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

Phylogeographic and phenotypic divergence between two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Iran

Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Central Iran. Our results showed high levels of phylogeographic and phenotypic variation in the contact zone. Two monophyletic clades including, clade 1 (T. g. zarudnyi) and clade 2 (T. g. buxtoni) were identified. Furthermore, four distinct subclades were found in T. g. buxtoni, across a wide geographic range. Divergence time analysis suggests that the two subspecies diverged from one another after the uplifting of the Zagros Mountains during the early Pliocene. Using neutrality tests and mismatch distribution analysis, we found no evidence of recent population expansion. Morphological associations among geographical populations in the contact zone found more distinctions, with some significant adaptive and non-adaptive morphological variations in these populations. These distinctive morphological populations can be considered as management units (MUs) to conserve the evolutionary potential of this species. Finer scale evolutionary studies are required to address the southern part of the Zagros mountain range, where the overlapping of mitochondrial clades and subclades has occurred. Such information is essential for effective conservation of T. graeca populations, preventing translocation or mixing of individuals without comprehensive genetic and morphological assessment.

Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe

Background

The application of molecular-phylogenetic approaches to taxonomy has had a dramatic effect on our understanding of the diversity of reptiles. These approaches have allowed researchers to reveal previously hidden lineages as well as taxonomic overestimation in morphologically plastic taxa. Slow worms, legless lizards of the genus Anguis (Squamata: Anguidae), were previously considered to comprise either one or two species, and morphology-based intraspecific taxonomy of Anguis fragilis remained controversial throughout the 20th century. After the discovery of deep genetic divergences within the genus, its taxonomy was reconsidered, and as a result, five extant species have been recognized. In order to better understand the patterns of their interspecific differentiation, here we studied phenotypic differences between the two most widespread of them—A. fragilis and A. colchica, and their putative hybrids across the contact zone of both species in Central Europe.

Methods

We used multivariate and univariate statistics and analyzed ten metric, eleven meristic, and six categorical phenotypic variables in material comprising a total of 326 individuals. We also genotyped individuals from the contact zone for one mitochondrial and two nuclear DNA fragments in order to delineate the distribution of individuals of hybrid and non-hybrid origin. The clines in morphological traits were studied using HZAR.

Results

We show that the two species are morphologically differentiated. Anguis fragilis has a less robust head, fewer scales covering the body, lower frequency of the external ear opening presence, lower frequency of separated prefrontal scales, higher frequency of prefrontal scales in contact with each other, and body coloration more similar to the juvenile coloration than A. colchica. Slow worms from the contact/hybrid zone are characterized by an intermediate morphology, with more similarities to A. fragilis than to A. colchica.

Discussion

None of the analyzed characters alone proved to be fully diagnostic, although more than 90% of all individuals could be successfully assigned to one or another species based on numbers of scales around the body. Our results indicate concordant, coincident, and steep clines in character states change. We present several hypotheses on the origin and evolutionary maintenance of the morphological divergence between both species and suggest that different evolutionary histories of the taxa rather than recently acting selection explain the observed morphological variation.

Morphological and genetic differentiation in the anguid lizard Pseudopus apodus supports the existence of an endemic subspecies in the Levant

The Levant represents one of the most important reptile diversity hotspots and centers of endemism in the Western Palearctic. The region harbored numerous taxa in glacial refugia during the Pleistocene climatic oscillations. Due to the hostile arid conditions in the warmer periods they were not always able to spread or come into contact with populations from more distant regions. One large and conspicuous member of the Levantine herpetofauna is the legless anguid lizardPseudopus apodus. This species is distributed from the Balkans to Central Asia with a portion of its range running along the eastern Mediterranean coast. Mitochondrial and nuclear DNA sequences, microsatellite genotypes, and morphology show that populations in this region differ from the two named subspecies and presumably had a long independent evolutionary history during the Quaternary. Here we describe the Levantine population as a new subspecies and present biogeographic scenarios for its origin and diversification. The new subspecies is genetically highly diverse, and it forms a sister lineage toPseudopusfrom the remaining parts of the range according to mtDNA. It is the largest-bodied of the three subspecies, but occupies the smallest range.

Cryptic diversity in the smooth snake (Coronella austriaca)

The smooth snake, Coronella austriaca, is a common snake species widespread in the Western Palearctic region. It does not form conspicuous morphological variants and, although several evolutionary lineages have been distinguished based on the analyses of the mitochondrial DNA sequences, only two subspecies with very limited distribution have been traditionally recognized. Here we present an mtDNA phylogeography of the species using geographically extended sampling while incorporating biogeographically important areas that have not been analyzed before, such as Anatolia, Crimea, and Iran. We find that the smooth snake comprises 14 distinct phylogenetic clades with unclear mutual relationships, characterized by complex genetic structure and relatively deep divergences; some of them presumably of Miocene origin. In general, the biogeographic pattern is similar to other Western Palearctic reptiles and illustrates the importance of the main European peninsulas as well as the Anatolian mountains, Caucasus, and Alborz Mts. in Iran for the evolution of the present-day diversity. Considerable genetic structure present in the smooth snake populations within these large areas indicates the existence of several regional Plio-Pleistocene refugia that served as reservoirs for dispersal and population expansions after the glacial periods. The current taxonomy of C. austriaca does not reflect the rich genetic diversity, deep divergences, and overall evolutionary history revealed in our study and requires a thorough revision. This will only be possible with an even higher-resolution sampling and integrative approach, combining analyses of multiple genetic loci with morphology, and possibly other aspects of the smooth snake biology.

Human-mediated secondary contact of two tortoise lineages results in sex-biased introgression

Human-mediated secondary contact of recently diverged taxa offers valuable opportunities for studying the evolutionary mechanisms involved in the establishment and maintenance of genetic boundaries between taxa. We used mitochondrial and microsatellite markers to examine a recently introduced population of the spur-thighed tortoise (Testudo graeca) of mixed origin in the Doñana National Park (SW Spain). The earliest records of tortoises in Doñana trace back to the 18th century, but several population reinforcements in the 20th century with animals from Morocco are well-documented. Consequently, different genetic lineages, which represent distinct subspecies, are thought to co-exist there. Our results confirmed the presence of distinct lineages by revealing that tortoises of the subspecies T. g. marokkensis were introduced into a local allochthonous T. g. graeca population. Unexpectedly, T. g. marokkensis haplotypes exclusively appeared in males, and admixture levels were statistically sex-biased toward males. The sex ratio of the population deviated from parity, with males being 2.36-fold more abundant than females. Our results indicated that population reinforcements had a strong effect on the genetic composition of this population and aggravated its sex ratio deviation. We predict that this sex-biased pattern of introgression is ephemeral and advocated to the near loss of T. g. marokkensis haplotypes.

Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'

Background

Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the ‘Azores Diversity Enigma’ (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries.

Results

In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa.

Conclusions

Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where genetic patterns reflected inter-island geographical isolation, and morphology reflected intra-island bioclimatic variation. The combined effects of differences in (i) the extent of geographical isolation, (ii) population sizes and (iii) geographical occupancy of bioclimatic niche space, coupled with the morphological plasticity of Pericallis, may all have contributed to generating the contrasting patterns observed in the archipelagos.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0766-1) contains supplementary material, which is available to authorized users.

Yalongjiang River Has Had an Important Role in the Dispersal and Divergence of Rosa soulieana in the Hengduan Mountains of China

The Hengduan Mountains are the core of the Sino-Himalayan Floristic Region. Rosa soulieana Crép. is an important wild rose species that is widely distributed in the Hengduan Mountains. To provide better future utilization of this wild rose, and also to add some possible proof of the effect of geomorphological and ecological characteristics of the Hengduan Mountains on the current spatial distribution and genetic diversity of local species, the genetic diversity and genetic structure of 556 individuals from 37 populations of R. soulieana were studied using fluorescent amplified fragment length polymorphisms (AFLPs). R. soulieana showed a moderately high level of genetic diversity and a high level of genetic differentiation at the species level. The total percentage of polymorphic loci, total heterozygosity (Ht), Shannon index (I), and heterozygosity value within populations (Hs) were 97.8%, 0.253, 0.339, and 0.139, respectively. More than half of the total genetic variation (54.0%) occurred within populations, and the overall gene differentiation coefficient (Gst) was 0.451. The genetic differentiation among populations was positively and significantly correlated with geographic distance. The neighbor-joining cluster and the Bayesian analysis divided all the populations and individuals into 3 groups, and did not support the morphology based intraspecific varieties. The results confirmed that the ancient R. soulieana of the third group survived in northwestern Yunnan and Yalongjiang valley and then moved upnorth along the valley. The spatial distribution of the other two groups was the result of allopatric divergence due to long period of adaptation to the different climatic conditions of its distribution at either side of the Yalongjiang River.

The desert tortoise trichotomy: Mexico hosts a third, new sister-species of tortoise in the Gopherus morafkai-G. agassizii group

Desert tortoises (Testudines; Testudinidae; Gopherusagassizii group) have an extensive distribution throughout the Mojave, Colorado, and Sonoran desert regions. Not surprisingly, they exhibit a tremendous amount of ecological, behavioral, morphological and genetic variation. Gopherusagassizii was considered a single species for almost 150 years but recently the species was split into the nominate form and Morafka’s desert tortoise, Gopherusmorafkai, the latter occurring south and east of the Colorado River. Whereas a large body of literature focuses on tortoises in the United States, a dearth of investigations exists for Mexican animals. Notwithstanding, Mexican populations of desert tortoises in the southern part of the range of Gopherusmorafkai are distinct, particularly where the tortoises occur in tropical thornscrub and tropical deciduous forest. Recent studies have shed light on the ecology, morphology and genetics of these southern ‘desert’ tortoises. All evidence warrants recognition of this clade as a distinctive taxon and herein we describe it as Gopherusevgoodeisp. n. The description of the new species significantly reduces and limits the distribution of Gopherusmorafkai to desertscrub habitat only. By contrast, Gopherusevgoodeisp. n. occurs in thornscrub and tropical deciduous forests only and this leaves it with the smallest range of the three sister species. We present conservation implications for the newly described Gopherusevgoodei, which already faces impending threats.