Development of anonymous nuclear markers from Illumina paired-end data for Seychelles caecilian amphibians (Gymnophiona: Indotyphlidae)

Lewis, Claire J.; Maddock, Simon T.; Day, Julia J.; Nussbaum, Ronald A.; Morel, Charles; Wilkinson, Mark; Foster, Peter G.; Gower, David J.

doi:10.1007/s12686-013-0127-y

Cited by 6 publications

(8 citation statements)

References 16 publications

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“…In addition, and because the samples were indexed, our MiSeq approach allowed us to attribute sequenced fragments to the mitogenome of each individual with almost complete certainty (assuming lack of contamination). This shotgun sequencing method also provides data that can be used for other purposes, such as development of anonymous nuclear loci [ 25 ], future development of microsatellite markers [ 50 ] or for SNP identification [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

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Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

et al. 2016

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Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina’s HiSeq and MiSeq, Roche’s 454 GS FLX, and Life Technologies’ Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.

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Section: Discussionmentioning

confidence: 99%

“…rostratus ), destined for shotgun sequencing, were prepared for Illumina MiSeq sequencing using a standard Illumina Nextera DNA kit. The primary aim of this sequencing run was to develop anonymous nuclear markers [ 25 ]. Paired-end reads (≤251bp long) were sequenced using a 500 cycle v.2 reagent kit on a single MiSeq flow cell.…”

Section: Methodsmentioning

confidence: 99%

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

et al. 2016

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“…Four nuclear loci-pro-opiomelanocortin (pomc), brain-derived neurotrophic factor (bdnf), and two anonymous nuclear markers (brev5 and rost5; [79])-were sequenced for a subset of the samples sequenced for cytb (Additional le 2). As expected, mtDNA nucleotide diversity is greater than for nuDNA (see Table 1).…”

Section: Molecular Datamentioning

confidence: 99%

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Maddock

Nussbaum

Day

et al. 2020

Preprint

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Background: Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65 – 62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles.Results: Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations.Conclusions: Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.

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“…Library preparation was performed by first extracting genomic DNA with a Qiagen DNeasy Blood and Tissue kit and then using a standard Illumina Nextera DNA kit to prepare the pooled sample for sequencing (see Lewis et al 2014). Sequencing was performed using a 500-cycle v.2 reagent kit on an Illumina MiSeq at the Core Research laboratories of the Natural History Museum, London.…”

Section: Dna Isolation and Microsatellite Identificationmentioning

confidence: 99%

Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data

Adamson

Saha

Maddock

et al. 2016

Conservation Genet Resour

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The Seychelles archipelago is unique among isolated oceanic islands because it features an endemic radiation of caecilian amphibians (Gymnophiona). In order to develop population genetics resources for this system, we identified microsatellite loci using unassembled Illumina MiSeq data generated from a genomic library of Grandisonia alternans, a species that occurs on multiple islands in the archipelago. Applying a recently described method (PALFINDER) we identified 8001 microsatellite loci that were potentially informative for population genetics analyses. Of these markers, we screened 60 loci using five individuals, directly sequenced several amplicons to confirm their identity, and then used eight loci to score allele sizes in 64 G. alternans individuals originating from five islands. A number of these individuals were sampled using non-lethal methods, demonstrating the efficacy of non-destructive molecular sampling in amphibian research. Although two loci satisfied our criteria as diploid, neutrally evolving loci with the statistical power to detect population structure, our success in identifying reliable loci was very low. Additionally, we discovered some issues with primer redundancy and differences between Illumina and Sanger sequences that suggest some Illumina-inferred loci are invalid. We investigated crossspecies utility for eight loci and found most could be successfully amplified, sequenced and aligned across other species and genera of caecilians from the Seychelles. Thus, our study in part supported the validity of using PALFIN-DER with unassembled reads for microsatellite discovery within and across species, but importantly identified major limitations to applying this approach to small datasets (ca. 1 million reads) and loci with small tandem repeat sizes.

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Development of anonymous nuclear markers from Illumina paired-end data for Seychelles caecilian amphibians (Gymnophiona: Indotyphlidae)

Cited by 6 publications

References 16 publications

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data

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