Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses

Libeskind-Hadas, Ran

doi:10.3390/life12030443

Cited by 4 publications

(2 citation statements)

References 34 publications

(46 reference statements)

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“…We found that between the different costs, the median MPRs produced quite different patterns based on the event costs set. The use of median MPRs and the clustering methods (not discussed here, but see [21]) help the user to explore the solutions output by e MP ress , however, deciding which of the different classes (i.e. which costs to set) remains challenging.…”

Section: Resultsmentioning

confidence: 99%

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Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths

2022

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Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. It is therefore crucial that we have a way of estimating their extinction risk. Attempts to do this have often relied on information about host extinction risk, without explicitly incorporating information about the parasites. However, assuming an identical risk may be misleading. Here, we apply a novel metric to estimate the cophylogenetic extinction rate, Ec , of parasites with their hosts. This metric incorporates information about the evolutionary history of parasites and hosts that can be estimated using event-based cophylogenetic methods. To explore this metric, we investigated the use of different cophylogenetic methods to inform the Ec rate, based on the analysis of polystome parasites and their anuran hosts. We show using both parsimony- and model-based approaches that different methods can have a large effect on extinction risk estimation. Further, we demonstrate that model-based approaches offer greater potential to provide insights into cophylogenetic history and extinction risk.

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Section: Resultsmentioning

confidence: 99%

“…[18]. In this context, reconciliation refers to mapping each node of the parasite tree onto a node or branch of the host tree [21]. Four evolutionary processes (events) are used to explain observed patterns between two trees: cospeciation, duplication, extinction and host switching [22] (figure 1).…”

Section: Introductionmentioning

confidence: 99%

Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths

2022

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Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

et al. 2023

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A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.

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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Sinaimeri,

Urbini,

Sagot

et al. 2023

Systematic Biology

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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 outcomes, 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 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.

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Tree Reconciliation Methods for Host-Symbiont Cophylogenetic Analyses

Cited by 4 publications

References 34 publications

Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths

Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths

Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

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