Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements.

The Amazonian poison frog genus Ameerega is one of the largest yet most understudied of the brightly colored genera in the anuran family Dendrobatidae, with 30 described species ranging throughout tropical South America. Phylogenetic analyses of Ameerega are highly discordant, lacking consistency due to variation in data types and methods, and often with limited coverage of species diversity in the genus. Here, we present a comprehensive phylogenomic reconstruction of Ameerega, utilizing state-of-the-art sequence capture techniques and phylogenetic methods. We sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. We generated topologies using maximum likelihood and coalescent methods and compared the use of maximum likelihood and Bayesian methods for estimating divergence times. Our phylogenetic inference diverged strongly from those of previous studies, and we recommend steps to bring Ameerega taxonomy in line with the new phylogeny. We place several species in a phylogeny for the first time, as well as provide evidence for six potential candidate species. We estimate that Ameerega experienced a rapid radiation approximately 7-11 million years ago and that the ancestor of all Ameerega was likely an aposematic, montane species. This study underscores the utility of phylogenomic data in improving our understanding of the phylogeny of understudied clades and making novel inferences about their evolution.

Speciation with introgression: Phylogeography and systematics of the Ameerega petersi group (Dendrobatidae).

The Tropical Andes contains exceptionally high diversity, much of it arising within the Quaternary period. The complex geology of the Andes and paleoclimate fluctuations within the Quaternary suggest complex speciation scenarios. This, in turn, has contributed to idiosyncratic speciation modes among shallowly diverged Amazonian taxa. Many relationships among these taxa remain poorly resolved. Here we use a sequence capture approach, ultraconserved elements (UCEs), to address the phylogenetic relationships among three recently diverged Peruvian Ameerega poison frog species (A. cainarachi, A. petersi, and A. smaragdina; family Dendrobatidae) and explore a possible mode of speciation in this group. We assess concordance among concatenated phylogenetic tree inference, gene-tree based species tree inference, SNP-based species tree inference, and Bayes factor lineage delimitation to resolve species boundaries. We complement these analyses with assessments of call divergence to address the presence of a prezygotic reproductive barrier. Additionally, we further explore the phylogeographic history of these species of Ameerega with demographic inference, considering evidence for admixture and population expansions. Our results support the synonymy of A. smaragdina as a junior synonym of A. petersi and we find that speciation in this group is characterized by admixture and signatures of a population bottleneck followed by expansion. We invoke the disturbance-vicariance hypothesis to explain the observed patterns and call for more, detailed investigations of in-situ speciation in the Tropical Andes.

Global determinants of insect mitochondrial genetic diversity.

Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.

The tadpole of Ameerega boehmei in southeastern Bolivia.

To date, half (16 of 32) of the species of Ameerega have had their tadpoles described: A. altamazonica, A. bassleri, A. bilinguis, A. braccata, A. cainarachi, A. flavopicta, A. hahneli, A. macero, A. parvula, A. petersi, A. picta, A. rubriventris, A shihuemoy. A. silverstonei, A. smaragdina, and A. trivittata (Lescure, 1976; Silverstone, 1976; Duellman, 1978; Myers Daly, 1979; Rodriguez Myers, 1993; Haddad Martins, 1994; Lötters et al., 1997; Duellman, 2005; Costa et al., 2006; Twomey Brown, 2008; Brown Twomey, 2009; Poelman et al., 2010; Schulze et al., 2015). Ameerega boehmei is a putative member of a clade containing Ameerega braccata, A. flavopicta, A. berohoka, A. munduruku, all of which inhabit various parts of the 'dry diagonal' between the Amazon and Atlantic rainforests (Prado Gibbs, 1993). Adult frogs in this group are morphologically similar, generally dark-bodied with yellow dorsolateral stripes, orange flash marks and some also possessing bright-yellow dorsal spots. Despite considerable research on their breeding behavior, acoustics and systematics (Lötters et al., 2009; Forti et al., 2013), the tadpole of Ameerega boehmei, the southern-most and western-most distributed species in this tentative group, has not been described.

Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus).

The ecological multifunctionality of colour often results in multiple selective pressures operating on a single trait. Most research on colour evolution focuses on males because they are the most conspicuous sex in most species. This bias can limit inferences about the ecological drivers of colour evolution. For example, little is known about population divergence in colour of female threespine stickleback (Gasterosteus aculeatus), which is among the most intensively-studied model vertebrates in evolution, ecology, and behaviour. In contrast, the evolution and ecology of colour in male stickleback has received considerable attention. One aspect of female colouration that is lacking previous research is non-ornamental body colour. Non-ornamental colour can play defensive and social roles, and indicate other aspects of female stickleback ecology. To remedy this knowledge gap, we measured the colour and brightness of one dorsal and one ventral lateral area on female stickleback from nine lake populations on Vancouver Island. We found that lake populations varied in overall colour brightness and dorso-ventral contrast. In addition, we found that female brightness increased with lake size, indicating potential ecological drivers of these colour differences. Our results demonstrate that there is substantial scope for future research on female colour diversification, which has been overlooked because past researchers focused on dramatic male nuptial colours.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses.

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model's discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have 'universal' analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates-to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.