Diversitree: comparative phylogenetic analyses of diversification in R

FitzJohn, Richard G.

doi:10.1111/j.2041-210x.2012.00234.x

Cited by 849 publications

(924 citation statements)

References 39 publications

(45 reference statements)

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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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“…MCMC sampling of the BiSSE model (31,33) indicates that migration was lost at a significantly higher rate than gained (SI Materials and Methods).…”

Section: Discussionmentioning

confidence: 99%

Temperate origins of long-distance seasonal migration in New World songbirds

Winger

Barker

Ree

2014

Proc. Natl. Acad. Sci. U.S.A.

107

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Migratory species exhibit seasonal variation in their geographic ranges, often inhabiting geographically and ecologically distinct breeding and nonbreeding areas. The complicated geography of seasonal migration has long posed a challenge for inferring the geographic origins of migratory species as well as evolutionary sequences of change in migratory behavior. To address this challenge, we developed a phylogenetic model of the joint evolution of breeding and nonbreeding (winter) ranges and applied it to the inference of biogeographic history in the emberizoid passerine birds. We found that seasonal migration between breeding ranges in North America and winter ranges in the Neotropics evolved primarily via shifts of winter ranges toward the tropics from ancestral ranges in North America. This result contrasts with a dominant paradigm that hypothesized migration evolving out of the tropics via shifts of the breeding ranges. We also show that major lineages of tropical, sedentary emberizoids are derived from northern, migratory ancestors. In these lineages, the winter ranges served as a biogeographic conduit for temperate-to-tropical colonization: winter-range shifts toward the tropics during the evolution of long-distance migration often preceded southward shifts of breeding ranges, the loss of migration, and in situ tropical diversification. Meanwhile, the evolution of long-distance migration enabled the persistence of old lineages in North America. These results illuminate how the evolution of seasonal migration has contributed to greater niche conservatism among tropical members of this diverse avian radiation.evolution of migration | historical biogeography | dispersal-extinction-cladogenesis | bird migration | tropical niche conservatism T he evolution of seasonal migratory behavior among animals involves a suite of behavioral, physiological, morphological, and neurological adaptations that enable migrants' extraordinary feats of endurance and navigation (1-3). However, the evolution of migration also is an inherently geographic process during which a species' breeding range and nonbreeding range (henceforth, winter range) become physically and ecologically separated (4). Understanding the evolution of migration therefore requires reconciling the fascinating adaptations of migratory individuals with the biogeographic factors that control the shifting boundaries of a species' range (5). The field of historical biogeography has shed considerable light on the geographic histories of organisms (6, 7) but has largely ignored migratory species due to the difficulty of simultaneously reconstructing the evolution of the breeding and winter ranges, which in migratory species are often ecologically disparate and separated by long distances (5). Consequently, progress in our understanding of the evolution of migration has been impeded by a biogeographic conundrum: testing hypotheses on the evolution of migration requires knowledge of the geographic histories of migratory species (4,8,9), but the existence of migratory b...

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“…Moreover, specialization on particular host species has led to genetic divergence within some cuckoo and honeyguide species into distinct host-specific races [16][17][18], and Krü ger et al [19] demonstrated that species of parasitic cuckoos had more subspecies than species of non-parasitic cuckoos. Since the appearance of these studies, novel phylogenies [20] and phylogenetic methods [3,21] have been developed.…”

Section: Introductionmentioning

confidence: 99%

Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites

Medina¹,

Langmore²

2015

Proc. R. Soc. B.

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Coevolution is often invoked as an engine of biological diversity. Avian brood parasites and their hosts provide one of the best-known examples of coevolution. Brood parasites lay their eggs in the nests of other species, selecting for host defences and reciprocal counteradaptations in parasites. In theory, this arms race should promote increased rates of speciation and phenotypic evolution. Here, we use recently developed methods to test whether the three largest avian brood parasitic lineages show changes in rates of phenotypic diversity and speciation relative to non-parasitic lineages. Our results challenge the accepted paradigm, and show that there is little consistent evidence that lineages of brood parasites have higher speciation or extinction rates than non-parasitic species. However, we provide the first evidence that the evolution of brood parasitic behaviour may affect rates of evolution in morphological traits associated with parasitism. Specifically, egg size and the colour and pattern of plumage have evolved up to nine times faster in parasitic than in non-parasitic cuckoos. Moreover, cuckoo clades of parasitic species that are sympatric (and share similar host genera) exhibit higher rates of phenotypic evolution. This supports the idea that competition for hosts may be linked to the high phenotypic diversity found in parasitic cuckoos.

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Diversitree: comparative phylogenetic analyses of diversification in R

Cited by 849 publications

References 39 publications

Evolution of the immune system influences speciation rates in teleost fishes

Evolution of the immune system influences speciation rates in teleost fishes

Temperate origins of long-distance seasonal migration in New World songbirds

Coevolution is linked with phenotypic diversification but not speciation in avian brood parasites

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