....
A new classification of<i>Carex</i>(Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree
Tamara Villaverde, Pedro Jiménez‐Mejías, Modesto Luceño et al. · 2020 · Botanical Journal of the Linnean Society · 93 citations
Abstract The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more afforda...
What is a Genus in Cypereae: Phylogeny, Character Homology Assessment and Generic Circumscription in Cypereae
A. Muthama Muasya, Alexander Vrijdaghs, David A. Simpson et al. · 2008 · The Botanical Review · 74 citations
El endemismo en las Liliopsida mexicanas
Adolfo Espejo‐Serna · 2017 · Acta Botanica Mexicana · 71 citations
Se presenta un listado actualizado de las Liliopsida endémicas de México. De las 4,542 especies silvestres que habitan en el territorio nacional, 2,010 son endémicas exclusivas y la cifra asciende ...
Phylogenetic relationships in Cyperus L. s.l. (Cyperaceae) inferred from plastid DNA sequence data
A. Muthama Muasya, David A. Simpson, Mark W. Chase · 2002 · Botanical Journal of the Linnean Society · 70 citations
The phylogeny of Cyperus and allied genera has been reconstructed using cladistic analysis of plastid rbcL gene, rps16 intron, trnL intron, and trnL-F intergenic spacer sequence data in 40 species ...
Taxonomic changes in C3 Cyperus (Cyperaceae) supported by molecular data, morphology, embryography, ontogeny and anatomy
Isabel Larridon, Marc Reynders, Wim Huygh et al. · 2011 · Plant Ecology and Evolution · 60 citations
Background and aims – Recent molecular studies validate a broad definition of Cyperus (Cyperaceae) uniting genera previously scattered in Cyperoideae. First indication of their affinity with Cyperu...
Reading Guide
Foundational Papers
Start with Muasya et al. (2002) for plastid basics in Cyperus s.l., then Simpson et al. (2007) rbcL family phylogeny, followed by Larridon et al. (2013) C4 delimitation to build core framework.
Recent Advances
Study Bauters et al. (2014) on Lipocarpha/Volkiella inclusion; Muasya et al. (2011) Dracoscirpoides for ontogeny; Villaverde et al. (2020) HybSeq methods adaptable to Cyperus.
Core Methods
Plastid (rbcL, trnL-F, rpl32-trnL), nuclear (ETS1f) sequencing; Bayesian/ML inference; embryography/ontogeny for morphology; species-tree reconstruction (Bauters et al., 2014).
How PapersFlow Helps You Research Cyperus Phylogenetic Relationships
Discover & Search
Research Agent uses searchPapers('Cyperus phylogenetic relationships') to retrieve Larridon et al. (2013), then citationGraph reveals 112 citing papers and backward citations to Muasya et al. (2002). findSimilarPapers on Simpson et al. (2007) uncovers rbcL-focused Cypereae studies; exaSearch('C4 Cyperus paraphyly ETS1f') surfaces niche preprints.
Analyze & Verify
Analysis Agent applies readPaperContent on Larridon et al. (2013) to extract ETS1f tree stats, then verifyResponse with CoVe cross-checks paraphyly claims against Muasya et al. (2002). runPythonAnalysis parses Newick trees from Simpson et al. (2007) rbcL data for bootstrap support visualization; GRADE assigns A-grade evidence to Bayesian inferences.
Synthesize & Write
Synthesis Agent detects gaps in C3 vs. C4 Cyperus integration from Larridon et al. (2011/2013), flags contradictions in plastid-nuclear trees. Writing Agent uses latexEditText for sectional phylogeny revisions, latexSyncCitations links Muasya papers, latexCompile generates PDF; exportMermaid diagrams clade relationships from Bauters et al. (2014).
Use Cases
"Compute bootstrap supports from rbcL sequences in Cyperus phylogenies"
Research Agent → searchPapers('Cyperus rbcL') → Analysis Agent → readPaperContent(Simpson 2007) → runPythonAnalysis(NumPy tree parsing, matplotlib bootstrap plot) → researcher gets CSV of node supports and divergence times.
"Draft LaTeX figure of C4 Cyperus clade from Larridon 2013"
Synthesis Agent → gap detection(Larridon 2013) → Writing Agent → latexEditText(clade description) → latexSyncCitations(Muasya papers) → latexCompile → researcher gets compiled PDF with TikZ phylogeny.
"Find code for Cyperus plastid alignment analysis"
Research Agent → searchPapers('Cyperus plastid phylogeny') → paperExtractUrls(Muasya 2002) → paperFindGithubRepo → githubRepoInspect → researcher gets R script for trnL-F alignment from cited repo.
Automated Workflows
Deep Research workflow scans 50+ Cyperus papers via searchPapers → citationGraph → structured report on paraphyly resolution (Larridon 2013 baseline). DeepScan's 7-step chain: readPaperContent(Simpson 2007) → runPythonAnalysis(rbcL parsimony) → CoVe verification → GRADE report on tree robustness. Theorizer generates hypotheses on hybridization from Muasya et al. (2008/2011) floral data.
Frequently Asked Questions
What defines Cyperus phylogenetic relationships?
Evolutionary reconstructions using rbcL, ETS1f, plastid markers, and morphology to resolve Cyperus s.l. paraphyly and sectional limits (Larridon et al., 2013; Muasya et al., 2002).
What molecular methods are used?
Maximum likelihood/Bayesian on ETS1f, rpl32-trnL; parsimony on rbcL, trnL-F; multi-locus for hybridization (Simpson et al., 2007; Bauters et al., 2014).
What are key papers?
Larridon et al. (2013, 112 citations) on C4 Cyperus; Simpson et al. (2007, 110 citations) rbcL phylogeny; Muasya et al. (2002, 70 citations) plastid relationships.
What open problems remain?
Full genome integration for hybridization; resolving C3/C4 conflicts; infrageneric taxa like Lipocarpha in Cyperus s.l. (Larridon et al., 2011; Bauters et al., 2014).
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