Spotlight on islands.On the origin and diversification of an ancient lineage of the Italian wall lizard Podarcis siculus in the western Pontine Islands

Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts

No association between candidate genes for color determination and color phenotype in Hierophis viridiflavus, and characterization of a contact zone

Genetic and phenotypic differentiation in allopatric conditions can be explained either by neutral phenomena or adaptative processes driven by selection. In reptiles, coloration can affect aspects directly related to their survival, representing a classical character under selection. In this context, secondary contact areas are natural laboratory to understand evolutionary processes underlying genetic permeability, especially when populations differ in phenotypic traits such as coloration. The western whip snake Hierophis viridiflavus presents two divergent mitochondrial clades, characterized by the presence of one of two main color phenotypes, namely one with black and yellow stripes and a fully melanic one. Here, we investigated whether melanogenesis-linked genes are determinant of the chromatic differences observed across the phenotypic variation of the species. In addition, we used a multilocus dataset, including 134 original ND4 sequences, to better define the overall genetic structure and to provide a characterization of a contact zone identified in Central Italy by estimating the amount of nuclear gene exchange. While we found no evidence supporting a direct association between target genes and coloration, a non-synonymous substitution polymorphism, at high frequency, was detected in the β melanocyte-stimulating hormone whose possible function has been discussed. Concerning the genetic structure, both mtDNA and nuDNA were partly concordant indicating introgression events occurring at the contact zone. When we measured the nuclear gene flow, we found a significant amount of gene exchange, mainly guided from one clade to the other, that is, asymmetric. These results might suggest the presence of ecological and/or behavioral processes driving the observed directional gene flow

Evolutionary and demographic correlates of Pleistocene coastline changes in the Sicilian wall lizard Podarcis wagleriana

Aim Emergence of coastal lowlands during Pleistocene ice ages might have provided conditions for glacial expansions (demographic and spatial), rather than contraction, of coastal populations of temperate species. Here, we tested these predictions in the insular endemic Sicilian wall lizard Podarcis wagleriana. Location Sicily and neighbouring islands. Methods We sampled 179 individuals from 45 localities across the whole range of P. wagleriana. We investigated demographic and spatial variations through time using Bayesian coalescent models (Bayesian phylogeographic reconstruction, Extended Bayesian Skyline plots, Isolation‐with‐migration models) based on multilocus DNA sequence data. We used species distribution modelling to reconstruct present and past habitat suitability. Results We found two main lineages distributed in the east and west portions of the current species range and a third lineage restricted to a small area in the north of Sicily. Multiple lines of evidence from palaeogeographic (shorelines), palaeoclimatic (species distribution models), and multilocus genetic data (demographic and spatial Bayesian reconstructions) indicate that these lineages originated in distinct refugia, located in the north‐western and south‐eastern coastal lowlands, during Middle Pleistocene interglacial phases, and came into secondary contact following demographic and spatial expansions during the last glacial phase. Main conclusions This scenario of interglacial contraction and glacial expansion is in sharp contrast with patterns commonly observed in temperate species on the continent but parallels recent findings on other Mediterranean island endemics. Such a reverse expansion–contraction (EC) dynamic has been likely associated with glacial increases of climatically suitable coastal lowlands, suggesting this might be a general pattern in Mediterranean island species and also in other coastal regions strongly affected by glacial marine regressions during glacial episodes. This study provides explicit predictions and some methodological recommendations for testing the reverse EC model in other region and taxa

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity

Who are you? The genetic identity of some insular populations of <em>Hierophis viridiflavus</em> s.l. from the Tyrrhenian Sea

This work investigates the genetic identity of Hierophis viridiflavus s.l. specimens from insular populations, to determine which of the two previously identified species is present on each island. Here, the authors hypothesise about times and modes of colonization and discuss the faunistic value of the obtained results. This follows the recent proposal to consider the two clades as two different species. Specimens from the islands of Favignana, Lipari and Vulcano belong to H. carbonarius and probably all belong to putative Sicilian source populations. Conversely, all individuals from the Pontine Islands (Ponza, Palmarola, Ventotene) should be considered to belong to H. viridiflavus. Even if genetically identical to the specimens from the Tyrrhenian Italian coast, these individuals show a darker colouration, very similar to the one usually shown by H. carbonarius specimens. Considering that the Pontine H. viridiflavus populations probably have a very recent origin, the dark livery of these individuals could be the result of a rapid morphological adaptation to insular environments

Who are you? The genetic identity of some insular populations of Hierophis viridiflavus s.l. from the Tyrrhenian Sea

This work investigates the genetic identity of Hierophis viridiflavus s.l. specimens from insular populations, to determine which of the two previously identified species is present on each island. Here, the authors hypothesise about times and modes of colonization and discuss the faunistic value of the obtained results. This follows the recent proposal to consider the two clades as two different species. Specimens from the islands of Favignana, Lipari and Vulcano belong to H. carbonarius and probably all belong to putative Sicilian source populations. Conversely, all individuals from the Pontine Islands (Ponza, Palmarola, Ventotene) should be considered to belong to H. viridiflavus. Even if genetically identical to the specimens from the Tyrrhenian Italian coast, these individuals show a darker colouration, very similar to the one usually shown by H. carbonarius specimens. Considering that the Pontine H. viridiflavus populations probably have a very recent origin, the dark livery of these individuals could be the result of a rapid morphological adaptation to insular environments

The intriguing biogeographic pattern of the Italian wall lizard Podarcis siculus (Squamata: Lacertidae) in the Tuscan Archipelago reveals the existence of a new ancient insular clade

The Tuscan Archipelago is one of the most ancient and ecologically heterogeneous island systems in the Mediterranean. The biodiversity of these islands was strongly shaped by the Pliocene and Pleistocene sea regressions and transgression, resulting in different waves of colonization and isolation of species coming from the mainland. The Italian wall lizard, Podarcis siculus, is present on the following islands of the Tuscan Archipelago: Elba, Giglio, Giannutri, Capraia, Montecristo and Cerboli. The species in the area displays a relatively high morphological variability that in the past led to the description of several subspecies. In this study, both the genetic and morphological diversity of P. siculus of the Tuscan Archipelago were investigated. Specifically, the meristic characters and the dorsal pattern were analyzed, while the genetic relationships among these populations were explored with mtDNA and microsatellite nuclear markers to reconstruct the colonization history of the Archipelago. Our results converge in the identification of at least two different waves of colonization in the Archipelago: Elba, and the populations of Cerboli and Montecristo probably originate from historical introductions from mainland Tuscany, while those of Giglio and Capraia are surviving populations of an ancient lineage which colonized the Tuscan Archipelago during the Pliocene and which shares a common ancestry with the P. siculus populations of south-eastern Italy. Giannutri perhaps represents an interesting case of hybridization between the populations from mainland Tuscany and the Giglio-Capraia clade. Based on the high phenotypic and molecular distinctiveness of this ancient clade, these populations should be treated as distinct units deserving conservation and management efforts as well as further investigation to assess their taxonomic status

Seeing the wood through the trees. Combining shape information from different landmark configurations

The geometric morphometric (GM) analysis of complex anatomical structures is an ever more powerful tool to study biological variability, adaptation and evolution. Here, we propose a new method (combinland), developed in R, meant to combine the morphological information contained in different landmark coordinate sets into a single dataset, under a GM context. combinland builds a common ordination space taking into account the entire shape information encoded in the starting configurations. We applied combinland to a Primate case study including 133 skulls belonging to 14 species. On each specimen, we simulated photo acquisitions converting the 3D landmark sets into six 2D configurations along standard anatomical views. The application of combinland shows statistically negligible differences in the ordination space compared to that of the original 3D objects, in contrast to a previous method meant to address the same issue. Hence, we argue combinland allows to correctly retrieve 3D-quality statistical information from 2D landmark configurations. This makes combinland a viable alternative when the extraction of 3D models is not possible, recommended, or too expensive, and to make full use of disparate sources (and views) of morphological information regarding the same specimens. The code and examples for the application of combinland are available in the Arothron R package

On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach