Where does diversity come from? Linking geographical patterns of morphological, genetic, and environmental variation in wall lizards

First genetic insights of Gonatodescaudiscutatus (Reptilia, Gekkota) in the Galapagos Islands and mainland Ecuador

Studies on genetic variability amongst native and introduced species contribute to a better understanding of the genetic diversity of species along their autochthonous distribution and identify possible routes of introduction. Gonatodescaudiscutatus is a gecko native to western Ecuador and introduced to the Galapagos Islands. Despite being a successful species in human-modified habitats along its native and non-native ranges, neither the colonisation process nor the genetic diversity of this gecko is known. In this study, we analysed 55 individuals from 14 localities in western Ecuador and six localities in San Cristobal Island, Galapagos - the only island with a large, self-sustaining population. We amplified and analysed the genetic variability of two nuclear genes (Cmos and Rag2) and one mitochondrial gene (16S). Cmos and Rag2 sequences presented little to none genetic variability, while 16S allowed us to build a haplotype network. We identified nine haplotypes across mainland Ecuador, two of which are also present in Galapagos. Low genetic diversity between insular and continental populations suggests that the introduction of G.caudiscutatus on the Islands is relatively recent. Due to the widespread geographical distribution of mainland haplotypes, it was not possible to determine the source population of the introduction. This study represents the first exploration of the genetic diversity of Gonatodescaudiscutatus, utilising genetic tools to gain insights into its invasion history in the Galapagos.

Phylogeographic and Paleoclimatic Modelling Tools Improve Our Understanding of the Biogeographic History of Hierophis viridiflavus (Colubridae)

Phylogeographic and paleoclimatic modelling studies have been combined to infer the role of Pleistocene climatic oscillations as drivers of the genetic structure and distribution of Mediterranean taxa. For the European whip snake, Hierophis viridiflavus, previous studies based on paleoclimatic modelling have depicted a low reliability in the pattern of past climatic suitability across the central Mediterranean Basin, which barely fits the species' genetic structure. In this study, we combined phylogeographic and paleoclimatic modelling tools to improve our understanding of the biogeographic history of H. viridiflavus, particularly extending the sampling and phylogeographic inferences to previously under-sampled regions. Phylogeographic analyses recovered two major clades that diverged at the beginning of the Pleistocene and had diversified in different ways by the late Pleistocene: the east clade (composed of three subclades) and the west clade (with no further structure). Paleoclimatic models highlighted the temperate character of H. viridiflavus, indicating range contractions during both the last inter-glacial and last glacial maximum periods. Range expansions from southern-located climatic refugia likely occurred in the Bølling-Allerød and Middle Holocene periods, which are supported by signals of demographic growth in the west clade and South-East-North subclade. Overall, this work improves our understanding of the historical biogeography of H. viridiflavus, providing further insights into the evolutionary processes that occurred in the Mediterranean Basin hotspot.

Identification of morphologically cryptic species with computer vision models: wall lizards (Squamata: Lacertidae: Podarcis) as a case study

Automated image classification is a thriving field of machine learning, and various successful applications dealing with biological images have recently emerged. In this work, we address the ability of these methods to identify species that are difficult to tell apart by humans due to their morphological similarity. We focus on distinguishing species of wall lizards, namely those belonging to the Podarcis hispanicus species complex, which constitutes a well-known example of cryptic morphological variation. We address two classification experiments: (1) assignment of images of the morphologically relatively distinct P. bocagei and P. lusitanicus; and (2) distinction between the overall more cryptic nine taxa that compose this complex. We used four datasets (two image perspectives and individuals of the two sexes) and three deep-learning models to address each problem. Our results suggest a high ability of the models to identify the correct species, especially when combining predictions from different perspectives and models (accuracy of 95.9% and 97.1% for females and males, respectively, in the two-class case; and of 91.2% to 93.5% for females and males, respectively, in the nine-class case). Overall, these results establish deep-learning models as an important tool for field identification and monitoring of cryptic species complexes, alleviating the burden of expert or genetic identification.

Evaluating the drivers and engines of morphological diversification in the invasive gecko Hemidactylus mabouia (Moreau de Jonnès, 1818) (Squamata: Gekkonidae)

Development determines the range of possible phenotypes that can be produced and exposed to selection and has a major role in the evolutionary trajectories of species. Nevertheless, development is itself subject to evolutionary forces. Here, we describe differences at the ontogenetic and population levels in head and limb proportions of the invasive gecko Hemidactylus mabouia, to assess the developmental mechanisms and extrinsic forces associated with morphological diversification during colonization of novel habitats. We have found that allometric trajectories of most skeletal traits remain constant throughout postnatal development. Linear morphometric analysis did not find multivariate differences between ontogenetic stages or sexes. When comparing populations, our results showed that the divergence of the corresponding external measures was explained by shifts in the intercept of static allometry curves, indicating that differences arose early in development. Populations aggregated into two morphological groups that did not correspond to the groups formed on the basis of genetic structure. Using two different approaches, we found support for an adaptive hypothesis when comparing observed patterns of morphological variation with that expected under neutral evolutionary models.

Microevolutionary variation in molar morphology of Onychomys leucogaster decoupled from genetic structure

In neutral models of quantitative trait evolution, both genetic and phenotypic divergence scale as random walks, producing a correlation between the two measures. However, complexity in the genotype-phenotype map may alter the correlation between genotypic and phenotypic divergence, even when both are evolving neutrally or nearly so. Understanding this correlation between phenotypic and genetic variation is critical for accurately interpreting the fossil record. This study compares the geographic structure and scaling of morphological variation of the shape of the first lower molar of 77 individuals of the northern grasshopper mouse Onychomys leucogaster to genome-wide SNP variation in the same sample. We found strong genetic structure but weak or absent morphological structure indicating that the scaling of each type of variation is decoupled from one another. Low P_ST values relative to F_ST values are consistent with a lack of morphological divergence in contrast to genetic divergence between groups. This lack of phenotypic structure and the presence of notable within-sample phenotypic variance are consistent with uniform selection or constraints on molar shape across a wide geographic and environmental range. Over time, this kind of decoupling may result in patterns of phenotypic stasis masking underlying genetic patterns.

Morphological diversification of Mediterranean anurans: the roles of evolutionary history and climate

Investigation of the ecological and evolutionary mechanisms governing the origin and diversification of species requires integrative approaches that often have to accommodate strong discordance among datasets. A common source of conflict is the combination of morphological and molecular characters with different evolutionary rates. Resolution of these discordances is crucial to assess the relative roles of different processes in generating and maintaining biodiversity. Anuran amphibians provide many examples of morphologically similar, genetically divergent lineages, posing questions about the relative roles of phylogeny and ecological factors in phenotypic evolution. We focused on three circum-Mediterranean anuran genera (Hyla, Alytes and Discoglossus), characterizing morphological and environmental disparity and comparing diversity patterns across biological levels of organization. Using a comparative phylogenetic framework, we tested how shared ancestry and climatic factors come together to shape phenotypic diversity. We found higher morphological differentiation within Hyla and Alytes than in Discoglossus. Body size and limb morphology contributed most to inter- and intraspecific morphological variation in Hyla and Alytes, but there was no strong phylogenetic signal, indicating that shared ancestry does not predict patterns of phenotypic divergence. In contrast, we uncovered a significant association between morphology and climatic descriptors, supporting the hypothesis that morphological disparity between species results from adaptive evolution.

From micro to macroevolution: drivers of shape variation in an island radiation of Podarcis lizards

Phenotypictraits have been shown to evolve in response to variation in the environment. However, the evolutionary processes underlying the emergence of phenotypic diversity can typically only be understood at the population level. Consequently, how subtle phenotypic differences at the intraspecific level can give rise to larger-scale changes in performance and ecology remains poorly understood. We here tested for the covariation between ecology, bite force, jaw muscle architecture, and the three-dimensional shape of the cranium and mandible in 16 insular populations of the lizards Podarcis melisellensis and P. sicula. We then compared the patterns observed at the among-population level with those observed at the interspecific level. We found that three-dimensional head shape as well as jaw musculature evolve similarly under similar ecological circumstances. Depending on the type of food consumed or on the level of sexual competition, different muscle groups were more developed and appeared to underlie changes in cranium and mandible shape. Our findings show that the local selective regimes are primary drivers of phenotypic variation resulting in predictable patterns of form and function. Moreover, intraspecific patterns of variation were generally consistent with those at the interspecific level, suggesting that microevolutionary variation may translate into macroevolutionary patterns of ecomorphological diversity.

How the African house gecko (Hemidactylus mabouia) conquered the world

Alien species are among the greatest threats to biodiversity, but the evolutionary origins of invasiveness remain obscure. We conducted the first range-wide sampling of Hemidactylus mabouia from more than 120 localities across Africa, Madagascar and the Neotropics to understand the evolutionary history of one of the most widely distributed, invasive vertebrates in the world. We used a multi-locus phylogeny, species delimitation, fossil-calibrated timetree, ancestral area reconstruction and species distribution models (SDMs) to determine how many putative species-level lineages are contained within H. mabouia, the timing and tempo of diversification, and the origins of commensality-providing insights into the evolutionary origins of invasiveness. Our analyses suggest 'H. mabouia' originated in the Miocene in the Zambezian biogeographic region and includes as many as 20 putative species-level lineages, of which only Hemidactylus mabouia sensu stricto is invasive and widely distributed, including all Neotropical records. Zambezia is the hotspot for diversity within the group with 14 species in southeastern Zambezia. SDMs suggest that H. mabouia was able to establish in the Neotropics due to habitat suitability, and globalization and the slave trade probably allowed it to cross the Atlantic. Distribution models for the H. mabouia complex overpredict the range of the invasive H. mabouia sensu stricto-highlighting the importance of taxonomy in invasive species management.

Macroevolutionary variation and environmental correlates of scalation traits in Eurasian vipers (Serpentes: Viperinae)

Understanding how phenotypic variation across species is shaped by the combination of shared evolutionary history and environmental factors is key to elucidating the processes that underlie biodiversity. In reptiles, morphological traits have traditionally been used to delimit species and make systematic inferences. Recent studies highlight the possibility that phenotypic variation, particularly in scalation traits, might instead be driven by environmental factors and therefore not reflect the phylogenetic relationships among species. In this study, we combined morphological and ecological data in a macroevolutionary framework, in order to describe the morphological variation across species of Eurasian vipers (Serpentes: Viperinae), investigate the phylogenetic structure of scalation traits and test the contribution of environmental factors in shaping morphological patterns. We found considerable variation in all examined traits, which, in most cases, agreed with the phylogenetic relationships among species, reinforcing their usefulness for taxonomic inferences. Interestingly, however, the number of ventral scales exhibited lower phylogenetic signal and a tight association with environmental factors of geographical ranges, suggesting potential adaptive or developmental sources of variation in the trait. This is the first comparative study of macroevolutionary variation in scalation traits in Eurasian vipers, validating the use of most of them for systematic inferences, but also indicating possible environmental factors that might shape phenotypic variation across species.

Eco-geographical determinants of the evolution of ornamentation in vipers

Multiple hypotheses have been proposed to explain the variation of dorsal patterns observed in snakes, but no studies yet have tested them over broad taxonomic and geographical scales. The Viperidae offer a powerful model group to test eco-evolutionary processes that lead to disruptive and cryptic ornaments. We developed a database reporting dorsal ornamentation, ecological habitus, habitat features and climatic parameters for 257 out of 341 recognized species. Three patterns of dorsal ornamentation were considered: “zig-zag”, “blotchy” and “uniform” patterns. Phylogenetic comparative analyses were based on 11 mitochondrial and nuclear genes. Forty-eight species presented a zig-zag pattern type, 224 a blotchy pattern type and 32 a uniform pattern type. All the patterns showed a strong phylogenetic signal. Character phylogenetic reconstruction analyses suggested an ancestral state for blotchy ornamentation, with multiple independent evolutions of the other patterns. The blotchy pattern was more frequent in terrestrial species living in warm climates and sandy habitats, supporting the hypothesis of a disruptive function. The zig-zag pattern evolved independently in several isolated taxa, particularly in species living in cold climates and in dense vegetation or water-related habitats, supporting the hypothesis of disruptive and aposematic functions. Uniform coloration was particularly frequent in arboreal species, supporting the hypothesis of a cryptic function.

Morphological variation in Cynodon dactylon (L.) Pers., and its relationship with the environment along a longitudinal gradient

Background

Geographical variation in morphological traits may reflect evolutionary patterns of morphological adaptability along environmental gradients. Comprehensive information on longitudinal patterns of morphological trait variation is very meaningful to explore morphological diversity and evolutionary trends in widespread bermudagrass.

Methods

To explore the spatial patterns of morphological traits, we investigated 10 morphological traits of bermudagrass and 10 soil nutrient indexes and collected local climate data for 13 different regions from 119°E to 105°E along the latitude 34°N.

Results

Considerable variations in morphological traits were observed at different longitudes, and the variations in most of the evaluated traits within populations were lower than those among populations. All of the 13 different longitudinal sites were divided into three groups based on morphological traits by cluster analysis. The major sources of diversity at the different longitudes were leaf length of the erect shoot, leaf width of the erect shoot, and the internode lengths of the erect shoot and stolon as determined by principal component analysis. Pearson correlation analysis also indicated that longitude was significantly and negatively correlated with these traits as well. Mean average rainfall was significantly correlated with leaf length of the erect shoot and the internode lengths of the erect shoot and stolon, while mean average temperature was only significantly correlated with internode length of the erect shoots. Available sulfur was significantly correlated with internode length of the erect shoot, plant height, and reproductive branch height, while the exchangeable Ca was significantly correlated with internode lengths of the erect shoot and stolon. Soil pH was significantly correlated with the internode length of the stolon. Longitude is an important factor that affects morphological trait variation in wild bermudagrass, and the leaves of the erect shoot and the internode length enlarged significantly with the collection sites moving from east to west.

Conclusion

Different combinations and interactions of environmental factors (soil and climate) along a longitudinal gradient may have strong effects on one or more morphological traits of bermudagrass.