Project 947: L. M. Dávalos, A. L. Cirranello, J. H. Geisler, N. B. Simmons. 2012. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews. 87 (4):991-1024.
Abstract
All characters and trait systems in an organism share a common evolutionary history that can be estimated using phylogenetic methods. However, differential rates of change and the evolutionary mechanisms driving those rates result in pervasive phylogenetic conflict. These drivers need to be uncovered because mismatches between evolutionary processes and phylogenetic models can lead to high confidence in incorrect hypotheses. Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species. For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict. Here, we develop and apply methods to minimize systematic biases, uncover the biological mechanisms underlying phylogenetic conflict, and outline data requirements for future phylogenomic and morphological data collection. We introduce new morphological data for phyllostomids and outgroups and expand previous molecular analyses to eliminate methodological sources of phylogenetic conflict such as taxonomic sampling, sparse character sampling, or use of different algorithms to estimate the phylogeny. We also evaluate the impact of biological sources of conflict: saturation in morphological changes and molecular substitutions, and other processes that result in incongruent trees, including convergent morphological and molecular evolution. Methodological sources of incongruence play some role in generating phylogenetic conflict, and are relatively easy to eliminate by matching taxa, collecting more characters, and applying the same algorithms to optimize phylogeny. The evolutionary patterns uncovered are consistent with multiple biological sources of conflict, including saturation in morphological and molecular changes, adaptive morphological convergence among nectar-feeding lineages, and incongruent gene trees. Applying methods to account for nucleotide sequence saturation reduces, but does not completely eliminate, phylogenetic conflict. We ruled out paralogy, lateral gene transfer, and poor taxon sampling and outgroup choices among the processes leading to incongruent gene trees in phyllostomid bats. Uncovering and countering the possible effects of introgression and lineage sorting of ancestral polymorphism on gene trees will require great leaps in genomic and allelic sequencing in this species-rich mammalian family. We also found evidence for adaptive molecular evolution leading to convergence in mitochondrial proteins among nectar-feeding lineages. In conclusion, the biological processes that generate phylogenetic conflict are ubiquitous, and overcoming incongruence requires better models and more data than have been collected even in well-studied organisms such as phyllostomid bats.Read the article »
Article DOI: 10.1111/j.1469-185X.2012.00240.x
Project DOI: 10.7934/P947, http://dx.doi.org/10.7934/P947
This project contains | Matrices |
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Download Project SDD File | Total scored cells: 12622 Total media associated with cells: 0 Total labels associated with cell media: 0 |
Characters | |
Total characters: 220 Total characters with associated media: 0 Total characters with media with labels: 0 Total character states: 547 Total character states with associated media: 0 Total character states with media with labels:0 Total unordered/ordered characters:220/0 |
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MorphoBank Project 947
MorphoBank Project 947
- Creation Date:
08 May 2013 - Publication Date:
21 April 2016 - Project views: 33183
- Matrix downloads: 31
This research
supported by
Authors' Institutions
- American Museum of Natural History
- Stony Brook University
- New York College of Osteopathic Medicine
Members
member name | taxa | specimens | media | chars | character
| cell scorings (scored, NPA, "-") | cell
| rules | ||||||||
Andrea Cirranello Project Administrator | 81 | 1 | 1 | 220 | 0 | 0 | 0 | 12622 (12622, 0, 0) | 0 | 0 | 0 | |||||
MorphoBank Curator Full membership | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 (0, 0, 0) | 0 | 0 | 0 |
Taxonomic Overview for Matrix 'M23687' (80 Taxa)
taxon | unscored cells |
scored cells |
no cell support |
NPA cells |
"-" cells | cell images | labels on cell images |
member access |
[1] Ametrida centurio Last Modified in 12/16/15 | 67 | 154 | 153 | 0 | 0 | 0 | 0 | 2 |
[2] Anoura caudifer Last Modified in 12/16/15 | 70 | 151 | 150 | 0 | 0 | 0 | 0 | 2 |
[3] Anoura geoffroyi Last Modified in 12/16/15 | 39 | 182 | 181 | 0 | 0 | 0 | 0 | 2 |
[4] Ardops nichollsi Last Modified in 12/16/15 | 69 | 151 | 151 | 0 | 0 | 0 | 0 | 2 |
[5] Ariteus flavescens Last Modified in 12/16/15 | 66 | 156 | 154 | 0 | 0 | 0 | 0 | 2 |
[6] Artibeus cinereus Last Modified in 12/16/15 | 71 | 149 | 149 | 0 | 0 | 0 | 0 | 2 |
[7] Artibeus concolor Last Modified in 12/16/15 | 77 | 145 | 143 | 0 | 0 | 0 | 0 | 2 |
[8] Artibeus hirsutus Last Modified in 12/16/15 | 119 | 101 | 101 | 0 | 0 | 0 | 0 | 2 |
[9] Artibeus jamaicensis Last Modified in 12/16/15 | 28 | 192 | 192 | 0 | 0 | 0 | 0 | 2 |
[10] Brachyphylla cavernarum Last Modified in 12/16/15 | 41 | 180 | 179 | 0 | 0 | 0 | 0 | 2 |
[11] Carollia brevicauda Last Modified in 12/16/15 | 77 | 143 | 143 | 0 | 0 | 0 | 0 | 2 |
[12] Carollia perspicillata Last Modified in 12/16/15 | 18 | 203 | 202 | 0 | 0 | 0 | 0 | 2 |
[13] Centurio senex Last Modified in 12/16/15 | 65 | 155 | 155 | 0 | 0 | 0 | 0 | 2 |
[14] Chiroderma villosum Last Modified in 12/16/15 | 71 | 151 | 149 | 0 | 0 | 0 | 0 | 2 |
[15] Choeroniscus godmani Last Modified in 12/16/15 | 60 | 161 | 160 | 0 | 0 | 0 | 0 | 2 |
[16] Choeronycteris mexicana Last Modified in 12/16/15 | 44 | 177 | 176 | 0 | 0 | 0 | 0 | 2 |
[17] Chrotopterus auritus Last Modified in 12/16/15 | 61 | 160 | 159 | 0 | 0 | 0 | 0 | 2 |
[18] Desmodus rotundus Last Modified in 12/16/15 | 32 | 189 | 188 | 0 | 0 | 0 | 0 | 2 |
[19] Diaemus youngi Last Modified in 12/16/15 | 79 | 143 | 141 | 0 | 0 | 0 | 0 | 2 |
[20] Diphylla ecaudata Last Modified in 12/16/15 | 69 | 151 | 151 | 0 | 0 | 0 | 0 | 2 |
[21] Ectophylla alba Last Modified in 12/16/15 | 84 | 137 | 136 | 0 | 0 | 0 | 0 | 2 |
[22] Enchisthenes hartii Last Modified in 12/16/15 | 66 | 155 | 154 | 0 | 0 | 0 | 0 | 2 |
[23] Erophylla sezekorni Last Modified in 12/16/15 | 46 | 174 | 174 | 0 | 0 | 0 | 0 | 2 |
[24] Furipterus horrens Last Modified in 12/16/15 | 70 | 151 | 150 | 0 | 0 | 0 | 0 | 2 |
[25] Glossophaga longirostris Last Modified in 12/16/15 | 90 | 130 | 130 | 0 | 0 | 0 | 0 | 2 |
[26] Glossophaga soricina Last Modified in 12/16/15 | 15 | 206 | 205 | 0 | 0 | 0 | 0 | 2 |
[27] Glyphonycteris daviesi Last Modified in 12/16/15 | 82 | 139 | 138 | 0 | 0 | 0 | 0 | 2 |
[28] Glyphonycteris sylvestris Last Modified in 12/16/15 | 73 | 148 | 147 | 0 | 0 | 0 | 0 | 2 |
[29] Hylonycteris underwoodi Last Modified in 12/16/15 | 56 | 164 | 164 | 0 | 0 | 0 | 0 | 2 |
[30] Lampronycteris brachyotis Last Modified in 12/16/15 | 75 | 146 | 145 | 0 | 0 | 0 | 0 | 2 |
[31] Leptonycteris yerbabuenae Last Modified in 12/16/15 | 48 | 174 | 172 | 0 | 0 | 0 | 0 | 2 |
[32] Lichonycteris obscura Last Modified in 12/16/15 | 55 | 167 | 165 | 0 | 0 | 0 | 0 | 2 |
[33] Lionycteris spurrelli Last Modified in 12/16/15 | 48 | 173 | 172 | 0 | 0 | 0 | 0 | 2 |
[34] Lonchophylla robusta Last Modified in 12/16/15 | 42 | 178 | 178 | 0 | 0 | 0 | 0 | 2 |
[35] Lonchophylla thomasi Last Modified in 12/16/15 | 73 | 148 | 147 | 0 | 0 | 0 | 0 | 2 |
[36] Lonchorhina aurita Last Modified in 12/16/15 | 63 | 160 | 157 | 0 | 0 | 0 | 0 | 2 |
[37] Lophostoma brasiliense Last Modified in 12/16/15 | 69 | 153 | 151 | 0 | 0 | 0 | 0 | 2 |
[38] Lophostoma silvicolum Last Modified in 12/16/15 | 69 | 152 | 151 | 0 | 0 | 0 | 0 | 2 |
[39] Macrophyllum macrophyllum Last Modified in 12/16/15 | 69 | 153 | 151 | 0 | 0 | 0 | 0 | 2 |
[40] Macrotus californicus Last Modified in 12/16/15 | 67 | 153 | 153 | 0 | 0 | 0 | 0 | 2 |
[41] Macrotus waterhousii Last Modified in 12/16/15 | 22 | 198 | 198 | 0 | 0 | 0 | 0 | 2 |
[42] Mesophylla macconnelli Last Modified in 12/16/15 | 71 | 150 | 149 | 0 | 0 | 0 | 0 | 2 |
[43] Metavampyressa nymphaea Last Modified in 12/16/15 | 75 | 146 | 145 | 0 | 0 | 0 | 0 | 2 |
[44] Micronycteris hirsuta Last Modified in 12/16/15 | 60 | 162 | 160 | 0 | 0 | 0 | 0 | 2 |
[45] Micronycteris megalotis Last Modified in 12/16/15 | 56 | 164 | 164 | 0 | 0 | 0 | 0 | 2 |
[46] Micronycteris minuta Last Modified in 12/16/15 | 71 | 149 | 149 | 0 | 0 | 0 | 0 | 2 |
[47] Mimon bennettii Last Modified in 12/16/15 | 70 | 150 | 150 | 0 | 0 | 0 | 0 | 2 |
[48] Mimon crenulatum Last Modified in 12/16/15 | 68 | 154 | 152 | 0 | 0 | 0 | 0 | 2 |
[49] Monophyllus redmani Last Modified in 12/16/15 | 43 | 177 | 177 | 0 | 0 | 0 | 0 | 2 |
[50] Mormoops megalophylla Last Modified in 12/16/15 | 54 | 167 | 166 | 0 | 0 | 0 | 0 | 2 |
[51] Musonycteris harrisoni Last Modified in 12/16/15 | 138 | 82 | 82 | 0 | 0 | 0 | 0 | 2 |
[52] Mystacina robusta Last Modified in 12/16/15 | 85 | 135 | 135 | 0 | 0 | 0 | 0 | 2 |
[53] Mystacina tuberculata Last Modified in 12/16/15 | 101 | 119 | 119 | 0 | 0 | 0 | 0 | 2 |
[54] Noctilio leporinus Last Modified in 12/16/15 | 49 | 171 | 171 | 0 | 0 | 0 | 0 | 2 |
[55] Phylloderma stenops Last Modified in 12/16/15 | 64 | 156 | 156 | 0 | 0 | 0 | 0 | 2 |
[56] Phyllonycteris aphylla Last Modified in 12/16/15 | 71 | 149 | 149 | 0 | 0 | 0 | 0 | 2 |
[57] Phyllonycteris poeyi Last Modified in 12/16/15 | 51 | 169 | 169 | 0 | 0 | 0 | 0 | 2 |
[58] Phyllops falcatus Last Modified in 12/16/15 | 47 | 175 | 173 | 0 | 0 | 0 | 0 | 2 |
[59] Phyllostomus discolor Last Modified in 12/16/15 | 48 | 173 | 172 | 0 | 0 | 0 | 0 | 2 |
[60] Phyllostomus hastatus Last Modified in 12/16/15 | 21 | 200 | 199 | 0 | 0 | 0 | 0 | 2 |
[61] Platalina genovensium Last Modified in 12/16/15 | 83 | 137 | 137 | 0 | 0 | 0 | 0 | 2 |
[62] Platyrrhinus helleri Last Modified in 12/16/15 | 47 | 174 | 173 | 0 | 0 | 0 | 0 | 2 |
[63] Pteronotus davyi Last Modified in 12/16/15 | 69 | 151 | 151 | 0 | 0 | 0 | 0 | 2 |
[64] Pteronotus parnellii Last Modified in 12/16/15 | 35 | 185 | 185 | 0 | 0 | 0 | 0 | 2 |
[65] Pygoderma bilabiatum Last Modified in 12/16/15 | 73 | 148 | 147 | 0 | 0 | 0 | 0 | 2 |
[66] Rhinophylla pumilio Last Modified in 12/16/15 | 72 | 148 | 148 | 0 | 0 | 0 | 0 | 2 |
[67] Saccopteryx bilineata Last Modified in 12/16/15 | 53 | 167 | 167 | 0 | 0 | 0 | 0 | 2 |
[68] Scleronycteris ega Last Modified in 12/16/15 | 148 | 72 | 72 | 0 | 0 | 0 | 0 | 2 |
[69] Sphaeronycteris toxophyllum Last Modified in 12/16/15 | 76 | 145 | 144 | 0 | 0 | 0 | 0 | 2 |
[70] Stenoderma rufum Last Modified in 12/16/15 | 74 | 146 | 146 | 0 | 0 | 0 | 0 | 2 |
[71] Sturnira lilium Last Modified in 12/16/15 | 37 | 184 | 183 | 0 | 0 | 0 | 0 | 2 |
[72] Thyroptera tricolor Last Modified in 12/16/15 | 59 | 161 | 161 | 0 | 0 | 0 | 0 | 2 |
[73] Tonatia saurophila Last Modified in 12/16/15 | 76 | 144 | 144 | 0 | 0 | 0 | 0 | 2 |
[74] Trachops cirrhosus Last Modified in 12/16/15 | 57 | 164 | 163 | 0 | 0 | 0 | 0 | 2 |
[75] Trinycteris nicefori Last Modified in 12/16/15 | 46 | 175 | 174 | 0 | 0 | 0 | 0 | 2 |
[76] Uroderma bilobatum Last Modified in 12/16/15 | 40 | 181 | 180 | 0 | 0 | 0 | 0 | 2 |
[77] Vampyressa pusilla Last Modified in 12/16/15 | 41 | 182 | 179 | 0 | 0 | 0 | 0 | 2 |
[78] Vampyriscus bidens Last Modified in 12/16/15 | 78 | 142 | 142 | 0 | 0 | 0 | 0 | 2 |
[79] Vampyrodes caraccioli Last Modified in 12/16/15 | 61 | 160 | 159 | 0 | 0 | 0 | 0 | 2 |
[80] Vampyrum spectrum Last Modified in 12/16/15 | 65 | 155 | 155 | 0 | 0 | 0 | 0 | 2 |
Project views
type | number of views | Individual items viewed (where applicable) |
Total project views | 33183 | |
Media views | 5774 | Media search (4698 views); M406366 (1076 views); |
Taxon list | 16426 | |
Project overview | 3017 | |
Matrix views | 2276 | Matrix landing page (1987 views); Phyllostomid morphology matrix (289 views); |
Documents list | 1765 | |
Specimen list | 2788 | |
Bibliography | 1127 | |
Views for media list | 10 |
Project downloads
type | number of downloads | Individual items downloaded (where applicable) |
Total downloads from project | 339 | |
Project downloads | 304 | |
Matrix downloads | 31 | Phyllostomid morphology matrix (31 downloads); |
Document downloads | 4 | Understanding phylogenetic incongruence: lessons from phyllostomid bats (4 downloads); |