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Non independence and convergence mislead morphological phylogenetics of phyllostomids
This document discusses issues with using morphological data to construct phylogenetic trees of phyllostomid bats. It finds that dental characters, while highly convergent, provide a strong phylogenetic signal that resolves relationships. This signal is amplified by the repetition of similar dental characters, which results in low dissimilarity among characters. In contrast, molecular characters show high dissimilarity. The authors hypothesize that the similarity among dental characters could arise from factors like occlusion, development along paths of least resistance, or strong negative selection due to ecological convergence.
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Non independence and convergence mislead morphological phylogenetics of phyllostomids
- 1. Lying through yourteeth: non independence and convergence mislead morphological phylogenetics of phyllostomids Liliana M. Dávalos —Stony Brook University Paul M. Velazco —American Museum of Natural History Omar M. Warsi —Stony Brook University Peter D. Smits —University of Chicago Nancy B. Simmons —American Museum of Natural History
- 2. Diphylla Diaemus Desmodus Brachyphylla Erophylla Phyllonycteris Platalina Lonchophylla Lionycteris Monophyllus Glossophaga Leptonycteris Anoura Hylonycteris Lichonycteris Scleronycteris Choeroniscus Musonycteris Choeronycteris Phylloderma Phyllostomus Macrophyllum Lonchorhina Mimon crenulatum Mimon bennettii Trachops Tonatia Chrotopterus Vampyrum Trinycteris Glyphonycteris Lampronycteris Macrotus Micronycteris minuta Micronycteris hirsuta Micronycteris megalotis Rhinophylla Carollia Sturnira Enchisthenes hartii Artibeus concolor Artibeus jamaicensis Artibeus cinereus Uroderma Platyrrhinus Vampyrodes Chiroderma Vampyressa bidens Vampyressa nymphaea Vampyressa pusilla Ectophylla Mesophylla Ametrida Centurio Sphaeronycteris Pygoderma Phyllops Stenoderma Ariteus Ardops MP bootstrap • • Macrotus Lampronycteris Micronycteris minuta Micronycteris schmidtorum Micronycteris hirsuta Microncyteris megalotis Diphylla Diaemus Desmodus Lonchorhina Macrophyllum Trachops Chrotopterus Vampyrum Lophostoma Tonatia Phylloderma Phyllostomus Mimon Erophylla Brachyphylla Monophyllus Glossophaga Leptonycteris Anoura Hylonycteris Choeroniscus Musonycteris Choeronycteris Lonchophylla Lionycteris Carollia Trinycteris Glyphonycteris daviesi Glyphonycteris sylvestris Rhinophylla Sturnira Chiroderma Vampyressa bidens Vampyressa brocki Uroderma Mesophylla Vampyressa Platyrrhinus Vampyrodes Enchisthenes Ectophylla Artibeus Dermanura Ariteus Ardops Stenoderma Centurio Pygoderma Ametrida Sphaeronycteris BYS posterior probability 0.97 • Baker et al. 2003 Occas Pap Mus TTU Datzmann et al. 2010 BMC Evol Biol Morphological Wetterer et al. 2000 B Am Mus Nat Hist Molecular
- 3. Genome not always available •Majority of species are extinct •Fossils are all that remain •Phylogenies must use morphology •How? Morgan Czaplewski 2012 Evolutionary History of Bats
- 4. Total evidence Conditionalcombination Hermsen Hendricks 2008 Ann Missouri Springer et al. 2007 Syst Biol Bot Gard
- 5. Assumptions of phylogeny •Homology: character changes reflect common descent •IID: Independent and Identically Distributed
- 6. Morphological Molecular Dávalos,Cirranello et al. 2012 Biol Rev
- 7. Saturation is not everything •If rates of evolution are high, then signal erased over time •Results in unresolved phylogeny •Other signal must emerge to resolve phylogeny • First position • Second position o Third position Dávalos Perkins 2008 Genomics
- 8. Macrophyllum Lonchorhina Trinycteris Neonycteris Glyphonycteris Micronycteris Lampronycteris Macrotus Micronycteris Mormoops Erophylla Phyllonycteris Brachyphylla Pygoderma Sturnira Uroderma Platyrrhinus Vampyrodes Enchisthenes Artibeus †Palynephyllum Glossophaga Lonchophylla Lionycteris Lonchophylla Monophyllus Leptonycteris Anoura Hylonycteris Lichonycteris Choeroniscus Musonycteris Xeronycteris Platalina Diphylla Desmodus Diaemus Carollia Rhinophylla 74 39 54 14 59 28 2 0 48 44 59 97 3 24 48 4 99 1 23 9 61 67 99 97 93 18 13 1 36 99 59 58 94 70 49 63 28 90 92 17 53 7 5 6 39 37 13 1 5 54 46 86 6 19 78 39 0 66 Rhinophylla Phyllonycteris Pygoderma Brachyphylla Uroderma Platyrrhinus Vampyrodes †Palynephyllum Enchisthenes Artibeus Choeronycteris Platalina Erophylla 55 Glossophaga Hylonycteris Lichonycteris Neonycteris Choeroniscus Glyphonycteris Musonycteris Xeronycteris Anoura Micronycteris 39 30 87 Diaemus Lionycteris Carollia Lampronycteris Desmodus Sturnira Lophostoma Monophyllus Macrotus Lonchophylla Lampronycteris Diphylla Leptonycteris 35 Trinycteris 95 79 30 50 51 94 22 48 13 74 10 44 18 91 25 60 31 82 34 89 39 87 66 19 11 99 67 59 80 77 15 92 35 83 14 59 78 24 30 97 19 27 86 70 45 40 23 24 87 41 26 25 88 24 63 80 36 95 75 22 40 31 31 13 36 53 83 14 35 48 95 60 47 17 Phyllonycteris Mormoops Uroderma Platyrrhinus Trinycteris Monophyllus Anoura Hylonycteris Choeroniscus Brachyphylla Neonycteris Lonchophylla Leptonycteris Diphylla Glyphonycteris Diaemus Macrotus Choeroniscus Choeronycteris Platalina Lophostoma Erophylla Lonchophylla Vampyrodes Lionycteris Carollia Enchisthenes Micronycteris Sturnira Lichonycteris Artibeus Musonycteris Desmodus Micronycteris Rhinophylla †Palynephyllum Glossophaga Xeronycteris Pygoderma 54 36 99 99 38 54 51 85 52 79 57 57 80 78 55 42 31 55 46 94 73 88 91 53 95 22 85 57 7 82 93 85 77 96 48 92 52 16 71 46 56 95 85 67 92 42 89 62 39 98 98 53 93 97 83 87 93 96 41 83 82 99 43 98 68 Bootstrap support 100 0 0.5 changes/character Supplementary Figure 4 B C Dávalos et al. Accepted Syst Biol Dental characters highly convergent
- 9. •9Kb from 7 chromosomes mt + 0.98 300 dental traits †Palynephyllum •= signal from dental traits •What makes this signal so strong? Vampyrum Macrophyllum Neonycteris Sturnira Enchisthenes Pygoderma Hylonycteris Lichonycteris Musonycteris Erophylla Phyllonycteris Leptonycteris Mimon crenulatum Hylonycteris Glyphonycteris Platyrrhinus 95 86 0.88 0.65 0.57 0.62 0.25 0.61 0.13 0.62 0.89 0.48 0.96 0.91 0.82 0.99 0.87 0.82 0.99 0.98 0.46 0.64 0.56 0.70 A B Figure 4 Mimon †Notonycteris Trachops Tonatia Mimon crenulatum Phylloderma Phyllostomus Lonchorhina Lonchophylla Carollia Glyphonycteris Rhinophylla Vampyrodes Artibeus Anoura Choeroniscus Platyrrhinus Choeronycteris Chrotopterus Platalina Uroderma Xeronycteris Lionycteris Trinycteris Brachyphylla Glossophaga Monophyllus Lophostoma Trinycteris Pygoderma Macrophyllum Lichonycteris Uroderma Platalina Lionycteris Chrotopterus Sturnira Xeronycteris Vampyrum Enchisthenes Choeronycteris †Palynephyllum Musonycteris †Notonycteris Trachops Tonatia Lophostoma Phylloderma Phyllostomus Lonchorhina Carollia Rhinophylla Vampyrodes Artibeus Lonchophylla Anoura Choeroniscus Brachyphylla Erophylla Phyllonycteris Monophyllus Leptonycteris Glossophaga Micronycteris Mimon Plant-visiting Support 100 47 % Posterior probability 1.00 0.13 Phyllostominae 95 59 89 97 98 99 90 73 82 58 71 91 99 96 82 91 91 79 77 91 99 86 98 99 47 72 87 79 93 99 99 92 95 99 75 99 59 99 99 56 changes/character 0.1 changes/character 0.93 0.80 0.77 0.34 0.98 0.69 0.49 0.63 0.89 0.42 0.97 0.52 0.93 0.98 0.91 0.77 0.99 0.99 0.77 0.44 0.58 0.99 0.99 0.78 0.48 0.98 0.97 0.980.95 0.99 0.98 0.51 0.96 0.63 0.45 0.99 0.85 0.96 0.57 0.98 0.86 0.74 0.57 0.51 0.99 Morphology has a strong signal Dávalos et al. Accepted Syst Biol
- 10. 15.6 10.4 5.2 8.5 6.3 4.2 0 Frequency (percent) Morphological 0 Molecular 2.1 10 A Dissimilarity between characters Relative density between morphological characters 0.0 0.2 0.4 0.6 0.8 1.0 8 6 4 2 0 B Figure 3 Signal is amplified by repetition •Measured dissimilarity between pairs of characters •High dissimilarity among molecular characters •Despite protein-coding loci •This is not the case for dental characters Dávalos et al. Accepted Syst Biol
- 11. How similarity arises •Hypotheses: •Occlusion •Negative selection •Ecological convergence •Positive selection •Development •Paths of least resistance 1! 2! 1! 2!
- 12. †Palynephyllum Diaemus Vampyrum Macrophyllum Neonycteris Sturnira Platyrrhinus Lichonycteris Erophylla Phyllonycteris Leptonycteris Desmodus 0 0 Hylonycteris ! ! ! ! ! Glyphonycteris 95 86 0.88 0.65 0.54 0.57 ! 0.80 ! 0.62 ! !! ! ! ! ! ! ! 0.25 0.61 ! ! ! 0.13 0.62 0.90 0.89 0.48 0.91 0.91 0.82 0.99 !! ! ! ! ! ! 0.87 0.82 ! 0.99 0.98 0.46 0.64 0.56 0.70 A ! ! ! !!! ! ! ! !! ! !! A B Premolars ! Significant Figure 4 Micronycteris Mimon †Notonycteris Trachops Tonatia Mimon crenulatum Phylloderma Phyllostomus Lonchorhina Lonchophylla Carollia Glyphonycteris Rhinophylla Vampyrodes Artibeus Anoura Choeroniscus Macrotus Pygoderma Choeronycteris Thyroptera Musonycteris Mormoops Hylonycteris Desmodus Enchisthenes Chrotopterus Noctilio Platalina Lampronycteris Diphylla Uroderma Xeronycteris Lionycteris Pteronotus Trinycteris Brachyphylla Glossophaga Monophyllus Lophostoma Trinycteris Pygoderma Macrophyllum Lichonycteris Uroderma Platalina Lionycteris Mormoops Diaemus Chrotopterus Sturnira Xeronycteris Vampyrum Enchisthenes Pteronotus Thyroptera Platyrrhinus Diphylla Choeronycteris Lampronycteris †Palynephyllum Noctilio Neonycteris Musonycteris Macrotus Micronycteris Mimon crenulatum †Notonycteris Trachops Tonatia Lophostoma Phylloderma Phyllostomus Lonchorhina Carollia Rhinophylla Vampyrodes Artibeus Lonchophylla Anoura Choeroniscus Brachyphylla Erophylla Phyllonycteris Monophyllus Leptonycteris Glossophaga Micronycteris Mimon Plant-visiting Support 100 47 % Posterior probability 1.00 0.13 Phyllostominae 95 59 89 95 97 98 99 90 73 67 82 58 71 91 99 96 82 95 91 95 98 91 79 77 91 99 86 98 99 47 67 72 74 87 79 93 99 99 92 95 99 75 99 98 59 99 99 56 Incisors 0.1 changes/character 0.1 changes/character 0.93 0.80 0.77 0.34 0.98 0.69 0.49 0.63 0.71 0.99 0.38 0.89 0.42 0.97 0.52 0.93 0.98 0.91 0.79 0.96 0.76 0.77 0.99 0.99 0.77 0.44 0.58 0.99 0.99 0.99 0.78 0.48 0.98 0.97 0.980.95 0.99 0.98 0.51 0.96 0.63 0.45 0.99 0.85 0.96 0.57 0.98 0.98 0.86 0.74 0.57 0.51 0.99 0.98 Dental characters ! ! Mandibular Maxillary ! Canine Molars B Dávalos et al. Accepted Syst Biol 0 Neonycteris in Micronycteris ï Support fRUQHFWDUïfeeding clade ! ! ! ! ! ! ! ! ! ! ! Support for Lonchorhina sitster to Phyllostominae ï !! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! !! ! ! ! ! !! !! !
- 13. Data modelsdon’t match •Less is more when collecting certain kinds of characters •Dental data violate key assumptions of phylogenetic models •Saturation, convergence, and non-independence •= model failure •New data models needed Czaplewski et al. 2003 Caldasia
- 14. No conflict Morphological phylogenies Statistical scaffold RQÀLFWLQJ characters Starting point Dependency Morphological Rates Data matrix Statistic from data matrix Phylogeny Statistic from phylogeny Phylogenetic analysis Other analysis Comparison Endpoint Alternative combined phylogenies )LJXUH Pairwise dissimilarity Bayesian State:step Simulations Distribution morphological dissimilarity Pairwise Bayesian dissimilarity Distribution molecular dissimilarity Agree? Yes No Null distribution difference per-character likelihoods Tree with Tree without Backbone constraints Bayesian Branch lengths Maximum likelihood Constrained phylogenies Molecular phylogenies Combined phylogenies Combined matrix without FRQÀLFWLQJ characters Variable sites Relative distribution RQÀLFWLQJ nodes Relative rates of evolution RQÀLFWLQJ nodes Branch lengths RQÀLFWLQJ morphological characters Statistical scaffold Morphological saturation plot Morphological Combined Molecular Analytical innovations •Statistical scaffolds = condition morphological resolution on molecular posterior •Morphological parametric bootstraps = uncover significantly conflicting characters
- 15. Thanks! • Funding • NSF—DEB • CIDER—SBU • Speciation diversification: A. Cirranello, E. Dumont, A. Russell, N. Gerardo, A. Wilson • Dávalos Lab • Phylogenetics: B. Baird, S. DelSerra, A. Goldberg, O. Warsi, L. Yohe