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The phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south-east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear mark-ers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in spe-cies delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera line-age from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.

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The process of speciation is often equated to the acquisition of reproductive isolation. This is a process typically envisioned as being correlated to divergence time: as time progresses the more likely it will be for diverging taxa to experience restrictions to gene exchange. This correlation has been tested and verified in a wide range of taxa; however, other aspects of differentiation, such as ecological divergence, have also been shown to correlate with reproductive isolation independently of divergence time or genomic differentiation. Characterizing reproductive isolation in multiple pairs of closely related taxa that are in different stages of the divergence process is a way of addressing these questions and disentangling the factors are more importante as engines of reproductive isolation. Wall lizards of genus Podarcis, particularly those belonging to the Iberian and North African group, are an appropriate model for this type of evaluations since they comprise various differentiated species with that establish a variety of natural contact zones. In this study we sampled and characterized patterns of hybridization in 9 contact zones between different species pairs using RADseq data. We found a generally low proportion of hybrids and contact zones were strongly bimodal in all cases, but with measurable differences in levels of gene flow among contact zones. Using data available from previous studies on this complex and in a multivariate statistical framework, we compared the level of hybridisation in each contact zone with several predictor variables: nuclear and mitochondrial genetic divergence, distribution overlap, and morphological, ecological and physiological distances between species. Our results show that, despite the general trend in other taxa, the level of hybridization in Podarcis contact zones does not seem to be correlated to divergence time. We discuss how other mechanisms may have influenced this pattern.

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Unravelling when divergent lineages constitute distinct species can be challenging, particularly in complex scenarios combining cryptic diversity and phylogenetic discordances between different types of molecular markers. Combining a phylogenetic approach with the study of contact zones can help to overcome such difficulties. The Podarcis hispanicus species complex has proven to be prosperous in independent evolutionary units, sometimes associated with cryptic diversity. Previous studies have revealed that one of the species of this complex, P. guadarramae, comprises two deeply divergent yet morphologically indistinguishable evolutionary units, currently regarded as subspecies (P. g. guadarramae and P. g. lusitanicus). In this study we used molecular data to address the systematics of the two lineages of Podarcis guadarramae and the closely related P. bocagei. Firstly, we reconstructed the species tree of these three and two additional taxa based on 30 nuclear loci using the multispecies coalescent with and without gene flow. Secondly, we used SNPs obtained from RADseq data to analyze the population structure across the distribution limits P. g. lusitanicus and P. g. guadarramae, and for comparison, a contact zone between P. bocagei and P. g. lusitanicus. Nuclear phylogenetic relationships between these three taxa are clearly difficult to determine due to the influence of gene flow, but our results give little support to the monophyly of P. guadarramae, potentially due to a nearly simultaneous divergence between them. Genetic structure and geographic cline analysis revealed that the two lineages of P. guadarramae replace each other abruptly across the sampled region and that gene flow is geographically restricted, implying the existence of strong reproductive isolation. Podarcis bocagei and P. g. lusitanicus show a similar degree of genetic differentiation and reproductive isolation, with very low levels of admixture in syntopy. These results support that all three forms are equally differentiated and reproductively isolated. In consequence, we conclude that the two former subspecies of Podarcis guadarramae constitute valid, yet cryptic species, that should be referred to as P. lusitanicus and P. guadarramae.

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Recent genetic works have suggested that the Iberian wall lizard Podarcis hispanicus (STEINDACHNER, 1870) sensu lato is a species complex. Several forms have already been elevated to species rank and linked to available nomina, but at least three still have to be formally named, including the western Iberian forms currently designated as Podarcis hispanicus“type 1A”, “type 1B” and “type 2”. The aim of the present work is to assign a valid nomen to these taxa. Using multivariate analyses, we first checked that the morphological differences reported in Portugal between type 1 and type 2 are main-tained over their distribution range. We then investigated phenotypic differentiation between type 1A and type 1B, which were found to be so similar that identification based on phenotype is currently not advisable. We propose to treat type 1 and type 2 as distinct species because of their level of genetic and phenotypic divergence, large area of distribution and ample evidence for reduced or absent introgression in contact zones. We maintain type 1A and 1B as subspecies for the time being, pending further analyses of their contact zone. The valid nomen for “Podarcis hispanica type 1 (sensu lato)” is Lacerta muralis guadarramae BOSCÁ, 1916 which becomes Podarcis guadarramae (BOSCÁ, 1916). Lineage type 1A is here described as a new taxon: P. guadarramae lusitanicus ssp. nov., inhabiting northern Portugal and northwestern Spain. The type 1B lineage corresponds to the nominotypical subspecies that inhabits Spain, mostly the Central Iberian Mountains. We were unable to locate an available nomen for “Podarcis hispanica type 2”, which is here described as Podarcis virescens sp. nov. This species is widely distributed in the plains and plateaus of central and parts of south-western Spain as well as central and southern Portugal.

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Identifying species is an important task in biology, medicine, pharmacology, agriculture and biodiversity conservation. Modern taxonomy, the discipline devoted to the description and identification of species, faces a decrease in its workforce while dealing with the challenge of describing the Earth’s vanishing biodiversity. In this context, automated identification of species becomes of major importance. Automated image identification is a thriving field of machine learning, with deep learning algorithms based on convolutional neural networks revolutionizing the field in recent years. These methods are also taking their first steps in the identification of images of biological taxa in a variety of different contexts and taxonomic scopes. In this work, we took a deep learning approach to classify images of Iberian and North African wall lizards, a group of cryptic species in which identification requires expert intervention. We addressed two problems: 1) a two-class problem focusing on the distinction between two species, Podarcis bocagei and Podarcis lusitanicus and 2) a nine-class problem involving all the species currently described in the group. Three different deep learning architectures were tested in both cases. In the two-class problem, classification success was high, reaching as high as 97.1% and 95.9% for ensemble models applied to male and female lizards, respectively. Classification in the nine-class problem was not as successful, highlighting the difficulties inherent to this group of cryptic species. However, results improved when predictions from different perspectives were combined, reaching 95.3% and 89.7% for males and females, respectively. These results suggest the utility of deep learning algorithms in the identification of cryptic species, providing promising resources in the taxonomical, evolutionary and conservation research.

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Die dem agonistischen Verhaltensrepertoire entlehnten Ausdrucksformen der Paarungsbalz und die Paarung selbst von Podarcis guadarramae lusitanicus im natürlichen Lebensraum (Serra de Montemuro/Nord-Portugal) werden beschrieben. Es besteht weitgehend Übereinstimmung mit dem Paarungsverlauf bei Podarcis hispanicus.

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Portugal ist ein beliebtes Urlaubsland. Vor allem die Metropole Lissabon und die Atlantikstrände des Algarve ziehen Touristen an. Aber das Land an der Südwestspitze Europas hat noch viel mehr zu bieten. Die Serra de Montemuro ist ein lohnendes Reiseziel auch für alle, die nach Amphibien und Reptiulien Ausschau halten.

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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.

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Sister species living in sympatry offer the opportunity to study the degree of divergence in their ecological, physiological and life-history traits. It has been hypothesized that closely related species with overlapping distribution should differ in their niche to reduce competition for resources. Furthermore, the investigation of sympatric species may shed light on how they may coexist without outcompeting each other. In the present study, we assess the degree of physiological divergence in two sympatric lacertid lizards, Podarcis bocagei and Podarcis guadarramae lusitanicus. These species share a Pliocenic ancestry and overlap at a both geographical and ecological scale. We assessed their thermal preferences and water loss rates, two physiological traits considered stable across congeneric species. We found that the two species differ in both traits, with P. bocagei selecting higher temperature than P. g. lusitanicus and losing more water than the latter at and above its preferred temperature. The results also showed that for both species body size has a relevant impact on thermal and hydric traits, with bigger individuals losing proportionally less water and selecting higher temperatures. These results, combined with previous evidence, suggest that physiological mechanisms, ecological preferences and morphology probably allow these two species to overlap in their distribution while selecting different microhabitats and thus decreasing possible competition between them.

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There is an increasing amount of evidence pointing towards the importance of bacteria and parasites in the ecology and dynamics of host populations. Complex microorganism communities living in intestinal tracts of the animals are known as the gut microbiome. These bacterial communities can impact the host’s fitness, immune system and behavior, whereas microbiome composition and diversity can be influenced by countless factors such as the host’s taxonomy, habitat, diet and social interactions with other individuals. In turn, blood parasites have a fundamental role in the ecosystem, weakening host fitness and reproductive ability, and thereby influencing population dynamics. Five lacertid lizard species were used for the present work, three endemic and two introduced: in Parque das Nações, Lisbon, the invasive Podarcis siculus (n=20) and the native Podarcis virescens (n=22); another introduced species, Teira dugesii (n=20), was captured from a distinct area of Lisbon (9 kilometres from the Parque das Naçoes); and in Moledo, Northern Portugal, two endemic and syntopic species were studied – Podarcis bocagei (n=33) and Podarcis lusitanicus (n=8). This thesis comprises two investigations. A first study was conducted in order to better understand the role and influence of environmental factors and the host in the gut microbiome composition and diversity of these five species. The second study had the objective of evaluating the effect of blood parasites on host behavior (using a mirror for the behavioral test), with the two syntopic species found in Moledo as models. This project allowed me to characterize the gut microbiome of these five species for the first time. Habitat/locality were the main factors driving gut microbiome differences between these species, and there was a greater microbiome diversity in species captured in Lisbon, the most urbanized studied site. I was able to verify a positive correlation between bacterial diversity and size in P. siculus, which indicates that it accumulates more bacteria, likely because bigger lizards explore more diverse environments. Additionally, I estimated bacteria transmission between sympatric lizards at Moledo and Parque das Nações. High transmission was verified for both populations. Results from the Lisbon population indicate that the invasive species, P. siculus might have acquired a higher proportion of local microbiota through the native species, P. virescens than vice versa. The second study highlighted the infection prevalence differences between P. bocagei and P. lusitanicus, with a larger number of infected individuals in the former. However, P. lusitanicus registered a higher average parasite intensity. The species that interacted with the mirror the most, and was therefore considered bolder, was P. lusitanicus. Contrary to what was expected, the individuals that interacted with the mirror the most, were more parasitized. This thesis aids in understanding the behavior and broadening the sphere of knowledge of microorganisms (bacteria and microparasites) and their interactions with the host. Such work is fundamentally important, and increased investment in these areas of knowledge is essential for species conservation.

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Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as taxonomy, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. In this study, we investigated the influence of taxonomy, sex, host size, locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal. We also analyzed the potential levels of microbial transmission between species that live in sympatry and syntopy. We studied Podarcis bocagei and Podarcis lusitanicus from northern Portugal (Moledo); and two invasive species, Podarcis siculus and Teira dugesii, and the native Podarcis virescens from Lisbon. We used a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Habitat/locality was found to be the main driver of the differences in composition and structure of gut bacterial communities of the studied lizards, with host effects more evident at finer taxonomic scales. Additionally, lizards from urbanized environments had higher microbiome diversity than lizards from rural areas. We detected a significant positive correlation between size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to higher exploratory behaviours. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota. These findings indicate that a diverse array of host and environmental factors can influence lizards gut microbiota.

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Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To accomplish these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e. species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards gut microbiota.