Multilocus phylogeny of the widely distributed South American lizard cladeEulaemus(Liolaemini,Liolaemus)

Description of the neuroanatomy of the brachial plexus in South American lizards. Phylogenetic implications

Few studies considered the anatomy of the nerve plexuses and musculature associated with them in ectothermic sauropsids. Based on differentiated Sudan Black B staining and conventional dissections, we describe the neuroanatomy of the brachial plexus, its main associated nerves, and muscles. For that, representatives of the genera Diplolaemus, Liolaemus, Phymaturus, and Tropidurus were selected. Based on this, potentially useful characters for phylogenetic analysis were described. Our results show that the brachial plexus can be formed by four, five, or six nerve branches. The brachial flexor trunk, circumflex, interosseous, median, radial, subscapulocoracoid, supracoracoid, and ulnar nerves were identified. Regarding the muscles innervated by the main nerves, the following muscles were identified: biceps brachii, deltoideus scapularis, latissimus dorsi, levator scapulae, pectoralis, serratus thoracis, trapezius, triceps longus caudalis, and triceps longus lateralis. Phylogenetic analyzes revealed 31 potential synapomorphies. There exists evidence that neuroanatomy studies in a phylogenetic context could provide useful information helping to elucidate the relationships between taxonomic groups.

Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade)

In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].

A new lizard species of the Liolaemus kingii group (Squamata: Liolaemidae) from northwestern Chubut province (Argentina)

We describe Liolaemus attenboroughi sp. nov., a lizard distributed in the northwestern Patagonian Steppe of Chubut province (Argentina) previously confused with L. kingii (Bell 1843). Recent studies based on molecular evidence supports its evolutionary independence. Here we provide a morphological diagnosis of this lineage, comparisons between three molecular species delimitation methods, and an updated phylogeny of the L. kingii group. Based on current knowledge of its distribution, this new species is allopatric with geographically close species of the L. kingii group.

Phylogenetic relationships of sleeper gobies (Eleotridae: Gobiiformes: Gobioidei), with comments on the position of the miniature genus Microphilypnus

Microphilypnus and Leptophilypnion are miniaturized genera within the family Eleotridae. The evolutionary relationships among these taxa are still poorly understood, and molecular analyses are restricted to mitochondrial genes, which have not been conclusive. We compiled both mitochondrial and nuclear genes to study the phylogenetic position of Microphilypnus and the evolutionary history and relationships of eleotrids. We propose that Microphilypnus and Leptophilypnus (a non-miniature genus) are not sister groups as suggested by previous studies, but rather separate lineages that arose in the early Eocene, with Leptophilypnus recovered as a sister group to the other analyzed eleotrids. In fact, Microphilypnus is currently associated with the Neotropical clade Guavina/Dormitator/Gobiomorus. We also identified a well-supported clade that indicated Gobiomorus and Hemieleotris as paraphyletic groups, besides a close relationship among Calumia godeffroyi, Bunaka gyrinoides, Eleotris and Erotelis species. This is the first comprehensive report about the evolutionary relationships in members of the family Eleotridae, including multiloci and multispecies approaches. Therefore, we provided new insights about the phylogenetic position of some taxa absent in previous studies, such as the miniature genus Microphilypnus and a recently described species of Eleotris from South America.

Vulnerability to global warming of the critically endangered Añelo Sand Dunes Lizard (Liolaemus cuyumhue) from the Monte Desert, Patagonia Argentina

The body temperature of lizards is strongly influenced by the thermal quality of microhabitats, exploiting the favourable environmental temperatures, and avoiding exposure to extreme thermal conditions. For these reasons, reptile populations are considered to be especially vulnerable to changes in environmental temperatures produced by climate change. Here, we study the thermal physiology of the critically endangered Añelo Sand Dunes Lizard (Liolaemus cuyumhue Avila, Morando, Perez and Sites, 2009). We hypothesise that (i) there is a thermal coadaptation between optimal temperature for locomotor performance of L. cuyumhue and its thermal preference; (ii) L. cuyumhue lives in an environment with low thermal quality; and (iii) a rise in environmental temperatures due to global warming will impose a decrement in locomotor speed represented by lower warming tolerance and narrower thermal safety margins, increasing their already high vulnerability. We recorded field body temperatures (T b), preferred body temperatures (T pref), the operative temperature (T e), and the thermal sensitivity of locomotion at different body temperatures. Our results indicate that this lizard is not currently under environmental stress or exceeding its thermal limits, but that it is thermoregulating below T pref to avoid overheating, and that an increase in environmental temperature higher than 3.5 °C will strongly affect the use of microhabitats with direct sun exposure.

Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels

Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies.

An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini)

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.

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.

Unravelling interspecific relationships among highland lizards: first phylogenetic hypothesis using total evidence of the Liolaemus montanus group (Iguania: Liolaemidae)

The South American lizard genus Liolaemus comprises > 260 species, of which > 60 are recognized as members of the Liolaemus montanus group, distributed throughout the Andes in central Peru, Bolivia, Chile and central Argentina. Despite its great morphological diversity and complex taxonomic history, a robust phylogenetic estimate is still lacking for this group. Here, we study the morphological and molecular diversity of the L. montanus group and present the most complete quantitative phylogenetic hypothesis for the group to date. Our phylogeny includes 103 terminal taxa, of which 91 are members of the L. montanus group (58 are assigned to available species and 33 are of uncertain taxonomic status). Our matrix includes 306 morphological and ecological characters and 3057 molecular characters. Morphological characters include 48 continuous and 258 discrete characters, of which 70% (216) are new to the literature. The molecular characters represent five mitochondrial markers. We performed three analyses: a morphology-only matrix, a molecular-only matrix and a matrix including both morphological and molecular characters (total evidence hypothesis). Our total evidence hypothesis recovered the L. montanus group as monophyletic and included ≥ 12 major clades, revealing an unexpectedly complex phylogeny.

Structure, variation, and systematic implications of the hemipenes of liolaemid lizards (Reptilia: Liolaemidae)

The structure of copulatory organs is widely used in systematics for both differentiating species and for studying phylogenetic relationships. We describe the hemipenes of 42 species belonging to the genus Liolaemus, representing most of their internal groups. We reported 42 characters, the majority not published previously. We constructed a metatree based on previously proposed phylogenetic studies and optimized the hemipenial characters in this topology. Among the most informative characters are presence or absence of flounces or calyces on the sulcate face, ornamentation of the apex, presence or absence of an asulcate face prominence, and presence of a thickening on the proximal region of the asulcate face. Furthermore, we performed a phylogenetic analysis exclusively with the hemipenial characters, not with the intention of making a phylogeny based on this single set of characters, but rather to demonstrate their significance for the reconstruction of relationships in Liolaemus. The obtained results show that the main clades are recovered. We also compared the hemipenial morphology between closely related species to evaluate its taxonomic importance. We conclude that in Liolaemus, the hemipenes can be used both for the differentiation of species and to provide additional evidence for establishing their phylogenetic relationships.

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

The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.