Biology subjects

Arntzen, J. W.

Publications and source records attributed to Arntzen, J. W..

8 recordsLinked to original sources

bioRxiv2025

Long term hybrid zone dynamics in red- and yellow-bellied toads estimated from environmental data at allopatric and parapatric scales

AimAims 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. LocationCentral and Eastern Europe, Croatia. TaxonThe red-bellied toad Bombina bombina and the yellow-bellied toad Bombina variegata. MethodsThe construction of two-species distribution models (TSDM) at allopatric and parapatric scales and the reconstruction of geographical clines across a low mountain range, in transects with and without extensive lowland forest cover. ResultsIt is confirmed that B. variegata is a mountain species and B. bombina is a lowland dweller, with hybrid populations in between, but traditional distribution models are oversimplistic. Environmental parameters selected with TSDM at both allopatric and parapatric scales are elevation and forestation. At transects with lowland forestation hybrid zones are positioned further away from elevated areas than in the absence of lowland forest. Bombina variegata stronghold areas are characterized not just by elevation but also by forestation. Out of 17 historical Bombina studies that are evaluated for promise in the study of hybrid zone dynamics several qualify for extended research. ConclusionsThe overall species mosaic with isolated mountain strongholds suggests that B. variegata was displaced from the surrounding lowlands upon its counterparts northward advance, following post-LGM climate amelioration. Initial hybrid zone formation will have been along the lower Danube River, distant from present-day positions. Because lowland forestation constitutes a buffering effect to species replacement, current hybrid zones may not have reached equilibrium conditions, depending on deforestation history and other characters of the landscape. Future genetic work on B. variegata enclaves may shed light on the pattern and process of hybrid zone movement and species replacement, though timing and the size and environmental signature of the enclaves will affect genetic introgression in ways that may be hard to disentangle.

ecology↗

bioRxiv2025

Assessment of environmental variables for species distribution modelling: insights from the mosaic distribution of red- and yellow-bellied toads

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 in Hungary with principal coordinate analysis we identified their differential ecological preferences as forested, hilly and mountainous for B. variegata and open lowland for B. bombina. These locally operating parameters we consider to be good proxies for the essential species difference which resides in breeding in ephemeral puddles (B. variegata) versus larger permanent ponds (B. bombina). With two-species distribution modelling - in which the presence of one species is contrasted with the presence of the counterpart species - we obtained excellent model fit (AUC) for climate and elevation / land cover datasets alike (AUC=0.98 versus 0.95). For both models fit values dropped upon transference to surrounding countries, yet the latter model kept significantly higher predictive power (AUC=0.91) than the climate model (AUC=0.79). Swapping elevation for hilliness as suggested in the literature had a significant negative effect on model performance. We conclude that an informed parameter selection enhances model transferability, therewith improving our understanding of species-habitat associations. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/650429v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@5caa3forg.highwire.dtl.DTLVardef@1ad3857org.highwire.dtl.DTLVardef@14df970org.highwire.dtl.DTLVardef@3352ca_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIRed- and yellow-bellied toads engage in a yin-yang-like mosaic distribution across Europe. C_LIO_LISpecies differential habitat characteristics were studied with principal coordinates. C_LIO_LISpecies distribution modelling was with climate data and with landscape variables. C_LIO_LIModels produced with atlas data for Hungary were assessed over neighbouring countries. C_LIO_LITransferred models with elevation and forestation performed better than climate-based ones. C_LI

ecology↗

bioRxiv2024

Genomic evidence suggests the balanced lethal system in Triturus newts originated in an instantaneous speciation event.

Triturus newts are afflicted by a balanced lethal system causing the spontaneous death of half of their offspring. How could such a maladaptive trait evolve? We construct genetic maps for Triturus and its sister genus Lissotriton, identifying genes involved in the balanced lethal system. Triturus chromosome 1 has diverged into two versions, which each carry a single massive deletion that is compensated for by duplication of the same region in the alternate version - indicating that the balanced lethal system arose instantaneously, in a single macromutation. Simulations show that, counterintuitively, the deleterious nature of the rearranged chromosomes protects them against competition with the ancestral arrangement via reproductive isolation. We conclude that the origin of the Triturus balanced lethal system also led to instantaneous speciation.

evolutionary biology↗

bioRxiv2023

Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.

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-defined clustering threshold. Because improper clustering of orthologs is expected to affect results in downstream analyses, it is crucial to design pipelines for empirically optimizing the clustering threshold. While this issue has been largely discussed from a population genomics perspective, it remains understudied in the context of phylogenomics and coalescent species delimitation. To address this issue, we generated RADseq assemblies of representatives of the amphibian genera Discoglossus, Rana, Lissotriton and Triturus using a wide range of clustering thresholds. Particularly, we studied the effects of the intra-sample Clustering Threshold (iCT) and between-sample Clustering Threshold (bCT) separately, as both are expected to differ in multi-species data sets. The obtained assemblies were used for downstream inference of concatenation-based phylogenies, and multi-species coalescent species trees and species delimitation. The results were evaluated in the light of a reference genome-wide phylogeny calculated from newly generated Hybrid-Enrichment markers, as well as extensive background knowledge on the species systematics. Overall, our analyses show that the inferred topologies and their resolution are resilient to changes of the iCT and bCT, regardless of the analytical method employed. Except for some extreme clustering thresholds, all assemblies yielded identical, well-supported inter-species relationships that were mostly congruent with those inferred from the reference Hybrid-Enrichment data set. Similarly, coalescent species delimitation was consistent among similarity threshold values. However, we identified a strong effect of the bCT on the branch lengths of concatenation and species trees, with higher bCTs yielding trees with shorter branches, which might be a pitfall for downstream inferences of evolutionary rates. Our results suggest that the choice of assembly parameters for RADseq data in the context of shallow phylogenomics might be less challenging than previously thought. Finally, we propose a pipeline for empirical optimization of the iCT and bCT, implemented in optiRADCT, a series of scripts readily usable for future RADseq studies.

evolutionary biology↗

bioRxiv2020

A genomic footprint of a moving hybrid zone in marbled newts

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 of the Vouga river estuary. This suggested the past presence of a hybrid zone, possibly coinciding with a natural river outlet at ca. 1200 A.D. Since 1808, the species contact has moved back south to a by then completed, man-made Vouga channel. We also found evidence for a T. marmoratus genomic footprint in T. pygmaeus from the Serra de Sintra, near Lisbon. In combination with a previously reported southern, relic occurrence of T. marmoratus in between both areas, the data point to the superseding with hybridization of T. marmoratus by T. pygmaeus. We estimate that the species hybrid zone has moved over a distance of ca. 215 km.

evolutionary biology↗

bioRxiv2019

Spatial variation in introgression along a toad hybrid zone in France

The barrier effect is a restriction of gene flow between diverged populations by barrier genes. Restriction of gene flow and asymmetric introgression over multiple transects indicates species wide (genetic) adaptations, whereas transect-specific barrier loci may indicate local adaptation to gene flow. Asymmetric introgression can be caused by selection, hybrid zone movement, asymmetric reproductive isolation, or a combination of these. We study two widely separated transects (northwest and southeast France) for the 900 km long hybrid zone between Bufo bufo and B. spinosus toads, using ~1200 markers from restriction-site associated DNA (RAD) sequencing data. Genomic and geographic clines were used to identify outlier markers which show restricted or elevated introgression. Twenty-six barrier markers are shared between transects (the union of 56 and 123 barrier markers identified in each transect), which is more than would be expected by chance. However, the number of barrier markers is twice as high in the southeast transect. In the northwest transect a high amount of (asymmetric) introgression from B. spinosus into B. bufo is consistent with hybrid zone movement or asymmetric reproductive isolation. In the southeast transect, introgression is symmetric and consistent with a stable hybrid zone. Differences between transects may be related to genetic sub-structure within B. bufo. A longer period of secondary contact in southeast France appears to result in a relatively stronger barrier effect than in the northwest. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier to gene flow from local reductions in gene flow.

evolutionary biology↗

bioRxiv2019

Drivers of amphibian population dynamics and asynchrony at local and continental scales

O_LIIdentifying 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., Moran effect), local factors including the level of density-dependence may reduce the level of synchrony. Although divergences in the scaling of population synchrony and spatial environmental variation have been observed, the regulatory factors that underlie such mismatches are poorly understood.\nC_LIO_LINo previous studies have investigated how density-dependent processes and population-specific responses to weather variation influence spatial synchrony at both local and continental scales. We addressed this issue in a pond-breeding amphibian, the great crested newt (Triturus cristatus). We used capture-recapture data collected through long-term surveys in five T. cristatus populations in Western Europe.\nC_LIO_LIWe found a low level of demographic synchrony at both local and continental levels. Weather has weak and spatially variable effects on survival, recruitment and population growth rate. In contrast, density-dependence was a common phenomenon (at least for population growth) in almost all populations and subpopulations.\nC_LIO_LIOur findings support the idea that Morans effect is low in species where the population dynamics more closely depends on local factors (e.g. population density and habitat characteristics) than on large-scale environmental fluctuation (e.g. regional climatic variation). Those demographic feature likely have far-reaching consequences for the long-term viability of the spatially structured populations and their ability to response to large-scale climatic anomalies.\nC_LI

ecology↗

bioRxiv2018

Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle

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 remained unclear. To resolve the phylogeny of Triturus, we generated a c. 6,000 transcriptome-derived marker data set using a custom target enrichment probe set, and conducted phylogenetic analyses using: 1) data concatenation with RAxML, 2) gene-tree summary with ASTRAL, and 3) species-tree estimation with SNAPP. All analyses produce the same, highly supported topology, despite cladogenesis having occurred over a short timeframe, resulting in short internal branch lengths. Our new phylogenetic hypothesis is consistent with the minimal number of inferred changes in NTV count necessary to explain the diversity in NTV observed today. Although a causal relationship between NTV, body form, and aquatic ecology has yet to be experimentally established, our phylogeny indicates that these features have evolved together, and suggest that they may underlie the adaptive radiation that characterizes Triturus.

evolutionary biology↗