High levels of genetic variability and inbreeding in two Neotropical dioecious palms with contrasting life histories

We characterized the population genetics of two Neotropical dioecious palm species of Chamaedorea with contrasting life strategies from the region that is both the northernmost extent and most species rich of the genus. Chamaedorea tepejilote is a common, wind-pollinated arboreal understory palm. Although most adult plants reproduce each year, only a few individuals produce the majority of flowers and seeds. Chamaedorea elatior, conversely, is an uncommon climbing subcanopy palm with entomophilous flowers (insect-pollinated characteristics). Most of the mature palms do not reproduce in consecutive years and fruiting is episodic. Isozymes with a total of 107 alleles for 27 loci of 17 enzymes from six populations were assessed. For both species, co-occurrence of high levels of genetic variation and homozygosity was observed (C. tepejilote: He: 0.385-0.442, f: 0.431-0.486; C. elatior: He: 0.278-0.342, f: 0.466-0.535). Genetic differentiation of C. elatior was much lower (theta=0.0315) than that for C. tepejilote (theta=0.152). The contrast in differentiation may be influenced by differences in the spatial scale of the genetic neighborhoods of the two species. The simultaneous maintenance of inbreeding and of a large number of alleles within the populations is attributable to the low and variable number of mating pairs. Demographic studies indicate that this pattern could be explained by low reproductive frequency among individuals and over years in C. elatior and by reproductive dominance in C. tepejilote.     

Spatial genetic structure of two sympatric neotropical palms with contrasting life histories

The spatial genetic structure within sympatric populations of two neotropical dioecious palm species with contrasting life histories was characterized to evaluate the influence of life history traits on the extent of genetic isolation by distance. Chamaedorea tepejilote is a common wind-pollinated arboreal understory palm. Chamaedorea elatior is an uncommon climbing subcanopy palm with entomophilous pollination syndrome. A total of 59 allozyme alleles for C. tepejilote and 53 alleles for C. elatior was analyzed using both unweighted (Iu) and weighted (Iw) Moran's I spatial autocorrelation statistics. The spatial genetic structure detected within these populations is consistent with those reported for highly dispersed plants. A significance test for differences between mean Moran's I-coefficients revealed less spatial genetic structure within the C. tepejilote population than that in the C. elatior population. Adjacent individuals of C. elatior exhibited significant spatial genetic autocorrelation (Iu=0.039, Iw=0.034), indicating a Wright's neighborhood size of about 100 individuals. For C. tepejilote, nonrandom genetic distribution among nearest neighbors was detected, even from small spatial autocorrelation values (Iu=0.008, Iw=0.009), consistent with a neighborhood size of about 300 individuals. For both species, seed dispersal, mortality among life cycle stages, overlapping generations, and contrasting traits of mating and reproduction influence the standing spatial genetic structure within populations.     

Biomass Allocation in the Dioecious Tropical Palm Chamaedorea tepejilote and Its Life History Consequences

Abstract The patterns of resource allocation are described for a dioecious tropical palm, Chamaedorea tepejilote. Resource allocation was measured by harvesting fifteen plants of C. tepejilote. The relative allocation of biomass in the stem increased with the size of the plant; that in the leaves decreased and that in the other structures remained roughly constant. Female plants showed a greater total reproductive effort, though male plants produced more inflorescences during the flowering season. Both male and female plants allocated more resources to prop root than to hypogeal roots. The annual productivity of reproductive and vegetative parts of C. tepejilote was estimated using allometric relationships for different plant structures and from demographic data obtained from the field. Annually, female plants allocated significantly more resources to leaves than male plants. Yearly productivity of inflorescences was higher for male plants, while female plants had greater total reproductive productivity (inflorescences and fruits). Correlation analysis showed an increase in reproductive effort with plant size, and an inverse relationship between fecundity and probability of survival, fecundity and residual reproductive value, and reproductive effort and life expectancy; these relationships suggested a cost in reproduction. Additionally, mature plants with different growth rates exhibited differences in fecundity: tall plants (>2.5m height) that grew more than 40 cm in height in four years had lower values of fecundity in comparison to plants of slower growth. These data were discussed in the context of the implications in the life history of a dioecious tropical plant.     

Population genetic structure of orchid bees (Euglossini) in anthropogenically altered landscapes

Habitat degradation and fragmentation are widespread phenomena in tropical regions. Negative effects on the biota are numerous, ranging from interruption of gene flow among populations, to the loss of genetic diversity within populations, to a decline in species richness over time. Orchid bees (Hymenoptera: Apidae: Euglossini) are of major conservation interest due to their function as pollinators of numerous orchid species and other tropical plants. Here, we used microsatellite markers to investigate the effects of geographic distance and habitat fragmentation on gene flow among populations. Populations of Euglossa dilemma in three geographic regions??the Yucat??n peninsula (Mexico), Veracruz (Mexico), and Florida (USA)??were genetically structured predominantly across the regions, with the strength of differentiation among populations being positively correlated with geographic distance. Within geographic regions only little substructure was found, suggesting that dispersal is substantial in the absence of geographic or ecological barriers. In a second study, patterns of genetic differentiation among eight species of Euglossa were not related to habitat fragmentation following deforestation in southern Mexico (Veracruz). Specifically, most bee populations in the 9,800?ha forest remnant of Los Tuxtlas (Volcano San Martin) were neither differentiated from, nor had less genetic diversity than, populations in near-continuous forest separated from Los Tuxtlas by 130?km of agricultural land. Either occasional long distance dispersal across open areas has buffered the expected genetic effects of fragmentation, or the history of fragmentation in southern Mexico is too recent to have caused measurable shifts in allelic composition.     

Studies in Annonaceae. XXVIII. Macromorphological variation of recent invaders in northern Central America: the case of Malmea (Annonaceae)

Cluster analysis is used to reveal patterns of macromorphological variation in a species complex of Malmea (Annonaceae) distributed in eastern Mexico, Guatemala, Belize, and Honduras. Of 53 characters, 24 are important for the clustering of 238 herbarium specimens into 12 clusters. No cluster is exclusively specified by any character or combination of characters. Neither can any geographical pattern be detected, except for the clustering of specimens from Los Tuxtlas Tropical Biological Station, Veracruz. A new subspecies from this area, M. depressa subsp. abscondita, is described. Malmea gaumeri and M. leiophylla are brought into synonymy with M. depressa. Distribution patterns of Mexican and Central American taxa of Malmea are largely concordant with those of South American taxa, which spread into Cental America after the Pliocene closure of the Isthmus of Panama. A phytogeographical novelty is presented, however, as the distribution of M. depressa subsp. abscondita within the Sierra de los Tuxtlas shows an hitherto unknown pattern: the new subspecies is distributed only on the northeastern slopes of this mountain range, and is geographically separated from M. depressa subsp. depressa, which occurs only on the southwestern slopes.     

Genetic analysis of an endemic archipelagic lizard reveals sympatric cryptic lineages and taxonomic discordance

The importance of genetic data in biodiversity conservation is well established, and knowledge of standing genetic variation within and between populations is important for designing conservation strategies. We investigated partitioning of genetic diversity in an endemic lizard (Leiocephalus psammodromus) distributed in the Turks and Caicos archipelago using mtDNA and AFLP data from 259 individuals sampled across 13 islands. Current taxonomy identifies six or more subspecies of L. psammodromus within the archipelago, several of which have undergone recent drastic reductions in range due to extirpation. However, our results indicate the presence of two independent lineages, one on each of the Turks and Caicos banks, and a third sympatric cryptic lineage on both banks. These lineages do not correspond to current taxonomy and alter our understanding of diversity and conservation of this species. Gross morphological data (mass and snout-vent length) indicate some variation in female size among lineages, indicating the possibility of cryptic morphological variation. Instead of initiating separate conservation measures for nominate subspecies, we recommend a more thorough investigation of the morphology and genetics of this group and a more inclusive conservation program. Our surprising results indicate that other endemic squamates in the Bahamas Archipelago might also exhibit sympatric cryptic diversity that does not correspond to current taxonomic understanding and could have significant impacts on our approach to conservation in this region.     

Effects of altitude and climate in determining elevational plant species richness patterns: A case study from Los Tuxtlas,Mexico

Altitudinal changes of composition and richness of montane plant assemblages are complex, depending on the taxonomic group and gradient conditions, with different factors involved that are directly altitude-dependent (e.g., temperatures, air pressure) and altitude-independent (e.g., precipitation, cloud cover, area). In order to assess the relative impacts of temperature, precipitation, air humidity, and area of altitudinal belts on plant diversity, we analyzed diversity patterns of five species-rich groups, mostly herbaceous plants, in 74 forest plots along three climatically contrasting elevational transects from humid tropical lowland vegetation up to cloud forests at Los Tuxtlas, Mexico. We recorded 278 plant species, with ferns being the most species-rich group followed by orchids, bromeliads, aroids, and piperoids. The most striking results were the contrasting patterns and model results for terrestrial and epiphytic taxa. Whereas the richness of all terrestrial species taken together did not change significantly with elevation, vascular epiphytes showed increasing species numbers with altitude. However, a number of individual terrestrial taxa showed also significant elevation-related changes: aroids showed a marked decline with hight, orchids and piperoids increased, and ferns displayed a hump-shaped pattern with highest richness in mid-altitudes. Among the epiphytes, aroids declined while most other groups increased with altitude. This distinction is relevant for projections of responses of plant communities to climate change, which will lead to increased temperatures and to changing precipitation and cloud condensation regimes and thus will likely affect terrestrial and epiphytic species in different ways.     

Phylogeographic patterns in widespread corvid birds

Intraspecific genetic diversity and phylogeography of Corvus corone was investigated using the mitochondrial (mt) control region as a molecular marker. A split into two distinct mt lineages was observed. One represents individuals from a wide geographic range spanning from England to the Russian Far East (Kamchatka), while the other one was found in the Primorye and Khabarovsk regions (southern parts of Russian Far East) as well as Japan. For comparison, we investigated several widespread Palearctic corvid taxa with respect to their phylogeographic patterns. A deep split into two lineages was revealed in five cases: Besides C. corone, within Corvus frugilegus, Pica pica, and between the species pairs Corvus monedula-Corvus dauuricus and Cyanopica cyanus-Cyanopica cooki. Although these taxa display a variety of distribution patterns, from disjunct, para/allopatric to continuous, the genetic pattern and level of divergence between clades is very similar. This implies that the differentiation started in about the same time range. In contrast, no differentiation into highly divergent lineages was detected in Corvus corax, Perisoreus infaustus, and Nucifraga caryocatactes. We try to explain the two phylogeographic patterns in corvid birds with ecological factors accompanying the changing climatic conditions during the Pleistocene. The deep genetic splits within several widely distributed Palearctic corvids are discussed with respect to taxonomic questions.     

PERMANENT GENETIC RESOURCES: Development of microsatellite markers of the Mexican understorey palm Chamaedorea elegans, cross-species genotyping, and amplification in congeners

With striking morphological diversity and adaptability, Chamaedorea palms constitute an ecologically and economically important understorey component of Neotropical forests. Nine loci developed for Chamaedorea elegans evaluated in three Veracruz populations resulted in a large number of alleles (8-18), and high expected heterozygosity (0.49-0.92), but low observed (0.27-0.65) heterozygosity. Deviations from Hardy-Weinberg and high inbreeding suggest a lack of panmixia. Eight loci optimized for Chamaedorea ernesti-augustii showed similar patterns of variation. All nine multiplexing loci amplified in other five congeneric species, which will facilitate comparisons within the genus and contribute to the conservation of its genetic resources.     

Digeneans (Plathelminthes: Trematoda) of seven sympatric species of anurans from Los Tuxtlas,Veracruz, Mexico

Digeneans of sympatric Bufo marinus, B. valliceps, Hyla picta, H. ebraccata, Smilisca baudini, Rana berlandieri, and R. vaillanti from Los Tuxtlas, Veracruz, Mexico, are reported. A total of 7 adult trematode species and 3 unidentified metacercariae was found in the different host species examined: Gorgoderina attenuata, G. parvicava, Cephalogonimus americanus, Haematoloechus medioplexus, Glypthelmins californiensis, Mesocoelium monas and Langeronia macrocirrus. Prevalence, mean intensity and abundance of the trematodes in each host species are given.     

The Influence of Large Tree Density on Howler Monkey (Alouatta palliata mexicana) Presence in Very Small Rain Forest Fragments

The populations of the Mexican mantled howler monkey ( Alouatta palliata mexicana ) in the Los Tuxtlas region, Mexico, have declined drastically due to habitat loss and fragmentation. Nevertheless, several troops still inhabit very small and isolated rain forest fragments. We identified the main vegetation attributes that can favor the presence of howlers within 18 small (< 10-ha) fragments that did not differ significantly in size, shape, and isolation (nine occupied and nine unoccupied by howlers). We found that habitat quality ( i.e. , food resources and vegetation structure) affected howler incidence in small fragments. Particularly, the occupied fragments showed greater density of big trees (dbh > 60 cm), greater total basal area, greater basal area of persistent tree species, and greater basal area of top food species than the unoccupied fragments; suggesting that even for small fragments the loss of big trees and particularly the decrease in size class of the top food species can negatively affect howler distribution in highly fragmented landscapes. These findings could be used to establish foreground conservation areas for this critically endangered subspecies in fragmented landscapes of Los Tuxtlas.     

Testing Species Delimitations in Four Italian Sympatric Leuciscine Fishes in the Tiber River: A Combined Morphological and Molecular Approach

Leuciscine fishes represent an important component of freshwater ichthyofauna endemic to northern Mediterranean areas. This lineage shows high intra-specific morphological variability and exhibits high levels of hybridization, two characteristics that contribute to systematic uncertainties, misclassification of taxa and, potentially, the mismanagement of biodiversity. This study focused on brook chub, Squalius lucumonis, an endemic taxon of Central Italy. The taxonomic status of this species has long been questioned, and a hybrid origin from sympatric leusciscines (S. squalus x Rutilus rubilio, or S. squalus x Telestes muticellus) has been hypothesised. A phenotypic (evaluating shape and meristic counts) and genetic (using mitochondrial and nuclear markers) investigation of these four taxa was conducted to test species delimitation in sympatric areas and to evaluate the taxonomic status of S. lucumonis. One hundred and forty-five individuals of all four taxa were collected within streams of the lowest portion of the Tiber River basin and analysed; this region encompasses a large portion of the S. lucumonis distribution. The different morphological and genetic approaches were individually examined, compared, and then combined in a quantitative model to both investigate the limits of each approach and to identify cases of misclassification. The results obtained confirm the cladogenetic non-hybrid origin of S. lucumonis, highlight the need for immediate conservation actions and emphasise the value of an integrated approach in the study of leuciscines evolution.     

A multivariate morphometric study on Corylus sieboldiana

Previous taxonomic treatments in Russia and China have considered Corylus mandshurica and C. sieboldiana to be distinct as independent species. A morphometric analysis was conducted to determine if the morphological differentiation from these taxa warrants specific taxonomic recognition with a large sample of field-collected leaves as well as specimens from several herbaria of northeastern Asia. One hundred and fifty two individuals representing Chinese, Korean, and Japanese geographic ranges of the species were scored for 18 morphological characters and the data matrix was used for principal components analysis. The entities that comprise C. sieboldiana complex exhibit widely overlapping ranges in all morphological attributes. The leaf and fruit data may reflect a lack of divergence between taxa. Therefore, we do not regard these to be sufficient for taxonomic splitting of C. mandshurica from C. sieboldiana to warrant the designation of the rank of a species based on morphology. The two taxa were not morphologically well differentiated and their ranges of distribution come together. Therefore, C. mandshurica should be recognized as an infraspecific taxon of C. sieboldiana. C. sieboldiana with short involucres in southern Korea and Japan is often treated as an independent species （C. hallaisanensis） or a variety (C. sieboldiana var. brevirostris), but should be only recognized as a form of C. sieboldiana because this involucral character is highly variable even within the same individual.     

毛榛复合体（桦木科）多变量形态学研究及分类学处理

Corylus mandshurica Maxim. & Rupr. 和 C. sieboldiana Blume 在中国和俄罗斯一直被处理为独立的种。本文对来自不同标本室的这两个种的腊叶标本及野外采集的大量叶片进行了形态学分析,以确定形态分化是否足够成为建立种的依据。对采自中国、韩国和日本覆盖两个种分布区的153份标本的18个形态学性状进行了统计,以构建数据矩阵用于主成分分析。结果表明,包含C. sieboldiana 复合体的数据单位（entities）在所有的形态学性状上均呈现出广泛的重叠区域。叶片和果实性状分析结果表明类群间缺乏分异性。基于形态学性状不足以把 C. mandshurica 从C. sieboldiana 中分离出去,并给予种的等级,也就是说这两个类群在形态上没有完全分化,而且它们的分布区也是相连的。 因此,应该把C. mandshurica作为C. sieboldiana 的种下分类群处理。C. sieboldiana在韩国南部和日本的具短总苞的植物常常被处理为独立的种或变种,但实际上应该作为C. sieboldiana 内的变型处理,因为总苞性状高度变异,即使在同一个体上也是如此。     

Diversity and biogeographical makeup of the dung beetle communities inhabiting two mountains in the Mexican Transition Zone

The role of horizontal and vertical colonization on the diversity and integration of the dung beetle fauna of two mountains in the Mexican Transition Zone (Los Tuxtlas and La Chinantla) are analyzed and compared. On each mountain standardized sampling was done using pitfall traps baited with dung and carrion along elevation gradients. On both mountains diversity decreased linearly with increasing elevation. The decrease in the number of genera and species was not different between mountains, but the cumulative total number for both taxonomic levels was significantly higher on La Chinantla. There, three well-defined groups were identified for which species turnover was mainly a result of species gain. On Los Tuxtlas there was no evident grouping pattern, and species turnover was determined by species loss. For both mountains the dominant biogeographic distribution pattern was Neotropical; however, at the higher elevations of La Chinantla, a clear replacement by lineages of Holarctic affinity was observed. We suggest that for La Chinantla—a mountain that is geographically connected to the Sierra Madre Oriental mountain range and is of ancient geological origin—the processes of horizontal and vertical colonization have had relatively different weights in terms of their effect on the pattern of diversity and the biogeographic integration of the beetle community, while on Los Tuxtlas, the limited role of horizontal colonization appears to be a consequence of its isolation and more recent geological origin. We discuss the potential use of these models for studying the effects of climate change on elevation gradients.     

Allopolyploid origin of Cardamine silana (Brassicaceae) from Calabria (southern Italy): karyological, morphological and molecular evidence

Endemic Cardamine silana from Calabria (southern Italy) previously reported to be related to C. raphanifolia was found to be hexaploid. Morphological characters and AFLP data were analysed to evaluate the degree of differentiation of C. silana from closely related taxa and to find parental taxa of this polyploid. Cardamine apennina from the C. pratensis group was examined as one putative parent, as indicated in previous studies of nuclear ITS sequences, along with other related taxa based on both cpDNA and ITS sequences. Both multivariate morphometric analyses of quantitative characters and evaluation of qualitative morphological characters showed: (1) closest position of C. silana to two diploids: C. acris from the Balkan Peninsula and C. apennina from Central Italy; (2) good extent of morphological separation of C. silana from related taxa; and (3) within C. acris subspecies, C. acris ssp. vardousiae from Central Greece as closest to C. silana . Neighbour-joining tree and PCoA ordinations of AFLP data, as well as patterns of AFLP bands sharing, corroborated results of multivariate morphometrics. This evidence supports an allopolyploid origin of C. silana , with C. apennina and C. acris as parental taxa. Its origin may be dated to Pleistocene glacial events, because of the presumably wider geographical distributions of its parental taxa during more humid periods at that time.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 101–116.     

Genetic structure of Eurasian and North American Leymus (Triticeae) wildryes assessed by chloroplast DNA sequences and AFLP profiles

Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve phylogenetic relationships between closely related species, with a curvilinear relationship expected between the proportion of shared bands and nucleotide substitution rate (D), up to about 0.100 D. The objective of this study was to compare D and phylogenetic relationships among 16 Leymus taxa, based on chloroplast DNA sequences and multi-locus AFLP genotypes. Estimates of chloroplast D between taxa were 0.002 and 0.013 within and among continental regions, respectively. Estimates of AFLP D between taxa were 0.076 and 0.093 compared within and between continental regions, respectively, versus 0.024 within taxa. Bayesian and neighbor-joining cluster analyses effectively separated all AFLP genotypes by species, but showed that North American L. ambiguus is a hybrid species with nearly equal contributions from sympatric L. cinereus and L. salinus taxa. Two hierarchical AFLP clades, containing six North American taxa and four Eurasian taxa, had more than 98% bootstrap confidence with 0.071 and 0.055 D among taxa. Three other Eurasian taxa clustered with 79% and 89% confidence, with up to 0.79 D between taxa. These estimates provide benchmarks for phylogenetic comparisons of AFLP profiles, but three taxa could not be reliably grouped, which may reflect concurrent radiation of multiple lineages or lack of homologous AFLP characters caused by a high D.     

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 23–38.     

Phylogeography of pollinator-specific sexually deceptive Chiloglottis taxa (Orchidaceae): evidence for sympatric divergence?

Divergence in sexually deceptive orchids is thought to occur through shifts in the attraction of specific pollinators, a process that is mediated by changes in the floral odours that lure sexually excited male insects. We investigated the origin of reproductive isolation in a sexually deceptive species complex of Chiloglottis R.Br. (Orchidaceae: Diurideae). Two geographically separated montane regions in eastern Australia were sampled, each containing sympatric pairs of orchid taxa presently found under the name, Chiloglottis pluricallata. Behavioural tests confirmed at least three distinct orchid taxa that specifically attract different pollinators. An artificial crossing experiment among two taxa from one region demonstrated their interfertility, and confirmed isolation to be a function of pollinator attraction. A phylogeographic analysis using amplified fragment length polymorphisms (AFLPs) indicated that samples from each geographical region are most closely related, a pattern consistent with in situ or sympatric divergence. However, an extensive population genetic study on two taxa from one region failed to entirely reject the possibility of intertaxon gene flow. Although clear genetic differentiation of the taxa is evident in two out of three sites where both grow in direct sympatry, overall, the two taxa are not strongly distinguished by AFLP markers. The reconstruction of a simple bifurcating pattern of divergence may be confounded by a combination of contemporary population-level processes operating within each taxon, the retention of ancestral polymorphism or intertaxon gene flow.     

AFLP analysis shows high incongruence between genetic differentiation and morphology‐based taxonomy in a widely distributed tortoise

Morphology has traditionally been used to diagnose the taxa of various taxonomic ranks. However, there is growing evidence that morphology is not always able to reveal cryptic taxa, and that pronounced morphological variation could reflect phenotypic plasticity rather than evolutionary divergence. Spur‐thighed tortoises (the Testudo graeca complex), distributed in the western Palaearctic region, are characterized by high morphological variability and complicated taxonomy, which are under debate. Previous molecular studies using mainly mitochondrial DNA (mtDNA) sequences have revealed incongruence between genetic differentiation and morphology‐based taxonomy, suggesting that morphological variability is the result of phenotypic plasticity and stabilizing selection, which masks the true genealogies. In the present study, we used a range‐wide sampling and nuclear Amplified fragment length polymorphism (AFLP) markers to investigate genetic differentiation within the T. graeca complex. We found that spur‐thighed tortoises are differentiated into four geographically well‐defined AFLP groups: Balkans–Middle Eastern, western Mediterranean, Caucasian and central‐eastern Iranian. Compared with the distribution of mtDNA lineages, the groups are largely concordant, although the AFLP markers are less sensitive and distinguish fewer groups than do mtDNA sequences. The AFLP groups show an allopatric or parapatric distribution. The AFLP differentiation conflicts with the previously proposed morphology‐based taxonomy of the complex, suggesting that local adaptation to different environmental conditions may have led to the great extent of morphological variation within the same lineages. We propose a re‐evaluation of the taxa that were confirmed genetically using a thorough morphological analysis corrected for phenotypic plasticity. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.