Systematic error and the contours of a theory of macroevolution
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The document discusses systematic and sampling errors in biological diversity and macroevolution research, focusing on the impact of these errors on estimating allele frequencies and phylogenetic relationships. It highlights how systematic errors can arise from incorrect models of gene evolution, leading to misleading results despite extensive data collection. Furthermore, it emphasizes the need for improved models and understanding of data to accurately analyze phenotypic evolution and macroevolutionary processes.
Systematic error and the contours of a theory of macroevolution
- 1. Systematic Error and the Contours of a Theory of Macroevolution ! Liliana M. Dávalos Associate Professor, Department of Ecology & Evolution SUNY, Stony Brook ! Field Museum of Natural History 17 December 2014
- 3. Two kinds of questions Biological diversity Diversification, speciation decrease Habitat lossincrease
- 4. Sampling error vs. systematic error Felsenstein 1978 Syst Zool
- 5. Thinking about errors • Let’s say we want to answer a question: • In a finite population, what is the frequency of an allele? Sampling vs. systematic
- 6. How to answer this question • We go out, get samples, genotype different individuals • Then we count the alleles • What is the main source of error? Sampling vs. systematic
- 7. This is sampling error • We want to get a better estimate of the allele frequency • => Sample more • We could sample the entire population • => Best possible estimate of allele frequency Sampling vs. systematic
- 8. Mycobacterium bovis BCG str. Pasteur 1173P2 M. tuberculosis H37Ra M. bovis BCG str. Tokyo 172 M. bovis AF212297 M. tuberculosis CDC1551 M. tuberculosis F11 M. tuberculosis KZN 1435 M. tuberculosis H37Rv M. avium subsp. paratuberculosis K10 M. avium 104 M. vanbaalenii PYR1 M. sp. Spyr1 M. smegmatis str. MC2 155 M. sp. KMS M. sp. MCS M. sp JLS Mycobacterium sp. * Nocardia farcinica IFM 10152 Gordonia bronchialis DSM 43247 Rhodococcus opacus B4 R. equi ATCC 33707 R. equi 103S Segniliparus rotundus DSM 44985 Bifidobacterium longum NCC2705 B. longum DJO10A B. longum subsp. infantis 157F B. longum subsp. longum JCM 121 B. longum subsp. longum BBMN68 B. longum subsp. infantis ATCC 558 B. longum subsp. longum JDM301 B. longum subsp. infantis ATCC 156 B. breve DSM 20213 B. dentium Bd1 B. dentium ATCC 100 100 84 96 42 100 63 63 65 55 84 10074 51 70 98 92 99 74 100 100 75 99 100 20 88 pathogenic (avium non-pathogenic Mycobacterium sme Phylogenetics • Testing relatedness • All of comparative biology • Historical biogeography • Evolutionary aspects of community ecology • Diagnostics and similar applications Corthals et al. 2012 PLoS One Sampling vs. systematic
- 9. Now let’s ask a different question • We want to find out how these 3000 microbial lineages relate to one another • We get their genomes, map out each of the single-copy genes, estimate a phylogeny Lang, Darling, Eisen 2013 PLoS One Sampling vs. systematic
- 10. But our results don’t make sense • Is it sampling error? • Can we sample more than the whole genome? • We discover the model of gene evolution we are using was wrong • What kind of error is this? Lang, Darling, Eisen 2013 PLoS One Sampling vs. systematic
- 11. This is systematic error • Even sampling whole genomes won’t fix the problem • Having more data can make the problem worse! • As long as we don’t change the model, we will keep obtaining the wrong answer Lang, Darling, Eisen 2013 PLoS One Sampling vs. systematic
- 12. Systematic error in molecular evolution Sullivan & Swofford 1997 J Mamm EvolD’Erchia et al. 1996 Nature
- 13. Systematic error = homoplasy that is not modeled
- 14. q p Homoplasy I: inconsistency! q pp Felsenstein 1978 Syst Biol Phenotypic evolution consistent Non consistent
- 15. A Background selection Amino acid position in alignment Supportfornectar-feedingclade -3 -2 -1 0 1 2 3 100 200 300 400 500 Significant support or rejection Selection shift Selection shift in Glossophaginae Type of codon CYTB COX1 Homoplasy II: ecological convergence • Phenotype exposed to selection • Selection from similar ecology produces similar phenotypes Dávalos, Cirranello et al. 2012 Biol Rev Phenotypic evolution
- 16. Homoplasy III: correlated evolution • Expected in protein- coding genes • Models in use for codons, aminoacids, ribosomal RNA secondary structure Dávalos & Perkins 2008 Genomics Phenotypic evolution
- 17. Example with favorite gene: mt cytb Agnarsson et al. 2011 PLoS Currents ToL
- 18. Dávalos 2010 Island Bats Evolution, Ecology, and Conservation Agnarsson et al. 2011 PLoS Currents ToL Molecular evolution © M. Tuttle© N. Simmons
- 19. One of these is evolving fast, very fast Dávalos, Gutiérrez & Velazco unpublished Molecular evolution
- 20. Speed cannot be the whole story • High rates of change randomize shared changes • Expect no resolution instead of actual conflict • For conflict, must reflect other forces • E.g., base composition Dávalos, Gutiérrez & Velazco unpublished Molecular evolution
- 21. Dávalos, Gutiérrez & Velazco unpublished Agnarsson et al. 2011 PLoS Currents ToL Molecular evolution © M. Tuttle© N. Simmons
- 22. Macrotus Lampronycteris Micronycteris minuta Micronycteris schmidtorum Micronycteris hirsuta Microncyteris megalotis Diphylla Diaemus Desmodus Lonchorhina Macrophyllum Trachops Chrotopterus Vampyrum Lophostoma Tonatia Phylloderma Phyllostomus Mimon Anoura Hylonycteris Choeroniscus Musonycteris Choeronycteris Erophylla Brachyphylla Monophyllus Glossophaga Leptonycteris Lonchophylla Lionycteris Carollia Trinycteris Glyphonycteris daviesi Glyphonycteris sylvestris Rhinophylla Sturnira Mesophylla Vampyressa Platyrrhinus Vampyrodes Uroderma Vampyressa bidens Vampyressa brocki Chiroderma Enchisthenes Ectophylla Artibeus Dermanura Ariteus Ardops Stenoderma Centurio Pygoderma Ametrida Sphaeronycteris < 0.97 BYS posterior probability Dumont, Dávalos et al. 2012 P R Soc B Molecular evolution Baker et al. 2003 Occas Pap Mus TTU Dávalos, Cirranello et al. 2012 Biol Rev
- 23. A B Background selection PercentcodonsofCYTBineachcodontype 0 20 40 60 Background selection Selection shift Significantly support Significantly reject Reject Support Type of codon Amino acid position in alignment -3 -2 -1 0 1 2 3 100 200 300 400 500 Significant support or rejection Selection shift Selection shift in Glossophaginae Type of codon CYTB COX1 Turns out: ecological convergence! • Brings together ecologically similar lineages • Mt cytochrome b gene of nectar- feeding bats • Link between molecular adaptation and support for node Dávalos, Cirranello et al. 2012 Biol Rev Molecular evolution
- 24. The genome is littered with such genes Parker et al. 2013 Nature © N. Simmons
- 25. 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 Anoura Hylonycteris Choeroniscus Musonycteris Choeronycteris Erophylla Brachyphylla Monophyllus Glossophaga Leptonycteris Lonchophylla Lionycteris Carollia Trinycteris Glyphonycteris daviesi Glyphonycteris sylvestris Rhinophylla Sturnira Mesophylla Vampyressa Platyrrhinus Vampyrodes Uroderma Vampyressa bidens Vampyressa brocki Chiroderma Enchisthenes Ectophylla Artibeus Dermanura Ariteus Ardops Stenoderma Centurio Pygoderma Ametrida Sphaeronycteris < 0.97 BYS posterior probability Baker et al. 2003 Occas Pap Mus TTU Dávalos, Cirranello et al. 2012 Biol Rev Wetterer et al. 2000 B Am Mus Nat Hist Systematic error in phenotype
- 26. Dated trees more important than ever • Dated trees need fossils • Why use dated trees? • Trait evolution • History of assemblages in time and space • Key innovations Dumont, Dávalos et al. 2012 P R Soc B Phenotypic evolution
- 27. • We use morphological characters • How do phenotypes evolve? • Characteristics of the data • Compare to models molecular evolution Fossils without genomes Dávalos & Russell 2012 Ecol Evol Phenotypic evolution
- 28. Species Characters These are morphological characters • They look like this —> • Discontinuous between species • Factors, not numbers • Difficult to model Phenotypic evolution © N. Simmons © M. Tuttle
- 29. The trouble with morphological characters • At first, only model was parsimony • Neutral Jukes-Cantor 1969 model implemented 2001 • Current model varies rates across characters • Applying this model does not solve conflict Dávalos, Cirranello et al. 2012 Biol Rev Phenotypic evolution
- 30. Could conflict arise from systematic error? Phenotypic evolution
- 31. Might systematic error affect morphological characters? Reviewer 1: I don't see the point. If the characters are good characters (meaning that they have some phylogenetic signal at some level), then there is nothing especially wrong with the fact that they are weighted a little more than other characters. Phenotypic evolution
- 32. Dávalos, Cirranello et al. 2012 Biol Rev Inconsistency! Phenotypic evolution
- 33. Dental characters ● ● Mandibular Maxillary ● Canine Incisors Molars Premolars ● Significant A 0 Supportffeedingclade ● ● ● ● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● A Background selection Amino acid position in alignment Supportfornectar-feedingclade -3 -2 -1 0 1 2 3 100 200 300 400 500 Significant support or rejection Selection shift Selection shift in Glossophaginae Type of codon CYTB COX1 Dávalos, Cirranello et al. 2012 Biol Rev Convergent evolution! Phenotypic evolution Dávalos, Velazco et al. 2014 Syst Biol
- 34. Correlated evolution! Phenotypic evolution Dissimilarity between characters -> ‘ Dávalos, Velazco et al. 2014 Syst Biol unpublished
- 35. Systematic error in phenotypes • Morphology = phenotype • Neutrality and independence wrong assumptions • Not neutral • Not independent Skelly et al. 2013 Genome Res Phenotypic evolution
- 36. The trouble with systematic error • In sampling error mode • More is more • More characters • = thousands of correlated phenotypes • This will fail, we have systematic error • Improve model • Improve data • Understand data Phenotypic evolution
- 37. The contours of a theory of macroevolution
- 38. Modern synthesis is about populations • Features of populations become important • Population size • Migration • Generations • Time • Mutation rate Dávalos & Russell 2014 J Mammal Contours of macroevolution
- 39. From micro to macro: successful example • Coalescent stochasticity • Genes may represent different histories by chance • No selective force, only population characteristics • Solution • Account for pop size (Ne), # generations (t), mutation rate (mu) Neigel & Avise 1986 Evolutionary Processes and Theory Contours of macroevolution
- 40. Another example • Phenotypic traits • Often expected to be under selection • Solution • Extend quantitative genetics • Compare Brownian motion to Ornstein- Uhlenbeck process • Model t, s, and optima Martins & Hansen 1997 Am Nat Butler & King 2004 Am Nat Contours of macroevolution
- 41. Dávalos, Velazco et al. 2014 Syst Biol unpublishedContours of macroevolution There is a limit to modeling these, though
- 42. The chasm genetics- phenotype • Biochemistry defines units and processes of genetics • Genetics defines units and processes of genotype evolution in population • What is there for (morphological) phenotypes? Contours of macroevolution Löytynoja & Goldman 2008 Science
- 43. Units and process • How to define units of morphological evolution? • Can using functional and developmental processes help? • Aren’t these also unknown? • Are such processes generalizable? • I.e., the way Ne, T and mu are Contours of macroevolution Rieppel & Kearney 2007 Biol Philos
- 44. Morphology ... Aminoacids Codons The challenge ahead Neutral genotype Model complexity Contours of macroevolution
- 45. Thank you for inviting me!