Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders

Weisrock, David W.; Hime, Paul M.; Nunziata, Schyler O.; Jones, Kenneth R.; Murphy, Mason O.; Hotaling, Scott; Kratovil, Justin D.

doi:10.1007/13836_2018_36

Cited by 25 publications

(21 citation statements)

References 75 publications

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“…This study also demonstrates the power of reduced representation genome scans for identifying sex-linked genes in organisms that lack pre-existing genetic resources. Our results further suggest that genome size may not necessarily be a limiting factor in generating informative genome-scale data to answer evolutionary questions in salamanders [see also Nunziata et al (2017); Murphy et al (2018); Weisrock et al (2018); Hu et al (2019)].…”

Section: Discussionmentioning

confidence: 75%

“…Reduced representation genomic approaches, such as restriction site-associated DNA sequencing (RADseq) (Baird et al 2008; Baxter et al 2011; Peterson et al 2012), have become a powerful alternative to WGS to identify sex chromosome-associated loci and to distinguish male- from female-heterogametic systems (Palaiokostas et al 2013; Brown et al 2016; Fowler and Buonaccorsi 2016; Gamble 2016; Lambert et al 2016; Brelsford et al 2017; Nielsen et al 2018; Stovall et al 2018; Jeffries et al 2018; Hu et al 2019). RADseq-based approaches involve inherent tradeoffs among the numbers of loci sequenced, their depths of sequencing coverage, and the numbers of individuals that can be effectively multiplexed on current high-throughput sequencing platforms (Weisrock et al 2018). Double digest RADseq (ddRADseq) protocols (Peterson et al 2012) are particularly well-suited to identify sex chromosome-associated regions in massive genomes because they can be readily tailored to target different numbers of loci in a given species by varying either of the restriction enzymes (REs) used and/or the particular fragment size-selection window (Figure S1).…”

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confidence: 99%

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Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

Hime

Briggler

Reece

et al. 2019

G3 Genes|Genomes|Genetics

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Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.

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Section: Discussionmentioning

confidence: 75%

mentioning

confidence: 99%

Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

Hime

Briggler

Reece

et al. 2019

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

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“…Most notably, while eight microsatellite markers and one mitochondrial gene allowed us to document basic patterns (e.g., little to no evidence for hybridization, likely expansion of P. cinereus ), these markers had limited resolution for evaluating more detailed demographic scenarios. In principle, population genomic approaches (e.g., Weisrock et al, 2018) could allow us to better estimate the rate of spread of P. cinereus and the rate of population growth within the contact zone. Second, our study was restricted to the high‐elevation contact zone at the northeastern edge of the range of P. hubrichti .…”

Section: Discussionmentioning

confidence: 99%

Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone

Page

Conarroe

Quintanilla

et al. 2020

Ecology and Evolution

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Climate change poses several challenges to biological communities including changes in the frequency of encounters between closely related congeners as a result of range shifts. When climate change leads to increased hybridization, hybrid dysfunction or genetic swamping may increase extinction risk—particularly in range‐restricted species with low vagility. The Peaks of Otter Salamander, Plethodon hubrichti, is a fully terrestrial woodland salamander that is restricted to ~18 km of ridgeline in the mountains of southwestern Virginia, and its range is surrounded by the abundant and widespread Eastern Red‐backed Salamander, Plethodon cinereus. In order to determine whether these two species are hybridizing and how their range limits may be shifting, we assessed variation at eight microsatellite loci and a 1,008 bp region of Cytochrome B in both species at allopatric reference sites and within a contact zone. Our results show that hybridization between P. hubrichti and P. cinereus either does not occur or is very rare. However, we find that diversity and differentiation are substantially higher in the mountaintop endemic P. hubrichti than in the widespread P. cinereus, despite similar movement ability for the two species as assessed by a homing experiment. Furthermore, estimation of divergence times between reference and contact zone populations via approximate Bayesian computation is consistent with the idea that P. cinereus has expanded into the range of P. hubrichti. Given the apparent recent colonization of the contact zone by P. cinereus, future monitoring of P. cinereus range limits should be a priority for the management of P. hubrichti populations.

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“…Naturally, WGS is the gold standard, as it provides the most comprehensive datasets, allowing for a deeper understanding of population history. However, factors such as large and/or complex genomes, the need for a certain minimum sample size (of sequenced individuals) for robust statistical analyses, and poor starting DNA quality are often prohibitive (Wandeler, Hoeck, & Keller, ; Weisrock et al, ) to this approach. This often leads researchers to employ RRL methods, where short genetic regions across the nuclear genome are sequenced, yielding a large number of (more or less) independent sites for comparisons across individuals and populations, while retaining the option of including a large number of individuals (Baird et al, ; Davey et al, ).…”

Section: Which Population Characteristics Can Currently Be Estimated mentioning

confidence: 99%

Population‐level inferences from environmental DNA—Current status and future perspectives

Sigsgaard

Jensen

Winkelmann

et al. 2019

Evolutionary Applications

129

141

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Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms.This approach offers several potential advantages compared with conventional tissuebased methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances.However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.

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Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders

Cited by 25 publications

References 75 publications

Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes

Genetic variation in Plethodon cinereus and Plethodon hubrichti from in and around a contact zone

Population‐level inferences from environmental DNA—Current status and future perspectives

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