Estimation of divergence times in Asparagales in the
presence of hybridization
Kate L. Hertweck, Michael R. McKain
Monocot...
Objectives
1) Describing lynchpins of monocot evolution
2) Informing Asparagales divergence times with lessons from
monoco...
Kate L. Hertweck, Michael S. Kinney, Sarah Mathews, Mark W. Chase,
M. A. Gandolfo, J. Chris Pires
Divergence time estimati...
Fossil calibrations for Asparagales
constraint Age (Ma) taxon
1 CG angiosperms 110.4 (Early-Middle Albian) Carpestella lac...
Monocot timetree
Single data partitions fail to
reconstruct deep relationships
Combined dataset yields high
confidence at ...
Monocot timetree: Maxage of angiosperms at 170 Ma
Outgroups constrained for
proper fossil placement
Confidence intervals:
...
Lynchpins in monocot divergence time estimation
● Taxonomic sampling
● Even sampling across lineages
● Represent early div...
Lynchpins in monocot divergence time estimation
● Taxonomic sampling
● Even sampling across lineages
● Represent early div...
Lynchpins in monocot divergence time estimation
● Taxonomic sampling
● Molecular sequence sampling
● Combining data partit...
Lynchpins in monocot divergence time estimation
● Taxonomic sampling
● Molecular sequence sampling
● Fossil calibrations
●...
Lynchpins in monocot divergence time estimation
● Taxonomic sampling
● Molecular sequence sampling
● Fossil calibrations
●...
Objectives
1) Describing lynchpins of monocot evolution
2) Informing Asparagales divergence times with lessons from
monoco...
Basic Asparagales divergence times
K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications...
Lynchpin 1: Taxonomic sampling in Asparagales
Chen S, Kim D-K, Chase MW, Kim J-H (2013) Networks
in a Large-Scale Phylogen...
●
Chen et al. 2013:
●
253 species, 201 genera, all families in Asparagales
●
29 species from monocot outgroups
●
Three cal...
• Variation in genome size
• Karyotype (chromosome structure, bimodality)
• Polyploidy (auto-, allo-, aneu- ploidy)
• Hybr...
Application of nuclear data to divergence time estimates
• ITS
• Low copy nuclear genes
• Transcriptomes
• PHYTOCHROME C (...
PHYC reconstructs relationships between families
K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3...
Intrafamilial relationships from PHYC are messy
Androstephium (Brodiaeoideae)
Brodiaea (Brodiaeoideae)
Drimia (Scilloideae...
Intrafamilial relationships from PHYC are messy
Androstephium (Brodiaeoideae)
Brodiaea (Brodiaeoideae)
Drimia (Scilloideae...
Lynchpin 3: Fossil calibrations
constraint Age (Ma) taxon
CG Orchidaceae 15 (Early-Middle Miocene) Meliorchis caribea
CG A...
Secondary calibrations can have unexpected results!
K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagale...
Recommendations for dating estimates in Asparagales
● Can any of uncertainty in three lynchpins be accommodated by
analyti...
Objectives
1) Describing lynchpins of monocot evolution
2) Informing Asparagales divergence times with lessons from
monoco...
Genomic changes occur repeatedly in Asparagales phylogeny
Hertweck,
Genome, 2013
K. Hertweck, NESCent, Asparagales diverge...
Dating transposable element proliferation
Hertweck,
Genome, 2013
K. Hertweck, NESCent, Asparagales divergence 1. Monocots ...
Divergence times provide the context for inferring evolutionary patterns
● From monocot 8 gene dataset:
● SymmeTREE (Chan ...
Summary
●
My personally favored estimate for CG Asparagales:
113 Ma (125-105)
●
Problems with dating in monocots are exace...
Basic Asparagales divergence times
K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications...
Acknowledgements
• J. Chris Pires and lab (U of Missouri)
• Victoria Docktor
• NESCent science and bioinformatics folks
• ...
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Hertweck Monocots V Presentation

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"Estimation of Divergence Times in Asparagales in the Presence of Hybridization," presented in symposium "Insights and Benefits from Monocot Palaeobiology: Fossils, DNA, and Phylogenies" at Monocots V (5th International Conference on Comparative Biology of Monocotyledons, The New York Botanical Garden, July 2013).

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Hertweck Monocots V Presentation

  1. 1. Estimation of divergence times in Asparagales in the presence of hybridization Kate L. Hertweck, Michael R. McKain Monocots V Blog: k8hert.blogspot.com Twitter @k8hert Google+ k8hertweck@gmail.com Slides available: http://www.slideshare.net/katehertweck Plantzafrica.comErica Wheeler
  2. 2. Objectives 1) Describing lynchpins of monocot evolution 2) Informing Asparagales divergence times with lessons from monocots 3) Applications of dating estimates What are the most important considerations in determining the context of diversification in monocots? K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  3. 3. Kate L. Hertweck, Michael S. Kinney, Sarah Mathews, Mark W. Chase, M. A. Gandolfo, J. Chris Pires Divergence time estimation in monocots ● Improved Chase et al. (2006) dataset with 8 genes (11459 bp) ● 1 mt, 4 cp, 2 nrDNA, 1 LCNG (PHYC) ● 151 total taxa (27 outgroup, including 10 eudicots) ● MUSCLE, RAxML/MrBayes (partitioned, GTRGAMMA) ● r8s (13 fossil constraints), PL (TN) with cross validation, BEAST ● Does a dataset representing all three genomic partitions accurately reconstruct evolutionary relationships? ● Can we improve divergence time estimations in monocots using comprehensive taxon sampling? K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  4. 4. Fossil calibrations for Asparagales constraint Age (Ma) taxon 1 CG angiosperms 110.4 (Early-Middle Albian) Carpestella lacunata 2 SL Nymphaeales 110.4 (Early-Middle Albian) Microvictoria svitkoana 3 SL Schisandraceae 89.3 (Cenomanian-Turonian) Illiciospermum pusillum 4 SL Chloranthaceae 130 (Hauterivian, Helez Fm.) Clavatipollenites minutus 5 SL Magnoliales 112 (Late Aptian) Endressinia brasiliana 6 SL Calycanthaceae 118.5 (Late Barremian-Early Aptian) Jerseyanthus calycanthoides 7 SL Lactoridaceae 70.6 (Early Turonian-Campanian) Lactoripollenites africanus 8 CG eudicots 99.6 (Late Albian) Spanomera marylandensis 9 SL Araceae 118.5 (Late Barremain-Early Aptian) Cobbania corrugata 10 CG Pandanales 89.3 (Turonian) Mabelia, Nuhliantha 11 SL Arecales 70.6 (Campanian) Sabalites magothiensis, Palmoxylon cliffwoodensis 12 SL Zingiberales 72.5 (Campanian, absolute age) Tricostatocarpon silvapinedae, Striatornata sanantoniensis 13 SL Poaceae 65.5 (Maastrichtian) phytoliths (Gandolfo, pers. comm.) K. Hertweck, NESCent, Asparagales divergence 1. Challenges 2. Data 3. Applications
  5. 5. Monocot timetree Single data partitions fail to reconstruct deep relationships Combined dataset yields high confidence at most nodes (except commelinids) K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  6. 6. Monocot timetree: Maxage of angiosperms at 170 Ma Outgroups constrained for proper fossil placement Confidence intervals: Maxage of angiosperms= 200 and 150 Ma CG monocots: 153 Ma (134-127) K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  7. 7. Lynchpins in monocot divergence time estimation ● Taxonomic sampling ● Even sampling across lineages ● Represent early diverging taxa in each lineage ● Sample lineages which are both species rich and poor ● Select optimal lineages for fossil calibrations K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  8. 8. Lynchpins in monocot divergence time estimation ● Taxonomic sampling ● Even sampling across lineages ● Represent early diverging taxa in each lineage ● Sample lineages which are both species rich and poor ● Select optimal lineages for fossil calibrations K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  9. 9. Lynchpins in monocot divergence time estimation ● Taxonomic sampling ● Molecular sequence sampling ● Combining data partitions more reliably estimates phylogeny, although constraining topology may still be necessary ● Variation in life history may affect rates of molecular evolution ● Multiple independent data partitions may smooth rate variation in individual genes K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  10. 10. Lynchpins in monocot divergence time estimation ● Taxonomic sampling ● Molecular sequence sampling ● Fossil calibrations ● Incongruence between molecular and fossil dates for divergence ● Most variation in divergence time estimation comes from implementation of fossil calibrations ● Calibrations at shallow nodes can be influential K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  11. 11. Lynchpins in monocot divergence time estimation ● Taxonomic sampling ● Molecular sequence sampling ● Fossil calibrations ● Some lynchpins are exacerbated in Asparagales ● What lessons learned from dating monocots can assist in improving divergence time estimates in Asparagales? K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  12. 12. Objectives 1) Describing lynchpins of monocot evolution 2) Informing Asparagales divergence times with lessons from monocots 3) Applications of dating estimates How can studies in monocots improve divergence time estimates in Asparagales? K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  13. 13. Basic Asparagales divergence times K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Monocot 8 gene dataset (Hertweck et al., unpub.) CG Asparagales: 113 Ma (125-105) CG “Core” Asparagales: 61 Ma (67-58) CG Asparagaceae: 52 Ma (58-49) CG Amaryllidaceae: 50 Ma (55-47) CG Xanthorrhoeaceae: 47 Ma (52-44) Broad taxonomic divergence time analyses (Janssen and Bremer 2004, Magallon and Castillo 2009, Bell et al. 2010) CG Asparagales: 92-127 my Datasets: Chen et al. 2013: many taxa, 4 cpDNA loci Seberg et al. 2013: many taxa, 3 cpDNA and 2 mtDNA loci * McKain plastome: some taxa, complete plastomes * McKain orthologs: fewer taxa, 19 nuclear orthologs
  14. 14. Lynchpin 1: Taxonomic sampling in Asparagales Chen S, Kim D-K, Chase MW, Kim J-H (2013) Networks in a Large-Scale Phylogenetic Analysis: Reconstructing Evolutionary History of Asparagales (Lilianae) Based on Four Plastid Genes. PLoS ONE 8(3): e59472. doi:10.1371/journal.pone.0059472 http://www.plosone.org/article/info:doi/10.1371/journal.p one.0059472 K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  15. 15. ● Chen et al. 2013: ● 253 species, 201 genera, all families in Asparagales ● 29 species from monocot outgroups ● Three calibrations: CG Asparagales and two outgroups Effect of many taxa K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Monocot 8 gene Chen BEAST CG Asparagales 113 Ma (125-105) 93 Ma (101-93) CG “Core” Asparagales 61 Ma (67-58) 63 Ma (75-53) CG Asparagaceae 52 Ma (58-49) 56 Ma (65-48) CG Amaryllidaceae 50 Ma (55-47) 51 Ma (62-42) CG Xanthorrhoeaceae 47 Ma (52-44) 56 Ma (66-48) More taxa increases accuracy of dating estimates?
  16. 16. • Variation in genome size • Karyotype (chromosome structure, bimodality) • Polyploidy (auto-, allo-, aneu- ploidy) • Hybridization (and other historically confounding evolutionary events) How do these genomic phenomena affect our ability to reconstruct phylogeny and other evolutionary patterns? Lynchpin 2: Molecular sequence sampling K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  17. 17. Application of nuclear data to divergence time estimates • ITS • Low copy nuclear genes • Transcriptomes • PHYTOCHROME C (PHYC) – Well characterized; red/far red light sensing – Single copy in almost all groups studied; orthology established – Phylogenetically informative – Degenerate primers in exon 1 of PHYC (Mathews et al., 1995) K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  18. 18. PHYC reconstructs relationships between families K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  19. 19. Intrafamilial relationships from PHYC are messy Androstephium (Brodiaeoideae) Brodiaea (Brodiaeoideae) Drimia (Scilloideae) Dianella (Hemerocallidoideae) Geitonoplesium (Hemerocallidoideae) Arthropodium (Laxmanniaceae) K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  20. 20. Intrafamilial relationships from PHYC are messy Androstephium (Brodiaeoideae) Brodiaea (Brodiaeoideae) Drimia (Scilloideae) Dianella (Hemerocallidoideae) Geitonoplesium (Hemerocallidoideae) Arthropodium (Laxmanniaceae) K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications • Hybridization and other types of reticulate networks may require a different approach to divergence time estimation • No methods explicitly incorporating networks for divergence times
  21. 21. Lynchpin 3: Fossil calibrations constraint Age (Ma) taxon CG Orchidaceae 15 (Early-Middle Miocene) Meliorchis caribea CG Agavoideae 12 (Middle Miocene) Protoyucca K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications ● Most botanists aren't paleobotanists ● Applying secondary calibrations might be problematic ● Evidence for additional fossil calibrations in Asparagales lineages ● Emerging support for both deep and shallow fossil calibrations across the phylogeny (except this requires representative taxon sampling) Ramirez et al. 2007
  22. 22. Secondary calibrations can have unexpected results! K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Monocot 8 gene McKain 19 single copy nuclear genes (two applicable fossils) McKain 19 single copy nuclear genes CG Asparagales 113 Ma (125-105) 87 Ma (102-72) 113 Ma (fixed age) CG “Core” Asparagales 61 Ma (67-58) 63 Ma (75-53) 78 Ma (74-81) CG Asparagaceae 52 Ma (58-49) 52 Ma (62-43) 63 Ma (60-66) CG Amaryllidaceae 50 Ma (55-47) 48 Ma (57-40) 59 Ma (56-61) CG Xanthorrhoeaceae 47 Ma (52-44) 56 Ma (66-46) 69 Ma (66-71)
  23. 23. Recommendations for dating estimates in Asparagales ● Can any of uncertainty in three lynchpins be accommodated by analytical techniques? – Easier to make comparisons with r8s (or other non-Bayesian algorithms) – *BEAST: explicitly incorporates coalescent to infer “species” tree, divergence times, population sizes – Different approach to prior assignment of fossils (exponential distribution, Chen et al. 2013) – Uncertainty better managed by Bayesian methods, but this benefit nullified by priors which are too complex! – Congruification (Eastman 2013): an alternative to running complete analysis – Look at relative diversification rather than absolute K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  24. 24. Objectives 1) Describing lynchpins of monocot evolution 2) Informing Asparagales divergence times with lessons from monocots 3) Applications of dating estimates K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Where do we go from here?
  25. 25. Genomic changes occur repeatedly in Asparagales phylogeny Hertweck, Genome, 2013 K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  26. 26. Dating transposable element proliferation Hertweck, Genome, 2013 K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Black: copia White: gypsy Rectangles: total repeats
  27. 27. Divergence times provide the context for inferring evolutionary patterns ● From monocot 8 gene dataset: ● SymmeTREE (Chan et al. 2005): tree topology and tree-wide species diversity ● One significant and one marginally significant shift in diversification, both in subfamily Agavoideae ● Other methods ● Incorporating divergence times ● Exploring relationships with morphological or life history traits ● Compounding uncertainty K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  28. 28. Summary ● My personally favored estimate for CG Asparagales: 113 Ma (125-105) ● Problems with dating in monocots are exacerbated in Asparagales ● Taxonomic sampling ● Molecular sequence sampling ● Fossil calibrations ● Can any of these problems be accommodated by analytical techniques? ● Careful balance between appropriate sampling and possibly compounding problems ● Think creatively, and try multiple approaches K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications
  29. 29. Basic Asparagales divergence times K. Hertweck, NESCent, Asparagales divergence 1. Monocots 2. Asparagales 3. Applications Monocot 8 gene dataset CG Asparagales: 113 Ma (125-105) CG “Core” Asparagales: 61 Ma (67-58) CG Asparagaceae: 52 Ma (58-49) CG Amaryllidaceae: 50 Ma (55-47) CG Xanthorrhoeaceae: 47 Ma (52-44)
  30. 30. Acknowledgements • J. Chris Pires and lab (U of Missouri) • Victoria Docktor • NESCent science and bioinformatics folks • Fossil consultation • S. Magallon • E. Friis • M. Beilstein • N. Nagalingum • Matt Dorrance K. Hertweck, NESCent, Asparagales divergence Repetitive elements in Asparagales: Poster 46! Blog: k8hert.blogspot.com Twitter @k8hert Google+ k8hertweck@gmail.com Slides available: http://www.slideshare.net/katehertweck

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