DOI: 10.6084/m9.figshare.14393309.v1
title: Dataset for ELE_EV_ELE13757

description: Methods: <br>A literature search was performed using Google Scholar on 19<sup>th</sup> March 2019, which identified 368 citations of the original paper for TreeMap (Page 1994), and 332 citations of the original paper for Parafit (Legendre<i> et al.</i> 2002), resulting in a total of 700 articles that were screened to extract metrics for inclusion in our meta-analysis. Articles that did not contain cophylogenetic analyses were immediately excluded. Studies focussing at the population level were also excluded, as these do not represent true cophylogenetic analyses at the macroevolutionary level. Additionally, studies that included less than four taxa were excluded from consideration, as these do not provide sufficient power for inclusion in the meta-analysis. Studies that did not report the test statistic for congruence were also necessarily excluded. A short citation of each study was recorded under ‘authors’, and the year of publication was recorded in ‘year’. Hosts and symbionts were classified broadly according to Linnean taxonomy for ‘host_tax_broad’ and ‘symbiont_tax_broad’ as either: invertebrate, vertebrate, plant or microbe (i.e. microscopic symbionts such as fungi, protozoa, bacteria, viruses). We adopted the mode of symbiosis and mode of transmission between host species specified by the authors in each individual study for ‘symbiosis’ and ‘mode_of_transmission_broad’. In cases where either mode of symbiosis or mode of transmission were not directly specified by authors, we consulted the literature for clarification. In a small number of studies restricted to bacterial intracellular symbionts, the mutualism-parasitism distinction was not defined by the authors and either no further information was available, or a symbiont was cited in the literature as being both a mutualist or a parasite, depending on which study was considered. The nature of the relationship between bacterial intracellular symbionts and their hosts is complex, and in some cases they may display both beneficial and detrimental effects simultaneously. In a few cases of conflict or where authors did not explicitly state mode of transmission for bacterial intracellular symbionts, we assumed a mode of transmission in line with the majority of available references. We only encountered one study where authors categorised the mode of symbiosis as commensalism. On the continuum of symbioses from pure parasitism (fitness losses for the host) to mutualism (fitness gains for the host), commensalism represents a single point where losses and gains for the host precisely equal zero. Consequently, commensalism is an unlikely and unstable state, easily tipped to one side or the other with any small change in external conditions. Thus, the lack of widely recognized groups of commensals is the likeliest explanation for the scarcity of studies on commensalism in our data (note that we did not include this category, commensalism, in our analyses). The total number of host tips that were linked to a symbiont taxon were summed to provide ‘host_tips_linked’, which in a very few cases was corrected to remove multiple sampling of the same host species, to provide ‘host_tips_linked_corrected’. The total number of symbiont tips with a link to a host taxon were summed to provide ‘symbiont_tips_linked’, while the total number of individual links between hosts and symbionts was recorded as ‘total_host_symbiont_links’. If all symbionts in a phylogeny were strict specialists, such that each one had a single link to a single host, ‘total_host_symbiont_links’ would simply equal ‘symbiont_tips_linked’. However, because symbionts are often associated with more than one host, the value of ‘total_host_symbiont_links’ was often higher than the total number of symbionts included in a study. Thus, a measure of symbiont generalism was captured using ‘host_range_link_ratio’, defined as ‘total_host_symbiont_links’ divided by ‘symbiont_tips_linked’, providing the mean number of host-symbiont links observed per symbiont taxon, with the measure increasing with increasing generalism. An alternative estimate of symbiont host specificity was captured using ‘host_range_taxonomic_breadth’, which considers Linnean taxonomic rank, and was calculated by assigning an incremental score to successive host taxonomic ranks per symbiont in turn (i.e. single host species = 1, multiple host species in the same genus = 2, multiple host genera = 3, multiple host families = 4, multiple host orders = 5), summing the total score across all symbionts, and dividing by ‘symbiont_tips_linked’ (i.e. the total number of symbionts). Consequently, ‘host_range_taxonomic_breadth’ increases with symbiont generalism, such that symbiont phylogenies containing symbionts capable of infecting hosts from a wide range of taxonomic ranks are assigned a greater score. The number of phylogenetic permutations performed by authors during cophylogenetic analyses was recorded as ‘no_randomizations’, which poses a unique problem in our meta-analysis (discussed in the section ‘Publication bias and sensitivity analysis’). The resultant <i>p</i> value from each study was recorded as ‘p_value’, whereby observed <i>p</i> values decrease with a decreasing likelihood of observing host-symbiont cophylogeny by chance alone (i.e., as calculated during permutation tests performed by authors during TreeMap or ParaFit analyses). <br><br>File '2021-09-01-source-data-dat.txt' is in tab-delimited text format.<br>File 'Supporting_Information.Rmd' is accompanying R code used for analysis of the source data.