Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Senczuk G

PROVIDER: S-EPMC6181948 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus.

Project description:The current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n?=?277 from 115 localities) and nuclear mc1r and ?-fibint7genes (n?=?262 and n?=?91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM).We identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula.Our population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.

| S-EPMC5216540 | biostudies-literature

The Intriguing Biogeographic Pattern of the Italian Wall Lizard <i>Podarcis siculus</i> (Squamata: Lacertidae) in the Tuscan Archipelago Reveals the Existence of a New Ancient Insular Clade.

Project description: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.

| S-EPMC9913114 | biostudies-literature

Phylogeography and conservation genetics of the common wall lizard, Podarcis muralis, on islands at its northern range.

Project description:Populations at range limits are often characterized by lower genetic diversity, increased genetic isolation and differentiation relative to populations at the core of geographical ranges. Furthermore, it is increasingly recognized that populations situated at range limits might be the result of human introductions rather than natural dispersal. It is therefore important to document the origin and genetic diversity of marginal populations to establish conservation priorities. In this study, we investigate the phylogeography and genetic structure of peripheral populations of the common European wall lizard, Podarcis muralis, on Jersey (Channel Islands, UK) and in the Chausey archipelago. We sequenced a fragment of the mitochondrial cytochrome b gene in 200 individuals of P. muralis to infer the phylogeography of the island populations using Bayesian approaches. We also genotyped 484 individuals from 21 populations at 10 polymorphic microsatellite loci to evaluate the genetic structure and diversity of island and mainland (Western France) populations. We detected four unique haplotypes in the island populations that formed a sub-clade within the Western France clade. There was a significant reduction in genetic diversity (HO, HE and AR) of the island populations in relation to the mainland. The small fragmented island populations at the northern range margin of the common wall lizard distribution are most likely native, with genetic differentiation reflecting isolation following sea level increase approximately 7000 BP. Genetic diversity is lower on islands than in marginal populations on the mainland, potentially as a result of early founder effects or long-term isolation. The combination of restriction to specific localities and an inability to expand their range into adjacent suitable locations might make the island populations more vulnerable to extinction.

| S-EPMC4319766 | biostudies-literature

Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Gunther, 1874) from the Balearic Islands (Spain).

Project description:The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.

| S-EPMC10214862 | biostudies-literature

Biological responses in pesticide exposed lizards (Podarcis siculus).

Project description:The release of contaminants as herbicides, fungicides and insecticides into the environment has been listed as one of the six major contributors to the global decline of reptiles. Although reptiles may face severe risk from contaminants due to their ecology and physiology, they are currently less studied than other vertebrate groups. In the present work, we investigated if and how different types of field treatment (conventional and organic) affected the health status of Italian wall lizard (Podarcis siculus) individuals in central Italy. We chose a multi-biomarker approach that evaluated the biological responses of lizards to the treatment by means of AChE activity in the nervous system, biotransformation enzymes activities and oxidative stress in the liver, micronuclei frequency measured in the erythrocytes, and rate of intestinal parasitic infection. Our findings showed evidence of effects of treatment in conventional areas and between sexes with significant oxidative stress due to hydroxyl radicals, that caused DNA damage. No difference of intestinal parasite infections was found among treatments. Podarcis siculus seems to be a good bioindicator in ecotoxicological studies and potentially in risk assessment of pesticides, although further analyses in laboratory and in the field are needed to achieve more accurate quantification of specific pesticide effects in relation to known exposure history and to understand if other mechanisms were involved in the toxicity and detoxification process of pesticides for this species.

| S-EPMC8295152 | biostudies-literature

Podarcis siculus

Project description:Podarcis siculus Genome sequencing and assembly

| PRJNA1032059 | ENA

Podarcis siculus

Project description:Podarcis siculus Raw sequence reads

| PRJNA470799 | ENA

Podarcis siculus

Project description:Podarcis siculus overview

| PRJNA470979 | ENA

Diet composition of the lizard Podarcis lilfordi (Lacertidae) on 2 small islands: an individual-resource network approach.

Project description:Despite it is widely accepted that intrapopulation variation is fundamental to ecological and evolutionary processes, this level of information has only recently been included into network analysis of species/population interactions. When done, it has revealed non-random patterns in the distribution of trophic resources. Nestedness in resource use among individuals is the most recurrent observed pattern, often accompanied by an absence of modularity, but no previous studies examine bipartite modularity. We use network analysis to describe the diet composition of the Balearic endemic lizard Podarcis lilfordi in 2 islets at population and individual levels, based on the occurrence of food items in fecal samples. Our objectives are to 1) compare niche structure at both levels, 2) characterize niche partition using nestedness and modularity, and 3) assess how size, sex, season, and spatial location influence niche structure. At population-level niche width was wide, but narrow at the level of the individual. Both islet networks were nested, indicating similar ranking of the food preferences among individuals, but also modular, which was partially explained by seasonality. Sex and body size did not notably affect diet composition. Large niche overlap and therefore possibly relaxed competition were observed among females in one of the islets and during spring on both islets. Likewise, higher modularity in autumn suggests that higher competition could lead to specialization in both populations, because resources are usually scarce in this season. The absence of spatial location influence on niche might respond to fine-grained spatio-temporally distribution of food resources. Behavioral traits, not included in this study, could also influence resource partitioning.

| S-EPMC7245015 | biostudies-literature

Unravelling the Role of Metallothionein on Development, Reproduction and Detoxification in the Wall Lizard Podarcis sicula.

Project description:Metallothioneins (MTs) are an evolutionary conserved multigene family of proteins whose role was initially identified in binding essential metals. The physiological role of MT, however, has been revealed to be more complex than expected, since not only are MTs able to bind to toxic heavy metals, but many isoforms have shown specialized and alternative functions. Within this uncertainty, the information available on MTs in non-mammalian vertebrates, particularly in neglected tetrapods such as the reptiles, is even more scant. In this review, we provide a summary of the current understanding on metallothionein presence and function in the oviparous lizard Podarcis sicula, highlighting the results obtained by studying MT gene expression in most representative adult and embryonic tissues. The results demonstrate that in adults, cadmium induces MT transcription in a dose- and tissue-specific manner. Thus, the MT mRNAs appear, at least in some cases, to be an unsuitable tool for detecting environmental ion contamination. In early embryos, maternal RNAs sustain developmental needs for MT protein until organogenesis is well on its way. At this time, transcription starts, but again in a tissue- and organ-specific manner, suggesting an involvement in alternative roles. In conclusion, the spatiotemporal distribution of transcripts in adults and embryos definitively confirms that MT has deserved the title of elusive protein.

| S-EPMC5536057 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data