Project 947: L. M. Davalos, A. L. Cirranello, J. H. Geisler, N. B. Simmons. 2012. Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews. 87 (4):991-1024.
Specimen: Artibeus phaeotis (unvouchered)

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.


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Article DOI: doi/10.1111/j.1469-185X.2012.00240

Project DOI: 10.7934/P947, http://dx.doi.org/10.7934/P947
This project containsMatrices
  • 1 Media
  • 1 Matrix
  • 1 Document
  • 81 Taxa
  • 1 Specimen
  • 220 Characters


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

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    Andrea Cirranello
    Project Administrator
    Last logged in 04/21/16
    811122000012622
    (12622, 0, 0)
    000
    MorphoBank Curator
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    Taxonomic Overview for Matrix 'M23687' (80 Taxa)

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    [1] Ametrida centurio
    Last Modified in 12/16/15
    6715415300002
    [2] Anoura caudifer
    Last Modified in 12/16/15
    7015115000002
    [3] Anoura geoffroyi
    Last Modified in 12/16/15
    3918218100002
    [4] Ardops nichollsi
    Last Modified in 12/16/15
    6915115100002
    [5] Ariteus flavescens
    Last Modified in 12/16/15
    6615615400002
    [6] Artibeus cinereus
    Last Modified in 12/16/15
    7114914900002
    [7] Artibeus concolor
    Last Modified in 12/16/15
    7714514300002
    [8] Artibeus hirsutus
    Last Modified in 12/16/15
    11910110100002
    [9] Artibeus jamaicensis
    Last Modified in 12/16/15
    2819219200002
    [10] Brachyphylla cavernarum
    Last Modified in 12/16/15
    4118017900002
    [11] Carollia brevicauda
    Last Modified in 12/16/15
    7714314300002
    [12] Carollia perspicillata
    Last Modified in 12/16/15
    1820320200002
    [13] Centurio senex
    Last Modified in 12/16/15
    6515515500002
    [14] Chiroderma villosum
    Last Modified in 12/16/15
    7115114900002
    [15] Choeroniscus godmani
    Last Modified in 12/16/15
    6016116000002
    [16] Choeronycteris mexicana
    Last Modified in 12/16/15
    4417717600002
    [17] Chrotopterus auritus
    Last Modified in 12/16/15
    6116015900002
    [18] Desmodus rotundus
    Last Modified in 12/16/15
    3218918800002
    [19] Diaemus youngi
    Last Modified in 12/16/15
    7914314100002
    [20] Diphylla ecaudata
    Last Modified in 12/16/15
    6915115100002
    [21] Ectophylla alba
    Last Modified in 12/16/15
    8413713600002
    [22] Enchisthenes hartii
    Last Modified in 12/16/15
    6615515400002
    [23] Erophylla sezekorni
    Last Modified in 12/16/15
    4617417400002
    [24] Furipterus horrens
    Last Modified in 12/16/15
    7015115000002
    [25] Glossophaga longirostris
    Last Modified in 12/16/15
    9013013000002
    [26] Glossophaga soricina
    Last Modified in 12/16/15
    1520620500002
    [27] Glyphonycteris daviesi
    Last Modified in 12/16/15
    8213913800002
    [28] Glyphonycteris sylvestris
    Last Modified in 12/16/15
    7314814700002
    [29] Hylonycteris underwoodi
    Last Modified in 12/16/15
    5616416400002
    [30] Lampronycteris brachyotis
    Last Modified in 12/16/15
    7514614500002
    [31] Leptonycteris yerbabuenae
    Last Modified in 12/16/15
    4817417200002
    [32] Lichonycteris obscura
    Last Modified in 12/16/15
    5516716500002
    [33] Lionycteris spurrelli
    Last Modified in 12/16/15
    4817317200002
    [34] Lonchophylla robusta
    Last Modified in 12/16/15
    4217817800002
    [35] Lonchophylla thomasi
    Last Modified in 12/16/15
    7314814700002
    [36] Lonchorhina aurita
    Last Modified in 12/16/15
    6316015700002
    [37] Lophostoma brasiliense
    Last Modified in 12/16/15
    6915315100002
    [38] Lophostoma silvicolum
    Last Modified in 12/16/15
    6915215100002
    [39] Macrophyllum macrophyllum
    Last Modified in 12/16/15
    6915315100002
    [40] Macrotus californicus
    Last Modified in 12/16/15
    6715315300002
    [41] Macrotus waterhousii
    Last Modified in 12/16/15
    2219819800002
    [42] Mesophylla macconnelli
    Last Modified in 12/16/15
    7115014900002
    [43] Metavampyressa nymphaea
    Last Modified in 12/16/15
    7514614500002
    [44] Micronycteris hirsuta
    Last Modified in 12/16/15
    6016216000002
    [45] Micronycteris megalotis
    Last Modified in 12/16/15
    5616416400002
    [46] Micronycteris minuta
    Last Modified in 12/16/15
    7114914900002
    [47] Mimon bennettii
    Last Modified in 12/16/15
    7015015000002
    [48] Mimon crenulatum
    Last Modified in 12/16/15
    6815415200002
    [49] Monophyllus redmani
    Last Modified in 12/16/15
    4317717700002
    [50] Mormoops megalophylla
    Last Modified in 12/16/15
    5416716600002
    [51] Musonycteris harrisoni
    Last Modified in 12/16/15
    138828200002
    [52] Mystacina robusta
    Last Modified in 12/16/15
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    [53] Mystacina tuberculata
    Last Modified in 12/16/15
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    [54] Noctilio leporinus
    Last Modified in 12/16/15
    4917117100002
    [55] Phylloderma stenops
    Last Modified in 12/16/15
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    [56] Phyllonycteris aphylla
    Last Modified in 12/16/15
    7114914900002
    [57] Phyllonycteris poeyi
    Last Modified in 12/16/15
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    [58] Phyllops falcatus
    Last Modified in 12/16/15
    4717517300002
    [59] Phyllostomus discolor
    Last Modified in 12/16/15
    4817317200002
    [60] Phyllostomus hastatus
    Last Modified in 12/16/15
    2120019900002
    [61] Platalina genovensium
    Last Modified in 12/16/15
    8313713700002
    [62] Platyrrhinus helleri
    Last Modified in 12/16/15
    4717417300002
    [63] Pteronotus davyi
    Last Modified in 12/16/15
    6915115100002
    [64] Pteronotus parnellii
    Last Modified in 12/16/15
    3518518500002
    [65] Pygoderma bilabiatum
    Last Modified in 12/16/15
    7314814700002
    [66] Rhinophylla pumilio
    Last Modified in 12/16/15
    7214814800002
    [67] Saccopteryx bilineata
    Last Modified in 12/16/15
    5316716700002
    [68] Scleronycteris ega
    Last Modified in 12/16/15
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    [69] Sphaeronycteris toxophyllum
    Last Modified in 12/16/15
    7614514400002
    [70] Stenoderma rufum
    Last Modified in 12/16/15
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    [71] Sturnira lilium
    Last Modified in 12/16/15
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    [72] Thyroptera tricolor
    Last Modified in 12/16/15
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    [73] Tonatia saurophila
    Last Modified in 12/16/15
    7614414400002
    [74] Trachops cirrhosus
    Last Modified in 12/16/15
    5716416300002
    [75] Trinycteris nicefori
    Last Modified in 12/16/15
    4617517400002
    [76] Uroderma bilobatum
    Last Modified in 12/16/15
    4018118000002
    [77] Vampyressa pusilla
    Last Modified in 12/16/15
    4118217900002
    [78] Vampyriscus bidens
    Last Modified in 12/16/15
    7814214200002
    [79] Vampyrodes caraccioli
    Last Modified in 12/16/15
    6116015900002
    [80] Vampyrum spectrum
    Last Modified in 12/16/15
    6515515500002


    Project views

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    Total project views14746
    Media views2718Media search (2191 views); M406366 (527 views);
    Taxon list6448
    Project overview1714
    Matrix views1268Matrix landing page (1133 views); Phyllostomid morphology matrix (135 views);
    Documents list976
    Specimen list1159
    Bibliography463




    Project downloads

    type number of downloads Individual items downloaded (where applicable)
    Total downloads from project168
    Project downloads141
    Matrix downloads24Phyllostomid morphology matrix (24 downloads);
    Document downloads3Understanding phylogenetic incongruence: lessons from phyllostomid bats (3 downloads);