John J Wiens

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• Anderson, S. R., & Wiens, J. J. (2017). Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates. Evolution, 71, 1944-1959.
• Bars-Closel, M., Kohlsdorf, T., Moen, D. S., & Wiens, J. J. (2017). Diversification rates are more strongly related to microhabitat than climate in squamate reptiles (lizards and snakes).. Evolution, 71, 2243–2261.
• Hutter, C. R., Lambert, S. M., & Wiens, J. J. (2017). Rapid diversification and time explain amphibian species richness at different scales in the Tropical Andes, Earth's most biodiverse hotspot. American Naturalist, 190, 828–843.
• Jezkova, T., & Wiens, J. J. (2017). What explains patterns of diversification and richness among animal phyla?. American Naturalist, 189, 201-212.
• Larsen, B. B., Miller, E. C., Rhodes, M. K., & Wiens, J. J. (2017). Inordinate fondness multiplied and redistributed: the number of species on Earth and the new Pie of Life. Quarterly Review of Biology, 92, 229–265.
• Lin, L., & Wiens, J. J. (2017). Comparing macroecological patterns across continents: evolution of climatic niche breadth in varanid lizards. Ecography, 40, 960–970.
• Miller, E. C., & Wiens, J. J. (2017). Extinction and time help drive the marine-terrestrial biodiversity gradient: is the ocean a deathtrap?. Ecology Letters, 20, 911-921.
• Moen, D. S., & Wiens, J. J. (2017). Microhabitat and climatic-niche change explain patterns of diversification among frog families. American Naturalist, 190, 29–44.
• Pontarp, M., & Wiens, J. J. (2017). The origin of species richness patterns along environmental gradients: uniting explanations based on time, diversification rate, and carrying capacity. Journal of Biogeography, 44, 722-735.
• Streicher, J. W., & Wiens, J. J. (2017). Phylogenomic analyses of more than 4,000 nuclear loci resolve the origin of snakes among lizard families. Biology Letters, 13, 20170393.
• Wiens, J. J. (2017). What explains patterns of biodiversity across the Tree of Life?. BioEssays, 39, 160012.
• Moen, D. S., Morlon, H., & Wiens, J. J. (2016). Testing Convergence Versus History: Convergence Dominates Phenotypic Evolution for over 150 Million Years in Frogs. SYSTEMATIC BIOLOGY, 65(1), 146-160.
• Streicher, J. W., Schulte, J. A., & Wiens, J. J. (2016). How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards. SYSTEMATIC BIOLOGY, 65(1), 128-145.
• Zheng, Y., & Wiens, J. J. (2016). Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. MOLECULAR PHYLOGENETICS AND EVOLUTION, 94, 537-547.
• Fisher-Reid, M. C., & Wiens, J. J. (2015). Is geographic variation within species related to macroevolutionary patterns between species?. JOURNAL OF EVOLUTIONARY BIOLOGY, 28(8), 1502-1515.
• Gomez-Rodriguez, C., Baselga, A., & Wiens, J. J. (2015). Is diversification rate related to climatic niche width?. GLOBAL ECOLOGY AND BIOGEOGRAPHY, 24(4), 383-395.
• Lambert, S. M., Reeder, T. W., & Wiens, J. J. (2015). When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny. MOLECULAR PHYLOGENETICS AND EVOLUTION, 82, 146-155.
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  Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates will differ. We predict such differences for branches in concatenated trees that are short, weakly supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard family, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial predictions, and suggest that simply considering uncertainty in concatenated trees may sometimes encompass the differences between these methods. We also found that relaxed-clock concatenated trees can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree estimates had slightly lower support values when based on many more genes (44 vs. 10) and a small (similar to 30%) reduction in taxon sampling. Thus, taxon sampling may be more important than gene sampling when applying species-tree methods to deep phylogenetic questions. Finally, our coalescent species-tree estimates tentatively support division of Scincidae into three monophyletic subfamilies, a result otherwise found only in concatenated analyses with extensive species sampling. (C) 2014 Elsevier Inc. All rights reserved.
• Qian, H., Wiens, J. J., Zhang, J., & Zhang, Y. (2015). Evolutionary and ecological causes of species richness patterns in North American angiosperm trees. ECOGRAPHY, 38(3), 241-250.
• Reeder, T. W., Townsend, T. M., Mulcahy, D. G., Noonan, B. P., Wood, P. L., Sites, J. W., & Wiens, J. J. (2015). Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa. PLOS ONE, 10(3).
• Wiens, J. J. (2015). Explaining large-scale patterns of vertebrate diversity. BIOLOGY LETTERS, 11(7).
• Wiens, J. J. (2015). Faster diversification on land than sea helps explain global biodiversity patterns among habitats and animal phyla. ECOLOGY LETTERS, 18(11), 1234-1241.
• Wiens, J. J., Lapoint, R. T., & Whiteman, N. K. (2015). Herbivory increases diversification across insect clades. NATURE COMMUNICATIONS, 6.
• Zheng, Y., & Wiens, J. J. (2015). Do missing data influence the accuracy of divergence-time estimation with BEAST?. MOLECULAR PHYLOGENETICS AND EVOLUTION, 85, 41-49.
• Bonett, R. M., Steffen, M. A., Lambert, S. M., Wiens, J. J., & Chippindale, P. T. (2014). EVOLUTION OF PAEDOMORPHOSIS IN PLETHODONTID SALAMANDERS: ECOLOGICAL CORRELATES AND RE-EVOLUTION OF METAMORPHOSIS. EVOLUTION, 68(2), 466-482.
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  Life-history modes can profoundly impact the biology of a species, and a classic example is the dichotomy between metamorphic (biphasic) and paedomorphic (permanently aquatic) life-history strategies in salamanders. However, despite centuries of research on this system, several basic questions about the evolution of paedomorphosis in salamanders have not been addressed. Here, we use a nearly comprehensive, time-calibrated phylogeny of spelerpine plethodontids to reconstruct the evolution of paedomorphosis and to test if paedomorphosis is (1) reversible; (2) associated with living in caves; (3) associated with relatively dry climatic conditions on the surface; and (4) correlated with limited range size and geographic dispersal. We find that paedomorphosis arose multiple times in spelerpines. We also find evidence for re-evolution of metamorphosis after several million years of paedomorphosis in a lineage of Eurycea from the Edwards Plateau region of Texas. We also show for the first time using phylogenetic comparative methods that paedomorphosis is highly correlated with cave-dwelling, arid surface environments, and small geographic range sizes, providing insights into both the causes and consequences of this major life history transition.
• Bonetti, M. F., & Wiens, J. J. (2014). Evolution of climatic niche specialization: a phylogenetic analysis in amphibians. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 281(1795).
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  The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e. g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.
• Cahill, A. E., Aiello-Lammens, M. E., Fisher-Reid, M. C., Hua, X., Karanewsky, C. J., Ryu, H. Y., Sbeglia, G. C., Spagnolo, F., Waldron, J. B., & Wiens, J. J. (2014). Causes of warm-edge range limits: Systematic review, proximate factors and implications for climate change. Journal of Biogeography, 41(3), 429-442.
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  Abstract: Aim: The factors that set species range limits underlie many patterns in ecology, evolution, biogeography and conservation. These factors have been the subject of several reviews, but there has been no systematic review of the causes of warm-edge limits (low elevations and latitudes). Understanding these causes is urgent, given that the factors that set these limits might also drive extinction at warm edges as global climate changes. Many authors have suggested that warm-edge limits are set by biotic factors (particularly competition) whereas others have stressed abiotic factors (particularly temperature). We synthesize the known causes of species' warm-edge range limits, with emphasis on the underlying mechanisms (proximate causes). Location: Global. Methods: We systematically searched the literature for studies testing the causes of warm-edge range limits. Results: We found 125 studies that address the causes of warm-edge limits, from a search including > 4000 studies. Among the species in these studies, abiotic factors are supported more often than biotic factors in setting species range limits at warm edges, in contrast to the widely held view that biotic factors are more important. Studies that test both types of factors support abiotic factors significantly more frequently. In addition, only 23 studies (61 species) identified proximate causes of these limits, and these overwhelmingly support physiological tolerances to abiotic factors (primarily temperature). Only eight species with identified proximate causes were tested for both biotic and abiotic factors, but the majority support abiotic factors. Main conclusions: Although it is often assumed that warm-edge limits are set by biotic factors, our review shows that abiotic factors are supported more often among the species in these 125 studies. However, few studies both identify proximate causes and test alternative mechanisms, or examine the interaction between biotic and abiotic factors. Filling these gaps should be a high priority as warm-edge populations are increasingly driven to extinction by climate change. © 2013 John Wiley & Sons Ltd.
• Chejanovski, Z. A., & Wiens, J. J. (2014). Climatic niche breadth and species richness in temperate treefrogs. JOURNAL OF BIOGEOGRAPHY, 41(10), 1936-1946.
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  AimPatterns of species richness are often closely linked with climate, but the specific mechanisms by which species' climatic niches underlie large-scale richness patterns remain poorly understood. It has been hypothesized that reduced temperature seasonality in the tropics promotes the evolution of species with narrow temperature niche breadths, and that this hypothesis helps explain high tropical richness. However, the relationship between species' climatic niche breadths and species richness has yet to be tested. We have addressed this issue using treefrogs (Hylidae) in eastern North America.
• Jiang, W., Chen, S., Wang, H., Li, D., & Wiens, J. J. (2014). Should genes with missing data be excluded from phylogenetic analyses?. MOLECULAR PHYLOGENETICS AND EVOLUTION, 80, 308-318.
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  Phylogeneticists often design their studies to maximize the number of genes included but minimize the overall amount of missing data. However, few studies have addressed the costs and benefits of adding characters with missing data, especially for likelihood analyses of multiple loci. In this paper, we address this topic using two empirical data sets (in yeast and plants) with well-resolved phylogenies. We introduce varying amounts of missing data into varying numbers of genes and test whether the benefits of excluding genes with missing data outweigh the costs of excluding the non-missing data that are associated with them. We also test if there is a proportion of missing data in the incomplete genes at which they cease to be beneficial or harmful, and whether missing data consistently bias branch length estimates. Our results indicate that adding incomplete genes generally increases the accuracy of phylogenetic analyses relative to excluding them, especially when there is a high proportion of incomplete genes in the overall dataset (and thus few complete genes). Detailed analyses suggest that adding incomplete genes is especially helpful for resolving poorly supported nodes. Given that we find that excluding genes with missing data often decreases accuracy relative to including these genes (and that decreases are generally of greater magnitude than increases), there is little basis for assuming that excluding these genes is necessarily the safer or more conservative approach. We also find no evidence that missing data consistently bias branch length estimates. (C) 2014 Elsevier Inc. All rights reserved.
• Rocio Pinto-Sanchez, N., Crawford, A. J., & Wiens, J. J. (2014). Using historical biogeography to test for community saturation. ECOLOGY LETTERS, 17(9), 1077-1085.
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  Saturation is the idea that a community is effectively filled with species, such that no more can be added without extinctions. This concept has important implications for many areas of ecology, such as species richness, community assembly, invasive species and climate change. Here, we illustrate how biogeography can be used to test for community saturation, when combined with data on local species richness, phylogeny and climate. We focus on a clade of frogs (Terrarana) and the impact of the Great American Biotic Interchange on patterns of local richness in Lower Middle America and adjacent regions. We analyse data on species richness at 83 sites and a time-calibrated phylogeny for 363 species. We find no evidence for saturation, and show instead that biotic interchange dramatically increased local richness in the region. We suggest that historical biogeography offers thousands of similar long-term natural experiments that can be used to test for saturation.
• Zeng, C., Gomez-Mestre, I., & Wiens, J. J. (2014). Evolution of Rapid Development in Spadefoot Toads Is Unrelated to Arid Environments. PLOS ONE, 9(5).
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  The extent to which species' life histories evolve to match climatic conditions is a critical question in evolutionary biology and ecology and as human activities rapidly modify global climate. GIS-based climatic data offer new opportunities to rigorously test this question. Superficially, the spadefoot toads of North America (Scaphiopodidae) seem to offer a classic example of adaptive life-history evolution: some species occur in extremely dry deserts and have evolved the shortest aquatic larval periods known among anurans. However, the relationships between the climatic conditions where spadefoots occur and the relevant life-history traits have not been explicitly tested. Here, we analyzed these relationships using GISbased climatic data, published life-history data, and a time-calibrated phylogeny for pelobatoid frogs. Surprisingly, we find no significant relationships between life-history variables and precipitation or aridity levels where these species occur. Instead, rapid development in pelobatoids is strongly related to their small genome sizes and to phylogeny.
• Blankers, T., Townsend, T. M., Pepe, K., Reeder, T. W., & Wiens, J. J. (2013). Contrasting global-scale evolutionary radiations: Phylogeny, diversification, and morphological evolution in the major clades of iguanian lizards. Biological Journal of the Linnean Society, 108(1), 127-143.
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  Abstract: Parallel evolutionary radiations in adjacent locations have been documented in many systems, but typically at limited geographical scales. Here, we compare patterns of evolutionary radiation at the global scale in iguanian lizards, the dominant clade of lizards. We generated a new time-calibrated phylogeny including 153 iguanian species (based on mitochondrial and nuclear data) and obtained data on morphology and microhabitats. We then compared patterns of species diversification, morphological disparity, and ecomorphological relationships in the predominantly Old World and New World clades (Acrodonta and Pleurodonta, respectively), focusing on the early portions of these radiations. Acrodonts show relatively constant rates of species diversification and disparity over time. In contrast, pleurodonts show an early burst of species diversification and less-than-expected morphological disparity early in their history, and slowing diversification and increasing disparity more recently. Analyses including all species (with MEDUSA) suggest accelerated diversification rates in certain clades within both Acrodonta and Pleurodonta, which strongly influences present-day diversity patterns. We also find substantial differences in ecomorphological relationships between these clades. Our results demonstrate that sister clades in different global regions can undergo very different patterns of evolutionary radiation over similar time frames.© 2012 The Linnean Society of London.
• Cahill, A. E., Aiello-Lammens, M. E., Fisher-Reid, M. C., Hua, X., Karanewsky, C. J., Ryu, H. Y., Sbeglia, G. C., Spagnolo, F., Waldron, J. B., Warsi, O., & Wiens, J. J. (2013). How does climate change cause extinction?. Proceedings. Biological sciences / The Royal Society, 280(1750), 20121890-.
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  PMID: 23075836;PMCID: PMC3574421;Abstract: Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies.
• Fisher-Reid, M. C., Engstrom, T. N., Kuczynski, C. A., Stephens, P. R., & Wiens, J. J. (2013). Parapatric divergence of sympatric morphs in a salamander: Incipient speciation on Long Island?. Molecular Ecology, 22(18), 4681-4694.
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  PMID: 23909857;Abstract: Speciation is often categorized based on geographic modes (allopatric, parapatric or sympatric). Although it is widely accepted that species can arise in allopatry and then later become sympatrically or parapatrically distributed, patterns in the opposite direction are also theoretically possible (e.g. sympatric lineages or ecotypes becoming parapatric), but such patterns have not been shown at a macrogeographic scale. Here, we analyse genetic, climatic, ecological and morphological data and show that two typically sympatric colour morphs of the salamander Plethodon cinereus (redback and leadback) appear to have become parapatrically distributed on Long Island, New York, with pure-redback populations in the west and pure-leadback populations in the east (and polymorphic populations in between and on the mainland). In addition, the pure-leadback populations in eastern Long Island are genetically, ecologically and morphologically divergent from both mainland and other Long Island populations, suggesting the possibility of incipient speciation. This parapatric separation seems to be related to the different ecological preferences of the two morphs, preferences which are present on the mainland and across Long Island. These results potentially support the idea that spatial segregation of sympatric ecotypes may sometimes play an important part in parapatric speciation. © 2013 John Wiley & Sons Ltd.
• Guerrero, P. C., Rosas, M., T., M., & Wiens, J. J. (2013). Evolutionary lag times and recent origin of the biota of an ancient desert (Atacama-Sechura). Proceedings of the National Academy of Sciences of the United States of America, 110(28), 11469-11474.
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  PMID: 23798420;PMCID: PMC3710863;Abstract: The assembly of regional biotas and organismal responses to anthropogenic climate change both depend on the capacity of organisms to adapt to novel ecological conditions. Here we demonstrate the concept of evolutionary lag time, the time between when a climatic regime or habitat develops in a region and when it is colonized by a given clade. We analyzed the time of colonization of four clades (three plant genera and one lizard genus) into the Atacama-Sechura Desert of South America, one of Earth's driest and oldest deserts. We reconstructed time-calibrated phylogenies for each clade and analyzed the timing of shifts in climatic distributions and biogeography and compared these estimates to independent geological estimates of the time of origin of these deserts. Chaetanthera and Malesherbia (plants) and Liolaemus (animal) invaded arid regions of the Atacama - Sechura Desert in the last 10 million years, some 20 million years after the initial onset of aridity in the region. There are also major lag times between when these clades colonized the region and when they invaded arid habitats within the region (typically 4-14 million years). Similarly, hyperarid climates developed ∼8 million years ago, but the most diverse plant clade in these habitats (Nolana) only colonized them ∼2 million years ago. Similar evolutionary lag timesmay occur in other organisms and habitats, but these results are important in suggesting that many lineages may require very long time scales to adapt to modern desertification and climatic change.
• Hua, X., & Wiens, J. J. (2013). How does climate influence speciation?. American Naturalist, 182(1), 1-12.
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  PMID: 23778222;Abstract: Variation in climatic conditions over space and time is thought to be an important driver of speciation. However, the role of climate has not been explored in the theoretical literature on speciation, and the theory underlying empirical studies of climate and speciation has come largely from informal, verbal models. In this study, we develop a quantitative model to test a relatively new but theoretically untested model of speciation (speciation via niche conservatism) and to examine the climatic conditions under which speciation via niche conservatism and speciation via niche divergence are most plausible. Our results have three broad implications for the study of speciation: (1) ecological similarity over time (niche conservatism) can be an important part of speciation, despite the traditional emphasis on ecological divergence, (2) long-term directional climate change promotes speciation via niche conservatism for species with low climatic-niche lability, whereas climatic oscillations promote speciation via niche divergence for species with high climatic- niche lability, and (3) population extinction can be a key component of speciation. © 2013 by The University of Chicago.
• Machac, A., Storch, D., & Wiens, J. J. (2013). Ecological causes of decelerating diversification in carnivoran mammals. Evolution, 67(8), 2423-2433.
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  PMID: 23888862;Abstract: Clade diversification is a central topic in macroevolutionary studies. Recently, it has been shown that diversification rates appear to decelerate over time in many clades. What causes this deceleration remains unclear, but it has been proposed that competition for limited resources between sympatric, ecologically similar species slows diversification. Employing carnivoran mammals as a model system, we test this hypothesis using a comprehensive time-calibrated phylogeny. We also explore several conceptually related explanations including limited geographic area and limited rates of niche evolution. We find that diversification slowdowns are strong in carnivorans. Surprisingly, these slowdowns are independent of geographic range overlap between related species and are also decoupled from rates of niche evolution, suggesting that slowdowns are unrelated to competition and niche filling. When controlling for the effects of clade diversity, diversification slowdowns appear independent of geographic area. There is a significant effect of clade diversity on diversification slowdowns, but simulations show that this relationship may arise as a statistical artifact (i.e., greater clade diversity increases the ability of the gamma statistic to refute constant diversification). Overall, our results emphasize the need to test hypotheses about the causes of diversification slowdowns with ecological data, rather than assuming ecological processes from phylogenies alone. © 2013 The Society for the Study of Evolution.
• Moen, D. S., Irschick, D. J., & Wiens, J. J. (2013). Evolutionary conservatism and convergence both lead to striking similarity in ecology, morphology and performance across continents in Frogs. Proceedings of the Royal Society B: Biological Sciences, 280(1773).
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  PMID: 24174109;PMCID: PMC3826223;Abstract: Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and South America), assessing the importance of dispersal and convergent evolution in explaining similarity across regions. We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems. © 2013 The Author(s) Published by the Royal Society. All rights reserved.
• Pyron, R. A., & Wiens, J. J. (2013). Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity. Proceedings of the Royal Society B: Biological Sciences, 280(1770).
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  PMID: 24026818;PMCID: PMC3779328;Abstract: Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates.We investigate the origins of high tropical diversity in amphibians, applying newphylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently. © 2013 The Author(s) Published by the Royal Society. All rights reserved.
• Pyron, R. A., Burbrink, F. T., & Wiens, J. J. (2013). A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evolutionary Biology, 13(1).
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  PMID: 23627680;PMCID: PMC3682911;Abstract: Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes. © 2013 Pyron et al.; licensee BioMed Central Ltd.
• Quintero, I., & Wiens, J. J. (2013). Corrigendum to Quintero & Wiens (2013). Ecology Letters, 16(12), 1516-1516.
• Quintero, I., & Wiens, J. J. (2013). Rates of projected climate change dramatically exceed past rates of climatic niche evolution among vertebrate species. Ecology Letters, 16(8), 1095-1103.
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  PMID: 23800223;Abstract: A key question in predicting responses to anthropogenic climate change is: how quickly can species adapt to different climatic conditions? Here, we take a phylogenetic approach to this question. We use 17 time-calibrated phylogenies representing the major tetrapod clades (amphibians, birds, crocodilians, mammals, squamates, turtles) and climatic data from distributions of > 500 extant species. We estimate rates of change based on differences in climatic variables between sister species and estimated times of their splitting. We compare these rates to predicted rates of climate change from 2000 to 2100. Our results are striking: matching projected changes for 2100 would require rates of niche evolution that are > 10 000 times faster than rates typically observed among species, for most variables and clades. Despite many caveats, our results suggest that adaptation to projected changes in the next 100 years would require rates that are largely unprecedented based on observed rates among vertebrate species. © 2013 John Wiley & Sons Ltd/CNRS.
• Quintero, I., & Wiens, J. J. (2013). What determines the climatic niche width of species? The role of spatial and temporal climatic variation in three vertebrate clades. Global Ecology and Biogeography, 22(4), 422-432.
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  Abstract: Aim: Climatic niche breadth (the range of climatic conditions that a species experiences over space and time) is a fundamental topic in ecology, biogeography and evolution. But what determines the climatic niche width of species? In 1967, Janzen suggested that climatic niche widths for temperature were determined by levels of seasonal fluctuation in temperature at each locality, such that niche breadths are narrow in tropical species and broad in temperate species. However, it is unclear whether climatic niche breadths of species are determined more by seasonal variability within sites as opposed to climatic variation between sites across the species' range. We address this question here. Location: Global. Methods: We analysed three vertebrate clades (plethodontid salamanders, hylid frogs and phrynosomatid lizards) for which we had phylogenetic information and climatic data from localities throughout each species' geographic range, collectively including 409 species. We tested how climatic niche breadths of localities (i.e. temporal variation) are related to overall species climatic niche breadths (i.e. temporal and spatial variation) using phylogenetic comparative methods, focusing both on temperature extremes and precipitation. Results: Across the three clades, we find that niche breadths for single localities generally span most of the species' climatic niche breadth, and are strongly correlated with overall species niche breadths. However, species with wider climatic niches also tend to show greater climatic divergence between localities. Main conclusions: The extent to which the climatic niche breadths of species are determined by variation within localities versus spatial variation between localities has been largely unexplored. Our results suggest that within-locality seasonal variation explains most variation in climatic niche breadths among species. However, between-locality variation and local adaptation may also play some role. These results require more general testing, but have several important implications. © 2012 Blackwell Publishing.
• Wiens, J. J., Kozak, K. H., & Silva, N. (2013). Diversity and niche evolution along aridity gradients in north american lizards (phrynosomatidae). Evolution, 67(6), 1715-1728.
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  PMID: 23730764;Abstract: Deserts occupy approximately 12% of the Earth's land surface, and are thought to have species poor but highly specialized biotas. However, few studies have examined the evolutionary origins of desert biotas and of diversity patterns along aridity gradients. Further, it is unclear if species occurring in more extreme conditions on a given niche axis (i.e., precipitation) are more specialized for those conditions (i.e., have narrower niche breadths). We address these questions here using a time-calibrated phylogeny and climatic data for 117 species of phrynosomatid lizards. Phrynosomatids are the most species-rich family of lizards in North America, and are found from deserts to rainforests. Surprisingly, we find that phrynosomatids have higher richness in more arid environments. This pattern occurs seemingly because they have been present in more arid habitats longer (~55 million years), and lineages in mesic environments are recently derived from more arid-dwelling ancestors. We find little support for the hypothesis that species in more extreme environments are more specialized. Instead, many desert-dwelling species are broadly distributed, and species in the most mesic environments have the broadest niche breadths. In summary, phrynosomatids offer a counterexample to the idea that arid regions are inhabited by a small number of recent and highly specialized lineages. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.
• Wiens, J., Hutter, C. R., Guayasamin, J. M., & Wiens, J. J. (2013). Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns. Ecology letters, 16(9).
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  The Tropical Andes are an important global biodiversity hotspot, harbouring extraordinarily high richness and endemism. Although elevational richness and speciation have been studied independently in some Andean groups, the evolutionary and ecological processes that explain elevational richness patterns in the Andes have not been analysed together. Herein, we elucidate the processes underlying Andean richness patterns using glassfrogs (Centrolenidae) as a model system. Glassfrogs show the widespread mid-elevation diversity peak for both local and regional richness. Remarkably, these patterns are explained by greater time (montane museum) rather than faster speciation at mid-elevations (montane species pump), despite the recency of the major Andean uplift. We also show for the first time that rates of climatic-niche evolution and elevational change are related, supporting the hypothesis that climatic-niche conservatism decelerates species' shifts in elevational distributions and underlies the mid-elevation richness peak. These results may be relevant to other Andean clades and montane systems globally.
• Wiens, J., Lambert, S. M., & Wiens, J. J. (2013). Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in phrynosomatid lizards. Evolution; international journal of organic evolution, 67(9).
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  The evolution of viviparity is a key life-history transition in vertebrates, but the selective forces favoring its evolution are not fully understood. With >100 origins of viviparity, squamate reptiles (lizards and snakes) are ideal for addressing this issue. Some evidence from field and laboratory studies supports the "cold-climate" hypothesis, wherein viviparity provides an advantage in cold environments by allowing mothers to maintain higher temperatures for developing embryos. Surprisingly, the cold-climate hypothesis has not been tested using both climatic data and phylogenetic comparative methods. Here, we investigate the evolution of viviparity in the lizard family Phrynosomatidae using GIS-based environmental data, an extensive phylogeny (117 species), and recently developed comparative methods. We find significant relationships between viviparity and lower temperatures during the warmest (egg-laying) season, strongly supporting the cold-climate hypothesis. Remarkably, we also find that viviparity tends to evolve more frequently at tropical latitudes, despite its association with cooler climates. Our results help explain this and two related patterns that seemingly contradict the cold-climate hypothesis: the presence of viviparous species restricted to low-elevation tropical regions and the paucity of viviparous species at high latitudes. Finally, we examine whether viviparous taxa may be at higher risk of extinction from anthropogenic climate change.
• Wiens, J., Pyron, R. A., & Wiens, J. J. (2013). Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity. Proceedings. Biological sciences / The Royal Society, 280(1770).
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  Many groups show higher species richness in tropical regions but the underlying causes remain unclear. Despite many competing hypotheses to explain latitudinal diversity gradients, only three processes can directly change species richness across regions: speciation, extinction and dispersal. These processes can be addressed most powerfully using large-scale phylogenetic approaches, but most previous studies have focused on small groups and recent time scales, or did not separate speciation and extinction rates. We investigate the origins of high tropical diversity in amphibians, applying new phylogenetic comparative methods to a tree of 2871 species. Our results show that high tropical diversity is explained by higher speciation in the tropics, higher extinction in temperate regions and limited dispersal out of the tropics compared with colonization of the tropics from temperate regions. These patterns are strongly associated with climate-related variables such as temperature, precipitation and ecosystem energy. Results from models of diversity dependence in speciation rate suggest that temperate clades may have lower carrying capacities and may be more saturated (closer to carrying capacity) than tropical clades. Furthermore, we estimate strikingly low tropical extinction rates over geological time scales, in stark contrast to the dramatic losses of diversity occurring in tropical regions presently.
• Blankers, T., Adams, D. C., & Wiens, J. J. (2012). Ecological radiation with limited morphological diversification in salamanders. Journal of Evolutionary Biology, 25(4), 634-646.
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  PMID: 22268991;Abstract: A major goal of evolutionary biology is to explain morphological diversity among species. Many studies suggest that much morphological variation is explained by adaptation to different microhabitats. Here, we test whether morphology and microhabitat use are related in plethodontid salamanders, which contain the majority of salamander species, and have radiated into a striking diversity of microhabitats. We obtained microhabitat data for 189 species that also had both morphometric and phylogenetic data. We then tested for associations between morphology and microhabitat categories using phylogenetic comparative methods. Associations between morphology and ecology in plethodontids are largely confined to a single clade within one subfamily (Bolitoglossinae), whereas variation in morphology across other plethodontids is unrelated to microhabitat categories. These results demonstrate that ecological radiation and morphological evolution can be largely decoupled in a major clade. The results also offer a striking contrast to lizards, which typically show close relationships between morphology and microhabitat. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.
• Fisher-Reid, M. C., Kozak, K. H., & Wiens, J. J. (2012). How is the rate of climatic-niche evolution related to climatic-niche breadth?. Evolution, 66(12), 3836-3851.
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  PMID: 23206141;Abstract: The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution. © 2012 The Society for the Study of Evolution.
• Gomez-Mestre, I., Pyron, R. A., & Wiens, J. J. (2012). Phylogenetic analyses reveal unexpected patterns in the evolution of reproductive modes in frogs. Evolution, 66(12), 3687-3700.
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  PMID: 23206128;Abstract: Understanding phenotypic diversity requires not only identification of selective factors that favor origins of derived states, but also factors that favor retention of primitive states. Anurans (frogs and toads) exhibit a remarkable diversity of reproductive modes that is unique among terrestrial vertebrates. Here, we analyze the evolution of these modes, using comparative methods on a phylogeny and matched life-history database of 720 species, including most families and modes. As expected, modes with terrestrial eggs and aquatic larvae often precede direct development (terrestrial egg, no tadpole stage), but surprisingly, direct development evolves directly from aquatic breeding nearly as often. Modes with primitive exotrophic larvae (feeding outside the egg) frequently give rise to direct developers, whereas those with nonfeeding larvae (endotrophic) do not. Similarly, modes with eggs and larvae placed in locations protected from aquatic predators evolve frequently but rarely give rise to direct developers. Thus, frogs frequently bypass many seemingly intermediate stages in the evolution of direct development. We also find significant associations between terrestrial reproduction and reduced clutch size, larger egg size, reduced adult size, parental care, and occurrence in wetter and warmer regions. These associations may help explain the widespread retention of aquatic eggs and larvae, and the overall diversity of anuran reproductive modes. © 2012 The Society for the Study of Evolution.
• Kozak, K. H., & Wiens, J. J. (2012). Phylogeny, ecology, and the origins of climate-richness relationships. Ecology, 93(8 SPEC. ISSUE), S167-S181.
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  Abstract: Many studies show that species richness is correlated with climate, especially among local sites within a region. However, few studies have addressed how these climate-diversity relationships actually arise. Only a few processes can directly change species richness (i.e., speciation, extinction, dispersal), and these processes may be best studied by incorporating a phylogenetic perspective. Here, we used a phylogenetic approach to address the causes of climate-diversity relationships in plethodontid salamanders by combining data on richness, climate, and phylogeny for 250 species. Our results suggest that species richness patterns in plethodontids are explained primarily by how long each region and climatic zone has been occupied, rather than by the effects of either area, species density (i.e., ecological limits), or climate on the rates of speciation or extinction. Across regions, diversity is related to time rather than climate. Within regions, significant climate-diversity relationships are also related to time, with higher richness in climatic regimes that have been occupied longer. Although some might think that phylogeny is unimportant at local scales and when climate and diversity are strongly correlated, we show that niche conservatism and phylogenetic history (time) combine to create species pools of different sizes in different habitats (climatic regimes), leading to variation in local species richness across these habitats within a region. © 2012 by the Ecological Society of America.
• Mulcahy, D. G., Noonan, B. P., Moss, T., Townsend, T. M., Reeder, T. W., Sites, J. W., & Wiens, J. J. (2012). Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles. Molecular Phylogenetics and Evolution, 65(3), 974-991.
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  PMID: 22982760;Abstract: Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to their relationships. Various dating methods have been used, but their relative performance remains understudied. Here, we generate and assemble an extensive phylogenomic data set for squamate reptiles (lizards and snakes) and evaluate two widely used dating methods, penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates among lineages (BEAST). We obtained sequence data from 25 nuclear loci (∼500-1000. bp per gene; 19,020. bp total) for 64 squamate species and nine outgroup taxa, estimated the phylogeny, and estimated divergence dates using 14 fossil calibrations. We then evaluated how well each method approximated these dates using random subsets of the nuclear loci (2, 5, 10, 15, and 20; replicated 10 times each), and using ∼1. kb of the mitochondrial ND2 gene. We find that estimates from r8s-PL based on 2, 5, or 10 loci can differ considerably from those based on 25 loci (mean absolute value of differences between 2-locus and 25-locus estimates were 9.0. Myr). Estimates from BEAST are somewhat more consistent given limited sampling of loci (mean absolute value of differences between 2 and 25-locus estimates were 5.0. Myr). Most strikingly, age estimates using r8s-PL for ND2 were ∼68-82. Myr older (mean = 73.1) than those using 25 nuclear loci with r8s-PL. These results show that dates from r8s-PL with a limited number of loci (and especially mitochondrial data) can differ considerably from estimates derived from a large number of nuclear loci, whereas estimates from BEAST derived from fewer nuclear loci or mitochondrial data alone can be surprisingly similar to those from many nuclear loci. However, estimates from BEAST using relatively few loci and mitochondrial data could still show substantial deviations from the full data set (>50. Myr), suggesting the benefits of sampling many nuclear loci. Finally, we found that confidence intervals on ages from BEAST were not significantly different when sampling 2 vs. 25 loci, suggesting that adding loci decreased errors but did not increase confidence in those estimates. © 2012 Elsevier Inc.
• Vega, G. C., & Wiens, J. J. (2012). Why are there so few fish in the sea?. Proceedings. Biological sciences / The Royal Society, 279(1737), 2323-2329.
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  PMID: 22319126;PMCID: PMC3350687;Abstract: The most dramatic gradient in global biodiversity is between marine and terrestrial environments. Terrestrial environments contain approximately 75-85% of all estimated species, but occupy only 30 per cent of the Earth's surface (and only approx. 1-10% by volume), whereas marine environments occupy a larger area and volume, but have a smaller fraction of Earth's estimated diversity. Many hypotheses have been proposed to explain this disparity, but there have been few large-scale quantitative tests. Here, we analyse patterns of diversity in actinopterygian (ray-finned) fishes, the most species-rich clade of marine vertebrates, containing 96 per cent of fish species. Despite the much greater area and productivity of marine environments, actinopterygian richness is similar in freshwater and marine habitats (15 150 versus 14 740 species). Net diversification rates (speciation-extinction) are similar in predominantly freshwater and saltwater clades. Both habitats are dominated by two hyperdiverse but relatively recent clades (Ostariophysi and Percomorpha). Remarkably, trait reconstructions (for both living and fossil taxa) suggest that all extant marine actinopterygians were derived from a freshwater ancestor, indicating a role for ancient extinction in explaining low marine richness. Finally, by analysing an entirely aquatic group, we are able to better sort among potential hypotheses for explaining the paradoxically low diversity of marine environments.
• Wiens, J. J., & Tiu, J. (2012). Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS ONE, 7(8).
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  PMID: 22900065;PMCID: PMC3416753;Abstract: Background: Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study). Methodology/Principal Findings: We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial. Conclusions: We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems. © 2012 Wiens, Tiu.
• Wiens, J. J., Hutter, C. R., Mulcahy, D. G., Noonan, B. P., Townsend, T. M., Sites Jr., J. W., & Reeder, T. W. (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species. Biology Letters, 8(6), 1043-1046.
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  PMID: 22993238;PMCID: PMC3497141;Abstract: Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets. © 2012 The Royal Society.
• Fisher-Reid, M. C., & Wiens, J. J. (2011). What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodon salamanders and 13 other vertebrate clades. BMC Evolutionary Biology, 11(1).
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  PMID: 21995558;PMCID: PMC3203092;Abstract: Background: The use of mitochondrial DNA data in phylogenetics is controversial, yet studies that combine mitochondrial and nuclear DNA data (mtDNA and nucDNA) to estimate phylogeny are common, especially in vertebrates. Surprisingly, the consequences of combining these data types are largely unexplored, and many fundamental questions remain unaddressed in the literature. For example, how much do trees from mtDNA and nucDNA differ? How are topological conflicts between these data types typically resolved in the combined-data tree? What determines whether a node will be resolved in favor of mtDNA or nucDNA, and are there any generalities that can be made regarding resolution of mtDNA-nucDNA conflicts in combined-data trees? Here, we address these and related questions using new and published nucDNA and mtDNA data for Plethodon salamanders and published data from 13 other vertebrate clades (including fish, frogs, lizards, birds, turtles, and mammals). Results: We find widespread discordance between trees from mtDNA and nucDNA (30-70% of nodes disagree per clade), but this discordance is typically not strongly supported. Despite often having larger numbers of variable characters, mtDNA data do not typically dominate combined-data analyses, and combined-data trees often share more nodes with trees from nucDNA alone. There is no relationship between the proportion of nodes shared between combined-data and mtDNA trees and relative numbers of variable characters or levels of homoplasy in the mtDNA and nucDNA data sets. Congruence between trees from mtDNA and nucDNA is higher on branches that are longer and deeper in the combined-data tree, but whether a conflicting node will be resolved in favor mtDNA or nucDNA is unrelated to branch length. Conflicts that are resolved in favor of nucDNA tend to occur at deeper nodes in the combined-data tree. In contrast to these overall trends, we find that Plethodon have an unusually large number of strongly supported conflicts between data types, which are generally resolved in favor of mtDNA in the combined-data tree (despite the large number of nuclear loci sampled). Conclusions: Overall, our results from 14 vertebrate clades show that combined-data analyses are not necessarily dominated by the more variable mtDNA data sets. However, given cases like Plethodon, there is also the need for routine checking of incongruence between mtDNA and nucDNA data and its impacts on combined-data analyses. © 2011 Fisher-Reid and Wiens; licensee BioMed Central Ltd.
• Pyron, R. A., & Wiens, J. J. (2011). A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution, 61(2), 543-583.
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  PMID: 21723399;Abstract: The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (~40% of the known extant species) from 432 genera (~85% of the ~500 currently recognized extant genera). Each sampled species contains up to 12,712. bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563. bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data. © 2011 Elsevier Inc.
• Pyron, R. A., Burbrink, F. T., Colli, G. R., Nieto, A., Vitt, L. J., Kuczynski, C. A., & Wiens, J. J. (2011). The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Molecular Phylogenetics and Evolution, 58(2), 329-342.
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  PMID: 21074626;Abstract: The superfamily Colubroidea (>2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5814. bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean = 67% per species), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees. © 2010 Elsevier Inc.
• Townsend, T. M., Mulcahy, D. G., Noonan, B. P., Sites, J. W., Kuczynski, C. A., Wiens, J. J., & Reeder, T. W. (2011). Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation. Molecular Phylogenetics and Evolution, 61(2), 363-380.
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  PMID: 21787873;Abstract: Iguanian lizards form a diverse clade whose members have been the focus of many comparative studies of ecology, behavior, and evolution. Despite the importance of phylogeny to such studies, interrelationships among many iguanian clades remain uncertain. Within the Old World clade Acrodonta, Agamidae is sometimes found to be paraphyletic with respect to Chamaeleonidae, and recent molecular studies have produced conflicting results for many major clades. Within the largely New World clade Pleurodonta, relationships among the 12 currently recognized major subclades (mostly ranked as families) have been largely unresolved or poorly supported in previous studies. To clarify iguanian evolutionary history, we first infer phylogenies using concatenated maximum-likelihood (ML) and Bayesian analyses of DNA sequence data from 29 nuclear protein-coding genes for 47 iguanian and 29 outgroup taxa. We then estimate a relaxed-clock Bayesian chronogram for iguanians using BEAST. All three methods produce identical topologies. Within Acrodonta, we find strong support for monophyly of Agamidae with respect to Chamaeleonidae, and for almost all relationships within agamids. Within Pleurodonta, we find strong Bayesian support for almost all relationships, and strong ML support for some interfamilial relationships and for monophyly of almost all families (excepting Polychrotidae). Our phylogenetic results suggest a non-traditional biogeographic scenario in which pleurodonts originated in the Northern Hemisphere and subsequently spread southward into South America. The pleurodont portion of the tree is characterized by several very short, deep branches, raising the possibility of deep coalescences that may confound concatenated analyses. We therefore also use 27 of these genes to implement a coalescent-based species-tree approach for pleurodonts. Although this analysis strongly supports monophyly of the pleurodont families, interfamilial relationships are generally different from those in the concatenated tree, and support is uniformly poor. However, a species-tree analysis using only the seven most variable loci yields higher support and more congruence with the concatenated tree. This suggests that low support in the 27-gene species-tree analysis may be an artifact of the many loci that are uninformative for very short branches. This may be a general problem for the application of species-tree methods to rapid radiations, even with phylogenomic data sets. Finally, we correct the non-monophyly of Polychrotidae by recognizing the pleurodont genus Anolis (sensu lato) as a separate family (Dactyloidae), and we correct the non-monophyly of the agamid genus Physignathus by resurrection of the genus Istiurus for the former Physignathus lesueurii. © 2011 Elsevier Inc.
• Wiens, J. J. (2011). Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluating dollo's law. Evolution, 65(5), 1283-1296.
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  PMID: 21521189;Abstract: Dollo's law states that structures that are evolutionarily lost will not be regained. Recent phylogenetic studies have revealed several potential examples in which Dollo's law seems to be violated, where lost structures appear to have been regained over evolutionary time. However, these examples have recently been questioned and suggested to be methodological artifacts. In this article, I document a striking and incontrovertible phylogenetic example of the re-evolution of a lost, complex structure: mandibular teeth in the frog genus Gastrotheca. I use a time-calibrated phylogeny for 170 amphibian species to show that mandibular teeth were lost in the ancestor of modern frogs at least 230 million years ago (Mya) and have been regained in the last ~5-17 My. I review recent studies on trait re-evolution and show that this long period of trait absence prior to re-acquisition is largely unprecedented. I also argue that there are several methodological issues that may cause trait re-evolution to be hardest to detect under those conditions when it is most likely to occur, leading to erroneous failures to reject Dollo's law. Finally, I discuss a mechanism that may facilitate trait re-evolution, and the evolution of mandibular teeth in frogs as an example of developmental constraint. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.
• Wiens, J. J. (2011). The causes of species richness patterns across space, time, and clades and the role of"ecological limits". Quarterly Review of Biology, 86(2), 75-96.
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  PMID: 21800635;Abstract: A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by"ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new"alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.© 2011 by The University of Chicago Press. All rights reserved.
• Wiens, J. J. (2011). The niche, biogeography and species interactions. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1576), 2336-2350.
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  PMID: 21768150;PMCID: PMC3130432;Abstract: In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even 'geographic barriers' must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally 'saturated' with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the 'competition-divergence-co-occurrence conundrum'). In general, the interface of biogeography and ecology could be a major area for research in both fields. © 2011 The Royal Society.
• Wiens, J. J., & Morrill, M. C. (2011). Missing data in phylogenetic analysis: Reconciling results from simulations and empirical data. Systematic Biology, 60(5), 719-731.
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  PMID: 21447483;
• Wiens, J. J., Pyron, R. A., & Moen, D. S. (2011). Phylogenetic origins of local-scale diversity patterns and the causes of Amazonian megadiversity. Ecology Letters, 14(7), 643-652.
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  PMID: 21535341;Abstract: What explains the striking variation in local species richness across the globe and the remarkable diversity of rainforest sites in Amazonia? Here, we apply a novel phylogenetic approach to these questions, using treefrogs (Hylidae) as a model system. Hylids show dramatic variation in local richness globally and incredible local diversity in Amazonia. We find that variation in local richness is not explained primarily by climatic factors, rates of diversification (speciation and extinction) nor morphological variation. Instead, local richness patterns are explained predominantly by the timing of colonization of each region, and Amazonian megadiversity is linked to the long-term sympatry of multiple clades in that region. Our results also suggest intriguing interactions between clade diversification, trait evolution and the accumulation of local richness. Specifically, sympatry between clades seems to slow diversification and trait evolution, but prevents neither the accumulation of local richness over time nor the co-occurrence of similar species. © 2011 Blackwell Publishing Ltd/CNRS.
• Wiens, J. J., Sparreboom, M., & Arntzen, J. W. (2011). Crest evolution in newts: Implications for reconstruction methods, sexual selection, phenotypic plasticity and the origin of novelties. Journal of Evolutionary Biology, 24(10), 2073-2086.
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  PMID: 21707814;Abstract: The dorsal crest of newts (Salamandridae) is a novel, phenotypically plastic, sexually selected trait that may evolve in association with complex courtship behaviours. We estimated a near-comprehensive, time-calibrated phylogeny for salamandrids and analysed the evolution of their crests and display behaviour. Different models give conflicting reconstructions for crest evolution, showing that likelihood can estimate incorrect ancestral states with strong statistical support. The best-fitting model suggests that crests evolved once and were lost repeatedly, supporting the hypothesis that sexually selected traits may be frequently lost. We demonstrate the correlated evolution of crests and courtship behaviour and show that species with larger numbers of crest-related traits have larger repertoires of behaviours. We also show that phenotypically plastic morphological traits can be maintained over long macroevolutionary timescales (~25-48Myr). Finally, we use salamandrids to address how novel structures may arise, and support a model involving the expansion and subdivision of pre-existing structures. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.