Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids

Haji, Diler; Vailionis, Jason; Stukel, Mark; Gordon, Eric R. L.; Lemmon, Emily Moriarty; Lemmon, Alan R.; Simon, Chris

doi:10.1038/s41598-022-24723-3

Cited by 4 publications

(4 citation statements)

References 86 publications

(113 reference statements)

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“…First, we consider applying the Jaccard‐inspired 4H index (incidence‐based) to our data sets (see Figure 2; Tables 1 and 2; Supplemental Video files Figures 2a.mp4–2f.mp4). Figure 2a shows quaternary plots (R version 4.2.1, phyloseq 1.41.1) comparing gut microbiota from F 1 crosses of Neotoma woodrats (brown) (Nielsen et al., 2023), Kikihia cicadas with evidence of mitochondrial introgression (black) (Haji et al., 2022) and a parthenogenetic Aspidoscelis lizard of hybrid origin (green, our own data). Table 1 shows the average values of the 4H indices for each system.…”

Section: Resultsmentioning

confidence: 99%

A conceptual framework for host‐associated microbiomes of hybrid organisms

Camper,

Laughlin,

Malagon

et al. 2024

Methods Ecol Evol

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Hybridization between organisms from evolutionarily distinct lineages can have profound consequences on organismal ecology, with cascading effects on fitness and evolution. Most studies of hybrid organisms have focused on organismal traits, for example, various aspects of morphology and physiology. However, with the recent emergence of holobiont theory, there has been growing interest in understanding how hybridization impacts and is impacted by host‐associated microbiomes. Better understanding of the interplay between host hybridization and host‐associated microbiomes has the potential to provide insight into both the roles of host‐associated microbiomes as dictators of host performance as well as the fundamental rules governing host‐associated microbiome assembly. Unfortunately, there is a current lack of frameworks for understanding the structure of host‐associated microbiomes of hybrid organisms. In this paper, we develop four conceptual models describing possible relationships between the host‐associated microbiomes of hybrids and their progenitor or ‘parent’ taxa. We then integrate these models into a quantitative ‘4H index’ and present a new R package for calculation, visualization and analysis of this index. We demonstrate how the 4H index can be used to compare hybrid microbiomes across disparate plant and animal systems. Our analyses of these data sets show variation in the 4H index across systems based on host taxonomy, host site and microbial taxonomic group. Our four conceptual models, paired with our 4H index and associated visualization tools, facilitate comparison across hybrid systems. This, in turn, allows for systematic exploration of how different aspects of host hybridization impact the host‐associated microbiomes of hybrid organisms.

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Section: Resultsmentioning

confidence: 99%

A conceptual framework for host‐associated microbiomes of hybrid organisms

Camper,

Laughlin,

Malagon

et al. 2024

Methods Ecol Evol

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“…To assemble mitochondrial genomes, we used off‐target AHE capture data from the SPAdes assemblies above (Haji et al, 2022; Lemmon et al, 2012; Simon et al, 2019). We identified mitochondrial contigs in the assemblies with a partial Kosemia yezoensis (Matsumura) [Cicadamorpha: Cicadidae: Cicadettinae: Cicadettini] reference mitochondrial genome—Genbank MG737723.1 (Łukasik et al, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…To assemble mitochondrial genomes, we used off-target AHE capture data from the SPAdes assemblies above (Haji et al, 2022;Lemmon et al, 2012;Simon et al, 2019). We identified mitochondrial contigs in the assemblies with a partial Kosemia yezoensis (Matsumura)…”

Section: Assembly Of Mitochondrial Genomes From Ahe Bycatchmentioning

confidence: 99%

Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito‐nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

Stukel,

Porczak,

Gordon

et al. 2023

Systematic Entomology

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Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use anchored hybrid enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly resolved radiation of the New Zealand cicada species in the genera Kikihia Dugdale and Maoricicada Dugdale. Compared with previous studies using only three to five Sanger‐sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. In addition, we find strong mito‐nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history of Kikihia and Maoricicada.

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“…Figure 2a shows quaternary plots (R version 4.2.1, phyloseq 1.41.1) comparing gut microbiomes from F1 crosses of Neotoma woodrats (brown) 122 , Kikihia cicadas with evidence of mitochondrial introgression (black) 160 , and a parthenogenetic Aspidoscelis lizard of hybrid origin (green, our own data). Table 1 shows the average values of the 4H indices for each system.…”

Section: Example Analysesmentioning

confidence: 99%

A Conceptual Framework for Host-Associated Microbiomes of Hybrid Organisms

Camper

Laughlin

Malagon

et al. 2023

Preprint

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Hybridization between organisms from evolutionarily distinct lineages can have profound consequences on organism ecology, with cascading effects on fitness and evolution. Most studies of hybrid organisms have focused on organismal traits, for example various aspects of morphology and physiology. However, with the recent emergence of holobiont theory, there has been growing interest in understanding how hybridization impacts and is impacted by host-associated microbiomes. Better understanding of the interplay between host hybridization and host-associated microbiomes has the potential to provide insight into both the roles of host-associated microbiomes as dictators of host performance as well as the fundamental rules governing host-associated microbiome assembly. Unfortunately, there is a current lack of frameworks for understanding the structure of host-associated microbiomes of hybrid organisms. In this paper, we develop four conceptual models describing possible relationships between the host-associated microbiomes of hybrids and their progenitor or parent taxa. We then integrate these models into a quantitative 4H index and present a new R package for calculation, visualization, and analysis of this index. Finally, we demonstrate how the 4H index can be used to compare hybrid microbiomes across disparate plant and animal systems.

show abstract

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids

Cited by 4 publications

References 86 publications

A conceptual framework for host‐associated microbiomes of hybrid organisms

A conceptual framework for host‐associated microbiomes of hybrid organisms

Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito‐nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

A Conceptual Framework for Host-Associated Microbiomes of Hybrid Organisms

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