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Untangling the morphological and genetic variation of two endemic lizards from the coastal sand dunes of Northeastern Brazil
Abstract
Studies in the Neotropical region consistently highlight high levels of endemism and biodiversity. However, challenges persist, particularly in uncovering the cryptic diversity among species. Various approaches are needed to address this, including morphological, genetic, and environmental data. This study focused on genetic and morphological variation in three endemic, sympatric lizard species: Tropidurus hygomi , Glaucomastix abaetensis , and Glaucomastix itabaianensis in the coastal sand dunes of Northeastern Brazil. These lizards are confined to sandy Pleistocene-formed environments with limited distribution. While earlier research revealed substantial genetic diversity, gaps remained in distribution sampling, morphological data, and understanding the correlation between this variation and environmental factors. We aimed to identify genetic clusters to assess the alignment of phenotypic differences with these clusters and explore potential relationships between climatic and geographical factors and morphometric variations. We utilized mtDNA data to assess population clusters. Geometric and linear morphometrics were employed to analyze morphological data, which was then correlated with climatic information. Results unveiled genetic and morphological variations signifying the presence of cryptic diversity. Our analyses also highlighted the influence of geography and climate on morphometric variations. These findings underscore hidden diversity and a complex evolutionary history within the confined Pleistocene sand dunes. Further genomic analyses could contribute to comprehending these patterns and enhancing the conservation strategies for these endangered species.
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The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.
Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.
Contact: peter@biomatters.com
In this study, we report additional cannibalism and predation events in Tropidurus hispidus
and, by reviewing our data with that found in the literature, we quantify the relative importance of vertebrate categories as prey for T. hispidus. In addition, we provide an ethogram for events related to territoriality, courting and copulation.
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses, which will be supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. We have now added a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface (GUI) has been made more responsive and interactive for very big datasets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled GUI and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
A combined approach based on karyology and DNA taxonomy allowed us to characterize the taxonomic peculiarities in 10 Mesoamerican lizard species, belonging to six genera and five families, inhabiting two Biosphere Reserve in Chiapas, Mexico: La Sepultura Biosphere Reserve, and Montes Azules Biosphere. The karyotypes of four species, Phyllodactylus sp. 3 ( P. tuberculosus species group) (2n = 38), Holcosus festivus (Lichtenstein et von Martens, 1856) (2n = 50), Anolis lemurinus Cope, 1861 (2n = 40), and A. uniformis Cope, 1885 (2n = 29–30) are described for the first time, the last one showing a particular X 1 X 1 X 2 X 2 /X 1 X 2 Y condition. In Aspidoscelis deppii (Wiegmann, 1834) (2n = 50) and Anolis capito Peters, 1863 (2n = 42), we found a different karyotype from the ones previously reported for these species. Moreover, in A. capito , the cytogenetic observation is concurrent with a considerable genetic divergence (9%) at the studied mtDNA marker (MT-ND2), which is indicative of a putative new cryptic species. The skink Scincella cherriei (Cope, 1893), showed high values of genetic divergence (5.2% at 16S gene) between the specimens from Montes Azules and those from Costa Rica and Nicaragua, comparable to the values typical of sister species in skinks. A lower level of genetic divergence, compatible with an intraspecific phylogeographic structure, has been identified in Lepidophyma flavimaculatum Duméril, 1851. These new data identify taxa that urgently require more in-depth taxonomic studies especially in these areas where habitat alteration is proceeding at an alarming rate.
Despite advances within particular groups, systematics of the Teiidae has long been unsatisfactory, because fewmorphological characters have been described for this family. Consequently, most species have been assigned to the large,polyphyletic, and poorly defined genera Ameiva and Cnemidophorus. We describe 137 morphological characters andscore them for most species of Neotropical Teiidae. Important, but previously undescribed, character suites include pupilshape; the frontal ridge; longitudinal division of the interparietal; the rostral groove; patterns of supraciliary fusion; thepreauricular skin fold; the “toothy” first supralabial; modified apical granules; the pectoral sulcus; expansion of scales atthe heel; tibiotarsal shields; scales between the digital lamellae along the postaxial edges of the toes; scale surfacemicrostructure of macrohoneycomb, macroridges, or lamellae; distribution patterns and morphology of lenticular scaleorgans; types of epidermal generation glands; and several hemipenial structures. We propose a new taxonomy of theTeiidae based on recovered evolutionary history and numerous morphological characters surveyed in this study. Werecognize three subfamilies: Callopistinae new subfamily, Teiinae Estes et al., and Tupinambinae Estes et al. To resolvepolyphyly of Ameiva and Cnemidophorus, we erect four new genera for various groups of Neotropical Teiidae: Ameivulanew genus, Aurivela new genus, Contomastix new genus, and Medopheos new genus. We resurrect Holcosus Cope fromthe synonymy of Ameiva and Salvator Duméril and Bibron from the synonymy of Tupinambis. On the basis of sharedderived characters, we propose new species groups of our redefined Ameiva and Cnemidophorus. We incorporate our newcharacters into a key to the genera and species groups of Teiidae. A phylogenetic hypothesis of Teiidae based onmorphological characters differs substantially from hypotheses based on mitochondrial DNA. The phylogeny based onmorphology is consistent with well-established biogeographic patterns of Neotropical vertebrates and explains extreme morphological divergence in such genera as Kentropyx and Aurivela.
Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation which is both easier to install and use, automating the entire pipeline. Additionally, we allow for the use of multiple processors, improve on the default settings of the algorithm, and provide an interface with the ggtree library to enable informative illustration of the clustering results. Our aim is that this package aids in the understanding and dissemination of the method, as well as enhancing the reproducibility of population structure analyses.
The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceeded heterogeneously. Here, we address these challenges as we diagnose and describe species in three co-occurring species groups of Australian lizards. By integrating genomic and morphological data with data on hybridization and introgression from contact zones, we explore several approaches - and their relative benefits and weaknesses - for testing the validity of cryptic lineages. More generally, we advocate that genetic delimitations of cryptic diversity must consider whether these lineages are likely to be durable and persistent through evolutionary time.
The Gran Chaco dry forest ecoregion corresponds to the southern portion of the South America diagonal belt of open formations, being one of the most threatened subtropical woodland savannas in the world. The area is still poorly known biologically and has been suffering with impressively high forest cover loss in the last 10 years. Integrating morphological and molecular data, we detected and describe a cryptic new species of lizard genus Ameivula endemic from the eastern part of this ecoregion, the called Humid Chaco. Ameivula apipensis sp nov. is characterised by a whitish brown vertebral stripe in adults and juveniles, a lateral field without ocelli and with overlapping spot, presence of an interfrontoparietal scale in 46.2% of the specimens, 12–17 femoral pores, an hemipenis without lateral sac, five xiphisternal ribs, and by a combination of meristic features as confirmed by discriminant analysis. The new species was recovered sister to a clade from Western Cerrado in our analysis, the first phylogenetic hypothesis for the Ameivula and Glaucomastix genera based on 1977 base pairs of three mitochondrial (12S, 16S and cyt-b) and one nuclear (c-mos) genes, including all the recognised species at the moment. Maximum parsimony and Bayesian inference recovered the monophyly of Ameivula and Glaucomastix with strong support. Reinforcing previous studies, our results suggest the presence of additional cryptic species in Ameivula from the Western Cerrado.
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
We created a new dataset of spatially interpolated monthly climate data for global land areas at a very high spatial resolution (approximately 1 km 2). We included monthly temperature (minimum, maximum and average), precipitation, solar radiation, vapour pressure and wind speed, aggregated across a target temporal range of 1970–2000, using data from between 9000 and 60 000 weather stations. Weather station data were interpolated using thin-plate splines with covariates including elevation, distance to the coast and three satellite-derived covariates: maximum and minimum land surface temperature as well as cloud cover, obtained with the MODIS satellite platform. Interpolation was done for 23 regions of varying size depending on station density. Satellite data improved prediction accuracy for temperature variables 5–15% (0.07–0.17 ∘ C), particularly for areas with a low station density, although prediction error remained high in such regions for all climate variables. Contributions of satellite covariates were mostly negligible for the other variables, although their importance varied by region. In contrast to the common approach to use a single model formulation for the entire world, we constructed the final product by selecting the best performing model for each region and variable. Global cross-validation correlations were ≥ 0.99 for temperature and humidity, 0.86 for precipitation and 0.76 for wind speed. The fact that most of our climate surface estimates were only marginally improved by use of satellite covariates highlights the importance having a dense, high-quality network of climate station data.
Blended learning, a convergence of e-learning approach and face-to-face learning, has been regarded as a new paradigm in modern education. The degree of learners' satisfaction with blended learning played a crucial role in evaluating the effectiveness of blended learning adoption. Therefore, this study examined the primary factors affecting learners' satisfaction in blended learning environment. A comprehensive questionnaire was used to assess the impact of six dimensions such as learner, instructor, course, technology, design and environment, on perceived e-learner satisfaction specifically on the e-learning component within the blended learning environment. The respondents for this study were generally young with an average age of 20 years old. Results from univariate regression analysis revealed all six dimensions to be positively associated with perceived e-learner satisfaction. Subsequent multivariate regression analysis evidenced only the design dimension to be the critical factor influencing perceived e-learner satisfaction. This study concluded younger generation prioritized the design dimension to be the most critical factor in their satisfaction towards e-learning component in blended learning environment. Therefore, it may be more strategic for institutions to emphasize on the design dimension in their e-learning implementations within the blended learning environment specifically for younger learners.
Cryptic diversity plagues estimates of biodiversity, conservation efforts and attempts to control diseases and invasive species. Here, we re-visit a decade-old assessment of whether or not cryptic species are homogeneously reported among higher metazoan taxa. We compiled information from an extensive survey of the literature to recover all reports of cryptic species among metazoans. After correcting for currently known species richness and research effort per taxon, we find that cryptic species are over-reported in some taxa and under-reported in others. Although several taxa showing either a lack or an excess of reported cryptic species were poorly studied invertebrate groups, we found that cryptic species were over-reported in amphibians, reptiles and crustaceans, all relatively well-studied groups. The observed heterogeneity in the distribution of reported cryptic species may reflect taxon-specific properties affecting either the propensity for cryptic species to be formed or their likelihood of being detected by conventional taxonomy. Either way, the implications of cryptic diversity may not apply equally across all taxonomic groups.
Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympat-ric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.
Tropidurus is a widespread genus of lizards in Brazilian biomes, particularly common in the state of Bahia, northeastern Brazil. However, genetic studies of populations and species of this group are still scarce. We used chromosomal and DNA barcoding analyses to examine 12 populations of five species of Tropidurus from semiarid (caatinga) and Atlantic forest portions of Bahia. All populations shared a karyotype with 2n = 36 divided into 12 metacentric and submetacentric chromosomes and 24 microchromosomes. The microchromosomes were acrocentric in most of species, but metacentric microchromosomes were observed in Tropidurus semitaeniatus, determining variation in fundamental number of arms from 48 to 52. One population of Tropidurus hispidus presented a supernumerary chromosome. Pericentromeric heterochromatin was detected in most microchromosomes and two pairs of macrochromosomes presented interstitial and pericentromeric C-bands. The nucleolar organizer regions (NORs) were single in Tropidurus erytrocephalus, T. semitaeniatus, and Tropidurus torquatus, and multiple in Tropidurus cocorobensis and T. hispidus. This is the first report of multiple NORs in both species. These results suggest a conserved pattern of karyotype macrostructure in Tropidurus, whereas microstructural features have undergone a more dynamic evolution, including non-Robertsonian rearrangements. DNA barcoding supported a clear distinction between analyzed species, except for the cryptic diversity indicated in the T. hispidus and T. torquatus cluster, in agreement with current taxonomic uncertainties. The diversity of this group of lizards is discussed based on their divergence and distribution patterns.
Tropidurus Wied, 1825, is one of the most ubiquitous lizard genera distributed in open habitats of tropical and subtropical South America. Nevertheless, the broad representation of specimens of this group in scientific collections is hardly reflected in our knowledge of its taxo- nomic diversity. Most species currently assigned to Tropidurus began to be uncovered in the early 1980’s and additional populations in need of formal taxonomic treatment have been cata- loged ever since. Herein, we name Tropidurus sertanejo, n. sp., a new species of the T. torquatus group endemic to the semiarid Brazilian Caatinga. Tropidurus sertanejo, n. sp., is currently known from two isolated populations in the municipalities of Caetité and Ibotirama, State of Bahia, Brazil. This is the only species of the T. torquatus group lacking granular mite pockets on the lateral neck, and it is also diagnosable by having a conspicuous bronze-colored head, a light-brown dorsal body with small pale salmon spots, and small body size in comparison with most congeners. Phylogenetic analyses recovered a paraphyletic Tropidurus, but firmly sup- ported T. sertanejo, n. sp., as member of a monophyletic T. torquatus species group. Trees gener- ated by independent analyses of nuclear and mitochondrial sequence data conflicted with our total evidence phylogenetic hypotheses. Since topological disagreements were detected among phylogenetic trees resulting from maximum parsimony (MP) and maximum likelihood (ML) reconstructions, and MP analyses do not require distinct evolutionary models or partition schemes to be defined prior to conduction of phylogenetic reconstruction, these factors were considered unlikely to explain all the variation in the observed results, favoring the interpreta- tion of conflicting phylogenetic signal. Because detailed information on the distribution, popu- lation size, and ecological requirements of T. sertanejo, n. sp., are currently unavailable, we recommend the species to be listed as “data deficient” following the rules proposed by IUCN.
Ecologists and evolutionary biologists are increasingly using big-data approaches to tackle questions at large spatial, taxonomic, and temporal scales. However, despite recent efforts to gather two centuries of biodiversity inventories into comprehensive databases, many crucial research questions remain unanswered. Here, we update the concept of knowledge shortfalls and review the tradeoffs between generality and uncertainty. We present seven key shortfalls of current biodiversity data. Four previously proposed shortfalls pinpoint knowledge gaps for species taxonomy (Linnean), distribution (Wallacean), abundance (Prestonian), and evolutionary patterns (Darwinian). We also redefine the Hutchinsonian shortfall to apply to the abiotic tolerances of species and propose new shortfalls relating to limited knowledge of species traits (Raunkiæran) and biotic interactions (Eltonian). We conclude with a general framework for the combined impacts and consequences of shortfalls of large-scale biodiversity knowledge for evolutionary and ecological research and consider ways of overcoming the seven shortfalls and dealing with the uncertainty they generate.
Phylogeographic research has advanced in South America, with increasing efforts on taxa from the dry diagonal biomes. However, the diversification of endemic fauna from the semiarid Caatinga biome in northeastern Brazil is still poorly known. Here we targeted saxicolous lizards of the Tropidurus semitaeniatus species group to better understand the evolutionary history of these endemic taxa and the Caatinga. We estimated a time-calibrated phylogeny for the species group based on two mitochondrial and two nuclear genes and jointly estimated the species limits and species tree within the group. We also devoted a denser phylogeographic sampling of the T. semitaeniatus complex to explore migration patterns, and the spatiotemporal diffusion history to verify a possible role of the São Francisco River as a promoter of differentiation in this saxicolous group of lizards.
Phylogenetic analysis detected high cryptic genetic diversity, occurrence of unique microendemic lineages associated with older highlands, and a speciation history that took place during the Pliocene-Pleistocene transition. Species delimitation detected five evolutionary entities within the T. semitaeniatus species group, albeit with low support. Thus, additional data are needed for a more accurate definition of species limits and interspecific relationships within this group. Spatiotemporal analyses reconstructed the geographic origin of the T. semitaeniatus species complex to be located north of the present-day course of the São Francisco River, followed by dispersal that expanded its distribution towards the northwest and south. Gene flow estimates showed higher migration rates into the lineages located north of the São Francisco River.
The phylogenetic and population structures are intrinsically associated with stable rock surfaces and landscape rearrangements, such as the establishment of drainage basins located to the northern and southern distribution ranges. The T. semitaeniatus complex preserved high genetic diversity during range expansion, possibly as a result of frequent long-distance dispersal events. Our results indicate that both the current course of the São Francisco River and its paleo-courses had an important role in promoting diversification of the Caatinga endemic T. semitaeniatus species group.
Resumo
This paper is a systematic revision of the lizards of the genus Tropidurus (torquatus group) occurring south of the Rio Amazonas. Following an analysis of meristic characters in five areas where lizards with different types of mite pockets occur synpatrically, eleven species are recognized, seven of which described as new. Diagnoses, descriptions and geographic distribution are given for each species, and an artificial key to species is presented. Ecologically, there seem to be two species assemblages: the first includes all species with wide geographic distribution, and the second includes species with restricted distributions, usually limited to mountain or sandy soil areas. Probably present climatic conditions are more suitable for the first group, than for the second. A model based on the geographic ecology of the recent past of a pair of species is proposed to explain the present complex distribution of some species of the torquatus group. The geographic differentiation of T. torquatus and T. hygomi is studied and a sequence of events proposed to explain its origin, ecologic differentiation and evolution.
Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as MANOVA, linear discriminant analysis, principal component analysis, canonical correlation, etc. It is important to assess multivariate normality in order to proceed with such statistical methods. There are many analytical methods proposed for checking multivariate normality. However, deciding which method to use is a challenging process, since each method may give different results under certain conditions. Hence, we may say that there is no best method, which is valid under any condition, for normality checking. In addition to numerical results, it is very useful to use graphical methods to decide on multivariate normality. Combining the numerical results from several methods with graphical approaches can be useful and provide more reliable decisions. Here, we present an R package, MVN, to assess multivariate normality. It contains the three most widely used multivariate normality tests, including Mardia’s, Henze-Zirkler’s and Royston’s, and graphical approaches, including chi-square Q-Q, perspective and contour plots. It also includes two multivariate outlier detection methods, which are based on robust Mahalanobis distances. Moreover, this package offers functions to check the univariate normality of marginal distributions through both tests and plots. Furthermore, especially for non-R users, we provide a user-friendly web application of the package. This application is available at http://www.biosoft.hacettepe.edu.tr/MVN/.
Male and female Ameiva exsul share overlapping home ranges. As a consequence sexually receptive females may have access to several males. We studied the effect of relative male size on paternity in five experimental populations of adult male and female A. exsul that were held in naturalistic 100 m2 enclosures. Each population, which initially consisted of three males and three females, was followed for a breeding season. Behavior was tallied from data gathered by focal animal observation. Progeny were obtained by harvesting clutches of eggs from the sand piles in which the animals denned. DNA samples from embryonic tissue and from blood of adults were compared to determine parentage using RAPD-PCR with bands scored as dominant markers. Body size was strongly associated with male reproductive success in the enclosures: the largest male in each enclosure sired the most progeny, and overall, with enclosures as statistical blocks, large males sired significantly more progeny than did medium or small males. Nevertheless, small males obtained some paternity, and so were not completely excluded from reproduction. We detected multiple paternity in one of the clutches.
This chapter provides a general overview of the tropical coast of Brazil, with emphasis on the marine realm. The described region extends for approximately 3000 km, and has three different sectors (northern, northeastern and eastern), each one with distinctive characteristics. The north and northeast sectors have a predominantly semi-arid climate, whereas the eastern sector is tropical and humid. Northeasterly trade winds occur mostly in the north sector, but in the northeast and east sectors southeasterly and easterly trade winds are more important. Three factors controlled sedimentation along the coast of tropical Brazil during Late Quaternary time: the sea-level history that played an important role in the evolution of the coastal zone and its related ecosystems over the last 5000 years; the sediment supply that is primarily regulated by the local relief and climate; and the climate itself, which is the major control of the large and active dune fields found in the northern sector. Coral reefs are one of the most prominent marine ecosystems of tropical Brazil, particularly because of the unique character of its low-diversity coral fauna which is rich in endemic species; it is a relic fauna from the Tertiary, which forms unusual mushroom-shaped coral pinnacles. They include the southernmost coral reef communities of the Atlantic, and a small atoll. A transition from siliciclastic dominant sediments on the coastline, to pure carbonates toward the middle and outer shelves, characterises the continental margin of tropical Brazil. Development was generally low until recently due to lack of roads and infrastructure, but new development has led to expansion in the area. Uncontrolled urban development, associated with heavy industrialisation and consequent pollution-uses which are not appropriate for these coastal marine ecosystems-and the accelerated deforestation of the Atlantic Rainforest are, today, the major threats to the tropical Coast of Brazil.
A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheettype data entry with univariate and multivariate statistics, curve fitting, time-series analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
Tropidurus melanopleurus is a highly dimorphic tropidurid lizard that is found on the eastern slopes of the Andes from Argentina to Peru. Adult males are larger than females and also have longer and wider heads. The hind legs show isometric growth in females and negative allometric growth in males, as do head width and head length of both sexes. Sexes differ in thermoregulation and diet. Males appear to be thermoregulators, whereas females are thermoconformers. Females are active over broader ranges of body temperature. Males prey upon a wide variety of arthropods, whereas females have a narrow myrmecophagous diet. At present, it is not possible to decide whether sexual or natural selection explains the sexual dimorphism observed in T. melanopleurus. Body size could be the product of sexual selection modified by ecological factors. /// Tropidurus melanopleurus es un representante de la familia Tropiduridae altamente dimórfico que habita en las laderas orientales de los Andes, desde Argentina hasta Perú. El macho es mayor que la hembra y posee una cabeza más larga y ancha. Aparentemente el crecimiento de las patas posteriores es isométrico en las hembras y, al igual que la longitud y anchura de la cabeza en ambos sexos, presenta un crecimiento alométrico negativo en los machos. Hemos hallado un notable dimorfismo sexual en algunas características ecológicas como la termorregulación y la dieta. El macho puede considerarse un buen termorregulador, mientras que la hembra se comporta como termoconformista. Además, los machos consumen una amplia variedad de artrópodos, mientras que las hembras poseen una estrecha dieta mirmecófaga. En el estado actual de nuestros conocimientos no es posible decantarse de modo definitivo por una de las dos hipótesis causales principales de las diferencias halladas entre machos y hembras de T. melanopleurus, la selección sexual o la selección natural. El dimorfismo sexual en el tamaño corporal puede ser un producto de la selección sexual quizás amplificado por determinados factores ecológicos.
Organisms adapted to open environments in South America have recently been used to understand the origins of the high Neotropical biodiversity. In the Caatinga, the largest continuous block of Seasonally Dry Tropical Forest in South America, phylogeographic studies have uncovered the role of historical climate changes and rivers (i.e., the São Francisco River, the largest perennial river in Caatinga), in promoting genetic differentiation and speciation of lizards and amphibians. We used mitochondrial data, demographic analyses, paleodistribution models, and landscape genetic methods to test the effects of spatial distances, historical climate fluctuations, and landscape heterogeneity on the genetic variation of the generalist lizard Tropidurus hispidus in the semi-arid Caatinga in northeastern Brazil. Four haplogroups with moderate geographical structure diverged in the Pleistocene, and exhibited high genetic diversity. Ecological niche models revealed large suitable climatic areas for T. hispidus in the past 790 thousand years, connecting the Caatinga and other regions via a narrow corridor. Part of the genetic differentiation in T. hispidus resulted from spatial distances among populations and isolation by resistance through climatic unsuitability areas in the Last Glacial Maximum (LGM), which probably reduced population connectivity and gene flow. Our findings highlight the role of the historical factors of the Caatinga, through LGM climate, and the generalist condition of species in shaping the genealogical histories of populations. Although the results are based on a single-locus approach, our study is a first step to shed light on the main drivers of the evolutionary history of T. hispidus, in a highly diverse and still poorly studied region. © The Trustees of the Natural History Museum, London 2022. All Rights Reserved.
Several species of Glaucomastix lizards have been described over the past decade, most of these inhabit inland Brazil. Glaucomastix abaetensis is a threatened whiptail endemic to Brazilian coastal “restinga” (sandy habitats) from Bahia State to Sergipe, with a distribution limited by riverine barriers. In order to investigate the differentiation and relationships in G. abaetensis, we integrated phylogeographic analysis, Bayesian species delimitation and morphological data to detect geographical patterns and historical events responsible for its present distribution. We recovered two highly divergent clades along its range, one of them unnamed. Glaucomastix itabaianensis sp. nov. has a a yellowish green tail, 13–16 scales in the lateral flank, 22–33 scales around tail, 28–35 femoral pores and usually four supraocular scales with the smaller one disposed posteriorly. Our results retrieved the monophyly of Glaucomastix, with G. venetacauda and G. cyanurus being sister species to a clade formed by G. littoralis and G. abaetensis. Divergence between Glaucomastix abaetensis and the new species occurred roughly 2.39 Myr ago; posterior shallow genetic divergences occurred mainly in Pleistocene. Finally, we present data on the conservation of this clade of whiptail lizards.
The species concept is the cornerstone of biodiversity science and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new ‘species’ paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category – which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a ‘process’ counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution, and species coexistence. It is time for incorporating multi-criteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.
Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes cryptic species based on their low levels of phenotypic (morphological) disparity relative to their degree of genetic differentiation and divergence times as compared with non-cryptic species. We discuss how application of a more rigorous definition of cryptic species in taxonomic practice will lead to more accurate estimates of their prevalence in nature, better understanding of their distribution patterns on the tree of life, and increased abilities to resolve the processes underlying their evolution.
The Quaternary period is marked by many extensive glaciations and sea level oscillations, mainly during the Pleistocene. Sea level oscillations possibly shaped landscapes in coastal regions, which may have played an important role in the diversification of organisms that live in these areas. In this study, we investigated the population history of the lizard Tropidurus hygomi, which is endemic to a narrow region of the northeastern coast of Brazil, inhabiting areas of white sandy coastal dunes in the Restinga formation. We specifically asked: how did sea level changes in the Quaternary shape population structure and historical demography of T. hygomi? We collected 72 tissue samples throughout the distribution of the species and obtained sequences from the mitochondrial gene cytochrome b. Different tests for population structure identified five distinct mitochondrial DNA clusters (mtDNA clusters) in T. hygomi. Divergence time estimate showed that splits among these mtDNA clusters took place in the Pleistocene, and exhibited temporal agreement with marine transgressive events during these periods. As T. hygomi is a threatened species and our data suggest the presence of five mtDNA clusters, further conservation actions for this species should consider these independent mtDNA clusters in order to preserve the evolutionary history and the diversity within the species.
The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.
Head shape in lizards correlates with a wide range of environmental pressures, supporting the hypothesis that patterns of phenotypic change represent adaptive responses to selective processes. However, natural selection promotes evolutionary adaptation only if the trait under selection has enough heritable variation. In this study we used geometric morphometrics and quantitative genetics to assess the heritability patterns of the head shape and size of common wall lizards (Podarcis muralis). Genetic and phenotypic components were estimated using animal models, which showed that more than half of the variation in head morphology is inheritable. Furthermore, at least five independent patterns of genetically determined phenotypic change were detected. These outcomes confirm that morphological differentiation in common wall lizards may reliably be regarded as the result of adaptive processes driven by natural selection.
Characters of scale surface microstructure are combined with 'traditional' morphological characters in a phylogenetic analysis of the Tropidurini. Tropidurid lizards show variation in types of coarse and fine scale surface microstructure, in the anatomical distribution of different scale surface features, and in scale organ morphology and distribution. The morphology of the inner surface zone of scales is here described for the first time using scanning electron microscopy. Our phylogeny differs considerably from those proposed in earlier studies. New characters and frequency coding of polymorphic characters help resolve the problematic relationships of several species. Statistical confidence supports recognition ot one large cis-Andean and one large trans-Andean clade of species. Based on our results, we synonymize Plesiomicrolophus with Microlophus and Uranoscodon with Tropidurus. The phylogenetic relationships of newly discovered Tropidurus are resolved: T. callathelys is the sister species of T. melanopleurus; T. xanthochilus is the sister species of T. spinulosus. Tropidurus spinulosus is found to be more closely related to T. strobilurus and a clade of Amazonian species than to T. melanopleurus. The species previously placed in Uracentron are more closely related to species previously placed in Plica than to T. strobilurus as previously thought.
Relative clutch mass (RCM) is an important life-history characteristic in lizards. Differential survivorship of females carrying clutches of eggs should partially determine RCM, and foraging mode and predator escape tactics play important roles in selection for a given RCM. RCM may vary within a population due to variation in resource availability or among populations of a species due to resource availability or geographic variation in escape tactics. Within species that forage widely, RCM is relatively low. RCM tends to be relatively high in species using the sit-and-wait foraging tactic. RCM variation in the latter group correlates with the manner in which crypsis is manifested. Where a streamlined morphology is advantageous (thin branch mimics or fossorial species), RCM may be low. Where crypsis does not involve a streamlined morphology, RCM tends to be high. Energetic costs associated with changes in RCM and variation in predation rates were estimated with a model of the daily net energy-intake of a lizard. Increasing RCM and/or predation intensity on gravid females reduces daily net energy-intake of wide foragers, but has little effect on species which are sit-and-wait foragers. -Authors
The cryptic concept refers to two or more species that have been classified as a single nominal species due to the fact that they are apparently morphologically indistinguishable. In recent years, the development of advanced morphometric tools has allowed researchers to differentiate subtle variations that cannot be distinguished by mere “eyeballing” as was carried out in in traditional cladistics. These robust statistical techniques alongside with molecular analyses have enabled the distinction of formerly “cryptic” species, thus highlighting the associated problems and overuse of this concept. In this article we used geometric morphometric (GM) methods to test if it was possible to distinguish two species of tenebrionid beetles (Nyctelia multicristata and Nyctelia confusa) that has been traditionally classified as cryptic. The goal of this study was twofold: on one hand it was expected to draw the attention of taxonomy researchers to be careful when using the concept of cryptic species. On the other hand, it was tested if the GM toolkit allows the differentiation of a species usually categorized as cryptic. Our results allowed the distinction between N. multicristata and N. confusa, hence rejecting the “cryptic” denomination. Based on our results it is possible to suggest that possibly many times species are classified as cryptic due inappropriate methodological designs and comparisons.
Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.