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Syst Biol. 2016 Jan;65(1):16-34. doi: 10.1093/sysbio/syv069. Epub 2015 Oct 22.

Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini).

Author information

1
Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA; david.marshall@uconn.edu.
2
Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA;
3
Entomology Department, Australian Museum, 6 College Street, Sydney NSW 2010, Australia;
4
Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA; Division of Biological Sciences, Health Sciences 304, U. Montana, Missoula, MT 59812;
5
Central Mindanao University, Sayre Highway, Bukidnon, Philippines.

Abstract

Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.

KEYWORDS:

Aridification; Australia; branch lengths; calibration; climate change; gamma distribution; maximum-likelihood; relaxed clock

PMID:
26493828
DOI:
10.1093/sysbio/syv069
[Indexed for MEDLINE]

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