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Ben Wielstra - One of the best experts on this subject based on the ideXlab platform.
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Triturus newts.
Current biology : CB, 2019Co-Authors: Ben WielstraAbstract:Ben Wielstra introduces Eurasian newts of the genus Triturus.
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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle.
Molecular phylogenetics and evolution, 2019Co-Authors: Ben Wielstra, Jan W. Arntzen, Evan Mccartney-melstad, Roger K. Butlin, Howard Bradley ShafferAbstract: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. 6000 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.
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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle
2018Co-Authors: Ben Wielstra, Jan W. Arntzen, Evan Mccartney-melstad, Roger K. Butlin, Howard Bradley ShafferAbstract:Abstract 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 a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny is still unresolved, the evolutionary pathway for NTV and annual aquatic period is unclear. To resolve the phylogeny of Triturus, we generate a c. 6,000 transcriptome-derived marker data set using a custom target enrichment probe set, and conduct phylogenetic analyses including: 1) data concatenation with RAxML, 2) gene tree summary with ASTRAL, and 3) species tree estimation with SNAPP. All analyses consistently result in the same, highly supported topology. Our new phylogenetic hypothesis only requires the minimal number of inferred changes in NTV count to explain the NTV radiation observed today. This suggests that, while diversification in body shape allowed ecological expansion in Triturus to encompass an increasingly aquatic life style, body shape evolution was phylogenetically constrained.
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Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts.
PloS one, 2014Co-Authors: Ben Wielstra, Jan W. Arntzen, Kristiaan J. Van Der Gaag, Maciej Pabijan, Wiesław BabikAbstract:The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
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parallel tagged amplicon sequencing of transcriptome based genetic markers for Triturus newts with the ion torrent next generation sequencing platform
Molecular Ecology Resources, 2014Co-Authors: Ben Wielstra, E Duijm, P Lagler, Y Lammers, W R M Meilink, Janine M ZiermannAbstract:Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.
Spartak N Litvinchuk - One of the best experts on this subject based on the ideXlab platform.
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Natural Autotriploidy in the Danube Newt, Triturus dobrogicus (Salamandridae)
Russian Journal of Herpetology, 2013Co-Authors: Spartak N Litvinchuk, Jury M. Rosanov, L. J. BorkinAbstract:A case of natural autotriploidy in Triturus dobrogicus from Transcarpathian Province (Ukraine) is described. This is the first record of polyploidy for the species.
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first record of paedomorphosis for the smooth newt Triturus vulgaris from ukraine
Russian Journal of Herpetology, 2013Co-Authors: Spartak N LitvinchukAbstract:Two paedomorphic males of the smooth newt ( Triturus vulgaris ) were found in Izmail, a town in Odessa Region (Danube River Valley). This is the first record of paedomorphosis in urodelans from Ukraine.
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tracing glacial refugia of Triturus newts based on mitochondrial dna phylogeography and species distribution modeling
Frontiers in Zoology, 2013Co-Authors: Spartak N Litvinchuk, Konstantinos Sotiropoulos, Ben Wielstra, Jelka Crnobrnjaisailovic, Bastian T Reijnen, Andrew K Skidmore, A G Toxopeus, Nikolay TzankovAbstract:The major climatic oscillations during the Quaternary Ice Age heavily influenced the distribution of species and left their mark on intraspecific genetic diversity. Past range shifts can be reconstructed with the aid of species distribution modeling and phylogeographical analyses. We test the responses of the different members of the genus Triturus (i.e. the marbled and crested newts) as the climate shifted from the previous glacial period (the Last Glacial Maximum, ~21 Ka) to the current interglacial. We present the results of a dense mitochondrial DNA phylogeography (visualizing genetic diversity within and divergence among populations) and species distribution modeling (using two different climate simulations) for the nine Triturus species on composite maps. The combined use of species distribution modeling and mitochondrial phylogeography provides insight in the glacial contraction and postglacial expansion of Triturus. The combined use of the two independent techniques yields a more complete understanding of the historical biogeography of Triturus than both approaches would on their own. Triturus newts generally conform to the ‘southern richness and northern purity’ paradigm, but we also find more intricate patterns, such as the absence of genetic variation and suitable area at the Last Glacial Maximum (T. dobrogicus), an ‘extra-Mediterranean’ refugium in the Carpathian Basin (T. cristatus), and areas where species displaced one another postglacially (e.g. T. macedonicus and western T. karelinii). We provide a biogeographical scenario for Triturus, showing the positions of glacial refugia, the regions that were postglacially colonized and the areas where species displaced one another as they shifted their ranges.
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Epicoracoid Overlap Indices in Newts of the Genus Triturus (Amphibia: Salamandridae)
Russian Journal of Herpetology, 2011Co-Authors: Valentin G. Borkhvardt, Spartak N LitvinchukAbstract:According to the epicoracoid overlap index, Triturus vulgaris , T. cristatus , T. dobrogicus , and T. karelinii form a rather homogenous group. Until now, members of the genus Triturus are the only arciferal amphibians in which the overlap index is less than 1.
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Spontaneous Triploidy in the Crested Newt, Triturus cristatus (Salamandridae)
Russian Journal of Herpetology, 2011Co-Authors: L. J. Borkin, Spartak N Litvinchuk, Jury M. RosanovAbstract:A triploid male was found among the offspring of a female of Triturus cristatus which was collected in the Ukrainian Transcarpathians. It is the first record of spontaneous triploidy for the species, and for salamanders of the former Soviet Union in general.
Jan W. Arntzen - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle.
Molecular phylogenetics and evolution, 2019Co-Authors: Ben Wielstra, Jan W. Arntzen, Evan Mccartney-melstad, Roger K. Butlin, Howard Bradley ShafferAbstract: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. 6000 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.
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Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle
2018Co-Authors: Ben Wielstra, Jan W. Arntzen, Evan Mccartney-melstad, Roger K. Butlin, Howard Bradley ShafferAbstract:Abstract 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 a higher NTV corresponds to a longer annual aquatic period. Because the Triturus phylogeny is still unresolved, the evolutionary pathway for NTV and annual aquatic period is unclear. To resolve the phylogeny of Triturus, we generate a c. 6,000 transcriptome-derived marker data set using a custom target enrichment probe set, and conduct phylogenetic analyses including: 1) data concatenation with RAxML, 2) gene tree summary with ASTRAL, and 3) species tree estimation with SNAPP. All analyses consistently result in the same, highly supported topology. Our new phylogenetic hypothesis only requires the minimal number of inferred changes in NTV count to explain the NTV radiation observed today. This suggests that, while diversification in body shape allowed ecological expansion in Triturus to encompass an increasingly aquatic life style, body shape evolution was phylogenetically constrained.
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Data concatenation, Bayesian concordance and coalescent-based analyses of the species tree for the rapid radiation of Triturus newts.
PloS one, 2014Co-Authors: Ben Wielstra, Jan W. Arntzen, Kristiaan J. Van Der Gaag, Maciej Pabijan, Wiesław BabikAbstract:The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
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The distribution of the crested and marbled newt species (Amphibia: Salamandridae: Triturus) – an addition to the New Atlas of Amphibians and Reptiles of Europe
Amphibia-Reptilia, 2014Co-Authors: Ben Wielstra, Neftalí Sillero, Judit Vörös, Jan W. ArntzenAbstract: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.
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A combination of techniques proves useful in the development of nuclear markers in the newt genus Triturus
Molecular ecology resources, 2009Co-Authors: G. Espregueira Themudo, Wiesław Babik, Jan W. ArntzenAbstract:To increase the number of markers available for study of phylogeny and phylogeography in the newt genus Triturus, we developed and tested 59 primer pairs using three different techniques. Primers were obtained from published sources, by designing exon-primed intron-crossing primers and from randomly cloned anonymous nuclear DNA fragments. Successful polymerase chain reaction products were cloned and sequenced. Five fragments were successfully amplified and sequenced for six species of Triturus: intron 7 of the β-fibrinogen gene (βfibint7), third intron of the calreticulin gene (CalintC), the 11th intron of the α-subunit of the platelet derived growth factor receptor (PDGFRα) and two anonymous markers (Cri1 and Cri4). The average percentage species divergence across all the markers is low (c. 3%), compared to what has been found in mitochondrial DNA (25-30%).
Cristina Giacoma - One of the best experts on this subject based on the ideXlab platform.
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THE DISTRIBUTION AND HABITATS OF THE NEWT (Triturus, AMPHIBIA) IN CALABRIA (SOUTHERN ITALY)
Monitore Zoologico Italiano-Italian Journal of Zoology, 2013Co-Authors: Cristina Giacoma, Orfeo Picariello, D. Puntillo, F. Rossi, Sandro TripepiAbstract:SUMMARY We provide data about the present day distribution and ecology of the Italian southern-most newt populations Triturus, Amphibia). In 1981–1986 the Calabrian wetlands were studied and classified. The presence/absence of the species were recorded as well as their main morphometric parameters. We observed and described 69 Triturus italicus (Peracca), 15 Triturus camifex (Laurenti) and 4 Triturus alpestris (Laurenti) breeding sites. Triturus italicus shows a high ecological plasticity and preferably colonizes man-made tanks or small seasonal pools below 800 m. In contrast, Triturus carnifex and Triturus alpestris are mostly found above 800 m and in ponds located in the beech woods. Ecological analysis highlighted how species density depends on climate and on the presence of predators.
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Limitation of similarity and feeding habits in three syntopic species of newts (Triturus, Amphibia)
Ecography, 1992Co-Authors: Pierre Joly, Cristina GiacomaAbstract:Differences in body size between both species and sex were observed to be close to Hutchinsonian ratios in an assemblage of three species of newts (Triturus italicus, T. alpestris and T. carnifex) in southern Italy. According to feeding, differences in body size were not related with a strict food niche segregation. The diet of larger newt included indeed all the prey eaten by smaller newts but showed new prey types. Differences between species were more marked than between sexes of the same species, despite a strong sexual dimorphism in body size. Larger newts foraged in a wider range of microhabitats and exhibited a greater diversity of foraging tactics. Triturus italicus fed essentially on plankton and chironomids in shallow water at the banks of the pond. Triturus alpestris foraged also in deeper water, particularly on isopods in vegetation. Prey fallen on the water surface constituted the main part of T. carnifex diet. According to recent data on newt evolution, speciation consisted in the reduction of body size. Our data show that this process has been related with a specialization of the diet and of habitat use.
Giuseppina Barsacchi - One of the best experts on this subject based on the ideXlab platform.
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Molecular cytogenetics of the ribosomal (18S + 28S and 5S) DNA loci in primitive and advanced urodele amphibians.
Genome, 1993Co-Authors: Stefania De Lucchini, Irma Nardi, Giuseppina Barsacchi, Renata Batistoni, F. AndronicoAbstract:In the present work we performed a cytogenetic analysis of the ribosomal (18S + 28S and 5S) loci in amphibian species belonging to the advanced family Salamandridae (genera Triturus, Salamandra, and Salamandrina) and in the primitive hynobiid Salamandrella keyserlingii (family Hynobiidae). In each analyzed karyotype the 5S rDNA sites appear to be stable, and definite in number, while an intraspecific variability both in number and chromosomal location of the 18S + 28S rDNA loci has been found in some Triturus species. In particular, an evolutionary trend toward a large intraspecific variability of the 18S + 28S rDNA loci has been found in the T. vulgaris species group. A structural analysis of the ribosomal repetition units demonstrates the occurrence of a length polymorphism within the 18S + 28S rDNA repeats in the examined species of the family Salamandridae; however, this polymorphism is rather limited, even in those Triturus species characterized by high intragenomic variability of the ribosomal sites...
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Two dispersed highly repeated DNA families of Triturus vulgaris meridionalis (Amphibia, Urodela) are widely conserved among Salamandridae
Chromosoma, 1991Co-Authors: Robert Vignali, Renata Batistoni, Filippo M. Rijli, Duccio Fratta, Federico Cremisi, Giuseppina BarsacchiAbstract:Two BamHI families of repeated sequences were characterized from the genome of the Italian smooth newt, Triturus vulgaris meridionalis (Amphibia, Urodela). The first family, which is divided into subfamilies, consists of tandemly arranged arrays whose basic repeat is around 398 bp long; these arrays are dispersed throughout the entire chromosome sets of the various species of Triturus tested. Moreover the family is widely conserved among Salamandridae, being detected by genomic DNA blotting of Notophthalmus viridescens, Taricha granulosa, Salamandrina terdigitata and Euproctus platycephalus . The second BamHI family is represented by a cloned sequence of 419 bp, which is dispersed in the chromosome set of several species of Triturus . The sequence is also conserved in S. terdigitata and in E. platycephalus but is not detectable in N. viridescens or T. granulosa . The cloned sequence is most probably only part of a longer unit interspersed within the Triturus genome.
