Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs

Cairns, Nicholas A.; Cicchino, Amanda S.; Stewart, Kathryn A.; Austin, James D.; Lougheed, Stephen C.

doi:10.1016/j.ympev.2020.107042

Cited by 8 publications

(8 citation statements)

References 97 publications

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“…In the present study, two individuals of D. japonicus displayed a high level of admixture, with D. Japonicus mtDNA haplotype and a predominantly D. suweonensis nuDNA background. Similar instances of genetic mismatches between mtDNA and nuDNA have been observed in other amphibian species ( Ambu et al, 2023 ; Cairns et al, 2021 ; Eto, Matsui & Sugahara, 2013 ). Majtyka et al (2022) showed that the introgression of mtDNA was a consequence of repeated backcrossing and some hybrids between Hyla arborea and H. orientalis exhibited instances of cyto-nuclear discordance.…”

Section: Discussionsupporting

confidence: 79%

Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids

Yoo,

Yoon,

Yoo

et al. 2024

PeerJ

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Background As hybridization can reduce biodiversity or cause extinction, it is important to identify both purebred parental species and their hybrids prior to conserving them. The Suwon tree frog, Dryophytes suweonensis, is an endangered wildlife species in Korea that shares its habitat and often hybridizes with the Japanese tree frog, D. japonicus. In particular, D. suweonensis, D. japonicus, and their hybrids often have abnormal ovaries and gonads, which are known causes that could threaten their existence. Methods We collected 57 individuals from six localities where D. suweonensis is known to be present. High-resolution melting curve (HRM) analysis of the mitochondrial 12S ribosomal RNA gene was performed to determine the maternal species. Thereafter, the DNA sequences of five nuclear genes (SIAH, TYR, POMC, RAG1, and C-MYC) were analyzed to determine their parental species and hybrid status. Results The HRM analysis showed that the melting temperature of D. suweonensis was in the range of 79.0–79.3 °C, and that of D. japonicus was 77.7–78.0 °C, which clearly distinguished the two tree frog species. DNA sequencing of the five nuclear genes revealed 37 single-nucleotide polymorphism (SNP) sites, and STRUCTURE analysis showed a two-group structure as the most likely grouping solution. No heterozygous position in the purebred parental sequences with Q values ≥ 0.995 were found, which clearly distinguished the two treefrog species from their hybrids; 11 individuals were found to be D. suweonensis, eight were found to be D. japonicus, and the remaining 38 individuals were found to be hybrids. Conclusion Thus, it was possible to unambiguously identify the parental species and their hybrids using HRM analysis and DNA sequencing methods. This study provided fundamental information for D. suweonensis conservation and restoration research.

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Section: Discussionsupporting

confidence: 79%

Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids

Yoo,

Yoon,

Yoo

et al. 2024

PeerJ

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“…Forester and Czarnowsky (1985) also did not detect positive SAM, despite having a robust sample size (n = 182 pairs), but we note that they pooled data across three years without checking for SAM within years (i.e., Green 2019). These previous studies were conducted in Ohio and Maryland, which represent divergent genetic lineages within the "Northern" clade of the Spring Peeper: the "Interior" and "Eastern" mtDNA lineages, respectively (Austin et al 2002, 2004, Cairns et al 2021). Unpublished data from a hybrid zone between the "Interior" and "Eastern" mtDNA lineages in Canada, nevertheless, found positive SAM using just 12 amplectant pairs, but this analysis was based on samples pooled across five sites that included both mtDNA lineages and hybrid populations (Hudson 2010).…”

Section: Resultsmentioning

confidence: 76%

Lack of Size-Assortative Mating in a Widespread Treefrog: Pseudacris Crucifer in Iowa

Moran,

La Rosa,

Hughes

2024

JNAH

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The Spring Peeper (Pseudacris crucifer) is a small treefrog native to much of the Central and Eastern USA. Here, we tested if Spring Peepers exhibit size-assortative mating—non-random mate pairings based on body size—from a population in eastern Iowa. We captured 75 amplecting pairs of Spring Peepers during the 2021 breeding season, measured their body sizes, and marked them for future recognition. We found that while sexual-size dimorphism exists between males and females, there was no evidence for size-assortative mating among amplectant pairs. Our study contributes to other recent work indicating that size-assortative mating is rare among most anurans, and that previous findings of this phenomenon in frogs should be interpreted with caution.

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Section: Discussionmentioning

confidence: 99%

“…Discordance between nuclear and mitochondrial genomes is a well-known phenomenon (reviewed in Toews and Brelsford 2012) and has been described in a range of taxa (e.g., Wielstra and Arntzen 2020;Cairns et al 2021;Morón-López et al 2022;Yi and Latch 2022). Mitochondrial genomes, due to differences in inheritance, recombination, and effective population size, exhibit distinct responses to selection, demographic changes, and drift (Toews and Brelsford 2012;Bonnet et al 2017).…”

Section: Mitonuclear Discordancementioning

confidence: 99%

“…Intraspecific variation, especially if it is recently derived, often necessitates large numbers of independent and variable loci to accurately infer population and demographic histories and to resolve spatial genomic variation (Hey and Nielsen 2004;Carling and Brumfield 2007;Gompert et al 2014;Garrick et al 2015;Satler et al 2021). Recent technological advances provide access to single nucleotide polymorphisms (SNPs) spread throughout the genome (Baird et al 2008;Peterson et al 2012;McCormack et al 2013;Garrick et al 2015) and have been used successfully to resolve spatial genetic variation in many widespread, nonmodel organisms (e.g., Bagley et al 2017;Lumley et al 2020;MacDonald et al 2020;Cairns et al 2021;Polic et al 2022).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide markers show continental structuring and mitonuclear discordance in the forest tent caterpillar (Malacosoma disstria Hübner) (Lepidoptera: Lasiocampidae)

et al. 2023

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The forest tent caterpillar, Malacosoma disstria Hübner (Lepidoptera: Lasiocampidae), is an irruptive forest pest found throughout North America. Widespread species such as M. disstria are exposed to historical and contemporary processes that are not uniform and can generate regionally distinct genomic variation. Previous analyses used a short mitochondrial fragment to infer broad-scale phylogeographic patterns in M. disstria, whereas nuclear markers have been previously applied only in a smaller geographic region. In this study, we quantified M. disstria population variation with genome-wide single nucleotide polymorphisms and cytochrome c oxidase from mitochondrial DNA. Using highly variable genome-wide markers, we resolved clear genomic differences among populations of M. disstria east of the Rocky Mountains that were not detected using mitochondrial variation alone. We also did not detect host-associated divergence in either our genomic or mitochondrial data. Our results highlight the utility of genome-wide markers to resolve intraspecific population structure within a widespread species and support the need for further biogeographic sampling of this forest insect pest.

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Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs

Cited by 8 publications

References 97 publications

Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids

Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids

Lack of Size-Assortative Mating in a Widespread Treefrog: Pseudacris Crucifer in Iowa

Genome-wide markers show continental structuring and mitonuclear discordance in the forest tent caterpillar (Malacosoma disstria Hübner) (Lepidoptera: Lasiocampidae)

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