Phylogeny, evolutionary history, and biogeography of Oriental–Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences

Alfaro, Michael E.; Karns, Daryl R.; Voris, Harold K.; Brock, Chad D.; Stuart, Bryan L.

doi:10.1016/j.ympev.2007.10.024

Cited by 63 publications

(62 citation statements)

References 53 publications

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“…The phylogenies of Malhotra and Thorpe (2004) and Castoe and Parkinson (2006) were used for Asian pitviper relationships, whereas the phylogeny of Castoe and Parkinson (2006) was used for New World pitviper relationships, and the phylogeny of Fenwick et al (2009) was used to place Bothrops and related taxa. The phylogeny of Alfaro et al (2008) was used for homalopsid relationships. Within the Elapidae, the phylogeny of Castoe et al (2007) was used for placement of the Elapinae, phylogenies of Lukoschek and Keogh (2006) and Metzger et al (2010) were used for relationships within the Hydrophiinae, and the morphological study by Kharin and Czeblukov (2006) was used for relationships within the genus Laticauda .…”

Section: Methodsmentioning

confidence: 99%

Gravity and the evolution of cardiopulmonary morphology in snakes

Lillywhite

Albert

Sheehy

et al. 2012

Comparative Biochemistry and Physiology Part A: Molecular &

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Physiological investigations of snakes have established the importance of heart position and pulmonary structure in contexts of gravity effects on blood circulation. Here we investigate morphological correlates of cardiopulmonary physiology in contexts related to ecology, behavior and evolution. We analyze data for heart position and length of vascular lung in 154 species of snakes that exhibit a broad range of characteristic behaviors and habitat associations. We construct a composite phylogeny for these species, and we codify gravitational stress according to species habitat and behavior. We use conventional regression and phylogenetically independent contrasts to evaluate whether trait diversity is correlated with gravitational habitat related to evolutionary transitions within the composite tree topology. We demonstrate that snake species living in arboreal habitats, or which express strongly climbing behaviors, possess relatively short blood columns between the heart and the head, as well as relatively short vascular lungs, compared to terrestrial species. Aquatic species, which experience little or no gravity stress in water, show the reverse – significantly longer heart–head distance and longer vascular lungs. These phylogenetic differences complement the results of physiological studies and are reflected in multiple habitat transitions during the evolutionary histories of these snake lineages, providing strong evidence that heart–to–head distance and length of vascular lung are co–adaptive cardiopulmonary features of snakes.

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Section: Methodsmentioning

confidence: 99%

Gravity and the evolution of cardiopulmonary morphology in snakes

Lillywhite

Albert

Sheehy

et al. 2012

Comparative Biochemistry and Physiology Part A: Molecular &

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“…The target group for the Florida grasshopper sparrow (Ammodramus savannarum floridanus) was defined as the range of full species Ammodramus savannarum (which ranges from Canada through Central America to northern South America), for the Florida scrub jay (Aphelocoma coerulescens) as the composite range of all Aphelocoma spp., for the piping plover (Charadrius melodus) as the composite range of all New World species of the genus Charadrius, for the wood stork (Mycteria americana) as the composite range of New World storks (family Ciconiidae), for the Audubon crested caracara (Caracara plancus audubonii) as the combined range of the northern and southern caracara (Caracara cheriway and Caracara plancus), for the Everglades snail kite (Rostrhamus sociabilis plumbeus) as all New World species of the subfamily Milvinae, for the whooping crane (Grus americana) as the composite range on New World species of the suborder Grui (e.g., the New World cranes, limpkins and trumpeters), and the red-cockaded woodpecker (Picoides borealis) as the composite range of closely related Picoides villosus and P. albolarvatus based on a recent Picoides phylogeny (Weibel and Moore, 2002). The target group range for the American crocodile (Crocodylus acutus) was defined as the composite range of all New World crocodilians, for the Florida sand skink (Neoseps reynoldsi) as North American species of the Eumeces + Neoseps clade from a recent skink phylogeny (Brandley et al, 2005), and for the eastern indigo snake (Drymarchon corais couperi) as the composite range of closely related species (Coluber constrictor, Spilotes pullatus, Phyllorynchus decurtatus, Masticophis flagellum and Drymarchon corais) as determined from two recent phylogenies (Lawson et al, 2005;Alfaro et al, 2008). We chose more exclusive taxonomic groupings for the definition for some species because the family level range would result in a domain covering most of the Western Hemisphere, an area much larger than the observed range of the species.…”

Section: Speciesmentioning

confidence: 99%

Do bioclimate variables improve performance of climate envelope models?

Watling

Romañach

Bucklin

et al. 2012

Ecological Modelling

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a b s t r a c tClimate envelope models are widely used to forecast potential effects of climate change on species distributions. A key issue in climate envelope modeling is the selection of predictor variables that most directly influence species. To determine whether model performance and spatial predictions were related to the selection of predictor variables, we compared models using bioclimate variables with models constructed from monthly climate data for twelve terrestrial vertebrate species in the southeastern USA using two different algorithms (random forests or generalized linear models), and two model selection techniques (using uncorrelated predictors or a subset of user-defined biologically relevant predictor variables). There were no differences in performance between models created with bioclimate or monthly variables, but one metric of model performance was significantly greater using the random forest algorithm compared with generalized linear models. Spatial predictions between maps using bioclimate and monthly variables were very consistent using the random forest algorithm with uncorrelated predictors, whereas we observed greater variability in predictions using generalized linear models.

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“…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%

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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Phylogeny, evolutionary history, and biogeography of Oriental–Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences

Cited by 63 publications

References 53 publications

Gravity and the evolution of cardiopulmonary morphology in snakes

Gravity and the evolution of cardiopulmonary morphology in snakes

Do bioclimate variables improve performance of climate envelope models?

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

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