Jan Willem Arntzen

• Naturalis Biodiversity Center

Aim: Aims of the study are to identify environmental parameters underlying the mutual distribution in a species pair engaged in a long and winding hybrid zone, to reconstruct pattern and process of species range developments following the Last Glacial Maximum (LGM), and to open research lines for the study of hybrid zone dynamics in a model system....

Species distribution modelling can possibly be improved through the preferential use of explanatory variables that reflect the natural history features of the species being modelled. Red- and yellow-bellied toads (genus Bombina ) engage in an intricate mosaic distribution across Europe. Analysing new atlas data on these species’ mutual distribution...

Amphibian populations are increasingly sampled with traps instead of the traditional dipnet, because of high yields at a comparatively low workload. Observations on sympatric newt species in the west of France uncovered a size effect in which the larger species Triturus cristatus and T. marmoratus were more frequently captured than the smaller spec...

Allometry, the relationship between body size and the size of other body parts, explains a significant portion of morphological variation across biological levels, at the individual level, within and between species. We used external morphology measurements of 6 Triturus (sub)species, focusing on the T. marmoratus species group, to explore allometr...

The balanced lethal system found in crested and marbled newts of the genus Triturus presents an intriguing mystery. All adults possess two distinct forms of their largest chromosome, resulting in 50% of offspring inheriting two copies of one of these forms. These homomorphic individuals undergo fatal developmental arrest during embryogenesis. How c...

The large-bodied newts Triturus cristatus and T. marmoratus possess ranges that overlap in western France where they frequently share breeding ponds. I test the hypothesis that the aquatic phenology differs between them, as associated with a more aquatic and terrestrial life style respectively. Total adult population sizes were determined in spring...

Two morphologically and genetically distinct salamander species (the crested newt, Triturus cristatus and the marbled newt, T. marmoratus ) engage over a large area in the west of France where they hybridize at ca. 4%. The species interaction is characterized by ecological differentiation and limited gene flow beyond the F 1 hybrid generation. Inco...

Wetland ecosystems worldwide are threatened by habitat alteration, climate change and the introduction of invasive species, even within protected areas. Unravelling the reliance of sensitive wetland‐dwelling species, such as amphibians, on habitat characteristics is thus essential to identify conservation targets. Here we assess the distribution of...

The herpetofauna of the Iberian Peninsula is relatively well-researched, yet detailed studies, at least in part relying on molecular genetic data, continue to reveal taxa new to science, mostly species and subspecies. Newts of the genus Triturus are one such group with undiscovered yet taxonomically relevant variation, as shown by the recent descri...

Iberian populations of large-bodied newts, with Triturus marmoratus in the north and T. pygmaeus in the south of the peninsula, were studied for external morphology, mitochondrial dna and for a panel of single nucleotide polymorphisms. This confirmed the species’ low level of interspecific hybridization and their parapatric, mosaic-like mutual rang...

European marbled newts come in two species that have abutting ranges. The northern species, Triturus marmoratus, is found in France and the northern part of the Iberian Peninsula, whereas the southern species, T. pygmaeus, is found in the southwestern corner of the Iberian Peninsula. We study the intraspecific genetic differentiation of the group b...

Morphological and genetic variation of organisms is generally lower in northern than in southern regions of the Palearctic. This ubiquitous geographical pattern has been associated with extinction and recolonization processes in the north versus persistence in the Mediterranean area, as governed by climate change in the Pleistocene. One area of dif...

When two putatively cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia, but a formal hybrid zone analysis has never been conducted. We sample populations throughou...

Illustration of the character states describing levels of calcification of the dorsal head skin and the parotoid glands that can be found in both sexes and species of European toads (Bufo bufo and B. spinosus)

When two putative cryptic species meet in nature, hybrid zone analysis can be used to estimate the extent of gene flow between them. Two recently recognized cryptic species of banded newt (genus Ommatotriton) are suspected to meet in parapatry in Anatolia but a formal hybrid zone analysis has never been conducted. We sample populations throughout t...

Serially homologous structures may have complex patterns of regionalization and morphological integration, influenced by developmental Hox gene expression and functional constraints. The vertebral column, consisting of a number of repeated, developmentally constrained, and highly integrated units-vertebrae-is such a complex serially homologous stru...

Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative...

Restriction site-Associated DNA sequencing (RADseq) has great potential for genome-wide systematics studies of non-model organisms. However, accurately assembling RADseq reads into orthologous loci remains a major challenge in the absence of a reference genome. Traditional assembly pipelines cluster putative orthologous sequences based on a user-de...

Micro-computed tomography is a powerful tool toward the detailed reconstruction of internal and external morphology, in particular for ossified and other dense tissues. Here, we document and compare the level of calcification in the skin of the head and the parotoids (the external skin glands) in males and females of common and spined toads, Bufo b...

The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognised pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acqui...

Related species often engage in abutting or overlapping contact zones with various strengths of interspecific competition. Biotic interactions such as these preclude the registration of the full profile of environmental variables that would describe the otherwise larger species ranges. Here, I advocate to forego full range species distribution mode...

We examined the cranial morphology and cranial kinesis of the common toads Bufo bufo and B. spinosus with micro-computed tomography and geometric morphometrics and compared the results with published data for related species in a phylogenetic context. The species significantly diverge in skull shape. The skull of B. spinosus is shorter and higher,...

Serially homologous structures, such as the vertebral column, often undergo functional and evolutionary diversification and are a good model-system for studies of regionalization and morphological integration. We studied these topics in the vertebral column (atlas, trunk and sacral vertebrae) of the closely related taxa of small-bodied newts – Liss...

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 population...

Theory suggests that spatial segregation of similar, co-occurring species may be driven by alternative innate life history and dispersal strategies, and that it operates through catastrophic events. An inventory of the evolutionary closely related small-bodied newts Lissotriton helveticus and L. vulgaris in the northwest of France demonstrated the...

The evolutionary biologist Paul Kammerer (1880–1926) purportedly demonstrated that environmentally induced character states are carried over to the next generation(s), therewith providing evidence for Lamarckian evolution. Kammerer’s work is generally seen as contentious but has also been valued as daring and insightful, and Kammerer has been heral...

Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression acro...

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influences on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males)...

Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species — the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus — with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically i...

The salamander vertebral column is largely undifferentiated, with a series of more or less uniform rib-bearing presacral vertebrae traditionally designated as the trunk region. We explored regionalisation of the salamander trunk in seven species and two subspecies of the salamander genus Lissotriton by the combination of micro computed tomography s...

Technological developments now make it possible to employ many markers for many individuals in a phylogeographic setting, even for taxa with large and complex genomes such as salamanders. The banded newt (genus Ommatotriton) from the Near East has been proposed to contain three species (O. nesterovi, O. ophryticus and O. vittatus) with unclear phyl...

Proteins encoded by Antigen Processing Genes (APGs) provide MHC class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain non-mammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathost...

Proteins encoded by Antigen Processing Genes (APGs) prepare antigens for presentation by the Major Histocompatibility Complex class I (MHC I) molecules. Coevolution between APGs and MHC I genes has been proposed as the ancestral gnathostome condition. The hypothesis predicts a single highly expressed MHC I gene and tight linkage between APGs and MH...

Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial pattern...

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 th...

Secondary contact between closely related species can lead to the formation of hybrid zones, allowing for interspecific gene flow. Hybrid zone movement can take place if one of the species possesses a competitive advantage over the other, ultimately resulting in species replacement. Such hybrid zone displacement is predicted to leave a genomic foot...

We developed a panel of 44 nuclear genetic markers and applied this to two hybridizing species of marbled newts in the north (Triturus marmoratus) and the south (Triturus pygmaeus) of the Iberian Peninsula, to investigate pattern and process of interspecific gene flow. The northernmost occurrence of T. pygmaeus genetic material was in a T. marmorat...

Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for...

Using a panel of 31 diagnostic nuclear SNP markers in 56 toad populations from the southern Alps and the northern and central Apennines, we document that the range of the spined toad, Bufo spinosus, extends along the Mediterranean coast from France into the northwest of Italy. This species, and the common toad B. bufo, engage in a unimodal hybrid z...

Integration of multilocus data and species distribution modelling into phylogeography allows mitochondrial DNA (mtDNA)-based scenarios to be fine-tuned. We address the question of whether extensive mtDNA substructuring in the crested newt Triturus macedonicus from the Balkan Peninsula is matched in the nuclear genome. We determine the intraspecific...

We developed a panel of 44 nuclear genetic markers and applied this to two species of marbled newts in the north (Triturus marmoratus) and the south (T. pygmaeus) of the Iberian Peninsula, to document pattern and process of interspecific gene flow. The northernmost occurrence of T. pygmaeus genetic material was in a T. marmoratus population north o...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The interplay between intrinsic (development, physiology, behavior) and extrinsic (landscape features, climate) factors determines the outcome of admixture processes in hybrid zones, in a continuum from complete genetic merger to full reproductive isolation. Here we assess the role of environmental correlates in shaping admixture patterns in the lo...

Identifying the drivers of population fluctuations in spatially distinct populations remains a significant challenge for ecologists. Whereas regional climatic factors may generate population synchrony (i.e. the Moran effect), local factors including the level of density dependence may reduce the level of synchrony. Although divergences in the scali...

A lightweight, collapsible funnel trap designed for crayfish was furnished with a smaller mesh and then used to study adult breeding populations of five species of newts in five ponds in France. Observations were made in spring, at the peak of breeding activity, over an 11-year period. Annual experiments involved on average 7.7 traps and 5.3 overni...

Serial homology or the repetition of equivalent developmental units and their derivatives is a phenomenon encountered in a variety of organisms, with the vertebrate axial skeleton as one of the most notable examples. Serially homologous structures can be viewed as an appropriate model system for studying morphological integration and modularity, du...

Adaptation to different ecological environments can, through divergent selection, generate phenotypic and genetic differences between populations, and eventually give rise to new species. The fire salamander (Salamandra salamandra) has been proposed to represent an early stage of ecological speciation, driven by differential habitat adaptation thro...

The interplay between intrinsic (development, physiology, behavior) and extrinsic (landscape features, climate) factors determines the outcome of admixture processes in hybrid zones, in a continuum from complete genetic merger to full reproductive isolation. Here we assess the role of environmental correlates in shaping admixture patterns in the lo...

Classical theory states that hybrid zones will be stable in troughs of low population density where dispersal is hampered. Yet, evidence for moving hybrid zones is mounting. One possible reason that moving zones have been underappreciated is that they may drive themselves into oblivion and with just the superseding species remaining, morphological...

Using micro-CT scanning and 3D geometric morphometrics of newt craniums and axial skeletons (first three vertebrae) we explored the pattern of morphological integration. We tested if i) directly connected serially homologous structures are more integrated than separated ones and ii) morphological integration coincides with regional differentiation....

Genomic heterogeneity of divergence between hybridizing species may reflect heterogeneity of introgression, but also processes unrelated to hybridization. Heterogeneous introgression and its repeatability can be directly tested in natural hybrid zones by examining multiple transects. Here, we studied hybrid zones between the European newts: Lissotr...

The barrier effect is a restriction of gene flow between diverged populations by barrier genes. Asymmetric introgression can point to selection, hybrid zone movement, asymmetric reproductive isolation, or a combination of these. Restriction of gene flow and asymmetric introgression over multiple transects point towards influence of intrinsic (genet...

We tested the hybrid superiority hypothesis in the zone of overlap and hybridization of the newts Triturus cristatus and T. marmoratus. To do so, we compared size, age, and growth‐related parameters in F1 hybrids and both parental species in Mayenne, France. We found significant differences in snout‐vent length (SVL), body mass and average lifespan...

Cryptic phylogeographic diversifications are unique models to examine the role of phylogenetic divergence on the evolution of reproductive isolation, without extrinsic factors such as ecology. Yet, to date very few comparative studies were attempted within such radiations. Here, we characterize a new speciation continuum in a group of widespread Eu...

Newts of the genus Triturus (marbled and crested newts) exhibit substantial variation in the number of trunk vertebrae (NTV) and a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny has thwarted resolution to date, the evolutionary history of NTV, annual aquatic period, and their potential coevolution has remai...

Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequil...

Understanding the course of eco-morphological evolution in adaptive radiations is challenging as the phylogenetic relationships among the species involved are typically difficult to resolve. Newts of the genus Triturus (marbled and crested newts) are a well-studied case: they exhibit substantial variation in the number of trunk vertebrae (NTV) and...

I document the contiguous distribution of the marbled newt species Triturus marmoratus and T. pygmaeus over the western part of the Iberian peninsula with a suite of morphological and molecular genetic data from altogether 141 populations. Morphological characters that identify the species are body size and the colour pattern character ‘Links’. Lin...

Relationships between phylogenetic relatedness, hybrid zone spatial structure, the amount of interspecific gene flow and population demography were investigated, with the newt genus Triturus as a model system. In earlier work, a bimodal hybrid zone of two distantly related species combined low interspecific gene flow with hybrid sterility and heter...

Raw output of the KASP genotyping protocol.

Input consensus sequences for Kraken.

Parameter values and 95% confidence intervals (CI) in the Von Bertalanffy growth curves for Triturus populations. Parameter values and 95% confidence intervals (CI) in the Von Bertalanffy growth curves for Triturus populations in the west and southeast of the genus’ range. Triturus cristatus and T. marmoratus are hybridizing in a wide area of range...

Skeletochronology results for Triturus macedonicus. Skeletochronology results for Triturus macedonicus from three populations in Montenegro, located away from areas in interspecific hybridization. The material is from the batrachalogical collection of the Institute of Biological Research “Siniša Stanković” and was collected in 1993–1996 (Džukić et...

Genetic data for a hybrid newt population in Serbia.

Skeletochronology results along with morphometric data and individual Structure scores.

The three species of banded newt (genus Ommatotriton) are endemic to the Near East. Recently an introduced banded newt population was discovered in Catalonia, Spain. To determine the species involved and the geographical source, we genotyped 11 individuals for one mitochondrial and two nuclear genetic markers, and compared the observed haplotypes t...

We document the distribution of the common toad Bufo bufo and the spined toad B. spinosus at their contact zone across France with data from a mitochondrial DNA RFLP assay, complementing similar work including nuclear markers in the northwest and southeast of France and in Italy. We also reconstruct geographical clines across the species’ contact z...

In a recent paper it was suggested that results published by Kam-merer (1911) on the midwife toad could be explained by epige-netics (Vargas et al., 2016). We show that data thought to be fitting are based on untested assumptions about the underlying genetic mechanisms. We cite recent studies on the genetics of life history traits, in particular eg...

We carried out a comparative morphometric analysis of 56 species of salamandrid salamanders, representing 19 out of 21 extant genera, with the aim of uncovering the major patterns of skull shape diversification, and revealing possible trends and directions of evolutionary change. To do this we used micro-computed tomography scanning and three-dimen...

The pervasive and unabated nature of global amphibian declines suggests common demographic responses to a given driver, and quantification of major drivers and responses could inform broad-scale conservation actions. We explored the influence of climate on demographic parameters (i.e., changes in the probabilities of survival and recruitment) using...

Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a sectio...

Much progress in speciation research stems from documenting patterns of morphological and genetic variation in hybrid zones. Contrasting patterns of marker introgression in different sections of the contact can provide valuable insights on the relative importance of various evolutionary mechanisms maintaining species differences in the face of hybr...

The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DN...

Habitat loss, together with less obvious land-use changes such as intensified farming practice, can have significant adverse impacts on biodiversity. An important factor in determining the ability of species to cope with such changes is their potential to sustain a populations network by dispersal across the landscape. Habitat quality and structure...

Speciation typically involves a stage in which species can still exchange genetic material. Interspecific gene flow is facilitated by the hybrid zones that such species establish upon secondary contact. If one member of a hybridizing species pair displaces the other, their hybrid zone would move across the landscape. Although theory predicts that m...

Figure S1. Results of the geographical cline analyses for individual markers and transects. Results for the northern and southern transect are in the left and right column (see Fig. 3 for details). Clines are shown from top to bottom for Structure Q score, mtDNA haplotype frequency, and allele frequency for the 12 diagnostic (amot ‐ taf8) and six n...

Table S1. Sampling details. Table S2. GenBank Accesion Numbers for mtDNA haplotypes. Table S3. Best fitting geographical cline models selected for the Structure Q score and the individual mtDNA and nuclear diagnostic (amot ‐ taf8) and semi‐diagnostic (chic ‐ wiz) markers. Table S4. Test whether there is more variation unaccounted for by the clin...

The use of hyper-variable markers across species is often hindered by low cross-species amplification success, a reduced level of polymorphism or a high frequency of null alleles. However , optimizing sets of reliable and informative markers that can be consistently amplified and scored across taxa is key to address questions about patterns of gene...

When related species meet upon postglacial range expansion, hybrid zones are frequently formed. Theory predicts that such zones may move over the landscape until equilibrium conditions are reached. One hybrid zone observed to be moving in historical times (1950–1979) is that of the pond-breeding salamanders Triturus cristatus and Triturus marmoratu...

Background Hybrid zones are regions where individuals of two species meet and produce hybrid progeny, and are often regarded as natural laboratories to understand the process of species formation. Two microevolutionary processes can take place in hybrid zones, with opposing effects on population differentiation. Hybridization tends to produce genet...

Genetic admixture between endangered native and non-native invasive species poses a complex conservation problem. Decision makers often need to quickly screen large numbers of individuals and distinguish natives from morphologically similar invading species and their genetically admixed offspring. We describe a protocol using the fast and economica...

Under a documented paleogeographic history of the Ria de Arosa archipelago, northwestern Spain, predictions can be made on the duration and strength of isolation of Podarcis guadarramae lizard populations that were ‘captured’ on the islands when sea-levels rose. We predict that genetic diversity: i) is lower on islands than on the mainland, ii) inc...

The Austrian biologist Paul Kammerer (1880-1926) would by now be long forgotten if Arthur Koestler had not published ‘The case of the Midwife toad’, in which he depicted Kammerer as a victim of the paradigm battle between neo-Darwinists and Lamarckists. Kammerer is still on the scientific agenda, with at least 10 publications since 2005. The questi...

We investigated the recent evolutionary history of the Danube crested newt, Triturus dobrogicus through reconstructions of: (1) the number and position of refugia at the last glacial maximum, (2) the role of major central European rivers in pattern of post-glacial dispersal, and (3) the present-day distribution pattern. We analysed sequences of mit...

Multilocus molecular data play a pivotal role in diagnosing cryptic species (i.e. genetically distinct but morphologically similar species). A multilocus phylogeographic survey has provided compelling evidence that Triturus ivanbureschi sensu lato comprises two distinct gene pools with restricted gene flow. We conclude that this taxon had better be...