Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data

Life Stages and Phylogenetic Position of the New Scale-Mite of the Genus Neopterygosoma (Acariformes: Pterygosomatidae) from Robert's Tree Iguana

A new pterygosomatid mite species, Neopterygosoma robertmertensi sp. n. (Acariformes: Pterygosomatidae) was collected from two specimens of Liolaemus robertmertensi (Liolaemidae) from Argentina. This new species is described based on active stages: adults (female and male) and juveniles (deutonymphs, protonymphs, and larvae) and quiescent stages (nymphchrysalis, deutochrysalis and imagochrysalis). The changes in morphological characters that occur during the ontogeny of N. robertmertensi have been analyzed in detail. A difference in larval sex morphology was observed for the first time in the family Pterygosomatidae (female larvae differ from male larvae in terms of the shape and size of the idiosoma and the position of the genital area). This new mite species is most similar to N. cyanogasteri but can be distinguished by the presence of different leg chaetotaxy patterns of genua IV and femora IV, four to six genital setae, three to five dorsomedial setae, and two to three ventromedial setae. Phylogenetic analysis was conducted based on 120 morphological characters of all Neopterygosoma spp. and four outgroup species using the maximum parsimony approach. The results indicated that this species is nested within mites of the chilensis group of Neopterygosoma associated with host species of the section chiliensis of Liolaemus s. str. An updated diagnosis of the chilensis group of Neopterygosoma and an identification key for all species of this genus has been provided.

Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles-lizards and snakes-recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards

Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.

Phylogenomic data resolve higher-level relationships within South American Liolaemus lizards

Phylogenomic approaches now generate hundreds of loci representative of the whole genome that can be used for phylogenetic analyses. The South American lizard genus Liolaemus is the most species-rich vertebrate radiation from temperate zones (more than 265 described species), yet most higher-level phylogenetic relationships within Liolaemus remain poorly resolved. In this study, we used 584 nuclear loci collected using targeted sequenced capture to estimate the phylogenetic relationships among 26 species representing the two subgenera within Liolaemus (Eulaemus + Liolaemus), and all major groups within Eulaemus. Previous molecular and morphological-based phylogenetic analyses of Eulaemus based on a limited number of characters resolved few higher-level relationships, although one point of agreement is that the early divergence within Eulaemus corresponds to the lineomaculatus section, followed by the diversification of eight main clades that are strongly supported and recognized. Liolaemus probably experienced relatively rapid divergences during parts of its evolutionary history, and a phylogenomic approach was used to resolve the relationships among the major groups. The new analyses presented here support the division of Liolaemus into two subgenera, and resolve relationships among many of the major clades of Eulaemus with strong support. A Bayesian divergence dating analysis using 44 protein-coding genes provides an estimation of the split of the two Liolaemus subgenera of approximately 19,7 ma (95% HPD = 16,94-23,04), while diversification within Eulaemus started at 15,05 ma (95% HPD = 12,94 - 17,59) among the L. lineomaculatus and the L. montanus series by Mid Miocene. A novel phylogenetic network analyses for SNP data identified two hybridizing edges among different groups of Eulaemus at different points in time. Having a solid phylogenetic hypothesis of the main Eulaemus clades opens new opportunities to test a variety of macroevolutionary questions for this unique radiation.

Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered

Johann Ludwig Christian Gravenhorst's herpetological collection at the Museum of Natural History, University of Wrocław included numerous important specimens of amphibians and reptiles. The majority, if not the entirety, of this collection has long been thought to be lost. However, we were able to rediscover some type specimens of lizards. The rediscovered specimens include the holotypes of Liolaemus conspersus and L. hieroglyphicus, one syntype of Callopistes maculatus (here designated as the lectotype) and two syntypes of L. lineatus (one of which is herein designated as the lectotype). Reexamination of these specimens indicates that previous synonymies proposed for L. conspersus and two syntypes of L. hieroglyphicus are problematic; furthermore, more complex taxonomic work is needed to resolve this issue. Two rediscovered syntypes of L. lineatus differ in several scalation traits and are possibly not conspecific. The type specimens of several other species of lizards from Gravenhorst's collection (Liolaemus marmoratus, L. unicolor and two other syntypes of L. lineatus, Leiocephalus schreibersii and Chalcides viridanus) were not found and are probably lost.

Phylogeny, time divergence, and historical biogeography of the South American Liolaemus alticolor-bibronii group (Iguania: Liolaemidae)

The genus Liolaemus comprises more than 260 species and can be divided in two subgenera: Eulaemus and Liolaemus sensu stricto. In this paper, we present a phylogenetic analysis, divergence times, and ancestral distribution ranges of the Liolaemus alticolor-bibronii group (Liolaemus sensu stricto subgenus). We inferred a total evidence phylogeny combining molecular (Cytb and 12S genes) and morphological characters using Maximum Parsimony and Bayesian Inference. Divergence times were calculated using Bayesian MCMC with an uncorrelated lognormal distributed relaxed clock, calibrated with a fossil record. Ancestral ranges were estimated using the Dispersal-Extinction-Cladogenesis (DEC-Lagrange). Effects of some a priori parameters of DEC were also tested. Distribution ranged from central Perú to southern Argentina, including areas at sea level up to the high Andes. The L. alticolor-bibronii group was recovered as monophyletic, formed by two clades: L. walkeri and L. gracilis, the latter can be split in two groups. Additionally, many species candidates were recognized. We estimate that the L. alticolor-bibronii group diversified 14.5 Myr ago, during the Middle Miocene. Our results suggest that the ancestor of the Liolaemus alticolor-bibronii group was distributed in a wide area including Patagonia and Puna highlands. The speciation pattern follows the South-North Diversification Hypothesis, following the Andean uplift.