Testing for heterogeneity among phenotypic correlations: a comparison of methods using Monte Carlo simulations

Heterogeneous phenotypic correlations may be suggestive of underlying changes in genetic covariance among life-history, morphology, and behavioural traits, and their detection is therefore relevant to many biological studies. Two new statistical tests are proposed and their performances compared with existing methods. Of all tests considered, the existing approximate test of homogeneity of product-moment correlations provides the greatest power to detect heterogeneous correlations, when based on Hotelling's z*-transformation. The use of this transformation and test is recommended under conditions of bivariate normality. A new distribution-free randomisation test of homogeneity of Spearman's rank correlations is described and recommended for use when the bivariate samples are taken from populations with non-normal or unknown distributions. An alternative randomisation test of homogeneity of product-moment correlations is shown to be a useful compromise between the approximate tests and the randomisation tests on Spearman's rank correlations: it is not as sensitive to departures from normality as the approximate tests, but has greater power than the rank correlation test. An example is provided that shows how choice of test will have a considerable influence on the conclusions of a particular study. This revised version was published online in July 2006 with corrections to the Cover Date.     

Complex patterns of morphological and mtDNA variation in Lacerta perspicillata (Reptilia; Lacertidae)

Lacerta perspicillata is a north-west African lacertid lizard that shows considerable intraspecific variation, with three subspecies described on the basis of colour pattern and body size. Recent observations of a population containing two morphological forms and more than one deep genetic lineage, as well as an apparent lack of concordance between forms and genetic lineages, suggest that the complexity is greater than previously thought. To analyse and quantify this variation, we studied the variability within this species at two levels: (1) external morphology (multivariate analysis of scalation, body dimensions, and colour pattern) and (2) mtDNA (sequencing and single-strand confirmation polymorphism analysis). Fifty-two individuals were studied at Taza, northern Morocco. Two morphological groupings (ostensibly representing two previously described subspecies) and two deep mtDNA lineages were detected at this site, with complete correspondence between the two. This, together with an apparent lack of hybrids, would normally support respective full species recognition. However, analysis of 98 individuals from other populations demonstrated that the situation is highly complex with the same genetic lineages having reversed morphotypes in other areas, making such a designation difficult. Across the other studied populations, we found no support for any of the currently recognized subspecies. The lack of congruence between mtDNA lineages and morphometric patterns (in some cases) and the morphological similarity among lizards from different lineages suggest ecophenotypic convergence or multiple introgressive hybridization. The study highlights the tremendous complexity that may exist within a taxon and the inadequacy of older alpha-taxonomy based designations in describing it.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 479–490.     

Reproductive cycles and reproductive strategies among populations of the Rose‐bellied Lizard Sceloporus variabilis (Squamata: Phrynosomatidae) from central Mexico

Species with wide distribution, generally show variations in life history characteristics, which can be attributed to environmental causes. In this study, we analyzed the reproductive cycle and reproductive characteristics from three populations (Atlapexco, San Pablo Tetlapayac, and Santa Catarina) of the lizard Sceloporus variabilis from central Mexico. The specific goal of this study was to evaluate life history characteristics such as reproductive period extent, SVL (snout‐vent length) at sexual maturity, clutch size, egg mass and volume, and RCM (relative clutch mass). The San Pablo Tetlapayac population showed a larger clutch size, RCM, egg mass, and a smaller SVL, body mass and reproductive period (January‐September), as well as egg volume than the Atlapexco and Santa Catarina populations. Reproductive cycle and reproductive characteristics were more similar between the Atlapexco and Santa Catarina populations. Differences found in the population of San Pablo Tetlapayac with respect to the Atlapexco and Santa Catarina populations could be attributed to environmental variations where lizard populations occur. Differences in the reproductive period and reproductive characteristics in each population could be the result of both historical (phylogenetic; e.g., reproductive mode) and nonhistorical (environmental; e.g., temperature, food availability) causes. This study showed that populations of the same species are under different selection pressures, and these affect the reproductive characteristics of populations. Our results also indicate that long‐term and targeted studies on predation, use and selection of food, are needed to determine the causes of these variations in populations of S. variabilis.     

Testing amniote models of prey transport kinematics: a quantitative analysis of mouth opening patterns in lizards

Two models have been proposed to describe the prey transport kinematics of terrestrial vertebrates (Bramble and Wake, 1985; Reilly and Lauder, 1990). The critical difference between the models is the presence or absence of a slow open-II phase (SO-II) in the gape profile during mouth opening. Each of these models has been applied to lizards, however to date, lizard feeding kinematics have not been adequately quantified to assess the utility of these models for this clade. Neither model has been sufficiently tested due to the lack of a methodology to assess the specific differences between the models. We describe a method that uses explicit mathematical criteria to define the kinematic phases in tetrapod feeding. This "slope analysis& is used to precisely quantify and compare the transport kinematics of seven lizard species. Lizard transport kinematics were highly variable both within and across taxa. However, several common gape cycle patterns were identified. The predominant patterns were slow-fast opening (37.3%), fast opening only (22.9%) and slow opening only (21.2%). The most common pattern explicitly fits the prediction of the Reilly and Lauder model while the other two are similar to patterns observed in salamanders. Thus, lizards possess both the slow opening-fast opening pattern predicted for amniotes and the more primitive, simple opening pattern characteristic of more basal tetrapods. Plateau phases were found in only 12.8% of the profiles and only a fourth of these (3.4% of the total) explicitly fit the Bramble and Wake model (slow opening, plateau, fast opening) and two species never exhibited plateaus in their gape cycles. Thus, it is clear that the Bramble and Wake model is not supported as a generalized model for lizards or generalized tetrapods.     

Clines: character number and the multivariate analysis of simple patterns of geographic variation

The stability of a clinal pattern geographic variation in relation to character number was investigated by the random selection of real characters. The characters used were selected from a set of 18 significant characters, drawn from four different character systems, and had a low within-group correlation. Principal component/coordinate analysis was used to elucidate the main pattern of geographic variation and the first principal coordinate was plotted against a geographical transect to illustrate this pattern. The existence of 'clinal' or 'monotically clinal' variation was assessed by the rank correlation between geographic position and coordinate score and the congruence between patterns of geographic variation was assessed by the correlation between the first principal coordinates of the appropriate analyses.
Two procedural models were used: A, the congruence between completely independent character sets based on 1–9 characters, and B, congruence between the 'total' analysis and those analyses based on 1–16 characters. The frequency of the types of pattern of geographic variation shown by these Model B analyses was also determined. Congruence is asymptotic in relation to character number and is described by various mathematical models, depending upon parameter and procedure. A broad pattern of clinal variation occurred in all analyses based on six or more characters and appears to be a stable feature of the racial affinities that is unlikely to be influenced by character choice. The details of the clinal pattern cannot be shown to be stable and may be influenced by the choice of character. This study had several findings in common with a previous study of categorical variation, e.g. the approximately hyperbolic relationship between character number and congruence in Model B, which may prove to be generally true in comparable situations.     

Complex clines: the predictivity of complicated patterns of geographic variation portrayed by multivariate analysis

The stability of complex patterns of geographic variation was investigated by assessing the congruence between multivariate ordinations derived from randomly chosen real characters. Two series of populations were analysed representing two situations with complex patterns of geographic variation. The first, a ‘Eurasian’ series of populations, showed a strongly structured hierarchical pattern, the second, an ‘eastern’ series of populations, showed a more subtle complex pattern of smooth clines and steps. The characters were selected from a total of 81 (Eurasian) or 61 (eastern) within-population independent characters from six different systems. The congruence between ordinations of the geographical populations was measured by the rotational fit statistic, R². Three procedures were used to compare ordinations based on from two to up to 80 characters randomly chosen to give: A, completely independent character sets; B, subsets compared to the total set; and C, potentially overlapping sets. All three procedures showed that congruence between the ordinations was asymptotic in relation to character number. This relationship was described by one of two mathematical models (procedure B did not result in a hyperbolic model as found with simple patterns of geographic variation). Generally speaking, once a sufficient number of characters are used, the complex patterns of geographic variation are stable, reliable and predictive and not substantially influenced by character choice. The strongly structured hierarchical pattern required 15 or so characters to achieve reliability whilst the more subtle patterns required 20 or so characters. However, the addition of further characters does improve reliability in both cases. The greater percentage of variance portrayed by three-dimensional ordinations compared to two-dimensional ordinations is achieved at the cost of lower congruence when a sufficient number of characters are used. If case studies of geographic variation were to adopt these procedures (preferably using completely independent character sets; procedure A) the reliability of their results would be indicated).     

Genetic patterns in the Lathyrus pannonicus complex (Fabaceae) reflect ecological differentiation rather than biogeography and traditional subspecific division

The endangered European relict species complex Lathyrus pannonicus shows distinct morphological variation, reflected by the number of subspecies recognized, and complicated patterns of genetic variation. The traditionally recognized subspecies appear to possess different ecological preferences and disjunct distributions, particularly in the western range of the species. In this study, L. pannonicus was investigated by the correlation of distance matrices based on phytosociological, ecological, molecular and morphological data. Ecological characteristics of selected stands of L. pannonicus throughout Europe were assessed using ‘Ellenberg values’ of all the constituent taxa in phytosociological relevés. Genetic distances were calculated using recently developed methods to analyse high degrees of intra‐individual nuclear‐encoded internal transcribed spacer variability. We found that the remarkable genetic (and morphological) diversity in L. pannonicus could not be explained solely by the fragmentation of the distributional range. Instead, patterns of morphological and genetic differentiation were a reflection of the moisture regime in the sampled stands. Two major lineages could be identified: (1) a lineage adapted to dry conditions (Ellenberg indicator F‐value ≤ 3.5) and (2) a lineage preferring moist conditions (F‐value ≥ 4.5). Although both lineages occurred in close proximity in the Pannonian area, they appeared to be reproductively isolated in general. Further data are needed to determine whether these genetically and ecologically defined lineages, or ecospecies, within the L. pannonicus species complex can be formalized as (Linnaean) species or subspecies. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 402–421.     

Morphological correlates of burst speed and field movement patterns: the behavioural adjustment of locomotion in wall lizards (Podarcis muralis)

Locomotion of lizards has clear morphological determinants and is important for developing activities such as feeding, social interaction and predator avoidance. Thus, morphological variation is believed to have fitness consequences through affecting locomotor performance. This paper firstly evaluates the dependence of burst speed on morphology, and secondly examines the movement patterns of free-ranging undisturbed wall lizards ( Podarcis muralis ) engaged in several kinds of activity. Body size was the most important correlate of burst speed as performed at the optimal temperature for running in the laboratory. After removing size effects from performance and morphological traits, the length of some particular limb segments had positive influence on burst speed, but these effects were weak, each trait explaining less than 16% of variance in burst speed. Free-ranging P. muralis exhibited intermittent locomotion, with movement sequences interrupted by frequent short pauses. Field movement patterns greatly differed depending upon the kind of activity and were in most aspects independent of the size and sex of the animal. P. muralis involved in thermoregulation performed short and low-speed displacements; exploratory activities were characterized by frequent, slow and short movements. On the contrary, lizards involved in intraspecific pursuits and predator escape developed comparatively high speeds, although only exceptionally did they attain the size-specific burst speed predicted from the laboratory trials. Speed of escape increased with distance to the refuge and the animals are able to assess predation risks to modulate approach distance, speed and pauses, so maximum exertion is seldom required. The evolution of locomotor capacities exceeding routine needs is discussed in the context of the principle of 'excessive construction'.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 135–146.     

Cranial morphological variation of Dromiciops gliroides (Microbiotheria) along its geographical distribution in south-central Chile: A three-dimensional analysis

We analyzed the variation in cranial morphology of the marsupial Dromiciops gliroides along its distribution in south-central Chile. We evaluated whether the cranial morphological variation is congruent with the phylogeographic structure previously observed in this species. We built three-dimensional models of 69 crania on which we digitized 30 landmarks. We used standard geometric morphometric methods to extract and analyze the shape and size components of the crania. Our data showed a subtle but consistent cranial size and shape variation along the studied distributional range, suggesting a geographic variation pattern rather than a phylogeographic structuring. Indeed, our multivariate analyses recovered a subtle morphological differentiation between island and mainland populations, contrary to what is suggested by a former phylogeographic study. We detected that either the cranial size variation, as well as the insularity and the latitude could be important factors underlying the cranial shape changes. We suggest that an interplay of historical and contemporary processes could be shaping the morphological pattern observed in this marsupial.     

Geographical distribution and phenotypic differentiation in populations of Dactylis glomerata L. in Japan

Although the perennial grass Dactylis glomerata L. has established dominant populations in Japan since its introduction in the 1870s, there have been marked reductions in its abundance in southern and northeastern regions. In order to examine the effects of climatic factors on distribution and differentiation of the naturalized populations of D. glomerata, abundance of 26 populations over a distance of 1500 km along a latitudinal gradient was recorded at each site, and life-history traits of each population were measured in a common garden. It was found that the reduction in abundance was related to the mean summer temperature in southern regions and to the lowest temperature before snow cover in northeastern regions. Recent climatic records in Japan show an increase in the mean summer temperature but no apparent changes in the lowest temperature before snow cover. These data suggest that, assuming the recent trend in climatic changes continues, the population abundance will decrease in southern regions and will change little in the northeastern regions. Germination speed, leaf width and reproductive allocations showed clinal variation over a geographical range, and the southern populations had more rapid germination, narrower leaves and lower reproductive allocation than did the northern populations. On the other hand, seed size and germination date showed margin-center differentiation. Marginal populations in both distributional borders had smaller seeds and lower germination rates than did the central populations. This revised version was published online in June 2006 with corrections to the Cover Date.     

Immunolocalization of a p53/p63‐like protein in the regenerating tail of the wall lizard (Podarcis muralis) suggests it is involved in the differentiation of the epidermis

During tail regeneration in lizards, the epidermis forms new scales comprising a hard beta‐layer and a softer alpha‐layer. Regenerated scales derive from a controlled folding process of the wound epidermis that gives rise to epidermal pegs where keratinocytes do not invade the dermis. Basal keratinocytes of pegs give rise to suprabasal cells that initially differentiate into a corneous wound epidermis and later in corneous layers of the regenerated scales. The immunodetection of a putative p53/63 protein in the regenerating tail of lizards shows that immunoreactivity is present in the nuclei of basal cells of the epidermis but becomes mainly cytoplasmic in suprabasal and in differentiating keratinocytes. Sparse labelled cells are present in the regenerating blastema, muscles, cartilage, ependyma and nerves of the growing tail. Ultrastructural observations on basal and suprabasal keratinocytes show that the labelling is mainly present in the euchromatin and nucleolus while labelling is more diffuse in the cytoplasm. These observations indicate that the nuclear protein in basal keratinocytes might control their proliferation avoiding an uncontrolled spreading into other tissues of the regenerating tail but that in suprabasal keratinocytes the protein moves from the nucleus to the cytoplasm, a process that might be associated to keratinocyte differentiation.     

Genetic and morphological differentiation patterns between sister species: the case of Onthophagus taurus and Onthophagus illyricus (Coleoptera, Scarabaeidae)

The present study investigated the morphological and genetic differentiation pattern between two sympatric dung beetle sister species, Onthophagus taurus and Onthophagus illyricus . The geometric morphometric approach coupled with the use of molecular markers allowed examination of the nature of interspecific relationships and an outline of the evolutionary and geographical processes that might have led to interspecific differentiation and the present-day partial sympatric and syntopic pattern of distribution. Geometric morphometrics failed to discrimininate the two species on the ground of external morphological traits, but revealed interspecific differences when the shape of the primary sexual traits was taken into account. The use of two different molecular markers (cytochrome oxidase subunit I gene and amplified fragment-length polymorphism) demonstrates that the two species are genetically well differentiated, forming two distinguishable lineages probably diverged during the Pliocene by allopatric speciation. No evidence of past or recent introgression and no support for hybridization were found, suggesting that sympatry was established subsequently, when speciation was accomplished. Both molecular markers and genital shape indicate that phenotypically intermediate individuals, despite their ambiguous appearance, are members of O. illyricus species rather than hybrids.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 197–211.     

Feeding biology of sunfishes: patterns of variation in the feeding mechanism

Fishes are generally believed to differ in their ability to alter (modulate) their feeding behaviour in response to different prey. We investigated modulation quantitatively in four species of sunfishes (Centrarchidae) by evaluating the variation in 11 electromyographic variables measured from recordings of electrical activity in head muscles during feeding on three prey types. The experimental design used allowed us to partition variation between species, among individuals within species, among prey types, and among feedings. Duration of activity of the sternohyoideus muscle was the only variable significantly different among the four species. All variables showed significant differences among individuals within species. The overall range of activity of each muscle activity variable was about the same for all four sunfishes. However, three species showed a significant ability to modulate most muscle variables while a fourth did not change its feeding response with respect to prey type. The results indicate that: (1) intraspecific variation is an important source of variability in functional attributes that should be accounted for in comparisons between species; (2) the ability of some species to modulate appears to be independent of the potential variability in muscle activity possessed by each species; (3) closely related species can differ considerably in their ability to alter muscle electrical activity patterns during feeding; and (4) a quantitative assessment of variation in electromyographic patterns is a powerful approach for asking questions about differences in feeding behaviour.     

Morphological variation in Gallotia atlantica from the volcanic island of Lanzarote: subspecies designations and recent lava flows

A detailed uni‐ and multivariate analysis of within‐island geographical variation in scalation and body dimensions of the lacertid lizard, Gallotia atlantica, from Lanzarote (and two neighbouring offshore islets) was carried out. Two main morphological groupings were detected: four populations clustered within a putative malpaís group, i.e. from relatively recent volcanic lava fields (seven populations were sampled from these areas), while the other 19 populations (including the three remaining malpaís populations, and those from the offshore islets of Montaña Clara and Alegranza) also clustered together. Thus, while there is a tendency for occupation of malpaís areas to be related to morphological variation, this model does have some inconsistencies. The differentiated malpaís group comprises populations from two geographically isolated areas, one from the central‐western part of the island (Timanfaya) and the other from the north (Malpaís de la Corona). The divergence of these populations is considered to have arisen recently, rather than their being relicts of an ancient, formerly widespread, lineage. The morphological variation partially supports the previous use of two different subspecies to describe the within‐island variation. However, if such a scheme were applied then one of the subspecies would need to encompass populations from the geographically separated southern Timanfaya and Malpaís de la Corona areas, as opposed to just the latter. We reject previous observations that either malpaís individuals in general, or those corresponding to the north‐eastern subspecies, are larger than individuals from other areas. The pattern of morphological variation of G. atlantica within Lanzarote is less pronounced but shows some similarities with patterns of morphological variation in lizards from neighbouring islands. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85 , 395–406.     

Comparing patterns of geographic variation in cave crickets by combining geostatistic methods and Mantel tests

Geographic variation patterns of biological characters and environmental variables are compared by using a procedure employing multivariate analyses, production of contour maps by the kriging method with enclosed validation of estimates, and Mantel tests to assess the significance of comparisons. As biological material we chose a sample of Dolichopoda cave crickets populations from Central-Southern Italy. The kriging technique provides estimates of the interpolation error for each true and estimated point. This profitable feature offers the opportunity to use, with ascertained levels of confidence, the estimated z -scores for further analysis and to compare data collected within the same area, but not exactly coincident in location or number. In such a way, we were able to use for subsequent comparisons by means of Mantel tests the maximum number of data points for all data sets, which originally differed in sampling sites. The interpretation of the contour maps and their statistical comparison suggested that allozymes and epiphallus shape data sets follow the phylogenetic pathways within the Dolichopoda populations, whereas variation in leg elongation is almost entirely under the control of an environmental gradient, synthetically described by the cave temperature.     

Genetic variation of Cordyceps sinensis, a fruit-body-producing entomopathogenic species from different geographical regions in China

Cordyceps sinensis is one of the most valuable medicinal fungi in the Orient. It is naturally distributed in the eastern extension area of the Qinghai-Tibet plateau, at an altitude over 4000 m high. In order to investigate genetic variation and evolutionary relationships of C. sinensis from different geographical regions, 17 isolates of C. sinensis were collected from different provinces and the complete sequences of rDNA ITS were determined. On the basis of 5.8S rDNA and ITS region analysis, it was clearly shown that the ITS sequences within C. sinensis are highly homologous regardless of geographical origin. The distance values between the sequences in this study were lower than 0.03. This implied that C. sinensis from different geographic regions are the same species; they are not different species or a species complex. The results also showed that distance values between C. sinensis and Hirsutella sinensis are of the same order as those within C. sinensis from different geographic regions. This confirmed our previous results that C. sinensis should only have H. sinensis as its asexual stage whatever the geographic region from which the samples were collected. An rDNA ITS clone library was established to obtain further evidence for the interpretation of the fungal community structure from C. sinensis and to confirm the accuracy of the taxonomic identities produced by directly sequencing the rDNA ITS region. The discrimination between intraspecies of C. sinensis might provide additional data for the authentication of medicinal material at the species or intraspecies level.     

Interspecific body size differentiation in species assemblages of the carabid subgenus Ohomopterus in Japan

Geographic variation and interspecific differentiation in body size (body length) were analyzed for 15 species of the carabid subgenus Ohomopterus (genus Carabus; Coleoptera, Carabidae) in Japan. Local species assemblages of this subgenus consist of up to 5 species of different size classes. These beetles exhibited sexual dimorphism in body size where females are larger than males, except Carabus uenoi, in which the male and female sizes were equivalent, possibly because of the exaggerated male genitalia. In 9 of 15 species, there was a positive correlation between mean body size and annual mean temperature of habitat, representing the converse of Bergmann's rule. However, in some cases this correlation does not hold over the range of a species because of regional differences. When allopatric and sympatric populations were compared, allopatric populations of Carabus albrechti and C. japonicus had larger bodies than sympatric populations. These intraspecific differences may have resulted from character displacement. In each local assemblage with 2 or more species, there was little interspecific overlap of body size, although the body size ratio between two species with adjacent body sizes seldom showed strict constancy. The mean size ratio between 2 adjacent species in an assemblage was reduced with the number of species, whereas the size ratio of the largest to smallest species in an assemblage increased with the number of species (i.e., the expansion of body size range). These results indicate that the body size of Ohomopterus species may have evolved in response to both climatic conditions and interspecific interactions. Because each species or species group represents the same size class over the distribution range and similar-sized species are parapatric or allopatric, the interspecific segregation in body size in local assemblages may have resulted mainly from a size assortment process during colonization. Received: June 8, 2000 / Accepted: October 10, 2000     

Atypical reproductive cycles in a population of Sceloporus grammicus (Squamata: Phrynosomatidae) from the Mexican Plateau

The spiny lizard Sceloporus grammicus (Squamata: Phrynosomatidae) is a small reptile from central México and the southern United States, occurring in a wide geographic area characterized by extensive variation in topographic and climatic regimes. Genetic variation among lineages from central México is substantial, though the extent to which this variation corresponds with life-history traits remains obscure. To address part of this puzzle, we studied a population of S. grammicus from Tepeapulco, Hidalgo, México. Male-biased sexual dimorphism was extensive in this population; males were larger than females overall, and expressed proportionately larger heads and longer limbs. Minimum size at sexual maturity was similar in the sexes (males: 43 mm; females: 42 mm). In contrast to other populations from the Central Plateau, reproductive activity of males and females was synchronous. Testicular recrudescence of adult males was initiated in October-November, and maximum testis size maintained from December to July. Female reproductive activity showed no clear seasonal pattern: females had vitellogenic follicles from October to July, and pregnant females were found throughout the year. Female body size was not related to litter size. Neither male nor female gonadal mass was correlated with any abiotic environmental variable examined. Differences in reproductive characteristics among populations of S. grammicus might be indicative of plasticity in response to local environmental conditions, local adaptation, or complex gene × environment interactions. We consider these results in the context of previously studied populations of S. grammicus from the Central Plateau and elsewhere, and propose directions for future research.     

Molecular survey of morphological subspecies reveals new mitochondrial lineages in Podarcis muralis (Squamata: Lacertidae) from the Tuscan Archipelago (Italy)

Recent analyses of molecular markers have significantly revised the traditional taxonomy of Podarcis species (Squamata: Lacertidae), leading to critically reconsider the taxonomic value of several subspecies described only on morphological bases. In fact, lizards often exhibit high morphological plasticity both at the intra‐specific and the intra‐population level, especially on islands, where phenotypic divergences are mainly due to local adaptation, rather than to evolutionary differentiation. The Common wall lizard Podarcis muralis exhibits high morphological variability in biometry, pholidosis values and colour pattern. Molecular analyses have confirmed the key role played by the Italian Peninsula as a multi‐glacial refuge for P. muralis, pointing out the lack of congruence between mitochondrial lineages and the four peninsular subspecies currently recognized. Here, we analyse a portion of the protein‐encoding cytochrome b gene in the seven subspecies described for the Tuscan Archipelago (Italy), in order to test whether the mitochondrial haplotypes match the morphologically based taxonomy proposed for Common wall lizard. We also compare our haplotypes with all the others from the Italian Peninsula to investigate the presence of unique genetic lineages in insular populations. Our results do not agree completely with the subspecific division based on morphology. In particular, the phylogenetic analyses show that at least four subspecies are characterized by very similar haplotypes and fall into the same monophyletic clade, whereas the other three subspecies are closer to peninsular populations from central Italy. From these results, we conclude that at least some subspecies could be better regarded as simple eco‐phenotypes; in addition, we provide an explanation for the distinctiveness of exclusive lineages found in the archipelago, which constituted a refuge for this species during last glacial periods.