Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling

Reynolds, R. Graham; Niemiller, Matthew L.; Revell, Liam J.

doi:10.1016/j.ympev.2013.11.011

Cited by 109 publications

(74 citation statements)

References 88 publications

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“…However, we recommend retaining the current classification until more species are sampled (Table 1) on the grounds that Cylindrophiidae + Anomochilidae share morphological features not present in Uropeltidae [35,84] and since strong support has been shown distinguishing them from Uropeltidae [15,23,32,41]. For boids, our analysis validates the taxonomic changes made in Pyron et al [30], but differs in topology from previous assessments in the placement of Calabariidae, Candoiidae, and Sanziniidae [15,23,53]. Although the relationship Erycidae + Boidae is recovered in all studies [15,23], except one [53], support for this relationship is low.…”

Section: Resultssupporting

confidence: 73%

“…In general, we substantiate many of the higher-level relationships reported in Pyron et al [15]; however, several differences also exist. Support for monophyly for each family and subfamily was above 88%, except for Gerrhopilidae (SHL = 48), and Cylindrophiidae was paraphyletic with Anomochilidae [23,35,53]. …”

Section: Resultsmentioning

confidence: 99%

“…Indeed, the first phylogenetic analysis including all families and subfamilies was only recently completed [32], and only included one representative from each rank. Over the years, researchers have emphasized resolving higher-level snake relationships [15,22,23,25,27,32–49], and topology within families: typhlopids [26,29,31,50]; boids [30,51–53]; acrochordids [54]; xenodermatids [55]; homalopsids [56,57]; pareatids [58]; viperids [59–61]; elapids and lamprophiids [28,62–64]; dipsads [65,66]; pseudoxendontids [67]; natricines [68]; sibynophiids [27]; and colubrids [39,40]. Despite these efforts, many unresolved nodes remain scattered throughout the entire snake tree, such as the monophyly of Scolecophidia [15], topology of Typhlopinae [29], monophyly of Cylindrophiidae and Anomochilidae [35], topology of Booidea [30,53], placement of Xenophidiidae and Bolyeridae [53], and several issues within Caenophidia [22,39,40].…”

Section: Introductionmentioning

confidence: 99%

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A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

et al. 2016

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BackgroundWith over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).ResultsIncreased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades.ConclusionOur analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

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Section: Resultssupporting

confidence: 73%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

et al. 2016

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“…The entire system was plumbed with minimally hygroscopic tubing (Bev-A-Line IV, Cole-Parmer, Vernon Hills, IL, USA). Air flow was adjusted for each metabolic chamber to replace 99 % of its Reynolds et al 2014) showing the presence (T) or absence (NT) of facultative thermogenesis in pythons. The results from previous studies are shown in gray (see text for references), while results from the present study are shown in black.…”

Section: Measurementsmentioning

confidence: 99%

“…The Pythonidae is divided between two primary phylogenetic clades, an Afro-Asian clade with two major lineages and an Indo-Australian clade with eight major lineages (Reynolds et al 2014; for recent review, see Barker et al 2015). The two species with confirmed facultative thermogenesis are in the different clades-P. molurus within the Afro-Asian group and M. spilota within the Indo-Australian group.…”

Section: Introductionmentioning

confidence: 99%

Facultative thermogenesis during brooding is not the norm among pythons

Brashears

DeNardo

2015

J Comp Physiol A

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Facultative thermogenesis is often attributed to pythons in general despite limited comparative data available for the family. While all species within Pythonidae brood their eggs, only two species are known to produce heat to enhance embryonic thermal regulation. By contrast, a few python species have been reported to have insignificant thermogenic capabilities. To provide insight into potential phylogenetic, morphological, and ecological factors influencing thermogenic capability among pythons, we measured metabolic rates and clutch-environment temperature differentials at two environmental temperatures-python preferred brooding temperature (31.5 °C) and a sub-optimal temperature (25.5 °C)-in six species of pythons, including members of two major phylogenetic branches currently devoid of data on the subject. We found no evidence of facultative thermogenesis in five species: Aspidites melanocephalus, A. ramsayi, Morelia viridis, M. spilota cheynei, and Python regius. However, we found that Bothrochilus boa had a thermal metabolic sensitivity indicative of facultative thermogenesis (i.e., a higher metabolic rate at the lower temperature). However, its metabolic rate was quite low and technical challenges prevented us from measuring temperature differential to make conclusions about facultative endothermy in this species. Regardless, our data combined with existing literature demonstrate that facultative thermogenesis is not as widespread among pythons as previously thought.

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Phylogenomics of Snakes

Streicher

Ruane

2018

Encyclopedia of Life Sciences

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Reduced representation genome sequencing has ushered in new methods for understanding how life evolved on earth. These methods utilise genetic data in the form of dozens, hundreds or even thousands of loci to estimate phylogenetic relationships. This approach, often termed phylogenomic analysis, has the potential to resolve controversial evolutionary relationships, particularly among ancient, rapid radiations. Among vertebrates, phylogenomic analyses are increasingly applied to an iconic group of reptiles, snakes. Phylogenomic analyses of snakes have begun to shed light on long‐standing questions including relationships among snake families, their origin among squamate reptiles and putative causes of speciation within recent radiations. In addition, these methods may even be used to obtain genetic data from archival museum specimens. This emerging approach for understanding snake evolution will be improved by whole genome sequencing initiatives that include a diverse group of snake species. Key Concepts Snakes are important study systems for human physiology and medicine. Snakes are important predators in ecosystems/important to maintaining ecosystem health. Robust phylogenetic hypotheses are necessary to understand snake evolution. Genome‐wide data offer unprecedented opportunities to resolve snake phylogeny and the tree of life. Phylogenomic analyses of snakes will aid biologists and medical researchers worldwide.

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Toward a Tree-of-Life for the boas and pythons: Multilocus species-level phylogeny with unprecedented taxon sampling

Cited by 109 publications

References 88 publications

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

Facultative thermogenesis during brooding is not the norm among pythons

Phylogenomics of Snakes

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