Papers by John G. Phillips
Journal of Molluscan Studies, 2020
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Journal of Heredity, 2020
Newly arrived species on young or remote islands are likely to encounter less predation and compe... more Newly arrived species on young or remote islands are likely to encounter less predation and competition than source populations on continental landmasses. The associated ecological release might facilitate divergence and speciation as colonizing lineages fill previously unoccupied niche space. Characterizing the sequence and timing of colonization on islands represents the first step in determining the relative contributions of geographical isolation and ecological factors in lineage diversification. Herein, we use genome-scale data to estimate timing of colonization in Naesiotus snails to the Galápagos islands from mainland South America. We test inter-island patterns of colonization and within-island radiations to understand their contribution to community assembly. Partly contradicting previously published topologies, phylogenetic reconstructions suggest that most Naesiotus species form island-specific clades, with within-island speciation dominating cladogenesis. Galápagos Naesiotus also adhere to the island progression rule, with colonization proceeding from old to young islands and within-island diversification occurring earlier on older islands. Our work provides a framework for evaluating the contribution of colonization and in situ speciation to the diversity of other Galápagos lineages.
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Journal of Biogeography, 2017
Aim: Habitat specialization can constrain patterns of dispersal and drive allopatric speciation i... more Aim: Habitat specialization can constrain patterns of dispersal and drive allopatric speciation in organisms with limited dispersal ability. Herein, we tested biogeo-graphic patterns and dispersal in a salamander with surface-dwelling larvae and obligate cave-dwelling adults. Location: Ozark Plateau, eastern North America. Methods: A population-level phylogeny of grotto salamanders (Eurycea spelaea complex) was reconstructed using mitochondrial (mtDNA) and multi-locus nuclear DNA (nucDNA), primarily derived from anchored hybrid enrichment (AHE). We tested patterns of molecular variance among populations and associations between genetic distance and geographic features. Results: Divergence time estimates suggest rapid formation of three major lineages in the Middle Miocene. Contemporary gene flow among divergent lineages appears negligible, and mtDNA suggests that most populations are isolated. There is a significant association between phylogenetic distance and palaeodrainages, contemporary drainages and sub-plateaus of the Ozarks, as all features explain a proportion of genetic variation. However, the greatest proportion of genetic variation is explained by the combined effects of palaeodrainages and sub-plateaus. Main conclusions: The geologic and hydrologic history of the Ozark Plateau has influenced lineage diversification in the grotto salamander, leading to genetic isolation among populations. Limited gene flow and strong phylogeographic structure in this complex may result from the restriction of highly specialized adults to caves.
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Proceedings of the Royal Society B, 2018
Life cycle strategies have evolved extensively throughout the history of metazoans. The expressio... more Life cycle strategies have evolved extensively throughout the history of metazoans. The expression of disparate life stages within a single ontogeny can present conflicts to trait evolution, and therefore may have played a major role in shaping metazoan forms. However, few studies have examined the consequences of adding or subtracting life stages on patterns of trait evolution. By analysing trait evolution in a clade of closely related salamander lineages we show that shifts in the number of life cycle stages are associated with rapid phenotypic evolution. Specifically, salamanders with an aquatic-only (paedomorphic) life cycle have frequently added vertebrae to their trunk skeleton compared with closely related lineages with a complex aquatic-to-terrestrial (biphasic) life cycle. The rate of vertebral column evolution is also substantially lower in biphasic lineages, which may reflect the functional compromise of a complex cycle. This study demonstrates that the consequences of life cycle evolution can be detected at very fine scales of divergence. Rapid evolutionary responses can result from shifts in selective regimes following changes in life cycle complexity.
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Nature Ecology & Evolution, 2020
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Diversity, 2019
Anoles are regarded as important models for understanding dynamic processes in ecology and evolut... more Anoles are regarded as important models for understanding dynamic processes in ecology and evolution. Most work on this group has focused on species in the Caribbean Sea, and recently in mainland South and Central America. However, the Eastern Tropical Pacific (ETP) is home to seven species of anoles from three unique islands (Islas Cocos, Gorgona, and Malpelo) that have been largely overlooked. Four of these species are endemic to single islands (Norops townsendi on Isla Cocos, Dactyloa agassizi on Isla Malpelo, D. gorgonae and N. medemi on Isla Gorgona). Herein, we present a phylogenetic analysis of anoles from these islands in light of the greater anole phylogeny to estimate the timing of divergence from mainland lineages for each species. We find that two species of solitary anoles (D. agassizi and N. townsendi) diverged from mainland ancestors prior to the emergence of their respective islands. We also present population-wide morphological data suggesting that both display sexual size dimorphism, similar to single-island endemics in the Caribbean. All lineages on Isla Gorgona likely arose during past connections with South America, and ecologically partition their habitat. Finally, we highlight the importance of conservation of these species and island fauna in general.
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Recently a comprehensive overview of reptiles and amphibians in Michigan was published. Unfortuna... more Recently a comprehensive overview of reptiles and amphibians in Michigan was published. Unfortunately, the distributions of the species represented were compiled before widespread accessibility to technological tools providing greater access to museum and historical records as well as citizen science efforts. To update the known ranges of Michigan herpetofauna, published literature, museum collections, and photographic vouchers submitted to an online database were examined and 339 new county and island records were added, updating the maps for 48 of Michigan’s 55 known species of reptiles and amphibians. I also present the first published list of Michigan amphibians that includes two new plethodontid salamanders, the Northern Dusky Salamander (Desmognathus fuscus) and Southern Two-lined Salamander (Eurycea cirrigera). This paper serves as an example of the wealth of information available to scientists that may have previously been unobtainable, and can be used for the distribution of herpetofauna elsewhere.
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Aim The Interior Highlands (Ouachita Mountains and Ozark Plateau) are major physiographical regio... more Aim The Interior Highlands (Ouachita Mountains and Ozark Plateau) are major physiographical regions of eastern North America and harbour many endemic species. Despite their close proximity, the Ozarks and Ouachitas have different geological histories and relatively distinct species pools. Few studies have tested the biogeographical origins of this region's fauna, and most researchers have treated the Interior Highlands as a single unit. Here, we inferred the sources and timing of colonization of the Ozarks and the Ouachi-tas by analysing the biogeography of three genera of plethodontid salamanders (Eurycea, Plethodon and Desmognathus). Location Eastern North America. Methods We constructed a well-sampled, time-calibrated phylogeny for the family Plethodontidae using three mitochondrial and three nuclear genes in beast. Genetic data were primarily taken from GenBank, although we also produced 76 novel sequences. Using lagrange, we reconstructed ancestral areas for North American plethodontids. We compared the frequency and timing of dispersal events between the Ozarks and Ouachitas to other putative sources such as the Eastern Highlands (Appalachian Mountains and associated limestone plateaus). Results We inferred nine dispersal events from the Eastern Highlands to the Interior Highlands, and just two dispersal events between the geographically proximate Ozarks and Ouachitas. Following one dispersal in the Oligocene, other inter-highland dispersal events occurred in the Miocene and Pliocene, including two periods of near-synchronous movements. Main conclusions Given the relatively limited faunal exchange between the Ozarks and Ouachitas, we conclude that either the river valley separating the Ozarks and Ouachitas is a more formidable barrier to plethodontid salamander dispersal than barriers separating the Interior Highlands from the Eastern Highlands, or ecological/community contingencies have limited dispersal within the Interior Highlands. In our study, geographical proximity of upland islands does not correspond with faunal similarity.
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Background: Caribbean anole lizards (Dactyloidae) have frequently been used as models to study qu... more Background: Caribbean anole lizards (Dactyloidae) have frequently been used as models to study questions regarding biogeography and adaptive radiations, but the evolutionary history of Central American anoles (particularly those of the genus Norops) has not been well studied. Previous work has hypothesized a north-to-south dispersal pattern of Central American Norops, but no studies have examined dispersal within any Norops lineages. Here we test two major hypotheses for the dispersal of the N. humilis/quaggulus complex (defined herein, forming a subset within Savage and Guyer’s N. humilis group).
Results: Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites.
Conclusions: The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within
N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles.
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Herpetological Review
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Herpetological Review, 2011
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Herpetological Review, 2013
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Papers by John G. Phillips
Results: Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites.
Conclusions: The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within
N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles.
Results: Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites.
Conclusions: The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within
N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles.