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Abstract Theory predicts that thermal developmental plasticity evolves in response to thermal heterogeneity, suggesting that plasticity may be an important trait for establishment in novel climates. However, few studies use multispecies comparisons to examine how plasticity evolves, meaning that there is little empirical basis with which to examine key theoretical predictions. We estimate patterns of thermal developmental plasticity in morphological and performance traits for 7 Anolis lizard species inhabiting South Florida, USA. We found interspecific differences as well as intraspecific variation in reaction norms across species. Neither temperature heterogeneity in present-day invasive ranges in Florida nor historical temperature heterogeneity from the contemporary native ranges predicted reaction norm variation. Phylogeny and species identity typically predicted around 90%–95% of reaction norm variation. Overall, these results suggest that thermal developmental plasticity in these traits exhibits variation that could be inconsistent with patterns expected under adaptive evolution to macroclimate. Examining the role of maternal nesting behavior and sampling of additional species can help to distinguish between neutral variation and selection toward multiple adaptive peaks. Our comparative study of thermal developmental plasticity in lizards provides new insights about macroevolutionary dynamics behind the evolution of developmental plasticity and the conditions under which adaptive plasticity is expected to evolve. 

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences. 

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences. 

A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions. 

An integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene ND2 recovered four new species of Hemiphyllodactylus Bleeker that are endemic to the Shan Plateau or Salween Basin in eastern Myanmar. Hemiphyllodactylus ngwelwini sp. nov. from the Shan Plateau is part of the earlier described “eastern Myanmar clade” renamed herein as the north lineage and H. kyaiktiyoensis sp. nov. and H. pinlaungensis sp. nov. of the Shan Plateau and H. zwegabinensis sp. nov. of the Salween Basin compose an entirely new Burmese clade herein referred to as the south lineage. Although the north and south lineages come within 46 km of one another on the Shan Plateau, they are not sister lineages but sequentially separated by two lineages from Yunnan, China and another from northwestern Thailand. Hemiphyllodactylus zwegabinensis sp. nov. is the first species of this genus to be recorded from the Salween Basin and is known only from a wind-blown cloud forest on the top of the insular, karstic mountain Zwegabin in Kayin State. All other Burmese species except for H. typus, are endemic to the various localities throughout the Shan Plateau. These four new species bring the total number of Hemiphyllodactylus in Myanmar to at least 10 which is certainly an extreme underestimate of the diversity of this genus given that we discover new species at every upland locality we survey.