Multiple origins of green blood in New Guinea lizards

Rodriguez, Zachary; Perkins, Susan L.; Austin, Christopher C.

doi:10.1126/sciadv.aao5017

Cited by 21 publications

(35 citation statements)

References 61 publications

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“…To demonstrate the use of gCF and sCF values, we first analysed a dataset containing 163 3,220 ultra-conserved elements (UCEs) from lizards, totalling 1,301,107 bp for 43 species 164 (Rodriguez et al 2018). To do this, we estimated a concatenated maximum likelihood (ML) 165 tree, 3,220 UCE trees, and the gCF, sCF, and bootstrap values with IQ-TREE ( Figure 2).…”

Section: Application To Empirical Datasets 162mentioning

confidence: 99%

New methods to calculate concordance factors for phylogenomic datasets

Minh

Hahn

Lanfear

2018

Preprint

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AbstractWe implement two measures for quantifying genealogical concordance in phylogenomic datasets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of “decisive” gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org).

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Section: Application To Empirical Datasets 162mentioning

confidence: 99%

New methods to calculate concordance factors for phylogenomic datasets

Minh

Hahn

Lanfear

2018

Preprint

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“…[14] The reasons for rapid bilin appearance in these small animals are debated [11] and range widely from a defense mechanism against predator attack to innate immunity. [13,19] Despite the ability of many non-mammalian animals to accumulate biliverdin, BVRA still occurs as evidence by the occurrence of bilirubin in these animals. [20]…”

Section: Non-mammalian Animal Bilinsmentioning

confidence: 99%

Heme‐Derived Bilins

Takemoto

Chang

Chen

et al. 2019

Israel Journal of Chemistry

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Living things on Earth depend on heme – the iron‐cyclic tetrapyrrole complex that harnesses iron's oxidizing powers. Heme is toxic, but Nature has evolved ways to control it. One way is breaking it with heme oxygenase which lowers its levels and begins the formation of linear tetrapyrroles called bilins. Bilins occur in many variations, often colorful, sometimes in abundance, and in animals, plants and microbes. Contrary to early notions, bilins are not only waste products of heme degradation. They are increasingly appreciated for their diverse roles such as sensing and gathering light, regulating growth and aging, responding to inflammatory conditions, and influencing behavior. The diverse functions of bilins are exploited with discoveries and uses of bioactive bilins for salutary benefits in medicine and agriculture. Opportunities for finding new bioactive bilins and applications will grow as knowledge of bilin biology and capabilities for producing bilins continue to expand.

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“…To illustrate this problem, we consider two cases of empirical incongruence of a binary trait. First, consider the case of New Guinea lizards that have evolved green blood from a red-blooded ancestor (Figure 1A; Rodriguez et al 2018). A clade of 15 taxa contains both the green-blooded species and red-blooded species (the ancestral state).…”

Section: Introductionmentioning

confidence: 99%

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

Hibbins

Gibson

Hahn

2020

Preprint

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The incongruence of character states with phylogenetic relationships is often interpreted as evidence of convergent evolution. However, trait evolution along discordant gene trees can also generate these incongruences -a phenomenon known as hemiplasy. Classic phylogenetic comparative methods do not account for discordance, resulting in incorrect inferences about the number of times a trait has evolved, and therefore about convergence. Biological sources of discordance include incomplete lineage sorting (ILS) and introgression, but only ILS has received theoretical consideration in the context of hemiplasy. Here, we derive expectations for the probabilities of hemiplasy and homoplasy with ILS and introgression acting simultaneously. We find that introgression makes hemiplasy more likely, suggesting that methods that account for discordance due to ILS alone will be conservative. We also present a method for making statistical inferences about the relative probabilities of hemiplasy and homoplasy in empirical datasets. Our method is implemented in the software package HeIST (Hemiplasy Inference Simulation Tool), and estimates the most probable number of transitions among character states given a set of relationships with discordance. HeIST can accommodate ILS and introgression simultaneously, and can be applied to large phylogenies. We apply this tool to a phylogeny of New Guinea lizards that have evolved green blood from a red-blooded ancestor, and find that hemiplasy is likely to explain the observed trait incongruence.

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Multiple origins of green blood in New Guinea lizards

Abstract: Green blood, a remarkable physiological trait, evolved multiple times in lizards.

Cited by 21 publications

References 61 publications

New methods to calculate concordance factors for phylogenomic datasets

New methods to calculate concordance factors for phylogenomic datasets

Heme‐Derived Bilins

Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression

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