D. Luke Mahler | University of California, Davis (original) (raw)
Papers by D. Luke Mahler
Whether the structure of ecological communities can exhibit stability over macroevolutionary time... more Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils—only three have been described to date— has precluded direct investigation of the stability of anole communitiesthrough time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.
Methods in Ecology and Evolution, 2013
1. We present a method, 'SURFACE', that uses the Ornstein-Uhlenbeck stabilizing selection model t... more 1. We present a method, 'SURFACE', that uses the Ornstein-Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. 2. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. 3. We demonstrate the method with an application to Hawaiian Tetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. 4. The R package surface is available as open source software from the Comprehensive R Archive Network.
Molecular Ecology, 2013
The pattern of reproductive character displacement (RCD)-in which traits associated with reproduc... more The pattern of reproductive character displacement (RCD)-in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation-is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example, Anolis caudalis appears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNA sequence data, information on dewlap phenotypes and GIS data on environmental variation to test the hypothesis of RCD generated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent with RCD at the southern and northern limits of the range of A. caudalis. We evaluate the evidence for reinforcement as the explanation for RCD in Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation in Haitian trunk anoles.
Biological Conservation, 2013
M. Böhm). 1 Here considered to include the various taxa that belong to the non-avian and nonmamma... more M. Böhm). 1 Here considered to include the various taxa that belong to the non-avian and nonmammalian amniotes: Crocodylia, Testudines and Lepidosauria (snakes, lizards, amphisbaenians, tuataras).
Evolution, 2012
This appendix contains the R source code used for our MCMC method (the function "evol.rate.mcmc()... more This appendix contains the R source code used for our MCMC method (the function "evol.rate.mcmc()" and several additional functions that are used to pre-process the posterior sample) as well as some very basic instructions on loading the source and using the method in R.
Global Ecology and Biogeography, 2012
Evolution, 2012
By limiting or directing covariation among component traits, modules are expected to represent ev... more By limiting or directing covariation among component traits, modules are expected to represent evolutionary building blocks and to play an important role in morphological diversification. But how stable are patterns of modularity over macroevolutionary timescales? Comparative analyses are needed to address the macroevolutionary effect of modularity, but to date few have been conducted. We describe patterns of skull diversity and modularity in Caribbean Anolis lizards. We first diagnose the primary axes of variation in skull shape and then examine whether diversification of skull shape is concentrated to changes within modules or whether changes arose across the structure as a whole. We find no support for the hypothesis that cranial modules are conserved as species diversify in overall skull shape. Instead we find that anole skull shape and modularity patterns independently converge.
Breviora, 2012
Until very recently, the horned anole of Ecuador, Anolis proboscis, was known from only six male ... more Until very recently, the horned anole of Ecuador, Anolis proboscis, was known from only six male specimens, the last collected in 1966. The species was rediscovered in 2005 and in subsequent years additional specimens have been collected in the general vicinity of the type locality. These include several females, which lack the conspicuous rostral appendage seen in males. Despite rediscovery, the natural history of this enigmatic anole remains almost completely unknown. We conducted an ecological and behavioral study of this species near Mindo, Ecuador. Anolis proboscis is an extremely slow-moving and cryptic species that often occurs high in the trees. The rostral horn notwithstanding, A. proboscis is indistinguishable from Greater Antillean anoles of the ''twig'' ecomorph class in morphology, ecology, and behavior. The possession of a horn only by males suggests a role in sexual selection. We found the horn in life to be soft and highly flexible and thus unsuitable for use as a weapon in male-male combat; hence, the horn most likely serves as a signal and may be involved in mate choice or territorial displays. However, we did not observe any social encounters during our observations and are thus unable to test these hypotheses. Given its cryptic morphology and behavior, it is not surprising that A. proboscis is so rarely observed.
IRCF Reptiles & Amphibians, 2012
International Journal for Parasitology, 2011
Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differen... more Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differences in morphology. These single-celled organisms often lack distinguishing morphological features, and this can encumber both species delimitation and identification. Six saurian malaria parasites have been described from the Caribbean island of Hispaniola. All six infect lizards in the genus Anolis, but only two of these parasites can be distinguished using morphology. The remaining four species overlap in morphology and geography, and cannot be consistently identified using traditional methods. We compared a morphological approach with a molecular phylogenetic approach for assessing the taxonomy of these parasites. We surveyed for blood parasites from 677 Anolis lizards, representing 26 Anolis spp. from a total of 52 sites across Hispaniola. Fifty-five of these lizards were infected with Plasmodium spp., representing several new host records, but only 24 of these infections could be matched to previously described species using traditional morphological criteria. We then estimated the phylogeny of these parasites using both mitochondrial (cytb and coxI) and nuclear (EF2) genes, and included carefully selected GenBank sequences to confirm identities for certain species. Our molecular results unambiguously corroborated our morphology-based species identifications for only the two species previously judged to be morphologically distinctive. The remaining infections fell into two well-supported and reciprocally monophyletic clades, which contained the morphological variation previously reported for all four of the morphologically ambiguous species. One of these clades was identified as Plasmodium floridense and the other as Plasmodium fairchildi hispaniolae. We elevate the latter to Plasmodium hispaniolae comb. nov. because it is polyphyletic with the mainland species Plasmodium fairchildi fairchildi and we contribute additional morphological and molecular characters for future species delimitation. Our phylogenetic hypotheses indicate that two currently recognised taxa, Plasmodium minasense anolisi and Plasmodium tropiduri caribbense, are not valid on Hispaniola. These results illustrate that molecular data can improve taxonomic hypotheses in Plasmodium when reliable morphological characters are lacking.
Molecular Ecology, 2011
Antarctic notothenioid fishes provide a fascinating evolutionary laboratory for the study of adap... more Antarctic notothenioid fishes provide a fascinating evolutionary laboratory for the study of adaptive radiation, as their diversification is linked to both isolation in an extreme environment and a key innovation that allows them to exploit it. In this issue of Molecular Ecology, Rutschmann et al. (2011) evaluate how dietary niche differences have evolved in notothenioids: rarely, or repeatedly in multiple lineages. The authors use stable isotopes to measure species' use of benthic vs. pelagic resources and map resource use onto a molecular phylogeny. Their findings indicate that pelagic diets have evolved in multiple lineages in at least two families, indicating that dietary niche diversification has occurred repeatedly and in parallel.
Herpetological Review, 2011
Evolution, 2010
The pace of phenotypic diversification during adaptive radiation should decrease as ecological op... more The pace of phenotypic diversification during adaptive radiation should decrease as ecological opportunity declines. We test this prediction using phylogenetic comparative analyses of a wide range of morphological traits in Greater Antillean Anolis lizards.
Evolution Since Darwin: The First 150 Years, 2010
Journal of Evolutionary Biology, 2010
The pattern of genetic variances and covariances among characters, summarized in the additive gen... more The pattern of genetic variances and covariances among characters, summarized in the additive genetic variance-covariance matrix, G, determines how a population will respond to linear natural selection. However, G itself also evolves in response to selection. In particular, we expect that, over time, G will evolve correspondence with the pattern of multivariate nonlinear natural selection. In this study, we substitute the phenotypic variance-covariance matrix (P) for G to determine if the pattern of multivariate nonlinear selection in a natural population of Anolis cristatellus, an arboreal lizard from Puerto Rico, has influenced the evolution of genetic variances and covariances in this species. Although results varied among our estimates of P and fitness, and among our analytic techniques, we find significant evidence for congruence between nonlinear selection and P, suggesting that natural selection may have influenced the evolution of genetic constraint in this species.
Evolutionary Ecology Research, 2010
In lizards, tail autotomy is used in defence against predators. Question: Can we infer predation ... more In lizards, tail autotomy is used in defence against predators. Question: Can we infer predation regime from the frequency and pattern of tail autotomy in five lizard species?
Proceedings of the Royal Society B, 2008
Phenacosaurus phylogenetically arise within Anolis Nicholson et al. 2005). Asterisks indicate tho... more Phenacosaurus phylogenetically arise within Anolis Nicholson et al. 2005). Asterisks indicate those species in the "randomly chosen" subset of Caribbean species.
Biological Journal of The Linnean Society, 2008
Most ecomorphological studies use a comparative approach to examine adaptation by studying variat... more Most ecomorphological studies use a comparative approach to examine adaptation by studying variation among species. A question of considerable interest is whether ecomorphological patterns observed among species also exist at the population level. We studied variation in morphology, performance, and behaviour in four populations of Leiocephalus personatus and two populations of Leiocephalus barahonensis in the Dominican Republic. We combined these data with measurements of predation intensity and habitat structure to test for convergence at the population level. We predicted that predation intensity would be higher in open habitats and that lizards in these habitats would have traits conferring higher predator evasion capacity (increased wariness, faster sprint speeds, and longer limbs). Principal components analysis suggests that sites tend to differ with respect to the abundance and spacing of low-lying vegetation (i.e. percentage of shrub cover and distance to nearest vegetation), but we did not detect any striking differences among sites in tail-break frequencies or attacks on clay lizard models. Consistent with predictions we find that in open habitats, lizards tend to have longer limbs, faster sprint speeds (relative to body size), and longer approach distances. These patterns corroborate findings in other ground-dwelling lizard species and indicate that they have evolved at least twice among populations of Leiocephalus lizards. The results of this study also suggest that these traits have evolved rapidly despite recent or ongoing gene flow. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 445–456.
Biotropica, 2007
The amount of space used by an organism is energetically determined. We utilized a population of ... more The amount of space used by an organism is energetically determined. We utilized a population of ant lion larvae in Costa Rica to test allometric theories concerning the use of space by organisms and how different densities of individuals affect the use of space. The area of ant lion trapping pits scaled with mass to the three-quarters power, supporting allometric theory for sessile organisms. Our analyses also show that larger ant lion larvae show spatial repulsion and facultative density dependent pit-building strategies.
Whether the structure of ecological communities can exhibit stability over macroevolutionary time... more Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved Anolis lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean Anolis fossils—only three have been described to date— has precluded direct investigation of the stability of anole communitiesthrough time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray microcomputed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.
Methods in Ecology and Evolution, 2013
1. We present a method, 'SURFACE', that uses the Ornstein-Uhlenbeck stabilizing selection model t... more 1. We present a method, 'SURFACE', that uses the Ornstein-Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. 2. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. 3. We demonstrate the method with an application to Hawaiian Tetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. 4. The R package surface is available as open source software from the Comprehensive R Archive Network.
Molecular Ecology, 2013
The pattern of reproductive character displacement (RCD)-in which traits associated with reproduc... more The pattern of reproductive character displacement (RCD)-in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation-is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example, Anolis caudalis appears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNA sequence data, information on dewlap phenotypes and GIS data on environmental variation to test the hypothesis of RCD generated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent with RCD at the southern and northern limits of the range of A. caudalis. We evaluate the evidence for reinforcement as the explanation for RCD in Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation in Haitian trunk anoles.
Biological Conservation, 2013
M. Böhm). 1 Here considered to include the various taxa that belong to the non-avian and nonmamma... more M. Böhm). 1 Here considered to include the various taxa that belong to the non-avian and nonmammalian amniotes: Crocodylia, Testudines and Lepidosauria (snakes, lizards, amphisbaenians, tuataras).
Evolution, 2012
This appendix contains the R source code used for our MCMC method (the function "evol.rate.mcmc()... more This appendix contains the R source code used for our MCMC method (the function "evol.rate.mcmc()" and several additional functions that are used to pre-process the posterior sample) as well as some very basic instructions on loading the source and using the method in R.
Global Ecology and Biogeography, 2012
Evolution, 2012
By limiting or directing covariation among component traits, modules are expected to represent ev... more By limiting or directing covariation among component traits, modules are expected to represent evolutionary building blocks and to play an important role in morphological diversification. But how stable are patterns of modularity over macroevolutionary timescales? Comparative analyses are needed to address the macroevolutionary effect of modularity, but to date few have been conducted. We describe patterns of skull diversity and modularity in Caribbean Anolis lizards. We first diagnose the primary axes of variation in skull shape and then examine whether diversification of skull shape is concentrated to changes within modules or whether changes arose across the structure as a whole. We find no support for the hypothesis that cranial modules are conserved as species diversify in overall skull shape. Instead we find that anole skull shape and modularity patterns independently converge.
Breviora, 2012
Until very recently, the horned anole of Ecuador, Anolis proboscis, was known from only six male ... more Until very recently, the horned anole of Ecuador, Anolis proboscis, was known from only six male specimens, the last collected in 1966. The species was rediscovered in 2005 and in subsequent years additional specimens have been collected in the general vicinity of the type locality. These include several females, which lack the conspicuous rostral appendage seen in males. Despite rediscovery, the natural history of this enigmatic anole remains almost completely unknown. We conducted an ecological and behavioral study of this species near Mindo, Ecuador. Anolis proboscis is an extremely slow-moving and cryptic species that often occurs high in the trees. The rostral horn notwithstanding, A. proboscis is indistinguishable from Greater Antillean anoles of the ''twig'' ecomorph class in morphology, ecology, and behavior. The possession of a horn only by males suggests a role in sexual selection. We found the horn in life to be soft and highly flexible and thus unsuitable for use as a weapon in male-male combat; hence, the horn most likely serves as a signal and may be involved in mate choice or territorial displays. However, we did not observe any social encounters during our observations and are thus unable to test these hypotheses. Given its cryptic morphology and behavior, it is not surprising that A. proboscis is so rarely observed.
IRCF Reptiles & Amphibians, 2012
International Journal for Parasitology, 2011
Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differen... more Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differences in morphology. These single-celled organisms often lack distinguishing morphological features, and this can encumber both species delimitation and identification. Six saurian malaria parasites have been described from the Caribbean island of Hispaniola. All six infect lizards in the genus Anolis, but only two of these parasites can be distinguished using morphology. The remaining four species overlap in morphology and geography, and cannot be consistently identified using traditional methods. We compared a morphological approach with a molecular phylogenetic approach for assessing the taxonomy of these parasites. We surveyed for blood parasites from 677 Anolis lizards, representing 26 Anolis spp. from a total of 52 sites across Hispaniola. Fifty-five of these lizards were infected with Plasmodium spp., representing several new host records, but only 24 of these infections could be matched to previously described species using traditional morphological criteria. We then estimated the phylogeny of these parasites using both mitochondrial (cytb and coxI) and nuclear (EF2) genes, and included carefully selected GenBank sequences to confirm identities for certain species. Our molecular results unambiguously corroborated our morphology-based species identifications for only the two species previously judged to be morphologically distinctive. The remaining infections fell into two well-supported and reciprocally monophyletic clades, which contained the morphological variation previously reported for all four of the morphologically ambiguous species. One of these clades was identified as Plasmodium floridense and the other as Plasmodium fairchildi hispaniolae. We elevate the latter to Plasmodium hispaniolae comb. nov. because it is polyphyletic with the mainland species Plasmodium fairchildi fairchildi and we contribute additional morphological and molecular characters for future species delimitation. Our phylogenetic hypotheses indicate that two currently recognised taxa, Plasmodium minasense anolisi and Plasmodium tropiduri caribbense, are not valid on Hispaniola. These results illustrate that molecular data can improve taxonomic hypotheses in Plasmodium when reliable morphological characters are lacking.
Molecular Ecology, 2011
Antarctic notothenioid fishes provide a fascinating evolutionary laboratory for the study of adap... more Antarctic notothenioid fishes provide a fascinating evolutionary laboratory for the study of adaptive radiation, as their diversification is linked to both isolation in an extreme environment and a key innovation that allows them to exploit it. In this issue of Molecular Ecology, Rutschmann et al. (2011) evaluate how dietary niche differences have evolved in notothenioids: rarely, or repeatedly in multiple lineages. The authors use stable isotopes to measure species' use of benthic vs. pelagic resources and map resource use onto a molecular phylogeny. Their findings indicate that pelagic diets have evolved in multiple lineages in at least two families, indicating that dietary niche diversification has occurred repeatedly and in parallel.
Herpetological Review, 2011
Evolution, 2010
The pace of phenotypic diversification during adaptive radiation should decrease as ecological op... more The pace of phenotypic diversification during adaptive radiation should decrease as ecological opportunity declines. We test this prediction using phylogenetic comparative analyses of a wide range of morphological traits in Greater Antillean Anolis lizards.
Evolution Since Darwin: The First 150 Years, 2010
Journal of Evolutionary Biology, 2010
The pattern of genetic variances and covariances among characters, summarized in the additive gen... more The pattern of genetic variances and covariances among characters, summarized in the additive genetic variance-covariance matrix, G, determines how a population will respond to linear natural selection. However, G itself also evolves in response to selection. In particular, we expect that, over time, G will evolve correspondence with the pattern of multivariate nonlinear natural selection. In this study, we substitute the phenotypic variance-covariance matrix (P) for G to determine if the pattern of multivariate nonlinear selection in a natural population of Anolis cristatellus, an arboreal lizard from Puerto Rico, has influenced the evolution of genetic variances and covariances in this species. Although results varied among our estimates of P and fitness, and among our analytic techniques, we find significant evidence for congruence between nonlinear selection and P, suggesting that natural selection may have influenced the evolution of genetic constraint in this species.
Evolutionary Ecology Research, 2010
In lizards, tail autotomy is used in defence against predators. Question: Can we infer predation ... more In lizards, tail autotomy is used in defence against predators. Question: Can we infer predation regime from the frequency and pattern of tail autotomy in five lizard species?
Proceedings of the Royal Society B, 2008
Phenacosaurus phylogenetically arise within Anolis Nicholson et al. 2005). Asterisks indicate tho... more Phenacosaurus phylogenetically arise within Anolis Nicholson et al. 2005). Asterisks indicate those species in the "randomly chosen" subset of Caribbean species.
Biological Journal of The Linnean Society, 2008
Most ecomorphological studies use a comparative approach to examine adaptation by studying variat... more Most ecomorphological studies use a comparative approach to examine adaptation by studying variation among species. A question of considerable interest is whether ecomorphological patterns observed among species also exist at the population level. We studied variation in morphology, performance, and behaviour in four populations of Leiocephalus personatus and two populations of Leiocephalus barahonensis in the Dominican Republic. We combined these data with measurements of predation intensity and habitat structure to test for convergence at the population level. We predicted that predation intensity would be higher in open habitats and that lizards in these habitats would have traits conferring higher predator evasion capacity (increased wariness, faster sprint speeds, and longer limbs). Principal components analysis suggests that sites tend to differ with respect to the abundance and spacing of low-lying vegetation (i.e. percentage of shrub cover and distance to nearest vegetation), but we did not detect any striking differences among sites in tail-break frequencies or attacks on clay lizard models. Consistent with predictions we find that in open habitats, lizards tend to have longer limbs, faster sprint speeds (relative to body size), and longer approach distances. These patterns corroborate findings in other ground-dwelling lizard species and indicate that they have evolved at least twice among populations of Leiocephalus lizards. The results of this study also suggest that these traits have evolved rapidly despite recent or ongoing gene flow. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 93, 445–456.
Biotropica, 2007
The amount of space used by an organism is energetically determined. We utilized a population of ... more The amount of space used by an organism is energetically determined. We utilized a population of ant lion larvae in Costa Rica to test allometric theories concerning the use of space by organisms and how different densities of individuals affect the use of space. The area of ant lion trapping pits scaled with mass to the three-quarters power, supporting allometric theory for sessile organisms. Our analyses also show that larger ant lion larvae show spatial repulsion and facultative density dependent pit-building strategies.