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Lying through your teeth: saturation and non independence in morphological data, and what to do about it
This document discusses issues with using morphological data to construct phylogenetic trees for bat species. It finds that morphological characters can be highly convergent due to similarities in ecology and function. This saturation of morphological signal over time makes resolving relationships difficult. However, the study finds that dental characters provide a strong phylogenetic signal, likely because they are repeated across the dentition and show less convergence than other traits. The repetition of dental characters amplifies phylogenetic signal and helps resolve relationships that would otherwise be unresolved using morphology alone.
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Lying through your teeth: saturation and non independence in morphological data, and what to do about it
- 1. Lying through yourteeth: saturation and non independence in morphological data, and what to do about it 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. B Figure 3 Vampyrum †Notonycteris Macrophyllum Morphology Trachops Tonatia has a strong signal Mimon crenulatum Phylloderma Phyllostomus Lophostoma Lonchorhina Lonchophylla Carollia †Palynephyllum Neonycteris Glyphonycteris Rhinophylla Sturnira Vampyrodes Enchisthenes Pygoderma Artibeus Anoura Hylonycteris Lichonycteris Choeroniscus Platyrrhinus Choeronycteris Musonycteris Chrotopterus Platalina Uroderma Xeronycteris Lionycteris Trinycteris Brachyphylla Erophylla Phyllonycteris Leptonycteris Glossophaga Monophyllus Macrophyllum Trinycteris Mimon crenulatum Platyrrhinus Pygoderma Hylonycteris Lichonycteris Uroderma Platalina Lionycteris Chrotopterus Sturnira Xeronycteris Vampyrum Enchisthenes Choeronycteris 89 †Palynephyllum Musonycteris †Notonycteris Trachops Tonatia Lophostoma Phylloderma Phyllostomus Lonchorhina Carollia Glyphonycteris Rhinophylla Vampyrodes Artibeus Lonchophylla Anoura Choeroniscus Brachyphylla Erophylla Phyllonycteris Monophyllus Leptonycteris Glossophaga Plant-visiting Support % Posterior probability 100 26 Phyllostominae 99 87 98 68 63 79 71 56 40 66 81 66 94 99 87 57 99 48 58 82 94 81 83 86 changes/character 1 1 94 78 99 57 95 92 92 59 99 98 99 55 57 44 94 84 91 44 49 94 99 52 99 76 99 93 66 98 91 93 54 63 99 62 57 97 99 54 81 93 95 71 63 28 95 99 99 95 96 26 99 99 63 66 0.05 changes/character •10Kb from 7 chromosomes mt + 300 dental traits •= signal from dental traits •What makes this signal so strong? Dávalos et al. Accepted Syst Biol
- 10. 19 9.5 0 3.9 2.6 1.3 0 Molecular Morphological Frequency (percent) A Figure B Pairwise dissimilarity between characters Relative density between morphological characters 0.0 0.2 0.4 0.6 0.8 1.0 2.5 2.0 1.5 1.0 0.5 0.0 Signal is amplified by repetition •Measured dissimilarity between pairs of characters •25% sequence characters are completely dissimilar •Despite protein-coding loci •This is not the case for dental characters Dávalos et al. Accepted Syst Biol
- 11. Vampyrum Macrophyllum Lophostoma †Palynephyllum Neonycteris Sturnira Platyrrhinus Lichonycteris Erophylla Phyllonycteris ! ! ! ! ! ! !! ! ! ! ! ! Hylonycteris 63 Dental characters ! ! Mandibular Maxillary Incisors ! Canine Premolars Molars ! Significant A 0 ! ! ! ! ! ! !! ! ! ! ! ! ! 0 ! ! ! !!! ! ! ! !! ! !! A B Figure 3 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 Diaemus Brachyphylla Leptonycteris Glossophaga Monophyllus Trinycteris Pygoderma Desmodus 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 Glyphonycteris Rhinophylla Vampyrodes Artibeus Lonchophylla Anoura Choeroniscus Brachyphylla Erophylla Phyllonycteris Monophyllus Leptonycteris Glossophaga Micronycteris Mimon Plant-visiting Support 100 40 % Posterior probability 100 26 Phyllostominae 99 87 98 83 68 63 79 94 71 56 40 66 94 81 66 94 99 87 57 94 64 99 48 58 90 82 94 94 81 83 86 0.05 changes/character 1 1 54 94 78 99 56 57 95 92 52 92 59 99 98 99 67 55 57 90 44 94 84 91 44 49 94 99 95 89 52 99 76 99 93 66 33 98 81 91 93 54 99 62 57 99 54 81 93 95 71 63 89 28 95 99 99 95 96 26 99 99 63 57 97 66 0.05 changes/character B Dávalos et al. Accepted Syst Biol 0 Neonycteris in Micronycteris ï Support fRUQHFWDUïfeeding clade ! ! ! ! ! ! ! ! ! ! ! Support for Lonchorhina sitster to Phyllostominae ï !! ! ! ! ! ! ! ! ! ! ! ! ! ! !! ! !! ! ! ! ! !! !! !
- 12. 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
- 13. Analytical innovations •Statisticalscaffolds = condition morphological resolution on molecular posterior •Morphological parametric bootstraps = uncover significantly conflicting characters
- 14. Thanks! • Funding • NSF—DEB • CIDER—SBU • Speciation diversification: A. Cirranello, E. Dumont, A. Russell, N. Simmons, P. Velazco • N. Gerardo, A. Wilson • Dávalos Lab • Phylogenetics: B. Baird, S. DelSerra, A. Goldberg, O. Warsi, L. Yohe