Biology subjects

Wielstra, B.

Publications and source records attributed to Wielstra, B..

13 recordsLinked to original sources

bioRxiv2025

Target capture sequencing provides insights into hybridogenetic water frogs

The European water frogs of the genus Pelophylax, with their propensity to hybridize and a non-orthodox inheritance system in some hybrids, present a genetic puzzle that has previously lacked strong genomic tools. This has limited investigation into the remarkable hybridogenetic system observed in the edible frog P. esculentus as well as inhibited monitoring of invasive populations in a genus that is critically vulnerable to this threat. In this study we explore whether a previously developed target capture bait set, FrogCap, can be used to answer genomic questions within the genus, by applying it to the three taxa of Pelophylax native to the Netherlands. We observe that the target capture data cleanly separates the three taxa, confirming significant introgression of P. lessonae mtDNA into P. ridibundus from the Netherlands. We also show that target capture is an efficient method for identifying polyploidy in P. esculentus and is effective at determining ancestral contribution within our sample population. Targeted sequence capture using FrogCap is a useful tool to unravel the intricate evolution of Pelophylax water frogs.

genomics↗

bioRxiv2024

Safeguarding Iguana diversity: Enabling rapid and low-effort tracking of non-native iguanas through terrestrial eDNA innovations

Reptiles have among the highest extinction risk across terrestrial vertebrates, with habitat fragmentation, habitat destruction, and invasive alien species being the primary causes of reptile species loss on a global scale. Invasive hybridization (i.e. hybridization between native and invasive alien species) is increasing globally, causing the extinction of native genotypes, and this phenomenon is particularly pervasive in Caribbean iguanas. The Lesser Antillean Iguana (Iguana delicatissima), a keystone species of Caribbean coastal ecosystems, has become critically endangered mainly due to ongoing hybridization with the invasive Common Green Iguana (I. iguana). For impactful conservation intervention, the need for early detection of invasive animals and their progeny, or detection of surviving pure native animals, is urgent. We aimed to develop a novel environmental DNA (eDNA) toolkit using Kompetitive Allele Specific PCR (KASP) technology, a method of allele-specific amplification for cost-effective and efficient sampling of terrestrial substrates to aid in mapping the distribution of native I. delicatissima, invasive I. iguana, and signal potential invasive hybridization. We demonstrate proof-of-concept and successfully identified I. delicatissima, I. iguana, and their hybrids via blood samples using our primer sets, as well as successful detection of I. delicatissima in several ex-situ (Rotterdam Zoo) and in-situ (St. Eustatius) eDNA samples, collected with environmental swabs and tape-lifting. We found that sampling potential perching spots yielded the highest number of positive detections via environmental swabbing and tape-lifting. Our toolkit demonstrates the potential of terrestrial eDNA sampling for iguana conservation, enabling faster detection of potential invasive hybridization. Additionally, the method holds promise for other terrestrial cryptic species, contributing to broader collection of population-level information.

ecology↗

bioRxiv2024

Identification of Y-chromosome turnover in newts fails to support a sex chromosome origin for the Triturus balanced lethal system

Non-recombining regions of the genome often have profound effects on evolution, resulting in phenomena such as sex chromosomes and supergenes. Amongst the strangest examples are balanced lethal systems, such as that found in newts of the genus Triturus. These systems halve reproductive output, and the evolution of such a deleterious trait is difficult to explain. For Triturus an intriguing model proposes that the balanced lethal system evolved from an ancestral Y-chromosome. To test this hypothesis, we identify the Y-chromosome of Triturus and verify whether it, or the balanced lethal system, is homologous to the Y-chromosome of its sister genus Lissotriton, which does not possess the balanced lethal system. We identify a set of candidate Y-linked markers in T. ivanbureschi and place them on a high-density linkage map that we construct with 7,233 RADseq markers. We validate male specificity of the markers across the genus, and then place both the Triturus and Lissotriton Y-linked regions within previously constructed target capture linkage maps that include genes linked to the balanced lethal system. We observe that neither the Triturus balanced lethal system, nor the Triturus Y-chromosome are homologous to the Lissotriton Y-chromosome. This is the first molecular evidence of a transition between Y-chromosome systems within salamanders. However, unless additional sex chromosome turnover events are involved, our data does not support a sex chromosome origin of the balanced lethal system.

evolutionary biology↗

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↗

bioRxiv2024

PAV-spotter: using signal cross-correlations to identify Presence/Absence Variation in target capture data

High throughput sequencing technologies have become essential in the fields of evolutionary biology and genomics. When dealing with non-model organisms or genomic gigantism, sequencing whole genomes is still relatively costly and therefore reduced-genome representations are frequently obtained, for instance by target capture approaches. While computational tools exist that can handle target capture data and identify small-scale variants such as single nucleotide polymorphisms and micro-indels, options to identify large scale structural variants are limited. To meet this need, we introduce PAV-spotter: a tool that can identify presence/absence variation (PAV) in target capture data. PAV-spotter conducts a signal cross-correlation calculation, in which the distribution of read counts per target between samples of different a priori defined classes - e.g. male versus female, or diseased versus healthy - are compared. We apply and test our methodology by studying Triturus newts: salamanders with gigantic genomes that currently lack an annotated reference genome. Triturus newts suffer from a hereditary disease that kills half their offspring during embryogenesis. We compare the target capture data of two different types of diseased embryos, characterized by unique deletions, with those of healthy embryos. Our findings show that PAV-spotter helps to expose such structural variants, even in the face of medium to low sequencing coverage levels, low sample sizes, and background noise due to mis-mapped reads. PAV-spotter can be used to study the structural variation underlying supergene systems in the absence of whole genome assemblies. The code, including further explanation, is available through the PAV-spotter GitHub repository: https://github.com/Wielstra-Lab/PAVspotter.

bioengineering↗

bioRxiv2024

Determining zygosity with multiplex Kompetitive Allele-Specific PCR (mxKASP) genotyping

We introduce multiplex Kompetitive Allele-Specific PCR (mxKASP): a modification of classical KASP genotyping that allows zygosity to be determined in diploid organisms. Rather than targeting a SNP associated with a single marker, mxKASP targets two non-homologous markers. We show proof of concept by applying mxKASP to the balanced lethal system in Triturus newts, in which individuals are known to possess either: (1) zero copies of the 1A version of chromosome 1 and two copies of the 1B version; (2) one copy of 1A and one copy of 1B; or (3) two copies of 1A and zero copies of 1B. mxKASP is successful in amplifying both a 1A and a 1B marker in a single reaction (if present), allowing the zygosity of individuals to be inferred. We independently confirm our mxKASP results with a multiplex PCR approach. We argue that mxKASP can be applied to rapidly and economically determine zygostity in diploid organisms, for a large number of samples at once.

molecular biology↗

bioRxiv2024

Conserved gene content and unique phylogenetic history characterize the 'bloopergene' underlying Triturus' balanced lethal system

In a balanced lethal system, half the reproductive output succumbs. Triturus newts are the best-known example. Their chromosome 1 comes in two distinct versions and embryos carrying the same version twice experience developmental arrest. Those possessing two different versions survive, suggesting that each version carries something uniquely vital. With target capture we obtain over 7,000 nuclear DNA markers across the genus Triturus and all main lineages of Salamandridae (the family to which Triturus belongs) to investigate the evolutionary history of Triturus chromosome 1 versus other chromosomes. Dozens of genes are completely missing from either one or the other version of chromosome 1 in Triturus. Furthermore, the unique gene content of 1A versus 1B is remarkably similar across Triturus species, suggesting that the balanced lethal system evolved before Triturus radiated. The tree topology of chromosome 1 differs from the rest of the genome, presumably due to pervasive, ancient hybridization between Triturus ancestor and other newt lineages. Our findings accentuate the complex nature of Triturus chromosome 1 - the bloopergene driving the evolutionarily enigmatic balanced lethal system.

evolutionary biology↗

bioRxiv2024

NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)

Salamanders have large and complex genomes, hampering whole genome sequencing. However, reduced representation sequencing provides a feasible alternative to obtain genome-wide data. We present NewtCap: a sequence capture bait set that targets c.7k coding regions across the genomes of all true salamanders and newts (the family Salamandridae, also known as salamandrids). We test the efficacy of NewtCap, originally designed for the Eurasian Triturus newts, in 30 species, belonging to 17 different genera, that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genus Triturus correlates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; 1) phylogenomics, by reconstructing the phylogeny of Salamandridae, 2) phylogeography, by sequencing the four closely related species comprising the genus Taricha, 3) hybrid zone analysis, by genotyping two Lissotriton species and different classes of interspecific hybrids, and 4) conservation genetics, by comparing Triturus ivanbureschi samples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.

genomics↗

bioRxiv2023

Migratory herbivorous waterfowl couple the seed wave and the green wave during spring migration

East Asian herbivorous waterfowl intensively use farmland in spring, next to their natural habitat. Accordingly, they might have expanded their migration strategy from merely tracking the green wave of newly emerging vegetation to also incorporating the availability of post-harvest agricultural seeds (here dubbed the seed wave). However, if and how waterfowl use multiple food resources to time their seasonal migration is still unknown. We test this migration strategy using 167 spring migration tracks of five East Asian herbivorous waterfowl species and mixed-effect resource selection function models. We find all study species arrive at their core stopover sites in the Northeast China Plain after agricultural seeds become available, extend their stay after spring vegetation emerges, and arrive at breeding sites around the emergence of vegetation. Moreover, the cue used in exploiting the availability of both food resources varies in different regions and among species. At the core stopover sites, larger-bodied species use the seed wave and smaller-bodied ones adopt the green wave. At the breeding sites, the former follow the green wave, and the latter track the snow-free time. Our findings suggest that waterfowl track multiple resource waves to finetune their migration, highlighting new opportunities for conservation.

ecology↗

bioRxiv2021

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through 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 such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

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↗

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↗