Estimating a Binary Character's Effect on Speciation and Extinction

Maddison, Wayne P.; Midford, Peter E.; Otto, Sarah P.

doi:10.1080/10635150701607033

Cited by 999 publications

(1,387 citation statements)

References 30 publications

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“…8 and Supplementary Note). To test whether high MHC I copy numbers are associated with lineages that have high diversification rates, we carried out BiSSE analyses 68 with the diversitree R package 69 . In these analyses, species were grouped into two categories for high and low MHC I copy numbers, on the basis of a given threshold value.…”

Section: Methodsmentioning

confidence: 99%

Evolution of the immune system influences speciation rates in teleost fishes

et al. 2016

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With over 32,000 extant species 1 , teleost fishes comprise the majority of vertebrate species. Their taxonomic diversity is matched by extensive genetic and phenotypic variation, including novel immunological strategies. Although the functionality of the adaptive immune system has been considered to be conserved since its emergence in the ancestor of all jawed vertebrates 2,3 , fundamental modifications of the immune gene repertoire have recently been reported in teleosts [4][5][6][7] . One of the most dramatic changes has occurred in Atlantic cod (Gadus morhua), involving complete loss of the MHC II pathway that is otherwise responsible for the detection of bacterial pathogens in vertebrates 4 . Moreover, this loss is accompanied by a substantially enlarged repertoire of MHC I genes, which normally encode molecules for protection against viral pathogens. It has thus been hypothesized that the expanded MHC I repertoire of cod evolved as a compensatory mechanism, whereby broader MHC I functionality makes up for the initial loss of MHC II (refs. 4,6). However, the questions of how and when MHC II was lost relative to the MHC I expansion, and whether these genomic modifications are causally related, have so far remained unresolved.As key components of the vertebrate adaptive immune system, the complex MHC pathways and their functionality are now well characterized 8-10 , but less is known about the causes of MHC copy number variation, which poses an immunological tradeoff 11,12 . Although an increase in the number of MHC genes facilitates pathogen detection, it will also decrease the number of circulating T cells [13][14][15][16] , resulting in an immune system that can detect a large number of pathogens at the expense of being less efficient in removing them. The evolution of MHC copy numbers is therefore likely driven toward intermediate optima determined by a tradeoff between detection and elimination of pathogens-as suggested by selection for 5-10 copies inferred in case studies of fish 17,18 and birds 19 . Because pathogen load and the associated selective pressures vary between habitats, the optimal number of MHC copies depends on the environment [20][21][22] . As a result, interbreeding between different locally adapted populations is expected to produce hybrids with excess (above optimal) MHC diversity that are characterized by T cell deprivation and low fitness. This process would introduce postzygotic reproductive isolation and promote reinforcement of premating isolation between the populations. Consequently, MHC genes have been suggested to have an important role in speciation 22,23 , but, to our knowledge, this role has never been tested comparatively in a macroevolutionary context.Here we report comparative analyses of 76 teleost species, of which 66 were sequenced to produce partial draft genome assemblies, including 27 representatives of cod-like fishes within the order Gadiformes. First, we use phylogenomic analysis to resolve standing controversy regarding early-teleost divergences and to firmly ...

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Section: Methodsmentioning

confidence: 99%

Evolution of the immune system influences speciation rates in teleost fishes

et al. 2016

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“…Nee et al ( 1994 ) illustrated how extinction rates could be estimated from phylogenetic trees (but see Rabosky 2010 ), but assumed constant rates model. New methods, for example, BiSSE (Maddison et al 2007 ) and GeoSSE (Goldberg et al 2011 ), relax this assumption, and allow us to estimate extinction and speciation rates simultaneously, for example, with the gain or loss of particular character states (BiSSE) or shifts in geographic distributions (GeoSSE). Phylogeny-based analysis of diversifi cation provides some limited evidence for increasing speciation through time (e.g.…”

Section: Speciation and Extinction As Two Natural Processesmentioning

confidence: 99%

Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?

Yessoufou

Davies

2016

Topics in Biodiversity and Conservation

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Analysing extinction within a phylogenetic framework may seem counter-intuitive because extinction is a priori a non-heritable trait. However, extinction risk is correlated with other traits, such as body size, that show a strong phylogenetic signal. Further, there has been much effort in identifying key traits important for diversifi cation, and recent evidence has demonstrated that the processes of speciation and extinction may be inextricably linked. A phylogenetic approach also allows us to quantify the impact of extinction, for example, as the loss of branches from the tree-of-life. Early work suggested that extinctions might result in little loss of evolutionary history, but subsequent studies indicated that nonrandom extinctions might prune more of the evolutionary tree. Loss of phylogenetic diversity might have ecosystem consequences because functional differences between species tend to be correlated with the evolutionary distances between them. Here we explore how extinction prunes the tree-of-life. Our review indicates that the loss of evolutionary history under non-random extinction (the emerging pattern in extinction biology) might be less pronounced than some previous studies have suggested. However, the loss of functional diversity might still be large, depending on the evolutionary model of trait change. Under a punctuated model of evolution, in which trait differences accrue in bursts at speciation, the number of branches lost is more important than their summed lengths. We suggest that evolutionary models need to be incorporated more explicitly into measures of phylogenetic diversity if we are to use phylogeny as a proxy for functional diversity.

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“…The BiSSE model computes the likelihood of a phylogenetic tree and the character states 177 of the tip taxa given a particular model of character evolution with up to six parameters: a 178 speciation rate under each state of a binary character (λ 0 and λ 1 ), an extinction rate under each 179 state (μ 0 and μ 1 ), and transition rates from each character state to the other (q 01 and q 10 ) 180 (Maddison et al, 2007). The six-parameter model (k = 6), hereafter referred to as the 181 unconstrained model, estimates all parameters using maximum likelihood.…”

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confidence: 99%

Lost and found: The third molars of Callimico goeldii and the evolution of the callitrichine postcanine dentition

Scott

2015

Journal of Human Evolution

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Estimating a Binary Character's Effect on Speciation and Extinction

Cited by 999 publications

References 30 publications

Evolution of the immune system influences speciation rates in teleost fishes

Evolution of the immune system influences speciation rates in teleost fishes

Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life?

Lost and found: The third molars of Callimico goeldii and the evolution of the callitrichine postcanine dentition

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