Development of polymorphic microsatellite loci markers for the Asp viper (Vipera aspis) using high-throughput sequencing and their use for other European vipers

Geser, Silvia; Kaiser, Laura; Zwahlen, Valérie; Ursenbacher, Sylvain

doi:10.1163/15685381-00002861

Cited by 10 publications

(13 citation statements)

References 23 publications

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“…When applying more relaxed comparison criteria between studies, 454‐based microsatellite loci development in the meadow viper resulted in only 14 applicable loci out of 37,000 sequence reads (0.037% success rate) and in a success rate of only 0.007% in the Asp viper (Geser et al. ) – both studies were performed without prior enrichment of genomic sublibraries. Accordingly, our obtained success rates are comparable quite high and seem to justify the applied enrichment procedure.…”

Section: Discussionmentioning

confidence: 99%

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina‐based approaches

Drechsler

Geller

Freund

et al. 2013

Ecology and Evolution

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The development of microsatellite loci has become more efficient using next-generation sequencing (NGS) approaches, and many studies imply that the amount of applicable loci is large. However, few studies have sought to quantify the number of loci that are retained for use out of the thousands of sequence reads initially obtained. We analyzed the success rate of microsatellite loci development for three amphibian species using a 454 NGS approach on tetra-nucleotide motif-enriched species-specific libraries. The number of sequence reads obtained differed strongly between species and ranged from 19,562 for Triturus cristatus to 55,626 for Lissotriton helveticus, with 52,075 reads obtained for Calotriton asper. PHOBOS was used to identify sequences with tetra-nucleotide repeat motifs with a minimum repeat number of ten and high quality primer binding sites. Of 107 sequences for T. cristatus, 316 for C. asper and 319 for L. helveticus, we tested the amplification success, polymorphism, and degree of heterozygosity for 41 primer combinations each for C. asper and T. cristatus, and 22 for L. helveticus. We found 11 polymorphic loci for T. cristatus, 20 loci for C. asper, and 15 loci for L. helveticus. Extrapolated, the number of potentially amplifiable loci (PALs) resulted in estimated species-specific success rates of 0.15% (T. cristatus), 0.30% (C. asper), and 0.39% (L. helveticus). Compared with representative Illumina NGS approaches, our applied 454-sequencing approach on specifically enriched sublibraries proved to be quite competitive in terms of success rates and number of finally applicable loci.

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Section: Discussionmentioning

confidence: 99%

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina‐based approaches

Drechsler

Geller

Freund

et al. 2013

Ecology and Evolution

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“…) and 11 for Vipera aspis (VA‐P8, VA‐P20, VA‐P25, VA‐P26, VA‐P20, VA‐P35, VA‐P51, VA‐P69, VA‐P70, VA‐P70, VA‐P91; see Geser et al . ) following the amplification conditions described in the previously mentioned publications. PCR products were analyzed on an ABI 3130xl automated sequencer (Applied Biosystems) and all sizes were determined using the program PeakScanner 3.1 (Applied Biosystems).…”

Section: Methodsmentioning

confidence: 99%

“…In order to evaluate the level of gene flow between both studied species, several microsatellite makers were amplified. We used nine markers specifically developed for Vipera berus (Vb-A8, Vb-A11, Vb-B'2, Vb-B'9, Vb-B10, Vb-B'10, Vb-B18, Vb-D'10 and Vb-D17; see Ursenbacher et al 2009) and 11 for Vipera aspis (VA-P8, VA-P20, VA-P25, VA-P26, VA-P20, VA-P35, VA-P51, VA-P69, VA-P70, VA-P70, VA-P91; see Geser et al 2013) following the amplification conditions described in the previously mentioned publications. PCR products were analyzed on an ABI 3130xl automated sequencer (Applied Biosystems) and all sizes were determined using the program PeakScanner 3.1 (Applied Biosystems).…”

Section: Dna Extraction and Amplificationmentioning

confidence: 99%

Hybridization between a Euro‐Siberian (Vipera berus) and a Para‐Mediterranean viper (V. aspis) at their contact zone in western France

Guiller¹,

Lourdais

Ursenbacher

2016

Journal of Zoology

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Western European vipers are well‐defined species with parapatric distributions that reflect contrasting thermal niches and climatic adaptations. Contact zones are usually narrow, coincide with steep ecological gradients and are associated with clear habitat segregation. Natural hybridization has been demonstrated between several species but has not been detected in others. The cold‐adapted adder (V. berus, subgenus Pelias) is not known to hybridize with the warm‐adapted aspic viper (V. aspis subgenus Vipera). For over 12 years, we have monitored sympatric populations of V. berus and V. aspis in western France where the two species exhibit very similar life cycles. We tested for possible hybridization because individuals with intermediate morphological traits have been reported in the past and were recently detected in the study population. Our results demonstrate that hybridization actually occurs and is directional since it involves females V. aspis viper and male V. berus in all analyzed cases. We discuss our results in the frame of previous findings on contact zones to evaluate in which conditions hybridization may occur.

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“…For each individual, the mitochondrial DNA (mtDNA) analysis allowed the maternal lineage to be assigned to one of the three viper species using BLAST (http://blast.ncbi.nlm.nih.gov). Analysis of the nuclear genome was conducted with 17 microsatellite markers previously developed for different viper species: Vb-A8, Vb-A11, Vb-B'2, Vb-B10, Vb-B'10, Vb-D'10, and Vb-D17 were specifically developed for V. berus (Ursenbacher, Monney & Fumagalli, 2009) and Va-P8, Va-P20, Va-P25, Va-P26, Va-P29, Va-P35, Va-P51, Va-P69, Va-P81, and Va-P91 were developed for V. aspis (Geser et al, 2013). Some of these primers have been shown to produce PCR products in other viper species (see Geser et al, 2013), but lack of amplification was also considered.…”

Section: Genetic Analysesmentioning

confidence: 99%

“…Analysis of the nuclear genome was conducted with 17 microsatellite markers previously developed for different viper species: Vb-A8, Vb-A11, Vb-B'2, Vb-B10, Vb-B'10, Vb-D'10, and Vb-D17 were specifically developed for V. berus (Ursenbacher, Monney & Fumagalli, 2009) and Va-P8, Va-P20, Va-P25, Va-P26, Va-P29, Va-P35, Va-P51, Va-P69, Va-P81, and Va-P91 were developed for V. aspis (Geser et al, 2013). Some of these primers have been shown to produce PCR products in other viper species (see Geser et al, 2013), but lack of amplification was also considered. The genetic diversity for each marker and each species was calculated using GenAlEx 6.5.1 (Peakall & Smouse, 2006, as was any deviation from Hardy Weinberg equilibrium.…”

Section: Genetic Analysesmentioning

confidence: 99%

The dynamics of coexistence: habitat sharing versus segregation patterns among three sympatric montane vipers

Mebert

Jagar²,

Grželj³

et al. 2015

Biol. J. Linn. Soc.

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Contact zones of closely related and ecologically similar species constitute rare opportunities to study the evolutionary consequences of past speciation processes. They represent natural laboratories in which strong competition could lead to the exclusion of one species, or the various species may switch into distinct ecological niches. Alternatively, if reproductive isolation has not yet been achieved, they may hybridize. We elucidate the degree of taxon integrity by comparing genetics and habitat use of three similar‐sized congeneric viper species, Vipera ammodytes, Vipera aspis, and Vipera berus, of Nadiza Valley in western Slovenia. No hybridization was detected for either mitochondrial or nuclear genomes. Similarly, external intermediacy by a single prestudy viper (probably V. ammodytes × V. aspis) indicates that hybridization occasionally occurs, but should be very rare. Populations of the three related viperids are partially allopatric in Nadiza Valley, but they also coexist in a narrow contact zone in the montane grassland along the south‐exposed slope of Mount Stol (1673 m a.s.l.). Here, the three species that occupy areas in or near patches of rocky microhabitats (e.g. stone piles, slides, and walls) live in syntopy. However, fine‐scale measurements of structural components show partial habitat segregation, in which V. berus becomes more dominant at elevations above 1400 m and occupies mostly the mountain ridge and north‐exposed slopes of Mount Stol, V. aspis occurs below 1300 m and is the only species to inhabit stoneless patches of grass and bushes around 1000 m and lower, and V. ammodytes occurs at all elevations up to 1500 m, but is restricted to a rocky microhabitat. We suggest that a high degree of microstructure divergence, slightly different environmental niches, and a generally favourable habitat for all three viper species, keep the pressure for mis‐mating and hybridization low, although mechanisms such as reduced hybrid inferiority and temporal mating segregation cannot yet be excluded.

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Development of polymorphic microsatellite loci markers for the Asp viper (Vipera aspis) using high-throughput sequencing and their use for other European vipers

Cited by 10 publications

References 23 publications

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina‐based approaches

What remains from a 454 run: estimation of success rates of microsatellite loci development in selected newt species (Calotriton asper, Lissotriton helveticus, and Triturus cristatus) and comparison with Illumina‐based approaches

Hybridization between a Euro‐Siberian (Vipera berus) and a Para‐Mediterranean viper (V. aspis) at their contact zone in western France

The dynamics of coexistence: habitat sharing versus segregation patterns among three sympatric montane vipers

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