Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.
Science (Impact Factor: 33.61). 02/2011; 331(6020):1032-5. DOI: 10.1126/science.1188545
Source: PubMed


Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary
biology for 150 years. If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover
the genetic and developmental mechanisms responsible. Similar phenotypes may be retained from common ancestry (homology),
but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution,
or less likely, that they experienced reversal. Such examples of homoplasy present opportunities to discover the foundations
of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces
the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated
exploration of the mechanisms by which similarity arises.

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    • "Higher-level avian systematic relationships have undergone considerable reshuffling over the past few decades, as molecular phylogenetic analyses have made it comparatively easier to resolve homoplasy resulting from convergent evolution (Wake et al., 2011). The overarching result has tended to be more rigorous formulations of relationships, as indicated by consistency of inferred relationships across studies. "
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    ABSTRACT: Muscicapa flycatchers and their allies (Bradornis, Dioptornis, Empidornis, Fraseria, Myioparus, Namibornis, and Sigelus) are widely distributed in Africa, Europe and Asia. This broad distribution and the wide variety of habitats occupied by the group, ranging from arid to tropical forests, presents an interesting opportunity to explore the evolution of biogeographic patterns and habitat associations. Sequence data (up to 3310 base pairs from two mitochondrial and two nuclear genes) were generated for 36 of 42 species which comprise the assemblage. Complementary data from an additional species was retrieved from GenBank, as was an additional gene which was available for 21 of our included taxa. Using model-based phylogenetic methods and molecular clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the lineage. Ancestral area reconstructions were performed on the phylogeny using LaGrange and BioGeoBEARS. Our results indicate that Bradornis, Fraseria, and Muscicapa are each non-monophyletic, with the latter being shown to comprise five separate clades each more closely related to other genera. Two new genera (Chapinia and Ripleyia) are erected to account for these results. Muscicapa and allies originated c. 7.4 Ma, most likely in Africa given that their sister lineage is almost entirely from there, and rapidly achieved a Eurasian distribution by c. 7.1 Ma. A second divergence at c. 6.1 Ma resulted in two clades. The first is a largely Eurasian clade that subsequently recolonized Africa, perhaps as the result of the loss of migration. The second is an African clade, and ancestral reconstructions suggest a Congolian (e.g. tropical forest) origin for this clade, with several subsequent diversifications into more arid habitats. This is a unique result, as most tropical forest lineages are confined to that habitat. As with other studies of African bird lineages, Afrotropical forest dynamics appear to have played a significant role in driving diversification in Muscicapa and allies, and our results include just the second recorded case of southern to northern African colonization patterns.
    Molecular Phylogenetics and Evolution 10/2015; 94(Pt B). DOI:10.1016/j.ympev.2015.09.026 · 3.92 Impact Factor
    • "Parallel/convergent phenotypic evolution – the independent and repeated evolution of similar traits in similar environments – provides strong evidence for a deterministic role of natural selection (Langerhans & DeWitt, 2004; Schluter et al., 2004; Arendt & Reznick, 2008; Losos, 2011; Wake et al., 2011). While recognizing that optimal use of the terms " parallel " versus " convergent " is debatable (Arendt & Reznick, 2008), we henceforth use " parallel " as it is standard for our study system (see below) and because we focus on phenotypic patterns, rather than the underlying genetic/developmental pathways. "
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    ABSTRACT: Parallel (and convergent) phenotypic variation is most often studied in the wild, where it is difficult to disentangle genetic versus environmentally-induced effects. As a result, the potential contributions of phenotypic plasticity to parallelism (and non-parallelism) are rarely evaluated in a formal sense. Phenotypic parallelism could be enhanced by plasticity that causes stronger parallelism across populations in the wild than would be expected from genetic differences alone. Phenotypic parallelism could be dampened if site-specific plasticity induced differences between otherwise genetically-parallel populations. We used a common-garden study of three independent lake-stream stickleback population pairs to evaluate the extent to which adaptive divergence has a genetic or plastic basis, and to investigate the enhancing versus dampening effects of plasticity on phenotypic parallelism. We found that lake-stream differences in most traits had a genetic basis, but that several traits also showed contributions from plasticity. Moreover, plasticity was much more prevalent in one watershed than in the other two. In most cases, plasticity enhanced phenotypic parallelism, whereas in a few cases plasticity had a dampening effect. Genetic and plastic contributions to divergence seem to play a complimentary, likely adaptive, role in phenotypic parallelism of lake-stream stickleback. These findings highlight the value of formally comparing wild-caught and lab-reared individuals in the study of phenotypic parallelism.This article is protected by copyright. All rights reserved.
    Journal of Evolutionary Biology 09/2015; DOI:10.1111/jeb.12767 · 3.23 Impact Factor
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    • "They are major patterns of phenotypic evolution. Such examples of homoplasy (Lankester 1870) present opportunities to discover the foundations of morphological traits and determine processes and mechanisms of evolution (Wake et al. 2011). Furthermore, understanding what is driving the high degree of homeomorphy within ammonoids is of great importance for taxonomy (e.g., Hewitt 1989; Webb 1994) and phylogeny as it might result in a high degree of homoplasy (Wake 1991; Yacobucci 2012). "

    Ammonoid Paleobiology: From macroevolution to paleogeography, Topics in Geobiology 44 edited by Christian Klug, Dieter Korn, Kenneth De Baets, Isabelle Kruta, Royal H. Mapes, 08/2015: chapter 5: pages 95-142; Springer., ISBN: 978-94-017-9632-3
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