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Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.

Supplemental Figures S1-S16

Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.

The integration of multilocus datasets and species distribution modelling in phylogeography allows for the reconstruction of more detailed historical biogeographical scenarios than based on mtDNA data alone. We here combine these approaches to investigate the range dynamics of the crested newt Triturus karelinii, an amphibian species endemic to the Pontocaspian region, whose range comprises three allopatric range sections: a Crimean, a Caucasian and a Caspian range section. In a previous mtDNA phylogeographical survey it was suggested that the Caucasian range section was colonized from the Caspian one and that the Crimean range section was subsequently colonized from the Caucasian one. Newly collected nuclear DNA data reveal little genetic differentiation between the three range sections and species distribution modelling suggests that they only recently became isolated. Taken together, our analyses agree with a recent colonization of the Crimean range section, but rather suggest long-term persistence in both the Caspian and Caucasian range sections, with extensive gene flow between the two.

Additional file 1: Figure S1. Geese select areas experiencing relatively low human pressure, at different distances to roosts. Table S1. Summary of GPS records obtained for 83 geese at their stopover and wintering regions.

In the recently published New Atlas of Amphibians and Reptiles of Europe (Sillero et al., 2014a), the distribution of the newt genus Triturus was not resolved at the level of the species. The main reason for this was the lack of high quality distribution data from in and around the parapatric contact zones between species, where interspecific hybridization occurs. We are working extensively on Triturus and the (particularly genetic) data we have accumulated allow us to map the individual Triturus species at the appropriate scale.We here provide a database composed of distribution data for the individual species, at generally high resolution, particularly from in and around contact zones. Based on this database we produce maps at the 50 × 50 km UTM grid resolution as used in the new atlas and highlight those grid cells in which more than one Triturus species occurs.

The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones

Facultative paedomorphism is regularly observed in salamanders, including newts of the Lissotriton vulgaris group. We document the first record of paedomorphism in L. (v.) kosswigi from a locality near Karasu, in the vicinity of Sakarya, Turkey. We compare measurements of 5 paedomorphic individuals with those of 10 metamorphic individuals from the same population and with measurements taken from the literature. Paedomorphs are on average bigger than metamorphs; intriguingly, the opposite pattern has been observed in the Turkish L. (v.) schmidtlerorum.

We provide results of a second survey of the hutan adat (forest traditionally exploited on a small scale by local people) situated in the Gunung Lumut Protection Forest, East Kalimantan, conducted in 2007 and closely following the first survey in 2005 (Wielstra & Pieterse 2009. Kukila 14: 1-15). An additional 29 species were observed, bringing the total number of species observed in GLPF to 217. These include two globally threatened (Vulnerable) species, 16 “Sundaic Lowland Forest” biomerestricted species and one “Sundaic montane forest” biome-restricted species. We confirmed the presence of over 1% of the biogeographic population of the congregatory waterbird Storm’s Stork Ciconia stormi. The findings provide further support for our previous suggestion to recognize Gunung Lumut Protection Forest as an Important Bird Area. We also provide some remarks on the potential conservation value of hutanadat and raise issues to be addressed in further studies.