DOI: 10.5061/dryad.5x69p8d6v
title: Cophylogeny reconstruction allowing for multiple associations through approximate Bayesian computation

description: Phylogenetic tree reconciliation is extensively employed for the
 examination of coevolution between host and symbiont species. An important
 concern is the requirement for dependable cost values when selecting
 event-based parsimonious reconciliation. Although certain approaches
 deduce event probabilities unique to each pair of host and symbiont trees,
 which can subsequently be converted into cost values, a significant
 limitation lies in their inability to model the invasion of diverse host
 species by the same symbiont species (termed as a spread event), which is
 believed to occur in symbiotic relationships. Invasions lead to the
 observation of multiple associations between symbionts and their hosts
 (indicating that a symbiont is no longer exclusive to a single host),
 which are incompatible with the existing methods of coevolution. 
 Here, we present a method called AmoCoala (an enhanced version of the tool
 Coala) that provides a more realistic estimation of cophylogeny event
 probabilities for a given pair of host and symbiont trees, even in the
 presence of spread events. We expand the classical 4-event coevolutionary
 model to include 2 additional spread events (vertical and horizontal
 spreads) that lead to multiple associations. In the initial step, we
 estimate the probabilities of spread events using heuristic frequencies.
 Subsequently, in the second step, we employ an approximate Bayesian
 computation (ABC) approach to infer the probabilities of the remaining 4
 classical events (cospeciation, duplication, host switch, and loss) based
 on these values. By incorporating spread events, our reconciliation model
 enables a more accurate consideration of multiple associations. This
 improvement enhances the precision of estimated cost sets, paving the way
 to a more reliable reconciliation of host and symbiont trees. To validate
 our method, we conducted experiments on synthetic datasets and
 demonstrated its efficacy using real-world examples. Our results showcase
 that AmoCoala produces biologically plausible reconciliation scenarios,
 further emphasizing its effectiveness.The software is accessible
 at https://github.com/sinaimeri/AmoCoala.
description: 4 biological datasets were extracted from the literature and
 provided as nexus files. <br><br>AP - Acacia &
 Pseudomyrmex. This dataset was extracted from Gomez-Acevedo et al.
 Neotropical mutualism between <em>Acacia</em> and
 <em>Pseudomyrmex</em>: Phylogeny and divergence times.
 Molecular Phylogenetics and Evolution, 2010. It displays the interaction
 between Acacia plants and <em>Pseudomyrmex</em>, a genus of
 ants. The host and symbiont trees include 9 and 7 leaves, respectively.
 The dataset has 22 multiple-associations.<br><br>MP - Myrmica
 & Phengaris. This dataset was extracted from Jansen et al. A
 phylogenetic test of the parasite-host associations between
 <em>Maculinea</em> butterflies (Lepidoptera: Lycaenidae) and
 <em>Myrmica</em> ants (Hymenoptera: Formicidae). European
 Journal of Entomology, 2011. It is composed of a pair of host and symbiont
 trees which have each 8 leaves. The dataset has 8
 multiple-associations.<br><br>SBL - Seabirds & Lice.
 This dataset was extracted from Paterson et al. Host-parasite
 co-speciation, host switching, and missing the boat. In D. H. Clayton and
 J. Moore, editors, Host-parasite evolution: General principles and avian
 models, Oxford University Press, 1997. The host and symbiont trees include
 15 and 8 leaves, respectively. The dataset has 15
 multiple-associations.<br><br>SFC - Smut Fungi &
 Caryophillaceus plants. This dataset was extracted from Refrégier et al.
 Cophylogeny of the anther smut fungi and their caryophyllaceous hosts:
 Prevalence of host shifts and importance of delimiting parasite species
 for inferring cospeciation. BMC Evolutionary Biology, 2008. The host and
 symbiont trees include 15 and 16 leaves, respectively. The dataset has 4
 multiple-associations.
description: The java code can be found at https://github.com/sinaimeri/AmoCoala