Genetic and morphological relationships of the Berlenga wall lizard (Podarcis bocagei berlengensis: Lacertidae)

Six biometric characters and 15 electrophoretic loci of three known subspecies of Podarcis bocagei were studied. Contrary to biometric indications, Podarcis bocagei berlengensis showed a closer genetic relationship with Podarcis bocagei carbonelli than with the nominal subspecies. The biometric results were confounded by the relative large size of P. b. berlengensis . Post-glacial colonization from two different areas might explain the greater genetic differentiation between the P. b. bocagei and P. b. carbonelli populations (Nei's D - 0.158 - near the species threshold). It might also explain the known colonization of these two lizards through the islands off the west coast of the Iberian penninsula and their present distributions to the north of (Galicia; Northern Portugal) and to the south of the valley of river Douro (central Portugal, western and Sistema Central), respectively.     

Contrasting patterns of population subdivision and historical demography in three western Mediterranean lizard species inferred from mitochondrial DNA variation

Pleistocene climatic oscillations were a major force shaping genetic variability in many taxa. We analyse the relative effects of the ice ages across a latitudinal gradient in the Western Mediterranean region, testing two main predictions: (i) species with historical distributions in northern latitudes should have experienced greater loss of suitable habitat, resulting in higher extinction of historical lineages than species distributed in southern latitudes, where the effects of the ice ages were not as drastic. This would be reflected in the observation of lower diversity and number of differentiated lineages in northern areas. (ii) a signature of demographic expansion following the climate amelioration should be obvious in northern species, whereas in the south evidence of long-term effective population size stability should be observed. We used as models three species of wall lizards (Podarcis bocagei, Podarcis carbonelli and Podarcis vaucheri) that replace each other along the study area. We investigated the patterns of mitochondrial DNA diversity and subdivision and obtained demographic parameter estimates for each species. Our results suggest that P. bocagei, the northernmost species, bears low genetic diversity, a shallow coalescent history and marks of a demographic expansion. In contrast, P. vaucheri, the species with a southernmost distribution, shows deeper coalescence events, complex geographical substructure and no evidence for population growth. The species with an intermediate distribution, P. carbonelli, shows average levels of diversity, substructure and population growth. Taken together, these results conform to our main predictions and are explained by a differential influence of the ice ages on distinct latitudes.     

Pheromonal discriminations of sex,reproductive condition,and species by the lacertid lizard Podarcis hispanica

In some vertebrate taxa, pheromones provide important information about species, sex, reproductive condition, kinship, and even individual identity. Because they possess highly developed nasal chemosensory systems, lizards are capable of many chemical discriminations, but many aspects of their pheromonal communication remain poorly understood even in major families. We report that males of a lacertid lizard, Podarcis muralis, are capable of differential response to surface chemical cues from conspecific males and females, from gravid and nongravid females, and from conspecific females and females of the closely related sympatric congener, P. bocagei carbonelli. In 60 sec trials in which stimuli from the femoral, cloacal, lateral, and upper body surfaces were presented to males on cotton swabs, males tongue-flicked at significantly higher rates to stimuli from conspecific females than males, from conspecific nongravid than gravid females, and from conspecific than heterospecific females. Responses to stimuli from conspecific males did not differ from those to distilled water. Together with previous findings that males can distinguish between chemical cues from familiar and unfamiliar males, these findings suggest that pheromones provide male P. hispanica important information regarding the presence of sexual rivals and the reproductive condition of potential mates without visually encountering other lizards. A growing body of literature indicates that lacertids are capable of sophisticated pheromonal discriminations that may play important roles in their social behavior.     

Comparing patterns of nuclear and mitochondrial divergence in a cryptic species complex: the case of Iberian and North African wall lizards (Podarcis, Lacertidae)

Combining different sources of information is essential for a complete understanding of the process of genetic differentiation between species. The Iberian and North African wall lizard ( Podarcis ) species complex has been the object of several studies regarding morphological and mitochondrial DNA variation but, so far, no large-scale survey of nuclear variation within this group has been accomplished. In this study, ten polymorphic allozyme loci were studied in 569 individuals collected across the Iberian Peninsula and North Africa. The obtained data were analysed using both conventional population genetic tools and recent Bayesian model-based clustering methods. Our results show that there are several well-differentiated entities corroborating the major splits observed in mtDNA analyses. These groups correspond not only to the fully recognized species Podarcis bocagei , Podarcis carbonelli , and Podarcis vaucheri but also to multiple forms within the polytypic Podarcis hispanica , all of which have a similar level of differentiation to that observed between the acknowledged species. However, relationships between forms are weakly supported both by population and individual clustering methods, suggesting a scenario of a rapid diversification that contrasts to the clear bifurcating model assumed from previous mtDNA analyses. Individual multilocus analyses report few individuals misassigned or apparently admixed, some of which are most likely explained by the persistence of high levels of ancestral polymorphism. Other admixed individuals, however, are probably the result of limited levels of gene flow between forms.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 121–133.     

Multivariate and geometric morphometrics in the analysis of sexual dimorphism variation in Podarcis lizards

Podarcis bocagei and P. carbonelli are two closely related lacertid species, very similar morphologically and ecologically. We investigated sexual dimorphism patterns presented by both species in allopatry and in sympatry. Sexual size and shape dimorphism patterns were analyzed using both multivariate and geometric morphometric techniques. Multivariate morphometrics revealed a marked sexual dimorphism in both species--males being larger with more robust habitus and females presenting a longer trunk. General patterns of sexual size dimorphism are not modified in sympatry, although there is evidence for some morphological change in male head size. The application of geometric morphometrics offered a more detailed image of head shape and revealed that males present a more developed tympanic area than do females, while females have a more rounded head. Differences in the degree of sexual shape dimorphism were detected in sympatry, but no consistent patterns were observed. From the results of the study, and based on previous knowledge on the populations studied, we conclude that the morphological differences observed are probably not caused by exploitative competition between the species, but rather appear attributable to the modification of the relative influence of sexual and natural selection on both sexes.     

Head shape allometry and proximate causes of head sexual dimorphism in Podarcis lizards: joining linear and geometric morphometrics

Podarcis bocagei and Podarcis carbonelli are two lacertid species endemic to the western Iberian Peninsula, and both show head size and shape sexual dimorphism. We studied immature and adult head sexual dimorphism and analysed ontogenetic trajectories of head traits with body and head size, aiming to shed light on the proximate mechanisms involved. Immatures were much less dimorphic than adults, but geometric morphometric techniques revealed that head shape sexual differences are already present at this stage. Males and females differed in allometry of all head characters with body size, with males showing a disproportionate increase of head size and dimensions. On the other hand, head dimensions and head shape changed with increasing head size following similar trends in both sexes, possibly indicating developmental restrictions. Consequently, adult sexual dimorphism for head characters in these species is the result of both shape differences in the immature stage and hypermetric growth of the head in relation to body size in males.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 111–124.     

Good species despite massive hybridization: genetic research on the contact zone between the watersnakes Nerodia sipedon and N. fasciata in the Carolinas, USA

Genomic markers generated with the amplified fragment length polymorphism method revealed extensive, panmictic-like hybridization along the narrow contact zone between the water snakes Nerodia sipedon and Nerodia fasciata in the Carolinas, USA. However, asymmetric distributions of diagnostic markers between both species and low frequencies of backcrossed hybrids with a high value of interspecific mixture infer selection against certain genotypes. This is consistent with a pronounced genetic and morphological preponderance of N. fasciata characters in the hybrid zone. Despite massive hybridization within the contact zone, the existence of nearly fixed genetic markers and the potential inferiority of certain hybrid genotypes support the species status of the two taxa and corroborate known, but nondiagnostic differences in morphology and ecology. This study stretches the applicability of species concepts to cases, where the genetic compatibility between two closely related species is very high, yet, they still evolve and persist as independent entities.     

Lack of congruence of genetic and niche divergence in Podarcis hispanicus complex

Niche divergence among closely related lineages can be informative on the ecological and evolutionary processes involved in differentiation, particularly in the case of cryptic species complexes. Here we compared phylogenetic relationships and niche similarity between pairs of lineages included in the Podarcis hispanicus complex to examine patterns of niche divergence and its role in the organization of current diversity patterns, as allopatric, parapatric, and sympatric lineages occur in the Western Mediterranean Basin. First, we used ecological niche models to characterize the realized climatic niche of each Podarcis hispanicus complex lineage based on topographic and climatic variables, to identify important variables, and to test for niche conservatism or divergence between pairs of lineages. Variables related to precipitation generally exhibited the highest contribution to niche models, highlighting the importance of rainfall levels in shaping distributions of Podarcis wall lizards. We found that most forms have significant differences in realized climatic niches that do not follow the pattern of mitochondrial divergence. These results lend support to the hypothesis that genetic divergence across Podarcis hispanicus complex most likely occurred in allopatric conditions, mostly with significant niche divergence. Competition after secondary contact is also suggested by the common occurrence of niche overlap between lineages that exhibit strictly parapatric distribution. The almost continuous distribution of Podarcis lizards in the study area appears to be a result of a combination of complementary suitable niches and competition, which seem two important mechanisms limiting geographic distributions and restricting the existence of extensive contact zones.     

Bidirectional introgressive hybridization between Lepus capensis and Lepus yarkandensis

Lepus capensis and Lepus yarkandensis are two well-established hare species with different habitat preferences and obvious morphological distinctions. L. capensis is common and widespread while L. yarkandensis is an endemic species with a restricted distribution in the Tarim Basin of western China. During field sampling, individuals with a distinct phenotype were found in the contact zone between the two species. To understand the origin of these unclassified individuals, we analyzed morphological and genetic data from 700 individuals including L. yarkandensis, L. capensis and the unclassified individuals. Morphological analyses of the unclassified individuals revealed that they lie between L. yarkandensis and L. capensis. Genetic analyses based on species-specific molecular markers (mitochondrial control region and SRY) showed that the unclassified populations have mtDNA and SRY genes from both L. capensis and L. yarkandensis, suggesting that the unclassified populations result from hybridization between the two species. Interestingly, many identical and/or very similar mtDNA haplotypes were shared between L. capensis populations and L. yarkandensis populations close to their contact zones, which further suggests the existence of extensive bidirectional mtDNA introgression. Similarly, we found evidence for SRY introgression, though it existed at a lower level compared to mtDNA introgression.     

Morphology and nuclear markers reveal extensive mitochondrial introgressions in the Iberian Wall Lizard species complex

Mitochondrial markers are still often used alone to identify evolutionary units, despite widespread evidence for processes such as incomplete lineage sorting or introgressive hybridization that may blur past population history. The combination of mitochondrial DNA data with other sources of information (morphology, nuclear genes) is a powerful tool to reveal when and why mitochondrial markers are potentially misleading. In this study, we evaluate the performance of mtDNA markers to unravel the evolutionary history of Spanish lizards from the Podarcis hispanicus species complex. We first uncover several cases of discordance between morphological and mitochondrial data in delimitation of taxa. To assess the origin of these discordances, we analysed the same populations using several independent nuclear loci. Both morphological and nuclear markers identified the same three evolutionary units in the region, while mitochondrial data revealed four deeply divergent lineages. We suggest here that the most likely scenario to explain this discordance is ancient mitochondrial introgression originating from a fourth evolutionary unit presently absent from the study area. Notably, this resulted in a complete replacement of the original lineage in a large part of the distribution of one of the taxa investigated. We discuss the potential evolutionary scenarios leading to this complete mitochondrial replacement and suggest why the previous studies have failed to recover the correct history of this species complex.     

Molecular phylogenetics of Iberian wall lizards (Podarcis): is Podarcis hispanica a species complex?

Phylogenetic relationships between species and morphotypes of Podarcis wall lizards from the Iberian Peninsula and north Africa were estimated using partial 12S rRNA and cytochrome b mitochondrial DNA sequences. All species except Podarcis hispanica form monophyletic units. P. hispanica is paraphyletic, although all identified morphotypes are monophyletic. These morphotypes represent highly divergent lineages showing 10-15% pairwise sequence divergence with the cytochrome b gene. The data suggest that P. hispanica is a species complex. We recommend using P. hispanica* until additional sampling delimits the number and ranges of species currently referred to P. hispanica. P. carbonelli, which has recently been raised to species status, is confirmed as a genetically distinct form. P. atrata is genetically distinct, but much more closely related to some populations of P. hispanica than previously thought.     

Can alternative mating tactics facilitate introgression across a hybrid zone by circumventing female choice?

Reproductive barriers and divergence in species’ mate recognition systems underlie major models of speciation. However, hybridization between divergent species is common, and classic mechanisms to explain permeable reproductive barriers rarely consider how an individual may attain reproductive success. Alternative mating tactics (AMTs) exist in various forms across animal taxa. Such tactics may allow poorer quality individuals to gain mating opportunities and facilitate introgression either through asymmetrical positive selection or by circumventing female choice altogether in areas of secondary contact. One such tactic is satellite behaviour in frogs, where silent males perch near advertisers in an attempt to intercept females. To test whether such satellite male tactics are context‐dependent and favoured by hybrids, we genotyped and quantified the morphology of 80 male spring peeper (Pseudacris crucifer) individuals involved in caller–satellite associations from a secondary contact zone between two intraspecific mitochondrial lineages. Irrespective of population, satellite behaviour was best predicted by size but not body condition. Within the contact zone, pure individuals showed a significantly greater probability of being active callers, whereas hybrids of one lineage were more likely to adopt the satellite tactic. We suggest that satellite behaviour in P. crucifer promotes introgression, breaks down reproductive isolating barriers and contributes to asymmetrical introgression in this secondary contact zone. AMTs may thus be an underexplored but important alternative to oft‐discussed causes of genetic discordance found in hybrid zones.     

Variation in the cranium shape of wall lizards (Podarcis spp.): effects of phylogenetic constraints, allometric constraints and ecology

We used geometric morphometrics to explore the influence of phylogenetic and allometric constraints as well as ecology on variation in cranium shape in five species of monophyletic, morphologically similar Podarcis lizards (Podarcis erhardii, Podarcis melisellensis, Podarcis muralis, Podarcis sicula and Podarcis taurica). These species belong to different clades, they differ in their habitat preferences and can be classified into two distinct morphotypes: saxicolous and terrestrial. We found (i) no phylogenetic signal in cranium shape, (ii) diverging allometric slopes among species, and (iii) a significant effect of habitat on cranium shape. The saxicolous species (P. erhardii and P. muralis) had crania with elongated parietals, elongated cranium bases, shortened anterior parts of the dorsal cranium, reduced chambers of the jaw adductor muscles and larger subocular foramina. These cranial features are adaptations that compensate for a flattened cranium, dwelling on vertical surfaces and seeking refuge in crevices. The crania of the terrestrial species (P. melisellensis, P. sicula and P. taurica) tended to be more elongate and robust, with enlarged chambers of the jaw adductor muscle, reduced skull bases and shortened parietals. Terrestrial species exhibited more variation in cranium shape than saxicolous species. Our study suggests that shape variation in Podarcis sp. lizards is largely influenced by ecology, which likely affects species-specific patterns of static allometry.     

Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil

Natural hybrid zones between distinct species have been reported for many taxa, but so far, few examples involve carnivores or Neotropical mammals in general. In this study, we employed mitochondrial DNA (mtDNA) sequences and nine microsatellite loci to identify and characterize a hybrid zone between two Neotropical felids, Leopardus geoffroyi and L. tigrinus, both of which are well-established species having diverged from each other c. 1 million years ago. These two felids are mostly allopatric throughout their ranges in South America, with a narrow contact zone that includes southern Brazil. We present strong evidence for the occurrence of hybridization between these species and identify at least 14 individuals (most of them originating from the geographical contact zone) exhibiting signs of interspecific genomic introgression. The genetic structure of Brazilian L. tigrinus populations seems to be affected by this introgression process, showing a gradient of differentiation from L. geoffroyi correlated with distance from the contact zone. We also corroborate and extend previous findings of hybridization between L. tigrinus and a third related felid, L. colocolo, leading to an unusual situation for a mammal, in which the former species contains introgressed mtDNA lineages from two distinct taxa in addition to its own.     

Mito‐nuclear discordance across a recent contact zone for California voles

To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi‐permeable. Using mitochondrial cytochrome b sequences and genome‐wide loci developed via ddRAD‐seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5–54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.     

Introgression at differentially aged hybrid zones in red-tailed chipmunks

Hybrid zones allow us to investigate the maintenance and the break down of reproductive isolation; they are a window into the speciation process. Tamias ruficaudus (red-tailed chipmunk) has a roughly ring-like distribution in the Inland Northwest and includes two morphologically well-differentiated subspecies, T. r. ruficaudus (in the eastern portion of its range) and T. r. simulans (in the western portion). These taxa meet at two contact zones: the Lochsa River in Idaho and 200 km to the north, near Whitefish, Montana. The Lochsa Zone is encompassed within the Clearwater River Drainage, which has been proposed as a glacial refugium for many taxa throughout the Pleistocene, whereas the Whitefish Zone was under the Cordilleran ice sheet during the most recent glacial maxima approximately 10,000 years ago. Mitochondrial DNA introgression has been documented at both contact zones, yet the subspecies remain significantly distinct with respect to bacular morphology and no intermediate morphologies have ever been reported. Here, we elucidate differentiation and introgression of the nuclear genome using ten microsatellite loci and compare findings to previously described mitochondrial DNA haplotype distribution and introgression. We found significant substructure in the nuclear data; each subspecies is divided into at least two genetically distinct demes. At the Lochsa contact zone, individuals restricted to the mtDNA zone of introgression form a distinct deme at microsatellite loci whereas in the younger, Whitefish contact zone, there is no hybrid-zone specific group. The genetic distances of the demes within these two subspecies indicate recent northward expansion.     

Multilocus and morphological analysis of south-eastern Iberian Wall lizards (Squamata,Podarcis)

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 markers 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 species 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 lineage 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.     

Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers

Contact zones between recently diverged taxa offer unique opportunities to test whether the forms are reproductively isolated and therefore distinct species. The Pacific‐slope flycatcher Empidonax difficilis and Cordilleran flycatcher Empidonax occidentalis are closely related taxa that were officially separated into two species in 1989, a treatment that has been controversial due to reports of phenotypically intermediate birds across the southern interior of British Columbia and Alberta. We present the first analysis of molecular variation across this region, in order to determine whether there is genetic introgression between the taxa. Allopatric populations of Pacific‐slope and Cordilleran flycatchers belong to distinct mitochondrial clades, and all of the individuals sampled in interior southwestern Canada have the Pacific‐slope haplotype. In contrast, variation in nuclear DNA (AFLPs) indicates hybridization between Pacific‐slope and Cordilleran flycatchers in this region. We suggest that the discordance between the mitochondrial and nuclear markers most likely results from stochastic loss of Cordilleran mitochondrial haplotype lineages facilitated by asymmetries in mating due to earlier arrival and greater abundance of Pacific‐slope flycatchers in the contact zone. The discovery of hybridization between Pacific‐slope and Cordilleran flycatchers in southwestern Canada may call into question the decision to split them into two species. On the other hand, allopatric populations are genetically distinct in both mitochondrial and nuclear DNA, and the hybridization might not affect populations outside of the contact zone. This study highlights the importance of employing multiple genetic markers in studies of contact zones between closely related species.     

PATTERNS OF VARIATION AND LINKAGE DISEQUILIBRIUM IN A FIELD CRICKET HYBRID ZONE

The distribution of multilocus genotypes found within a natural hybrid zone is determined by the sample of genotypes present when the hybrid zone first formed, by subsequent patterns of genetic exchange between the hybridizing taxa, and by drift and selection within each of the hybrid zone populations. We have used anonymous nuclear DNA restriction fragment polymorphisms (RFLPs) to characterize the array of multilocus genotypes present within a well-studied hybrid zone between two eastern North American field crickets, Gryllus pennsylvanicus and Gryllus firmus. These crickets hybridize along a zone of contact that extends from New England to Virginia. Previous studies have shown that both premating and postmating barriers exist between the two cricket species, but the absence of diagnostic morphological and allozyme markers has made it difficult to assess the consequences of these barriers for genetic exchange. Analyses based on four diagnostic anonymous nuclear markers indicate that hybrid zone populations in Connecticut contain few F₁ hybrids, and that nonrandom associations persist among nuclear gene markers, between nuclear and cytoplasmic markers, and between molecular markers and morphology. Field cricket populations within the hybrid zone are not “hybrid swarms” but consist primarily of crickets that are very much like one or the other of the parental species. Despite ample opportunity for genetic exchange and evidence for introgression at some loci, the two species remain quite distinct. Such a pattern appears to be characteristic of many natural hybrid zones.     

Chemical communication,sexual selection,and introgression in wall lizards

Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters, but the associations were variable and inconsistent between lineages. In experimental contact zones, chemical composition was weakly associated with male reproductive success, and did not predict the likelihood of hybridization. Consistent with these results, introgression of chemical profiles in a natural hybrid zone resembled that of neutral nuclear genetic markers overall, but one compound in particular (tocopherol methyl ether) matched closely the introgression of visual sexual characters. These results imply that associations among male chemical profiles, sexual characters, and reproductive success largely reflect transient and environmentally driven effects, and that genetic divergence in chemical composition is largely neutral. We therefore suggest that femoral secretions in wall lizards primarily provide information about residency and individual identity rather than function as sexual signals.