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FIGURE 2 in A morphological and molecular revision of lizards of the genus Marisora Hedges & Conn (Squamata: Mabuyidae) from Central America and Mexico, with descriptions of four new species

FIGURE 2. General lateral-dorsolateral pattern elements in Marisora (Mabuyidae, Mabuyinae). Adapted from Hedges & Conn (2012).

FIGURE 3B in A morphological and molecular revision of lizards of the genus Marisora Hedges & Conn (Squamata: Mabuyidae) from Central America and Mexico, with descriptions of four new species

FIGURE 3B. Phylogenetic tree of the genus Marisora from a maximum-likelihood analysis of DNA sequences of three mitochondrial genes (12S rRNA, 16S rRNA, and cyt b) and three nuclear genes (NGFB, R35, and RAG2) in 140 individuals (4,029 bp). A scale bar (2% sequence divergence) is indicated. The numbers at left of nodes are bootstrap support values. The tree is rooted with Mabuya dominicana. Species delimited using ABGD indicated by black vertical lines at right; samples with horizontal bars missing cytochrome b. Figure continues on two pages.

FIGURE 3A in A morphological and molecular revision of lizards of the genus Marisora Hedges & Conn (Squamata: Mabuyidae) from Central America and Mexico, with descriptions of four new species

FIGURE 3A. Phylogenetic tree of the genus Marisora from a maximum-likelihood analysis of DNA sequences of three mitochondrial genes (12S rRNA, 16S rRNA, and cyt b) and three nuclear genes (NGFB, R35, and RAG2) in 140 individuals (4,029 bp). A scale bar (2% sequence divergence) is indicated below. The numbers at left of nodes are bootstrap support values. The tree is rooted with Mabuya dominicana. Species delimited using ABGD indicated by black vertical lines at right; samples with horizontal bars missing cytochrome b Figure continues on two pages.

FIGURE 1 in A morphological and molecular revision of lizards of the genus Marisora Hedges & Conn (Squamata: Mabuyidae) from Central America and Mexico, with descriptions of four new species

FIGURE 1. Head scalation in Neotropical skinks (Mabuyidae, Mabuyinae, Marisora). Locations and names of head scales on side (A) and top (B) of head. Abbreviations are AL (anterior loreal), F (frontal), FN (frontonasal), FP (frontoparietal), IP (interparietal), LST (lower secondary temporal), M (mental), NU (nuchal), P (parietal), PF (prefrontal), PL (posterior loreal), PT (primary temporal), R (rostral), UST (upper secondary temporal), and UTT (upper tertiary temporal). Chin scale configuration: (C) no contact between chin shields and infralabials; (D) two chin shields (each side) in contact with infralabials. In the former case, the sublabials contact the postmental whereas in the latter case they are separated by two chin shields. Nuchal scales: (E) one transverse row; (F) three transverse rows; note presence of enlarged dorsals (not scored as nuchals) in both cases. Adapted from Hedges & Conn (2012).

FIGURE 8 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 8. (A) An individual of U. thurmanae in its natural habitat. (B) Sand dune habitat of U. thurmanae (camera pointed east with the Mohawk Dunes in the midground and the Mohawk Mountains in the background). Photographs by A. Gottscho.

FIGURE 6 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 6. Holotype (USNM 590033) of Uma thurmanae showing (A) dorsal and (B) ventral head; (C) dorsal right hindfoot and (D) dorsal right forefoot showing toe fringes. Photographs by E. Langan and J. Poindexter.

FIGURE 7 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 7. Satellite map of collecting localities for the type series of Uma thurmanae. Locations where specimens were collected, denoted by red stars, lie along the Mohawk Dunes, a long strip running northwest to southeast. The lizards are isolated in this dune system by the parallel Mohawk Mountains to the east, the Gila River and Interstate-8 to the north, and alluvial fans to the west and south, ultimately resulting in speciation. Source: "Mohawk Dunes," 32° 34' N, 113° 38' W, Google Earth. Imagery date: May 29, 2016. Accessed: July 3, 2018.

FIGURE 5 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 5. (A) Dorsal and (B) ventral view of the adult female holotype (USNM 590033) of Uma thurmanae. Photographs by E. Langan and J. Poindexter.

FIGURE 3 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 3. Box-and-whisker plots for discrete morphological characters that exhibited significant pairwise differences between OTUs. See Appendix 2 for details of how the characters were measured. SPLB=Supralabial Scales; SPCIL=Supraciliary Scales; INS=Internasal Scales; FP=Femoral Pores.

FIGURE 4 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 4. Locations of Uma specimens in the morphospace defined by the first two axes of a Discriminant Function Analysis of morphological characters. Top: when specimens with broken tails are included and TL excluded (n=57), U. inornata can still be distinguished from other OTUs, but U. notata overlaps considerably with U. rufopunctata and U. cowlesi overlaps considerably with U. sp. Bottom: analysis of only the specimens with intact tails such that tail length (TL) could be measured (n=32) allows each OTU to be distinguished.

FIGURE 1 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)

FIGURE 1. Approximate geographic distributions of members of the U. notata species complex and its sister species, U. scoparia (adapted from Gottscho et al. 2017). Actual geographic distributions are more fragmented than shown by the shaded areas as the lizards are restricted to windblown sand habitats within those areas.

opencc-zeroJul 2020View details →

Data from: Metropolitan lizards? Urbanization gradient and the density of lagartixas (Tropidurus hispidus) in a tropical city

Urbanization, with its cohort of environmental stressors, has a dramatic effect on wildlife, causing loss of biodiversity and decline in population abundance customarily associated with increasing levels of impervious surface and fragmentation of native habitats. Some studies suggest that faunal species from open habitats, and with higher abundance in natural environments, seem more likely to tolerate and live in urban environments. Here I evaluate how the level of urbanization affects lagartixas (Tropidurus hispidus) one of the most common lizards found in open vegetation ecosystems in NE Brazil. I surveyed a total of 47 transects across sites that differed in proportion of impervious surface (high, mild, peri-urban and rural). I also collected specific biotic (herbaceous cover, tree and arthropod abundance) and abiotic (amount of shelters and impervious surfaces) factors that could affect lagartixas abundance. Ants were the most common arthropod both in the rural and urban environment. Lagartixas thrive in urban environments and trees and shelter were key predictors of their abundance. Lagartixas show a clear association with use of artificial structures. The low densities of lagartixas in rural areas and higher density in urbanized areas suggests that they colonized urban areas due to the hard surfaces and they probably are not exploiting a novel habitat, but somewhat responding to conditions resembling those in which they evolved. Finally, lagartixas are extremely common in tropical cities, they have a suite of features that are associated with selective pressures in cities and they might play a key functional role in urban ecosystems making this lizard an excellent system for the study of ecology and adaptation to the urban environments.

opencc-zeroJun 2020View details →

Data from: Transcriptome sequencing reveals signatures of positive selection in the spot-tailed earless lizard

The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.

opencc-zeroJun 2020View details →

Data from: The global biogeography of lizard functional groups

Aim - Understanding the mechanisms determining species richness is a primary goal of biogeography. Richness patterns of sub-groups within a taxon are usually assumed to be driven by similar processes. However, if richness of distinct ecological strategies respond differently to the same processes, inferences made for an entire taxon may be misleading. We deconstruct the global lizard assemblage into functional groups and examine the congruence among richness patterns between them. We further examine the species richness – functional richness relationship to elucidate the way functional diversity contributes to the overall species richness patterns. Location – Global. Methods – Using comprehensive biological trait databases we classified the global lizard assemblage into ecological strategies based on body size, diet, activity times and microhabitat preferences, using Archetypal Analysis. We then examined spatial gradients in the richness of each strategy at the one-degree grid cell, biomes and realm scales. Results – We found that lizards can best be characterized by seven 'ecological strategies': scansorial, terrestrial, nocturnal, herbivorous, fossorial, large and semi-aquatic. There are large differences among the global richness patterns of these strategies. While the major richness hotspot for lizards in general is in Australia, several strategies exhibit highest richness in the Amazon Basin. Importantly, the global maximum in lizard species richness is achieved at intermediate values of functional diversity and increasing functional diversity further result in a shallow decline of species richness. Main conclusions - The deconstruction of the global lizard assemblage along multiple ecological axes offers a new way to conceive lizard diversity patterns. It suggests that local lizard richness mostly increases when species belonging to particular ecological strategies become hyper-diverse there, and not because more ecological types are present in the most species rich localities. Thus maximum richness and maximum ecological diversity do not overlap. These results shed light on the global richness pattern of lizards, and highlight previously unidentified spatial patterns in understudied functional groups.

opencc-zeroAug 2020View details →

Phylogenomics of monitor lizards and the role of competition in dictating body size disparity

Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly on macroevolutionary timescales and across broad geographic spaces. Here we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. Incorporating both exon-capture molecular and morphological datasets we use a combined evidence approach to estimate the relationships among living and extinct varaniform lizards. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.

opencc-zeroAug 2020View details →

Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with ultraconserved elements and two morphological matrices. In unweighted maximum likelihood and Bayesian combined-evidence analyses, morphological signal was dwarfed by the ultraconserved elements, and some node support values were reduced relative to ultraconserved element-only analyses. Increasing the weight of morphological characters allowed those data to influence the tree, but weighting subjectivity should be considered in future analyses. More attempts should be made to simultaneously analyze genomic and morphological datasets.

opencc-zeroSep 2020View details →

Data from: Mite load predicts the quality of sexual color and locomotor performance in a sexually dichromatic lizard

Since Darwin, the maintenance of bright sexual colors has recurrently been linked to mate preference. However, the mechanisms underpinning such preferences for bright colors would not be resolved for another century. Likely, the idea of selection for colors that could decrease the chances of survival (e.g. flashy colors that can inadvertently attract predators) was perceived as counterintuitive. It is now widely-accepted that these extreme colors often communicate to mates the ability to survive despite a 'handicap' and act as honest signals of individual quality when they are correlated with the quality of other traits that are directly linked to individual fitness. Sexual colors in males are frequently perceived as indicators of infection resistance, in particular. Still, there remains considerable discord among studies attempting to parse the relationships between the variables associating sexual color and infection resistance, such as habitat type and body size. This discord may arise from complex interactions between these variables. Here, we ask if sexual color in male Florida scrub lizards (Sceloporus woodi) is an honest signal of resistance to chigger mite infection. To this end, we use linear modeling to explore relationships between mite load, different components of sexual color, ecological performance, body size, and habitat type. Our data show that that the brightness of sexual color in scrub lizards is negatively associated with the interaction between mite load and body size, and scrub lizards suffer decreased endurance capacity with increases in mite load. Our data also indicate that mite load, performance, and sexual color in male scrub lizards can vary between habitat types. Collectively these results suggest that sexual color in scrub lizards is an honest indicator of individual quality and further underscore the importance of considering multiple factors when testing hypotheses related to the maintenance of sexual color.

opencc-zeroSep 2020View details →

Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts

Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacteria species that are highly similar to each other metabolically. This pattern in the bacteria microbiome could represent an early step in the taxonomic shifts in bacteria microbiome that occur when host lineages change their in diet niche over evolutionary timescales.

opencc-zeroOct 2020View details →

Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).

Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.