Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards.

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex).

Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of single nucleotide polymorphisms, mitochondrial sequences, and comprehensive morphological data to characterize the evolutionary history of the ridge-tailed monitors in the Varanus acanthurus complex (V. acanthurus, V. baritji, and V. storri), a group of saxicolous lizards with a wide distribution in Australia, the driest vegetated continent. We found substantial genetic structure in the group and identify nine geographically clustered populations. Based on admixture patterns and species delimitation analyses we propose a taxonomic scheme that differs from current taxonomy. We consider V. acanthurus as monotypic, synonymize V. baritji with V. a. insulanicus (as a redefined V. insulanicus), elevate the subspecies of V. storri to full species (V. storri and V. ocreatus), and describe a new species from a previously identified center of endemism. The relationships among the species remain unresolved, likely as a result of fast speciation. Our study highlights the capability of large datasets to illuminate admixture patterns, biogeographic history, and species limits, even when phylogeny is not completely resolved. Furthermore, our results highlight the impact that the Cenozoic aridification of Australia had on saxicolous taxa and the role of mesic rocky escarpments as refugia. These habitats apparently allowed the persistence of lineages that became sources of colonization for arid environments.

Ontogenetic drivers of morphological evolution in monitor lizards and allies (Squamata: Paleoanguimorpha), a clade with extreme body size disparity.

BACKGROUND: Heterochrony, change in the rate or timing of development, is thought to be one of the main drivers of morphological evolution, and allometry, trait scaling patterns imposed by size, is traditionally thought to represent an evolutionary constraint. However, recent studies suggest that the ontogenetic allometric trajectories describing how organisms change as they grow may be labile and adaptive. Here we investigated the role of postnatal ontogenetic development in the morphological diversification of Paleoanguimorpha, the monitor lizards and allies, a clade with extreme body size disparity. We obtained linear and geometric morphometric data for more than 1,600 specimens belonging to three families and 60 species, representing ~ 72% of extant paleoanguimorph diversity. We used these data to undertake one of the largest comparative studies of ontogenetic allometry to date. RESULTS: Heterochrony is likely dictating morphological divergence at shallow evolutionary scales, while changes in the magnitude and direction of ontogenetic change are found mainly between major clades. Some patterns of ontogenetic variation and morphological disparity appear to reflect ontogenetic transitions in habitat use. Generally, juveniles are more similar to each other than adults, possibly because species that differ in ecology as adults are arboreal as juveniles. The magnitude of ontogenetic change follows evolutionary models where variation is constrained around an optimal value. Conversely, the direction of ontogenetic change may follow models with different adaptive optima per habitat use category or models where interspecific interactions influence its evolution. Finally, we found that the evolutionary rates of the ontogenetic allometric trajectories are phylogenetically variable. CONCLUSIONS: The attributes of ontogenetic allometric trajectories and their evolutionary rates are phylogenetically heterogeneous in Paleoanguimorpha. Both allometric constraints and ecological factors have shaped ontogeny in the group. Our study highlights the evolutionary lability and adaptability of postnatal ontogeny, and teases apart how different evolutionary shifts in ontogeny contribute to the generation of morphological diversity at different evolutionary scales.

Competition and geography underlie speciation and morphological evolution in Indo-Australasian monitor lizards.

How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolution. Here, we use a near complete phylogenomic-scale phylogeny and a comprehensive morphological dataset comprising more than a thousand specimens to assess the role of biotic and abiotic processes in the diversification of monitor lizards (Varanidae). This charismatic group of lizards shows striking variation in species richness among its clades and multiple instances of endemic radiation in Indo-Australasia (i.e., the Indo-Australian Archipelago and Australia), one of Earth's most biogeographically complex regions. We found heterogeneity in diversification dynamics across the family. Idiosyncratic biotic and geographic conditions appear to have driven diversification and morphological evolution in three endemic Indo-Australasian radiations. Furthermore, incumbency effects partially explain patterns in the biotic exchange between Australia and New Guinea. Our results offer insight into the dynamic history of Indo-Australasia, the evolutionary significance of competition, and the long-term consequences of incumbency effects.

A return-on-investment approach for prioritization of rigorous taxonomic research needed to inform responses to the biodiversity crisis.

Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach for prioritizing rigorous taxonomic research for conservation. We implement this approach in a highly diverse vertebrate group-Australian lizards and snakes. Of 870 species assessed, we identified 282 (32.4%) with taxonomic uncertainty, of which 17.6% likely comprise undescribed species of conservation concern. We identify 24 species in need of immediate taxonomic attention to facilitate conservation. Using a broadly applicable return-on-investment framework, we demonstrate the importance of prioritizing the fundamental work of identifying species before they are lost.

Phylogeography, historical demography and systematics of the world's smallest pythons (Pythonidae, Antaresia).

Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousands of genome-wide SNPs and linear and geometric morphometrics on Antaresia, a clade of four currently recognised dwarf pythons from Australia and New Guinea (Antaresia childreni, A. stimsoni, A. maculosa and A. perthensis). Our integrative analyses of phylogenetics, population structure, species delimitation, historical demography and morphometrics revealed that the true evolutionary diversity is not well reflected in the current appraisal of the diversity of the group. We find that Antaresia childreni and A. stimsoni comprise a widespread network of populations connected by gene flow and without evidence of species-level divergence among them. However, A. maculosa shows considerable genetic structuring which leads us to recognise two subspecies in northeastern Australia and a new species in Torres Strait and New Guinea. These two contrasting cases of over and under estimation of diversity, respectively, illustrate the power of thorough integrative approaches into understanding evolution of biodiversity. Furthermore, our analyses of historical demographic patterns highlight the importance of the Kimberley, Pilbara and Cape York as origins of biodiversity in Australia.

A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth's Largest Lizards.

Hybridization between species occurs more frequently in vertebrates than traditionally thought, but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprise $>$300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with $V$. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and $V$. komodoensis. Biogeographic analyses suggest that $V$. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes, and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.[Biogeography; introgression; Komodo dragon; phylogenetic networks; phylogenomics; reticulation; Varanus.].

Does breeding season variation affect evolution of a sexual signaling trait in a tropical lizard clade?

Sexually selected traits can be expected to increase in importance when the period of sexual behavior is constrained, such as in seasonally restricted breeders. Anolis lizard male dewlaps are classic examples of multifaceted signaling traits, with demonstrated intraspecific reproductive function reflected in courtship behavior. Fitch and Hillis found a correlation between dewlap size and seasonality in mainland Anolis using traditional statistical methods and suggested that seasonally restricted breeding seasons enhanced the differentiation of this signaling trait. Here, we present two tests of the Fitch-Hillis Hypothesis using new phylogenetic and morphological data sets for 44 species of Mexican Anolis. A significant relationship between dewlap size and seasonality is evident in phylogenetically uncorrected analyses but erodes once phylogeny is accounted for. This loss of strong statistical support for a relationship between a key aspect of dewlap morphology and seasonality also occurs within a species complex (A. sericeus group) that inhabits seasonal and aseasonal environments. Our results fail to support seasonality as a strong driver of evolution of Anolis dewlap size. We discuss the implications of our results and the difficulty of disentangling the strength of single mechanisms on trait evolution when multiple selection pressures are likely at play.

Speciation across mountains: Phylogenomics, species delimitation and taxonomy of the Liolaemus leopardinus clade (Squamata, Liolaemidae).

Organisms rapidly diversifying across unstable environments such as mountain tops provide substantial challenges for resolving evolutionary histories and delimiting species. The Liolaemus leopardinus clade is a group of five species of lizards adapted to high altitudes in central Chile, with most species found in the Andes, but one species, L. frassinettii is found in the independent Costa Cordillera. Despite their allopatric distributions, they display shallow mitochondrial divergences, making phylogenetics and species delimitation of this clade hard to resolve. We use an integrative approach to delimit species by considering morphological data (linear and landmark-based), mitochondrial DNA (mtDNA), and nuclear DNA (Sequences and SNPs collected with ddRADseq). We find strong conflicting signals between phylogenetic analyses of the nuclear and mtDNA data. While mtDNA places L. frassinettii as sister to the rest of the clade, the SNPs support a south to north order of divergences, with southernmost species (new taxon described here) as sister to the rest of the clade. Moreover, species delimitation using mtDNA only supports two species (one in the Costa and one in the Andes), whereas combined analyses using the nuclear data and morphology support multiple Andean taxa, including a new one we describe here. Based on these results, population structure analyses and our knowledge of the geological and climatic history of the Andes, we argue that this mito-nuclear discordance is explained by past introgression among the Andean taxa, likely during glacial periods that forced these lizards to lower altitudes where they would hybridize. The complete isolation between the Costa and Andes cordilleras has prevented any further contact between taxa on either mountain chain. Our study highlights the importance of using multiple lines of evidence to resolve evolutionary histories, and the potential misleading results from relying solely on mtDNA.

Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae).

Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.

A new rare species of the Rhadinaeadecorata group from the Sierra Madre del Sur of Guerrero, Mexico (Squamata, Colubridae).

A new species of the Rhadinaeadecorata group is described based on two specimens from the Sierra Madre del Sur, Guerrero, Mexico. The new species differs from all other members of the genus Rhadinaea by having: eight supralabials; 149-151 (male) ventrals; 63-77 (male) subcaudals; two large pale nuchal blotches, forming an incomplete collar that occupies two scales laterally and is bissected along the dorsal midline; a postocular pale marking consisting of a well-defined, narrow line beginning behind the upper posterior margin of the eye and extending posteriorly nearly horizontally until connecting with the nuchal blotches; and the dark ground color of the flanks extending to the lateral portion of the ventrals. The large nuchal blotches distinguish the new species from the other members of the R.decorata group, except for R.cuneata and some individuals of R.hesperia (pale nuchal marking one-scale wide in R.marcellae, absent in the other species). The condition of the postocular pale marking distinguishes it from R.cuneata and R.hesperia (postocular pale marking wedge-shaped in R.cuneata, not connected with the pale post-cephalic markings in R.hesperia). Furthermore, the number of subcaudals and the coloration of the lateral portion of the ventrals distinguish it from R.omiltemana and R.taeniata, the remaining congeners found in Guerrero (85-90 in males of R.omiltemana and 91-121 in R.taeniata; dark color of the flanks not reaching ventrals in the former species, occasionally and faintly in R.taeniata). Additionally, a new combination for R.stadelmani is proposed. The new species is the first described in the genus Rhadinaea in more than 40 years.

A new species of Plestiodon (Squamata: Scincidae) from the Balsas Basin, Mexico.

We describe a new species of Plestiodon in the P. brevirostris group from the Balsas Basin in central Mexico. It is distinguished from the other species in the group by the following combination of traits: supraoculars four; interparietal enclosed posteriorly by parietals; primary temporal present; seventh supralabial usually contacting upper secondary temporal; longitudinal dorsal scale rows around midbody 23-26; Toe-IV lamellae 13-15; limbs not overlapping when adpressed against body; dorsolateral light line extending posteriorly to level of posterior end of anterior fourth of body or beyond; light median line absent in all growth stages; primary lateral dark lines separated medially by six dorsal scale rows and upper half of adjacent row on each side at level of midbody; lower secondary dark line faint at level of neck; and light coloration of supralabials extending ventrally to lip border. Analyses based on DNA sequences of three loci support the distinctiveness of the new species, as well as its sister species relationship with P. ochoterenae. The Environmental Vulnerability Score of the new species places it in the high vulnerability category.

A new species of earth snake (Dipsadidae, Geophis) from Mexico.

A new species of the Geophis dubius group is described from the mountains of the Sierra Zongolica in west-central Veracruz and the Sierra de Quimixtlán in central-east Puebla. The new species is most similar to Geophis duellmani and Geophis turbidus, which are endemic to the mountains of northern Oaxaca and the Sierra Madre Oriental of Puebla and Hidalgo, respectively. However, the new species differs from Geophis duellmani by the presence of postocular and supraocular scales and from Geophis turbidus by having a bicolor dorsum. With the description of the new species, the species number in the genus increases to 50 and to 12 in the Geophis dubius group. Additionally, a key to the species of the Geophis dubius group is provided.