The mitochondrial genomes of five frog species of the Neotropical genus <i>Ischnocnema</i> (Anura: Brachycephaloidea: Brachycephalidae)

Taucce, Pedro P. G.; Canedo, Clarissa; Haddad, Célio F. B.; Lemmon, Alan R.; Lemmon, Emily Moriarty; Vences, Miguel; Lyra, Mariana L.

doi:10.1080/23802359.2018.1501312

Cited by 4 publications

(3 citation statements)

References 29 publications

(32 reference statements)

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“…The remaining portion of the sequence data, that is off‐target sequences, is often ignored in many sequence capture studies, but several recent studies have exploited this by‐catch to extract legacy loci used in past phylogenetic studies (e.g. Barrow et al., 2017; Branstetter et al., 2021; Caparroz et al., 2018; Gasc et al., 2016; Guo et al., 2012; Łukasik et al., 2019; Lyra et al., 2017; Matsuura et al., 2018; Percy et al., 2018; Simon et al., 2019; Taucce et al., 2018). Our study sought to recover legacy loci from off‐target sequences in a sequence capture data set using published legacy data, explore approaches to improve legacy locus recovery, and perform a phylogenetic analysis on a concatenated data set comprised of legacy loci and UCE data.…”

Section: Discussionmentioning

confidence: 99%

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

et al. 2021

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Sequence capture studies result in rich data sets comprising hundreds to thousands of targeted genomic regions that are superseding Sanger‐based data sets comprised of a few well‐known loci with historical uses in phylogenetics (‘legacy loci’). However, integrating sequence capture and Sanger‐based data sets is of interest as legacy loci can include different types of loci (e.g. mitochondrial and nuclear) across a potentially larger sample of species from past studies. Sequence capture data sets include nontargeted sequences, and there has been recent interest in extracting legacy loci from invertebrate data sets. Here, we use published legacy data from leaf‐footed bugs (Hemiptera: Coreoidea) to recover 15 mitochondrial and seven nuclear legacy loci from off‐target sequences in a sequence capture data set, explore approaches to improve legacy locus recovery, and combine these loci with sequence capture data for phylogenetic analysis. Two nuclear loci were determined to already be targeted by sequence capture baits. Most of the remaining loci were successfully recovered from off‐target sequences, but this recovery varied greatly. Additionally, complementing complete mitogenomes with additional reference mitochondrial sequences from a genetic depository did not offer improvement for most of our taxa; however, supplementing these reference sequences with extracted legacy loci offered ≥6% improvement across taxa for a given mitochondrial locus (negligible improvement for nuclear loci). Phylogenetic analysis of legacy and sequence capture data produced a topology generally congruent with recent studies, but support was lower. Thus, future studies may employ the approaches used in this study to integrate legacy data with newly generated sequence capture data sets without added expenses.

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Section: Discussionmentioning

confidence: 99%

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

et al. 2021

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“…As mitochondrial DNA is naturally enriched, sequencing reads of target‐enriched libraries typically include background mitochondrial sequences as byproducts. For example, Allio et al (2019) were able to extract COI barcodes and other mitochondrial genes from 501 hybrid‐capture libraries in ants (Formicidae), and Taucce et al (2018) assembled mitogenomes for five frog species (Anura) from hybrid‐capture libraries. Here, we show that mitochondrial genes other than COI could be recovered for all samples in this study (Figure S2).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Quek

Jain

Neo

et al. 2020

Molecular Ecology Resources

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Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross‐contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.

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“…Mitochondrial bycatch from exome capture methods can be an appreciable source of mitogenomic data 70 . To take advantage of these data, we assembled mitochondrial genomes from raw reads using custom scripts built around existing assembly and alignment software.…”

Section: Whole Mitochondrial Genomesmentioning

confidence: 99%

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

Novikova

Brennan

Booker

et al. 2019

Preprint

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Polyploidy plays an important role in evolution because it can lead to increased genetic complexity and speciation. It also provides an extra copy buffer and increases genetic novelty. While both common and well-studied in plants, polyploidy is rare in animals, and most polyploid animals reproduce asexually. Amphibians represent a dramatic vertebrate exception, with multiple independent sexually reproducing polyploid lineages, but very few cases have been studied in any detail. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful model animal polyploid system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on evolution of adaptation in animals.

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The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae)

Cited by 4 publications

References 29 publications

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

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