East Asian migratory waterfowl have greatly declined since the 1950s, especially the populations that winter in China. Conservation is severely hampered by the lack of primary information about... Show moreEast Asian migratory waterfowl have greatly declined since the 1950s, especially the populations that winter in China. Conservation is severely hampered by the lack of primary information about migration patterns and stopover sites. This study utilizes satellite tracking techniques and advanced spatial analyses to investigate spring migration of the greater white-fronted goose (Anser albifrons) and tundra bean goose (Anser serrirostris) wintering along the Yangtze River Floodplain. Based on 24 tracks obtained from 21 individuals during the spring of 2015 and 2016, we found that the Northeast China Plain is far-out the most intensively used stopover site during migration, with geese staying for over 1month. This region has also been intensely developed for agriculture, suggesting a causal link to the decline in East Asian waterfowl wintering in China. The protection of waterbodies used as roosting area, especially those surrounded by intensive foraging land, is critical for waterfowl survival. Over 90% of the core area used during spring migration is not protected. We suggest that future ground surveys should target these areas to confirm their relevance for migratory waterfowl at the population level, and core roosting area at critical spring-staging sites should be integrated in the network of protected areas along the flyway. Moreover, the potential bird-human conflict in core stopover area needs to be further studied. Our study illustrates how satellite tracking combined with spatial analyses can provide crucial insights necessary to improve the conservation of declining Migratory species. Show less
Riemsdijk, I. van; Nieuwenhuize, L. van; Martinez-Solano, I.; Arntzen, J.W.; Wielstra, B.M. 2018
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... Show moreThe 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 to a range-wide phylogeography of Ommatotriton. All haplotypes identified in Spain are identical to haplotypes known from the native range. The mitochondrial haplotypes derive from O. ophryticus and were originally recorded in northeast Turkey. The nuclear haplotypes reveal that all individuals are genetically admixed between O. ophryticus and O. nesterovi. While the geographical resolution for the nuclear markers is low, the source of the O. nesterovi ancestry must be Turkey, as this species is a Turkish endemic. Species distribution models suggest a large potential distribution for the two Ommatotriton species, extending over northern Iberia and southern France. The ecology of hybrids can differ substantially from that of the parent species, making the impact of the Spanish hybrid banded newt population difficult to predict. Show less
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... Show moreUnderstanding 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 section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future. Show less
Riemsdijk, I. van; Arntzen, J.W.; Bogaerts, S.; Franzen, M.; Litvinchuk, S.N.; Olgun, K.; Wielstra, B.M. 2017
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... Show moreThe 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 DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at similar to 25 Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated similar to 8-13 Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity. (C) 2017 The Authors. Published by Elsevier Inc. Show less
The highly pathogenic avian influenza subtype H5N1 (HPAI H5N1) is a worldwide zoonotic infectious disease, threatening humans, poultry and wild birds. The role of wild birds in the spread of HPAI... Show moreThe highly pathogenic avian influenza subtype H5N1 (HPAI H5N1) is a worldwide zoonotic infectious disease, threatening humans, poultry and wild birds. The role of wild birds in the spread of HPAI H5N1 has previously been investigated by comparing disease spread patterns with bird migration routes. However, the different roles that the southward autumn and northward spring migration might play in virus transmission have hardly been explored. Using direction analysis, we analyze HPAI H5N1 transmission directions and angular concentration of currently circulating viral clades, and compare these with waterfowl seasonal migration directions along major waterfowl flyways. Out of 22 HPAI H5N1 transmission directions, 18 had both a southward direction and a relatively high concentration. Differences between disease transmission and waterfowl migration directions were significantly smaller for autumn than for spring migration. The four northward transmission directions were found along Asian flyways, where the initial epicenter of the virus was located. We suggest waterfowl first picked up the virus from East Asia, then brought it to the north via spring migration, and then spread it to other parts of world mainly by autumn migration. We emphasize waterfowl autumn migration plays a relatively important role in HPAI H5N1 transmission compared to spring migration. Show less
The Danube crested newt Triturus dobrogicus has been proposed to comprise two subspecies: T. d. dobrogicus and T. d. macrosoma. Uncertainty exists in the literature over their distribution and... Show moreThe Danube crested newt Triturus dobrogicus has been proposed to comprise two subspecies: T. d. dobrogicus and T. d. macrosoma. Uncertainty exists in the literature over their distribution and diagnosability. We conduct a multilocus phylogeographical survey and review published data to determine whether a two taxon treatment is warranted. Newly produced and published nuclear DNA data suggest intraspecific variation in the Pannonian Plain part of the range, but with extensive genetic admixture, whereas mitochondrial DNA data shows a lack of geographical structuring in T. dobrogicus altogether. None of the studied morphological characters suggest the presence of two geographical groups in T. dobrogicus unequivocally. Although Danube Delta newts do have relatively short bodies compared to the remainder of the range (the Pannonian and Lower Danube Plains and the Dnepr Delta), we argue that this finding can be explained by phenotypic plasticity - particularly in light of the incongruent evolutionary scenario suggested by genetic data. We conclude that the total body of evidence does not support the two subspecies hypothesis and recommend that T. dobrogicus is treated as a monotypic species. Show less
Genetic pollution of a native species through hybridization with an invasive species poses an insidious conservation threat. To expose genetic pollution, molecular methods employing multilocus data... Show moreGenetic pollution of a native species through hybridization with an invasive species poses an insidious conservation threat. To expose genetic pollution, molecular methods employing multilocus data are required. We present a case study of genetic pollution via hybridization of a native crested newt species, Triturus cristatus, by the invasive Triturus carnifex on the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next generation sequencing and one mitochondrial marker by Sanger sequencing for four populations from the native range of both parent species and eleven ponds on the Veluwe. We use three population genetic approaches (HIest, BAPS and Structure) to determine the genetic composition of the Veluwe newts based on all nuclear markers, a subset of 18 diagnostic markers and the complementary 32 non-diagnostic markers, with and without parental populations. BAPS underestimates genetic pollution, whereas Structure is comparatively accurate compared to HIest, although Structure's relative advantage decreases with the diagnosticity of the markers. Data simulation confirms these findings. Genetic composition of the Veluwe ponds ranges from completely native, via different degrees of genetic admixture, to completely invasive. The observed hybrid zone appears to be bimodal, suggesting negative selection against hybrids. A genetic footprint of the native species is present in invasive populations, evidencing that the invasive locally replaced the native species. Genetic pollution is currently confined to a small area, but the possibility of further expansion cannot be excluded. Removal of genetic pollution will not be easy. We emphasize the need for legal guidance to manage genetic pollution. (C) 2015 The Authors. Published by Elsevier Ltd. Show less
We assess the role of the Carpathians as an extra-Mediterranean glacial refugium for the crested newt Triturus cristatus. We combine a multilocus phylogeography (one mitochondrial protein-coding... Show moreWe assess the role of the Carpathians as an extra-Mediterranean glacial refugium for the crested newt Triturus cristatus. We combine a multilocus phylogeography (one mitochondrial protein-coding gene, three nuclear introns, and one major histocompatibility complex gene) with species distribution modelling (projected on current and Last Glacial Maximum climate layers). All genetic markers consistently show extensive genetic variation within and genetic depletion outside the Carpathians. The species distribution model suggests that most of the current range was unsuitable at the Last Glacial Maximum, but a small suitable area remained in the Carpathians. Triturus cristatus dramatically expanded its postglacial range, colonizing much of temperate Eurasia from a glacial refugium in the Carpathians. Within the Carpathians, T.cristatus persisted in multiple geographically discrete regions, providing further support for a Carpathian refugia within refugia' scenario.(c) 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114, 574-587. Show less
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... Show moreFacultative 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. Show less
Two and perhaps three taxa of Lissotriton newt occur in Turkey. Their species status is controversial. The distribution of these taxa and the taxonomic status of each are reviewed and discussed. A... Show moreTwo and perhaps three taxa of Lissotriton newt occur in Turkey. Their species status is controversial. The distribution of these taxa and the taxonomic status of each are reviewed and discussed. A database of 128 Turkish Lissotriton localities was compiled and species distribution models were constructed. We reiterate that the presence of L. (v.) lantzi in Turkey is disputed and needs confirmation. The range of L. (v.) kosswigi is restricted to north-western Anatolia - given the small global range of this Turkey endemic, a closer look at its conservation status is warranted. The distribution of L. v. schmidtleri covers western Asiatic and European Turkey. The findings support an allopatric distribution of the Turkish Lissotriton species. We reflect on the biological significance of previously reported morphological intermediates between L. (v.) kosswigi and L. v. schmidtleri in the light of the recent proposal to recognize kosswigi at the species level. The available data are in line with species status for L. (v.) lantzi and L. (v.) kosswigi. Although L. v. schmidtleri is a genetically diverged taxon as well, the extent of gene flow with parapatric European Lissotriton taxa is as yet unknown. Show less
Vukov, T.D.; Cvijanovic, M.; Wielstra, B.M.; Kalezic, M.L. 2014
Assessing the origin of trait variation during evolutionary history is an important first step in understanding evolutionary diversification. Here, we tested the influence of shared ancestry and... Show moreAssessing the origin of trait variation during evolutionary history is an important first step in understanding evolutionary diversification. Here, we tested the influence of shared ancestry and climate, and the interplay of both, on the variation of ten life history traits in Triturus newts. We showed that (1) climate alone has driven the evolution of variation in live life history traits, (2) phylogenetic signal partly explains the variation in two traits (vitellus diameter and snout-vent length of larvae at metamorphosis), and (3) the interplay of shared ancestry and climate explains the variation in one trait (snout-vent length of larvae at metamorphosis). This study highlights the coarse-grained influence of shared ancestry and climate on the structure of phenotypic trait variation in Triturus and provides a handle for more detailed, fine grained studies on the evolution of phenotypic trait variation. Show less
Wielstra, B.M.; Arntzen, J.W.; van der Gaag, K.J.; Pabijan, M.; Babik, W. 2014
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.... Show moreThe 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. Show less
The shape of hybrid zones provides insight into genetic isolation between the evolutionary lineages involved: the greater the limitation to gene flow, the farther along the unimodal to bimodal... Show moreThe shape of hybrid zones provides insight into genetic isolation between the evolutionary lineages involved: the greater the limitation to gene flow, the farther along the unimodal to bimodal continuum. We study hybrid zone modality in a group of closely related species at a variety of levels of genetic divergence. We explore the degree and the geography of hybridization in 12 transects of Triturus newts, for nine of the ten secondary contact zones in Europe, using nuclear and mitochondrial encoded genetic data and morphological characteristics. Species status is verified by examining the correlation between the three marker systems in a geographical context. At 40 allozyme loci, two transects classify as unimodal, three as bimodal and two as intermediate, while the signal for hybridization is weak or absent in five transects. One zone studied in duplicate was classified as intermediate in one region and as bimodal in another region. mtDNA introgression is frequent and extends beyond nuclear introgression in two transects. Morphology provides additional evidence for hybridity, including one transect for which the signal of nuclear gene flow is weak. Compared to simulations allowing panmixia, the observed allozyme transitions at contact zones show a deficit of backcrossing to various degrees. Over all transects, there is a weak negative relationship between the level of hybridization and allozyme genetic distance for species pairs, consistent with Bateson-Dobzhansky-Muller effects. This observation, based upon highly comparable data for a single genus, supports conclusions derived from analyses over a wide variety of other taxa.(c) 2014 The Authors. Biological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113, 604-622. Show less
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... Show moreNext-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. Show less
We collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality... Show moreWe collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality at Vrtovac in eastern Serbia. We compare these data to a reference set composed of the four crested newt species distributed in eastern Serbia namely T. cristatus, T. dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of these species the newts from the type locality of T. arntzeni should be attributed. The majority of alleles in individuals from Vrtovac is derived from T. macedonicus, but a considerable number of T. ivanbureschi alleles is also present; alleles typical for T. cristatus and T. dobrogicus are found at low frequency. Accordingly, we interpret Vrtovac as a T. macedonicus - T. ivanbureschi hybrid population, albeit not composed of F1 hybrids but of genetically admixed individuals derived through multiple generations of backcrossing. The data support the notion that the name T. arntzeni should not be applied to a species newly distinguished in T. karelinii sensu lato (to which the name T. ivanbureschi has been given). We conclude that because of the hybrid nature of the individuals from Vrtovac, the name T. arntzeni should be placed not only in the synonymy of T. macedonicus but also in the synonymy of T. ivanbureschi. In this study we demonstrate that next-generation sequencing can provide high quality data for type material with degraded DNA and therefore can play an important role in taxonomy. Show less
If potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species.... Show moreIf potential morphologically cryptic species, identified based on differentiated mitochondrial DNA, express ecological divergence, this increases support for their treatment as distinct species. However, mitochondrial DNA introgression hampers the correct estimation of ecological divergence. We test the hypothesis that estimated niche divergence differs when considering nuclear DNA composition or mitochondrial DNA type as representing the true species range. We use empirical data of two crested newt species (Amphibia: Triturus) which possess introgressed mitochondrial DNA from a third species in part of their ranges. We analyze the data in environmental space by determining Fisher distances in a principal component analysis and in geographical space by determining geographical overlap of species distribution models. We find that under mtDNA guidance in one of the two study cases niche divergence is overestimated, whereas in the other it is underestimated. In the light of our results we discuss the role of estimated niche divergence in species delineation. Show less
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... Show moreIn 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 x 50 km UTM grid resolution as used in the new atlas and highlight those grid cells in which more than one Triturus species occurs. Show less
We present a taxonomic revision of the crested newt Triturus karelinii sensu lato. Based on the presence of discrete nuclear DNA gene pools, deep genetic divergence of mitochondrial and nuclear DNA... Show moreWe present a taxonomic revision of the crested newt Triturus karelinii sensu lato. Based on the presence of discrete nuclear DNA gene pools, deep genetic divergence of mitochondrial and nuclear DNA, and no indication of gene flow, we interpret this taxon as comprising two species: one covering the southern Caspian Sea shore, the Caucasus and the Crimea, i.e. the eastern part of the total range and another covering northern Asiatic Turkey and western Asiatic Turkey plus the southeastern Balkan Peninsula, i.e. the central and western part of the total range. We acknowledge that the central/western species should likely be further subdivided into a central and a western taxon, but we prefer to await a more detailed genetic analysis of the putative contact zone, positioned in northwestern Asiatic Turkey. The name T. karelinii (Strauch, 1870) applies to the eastern species as the type locality is positioned along the coast of the Gulf of Gorgan, Iran. The name T. arntzeni has been applied to the central/western species with Vrtovac, Serbia as the type locality. We show that not T. karelinii sensu lato but T. macedonicus occurs at Vrtovac. Hence, the name T. arntzeni Litvinchuk, Borkin, Dzukic and Kalezic, 1999 (in Litvinchuk et al., 1999) is a junior synonym of T. macedonicus (Karaman, 1922) and should not be used for the central/western species. We propose the name T. ivanbureschi sp. nov. for the central/western species and provide a formal species description. Show less
The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages:... Show moreThe crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species. (C) 2013 Elsevier Inc. All rights reserved. Show less
