Putting the genome in insect phylogenomics

Johnson, Kevin P.

doi:10.1016/j.cois.2019.08.002

Cited by 22 publications

(11 citation statements)

References 56 publications

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“…Mitochondrial genomes have been widely used for inferring higher‐level phylogeny (Cameron et al, 2007; Castro & Dowton, 2006; Liu et al, 2019), which is characterized by small genome size, maternal inheritance, and rapid evolutionary rate (Brown et al, 1979; Curole & Kocher, 1999). Currently, with the development of high‐throughput sequencing technology, massive amounts of genetic data have been sequenced to study insect systematics (Johnson, 2019). However, there are a few studies on the phylogeny for Coreidae or Alydidae based on mitogenomes that only include fewer taxa (Liu et al, 2019; Yuan et al, 2015; Zhao et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Xue

Wang

Tang

et al. 2022

Arch Insect Biochem Physiol

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Coreoidea (Insecta: Hemiptera: Heteroptera) is a widely distributed and agriculturally important bugs. However, the phylogeny of Coreoidea lacked consensus on higher‐level relationships and several studies by comparative morphological characters and molecular data suggested the non‐monophyly of two families: Coreidae and Alydidae. The mitochondrial genome (mitogenome) has long been thought to be a significant marker to understand phylogenetic relationships, but the mitogenome in Alydidae is scarce to date. In the present study, we gathered the mitogenomes of 28 species from four families of Coreoidea excluding Hyocephalidae (Alydidae, Coreidae, Rhopalidae, and Stenocephalidae), including four newly sequenced mitogenomes of Alydidae, and conducted mitogenomic organization and phylogenetic studies. We used maximum likelihood and Bayesian inference methods to infer the higher‐level phylogeny from the perspective of mitogenomes, primarily to investigate the phylogenetic relationship betweeen Coreidae and Alydidae. We add evidence that neither Alydidae nor Coreidae are monophyletic based on mitogenomes. Newly sequenced mitogenomes of Alydidae have traditional gene structure and gene rearrangement was not found. Alydinae was always recovered as closely related to Pseudophloeinae of the coreid subfamily with high support. The placement of the coreid subfamily Hydarinae and alydid subfamily Micrelytrinae are unstable depending on approach used. In terms of the length and nucleotide composition of the protein coding genes in mitogenomes, Pseudophloeinae and Hydarinae of coreid were more similar to Alydidae. The unsettled classification issues of Coreidae and Alydidae by mitogenomes were demonstrated in this work, indicating that further study is needed.

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Section: Introductionmentioning

confidence: 99%

“…Currently, with the development of high-throughput sequencing technology, massive amounts of genetic data have been sequenced to study insect systematics (Johnson, 2019). However, there are a few studies on the phylogeny for Coreidae or Alydidae based on mitogenomes that only include fewer taxa (Liu et al, 2019;Yuan et al, 2015;Zhao et al, 2018).…”

mentioning

confidence: 99%

Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Xue

Wang

Tang

et al. 2022

Arch Insect Biochem Physiol

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“…While these approaches have been extensively used in free-living species, to our knowledge, extinction rates from phylogenies have almost not been yet used in symbiont studies (but see Alcala et al, 2017). Thus, even though these estimates on extinction risk from phylogenies should be treated with caution (particularly when including non-sequenced species; Rabosky, 2016), the increasing availability of robust-comprehensive phylogenetic trees offers an opportunity to use these phylogenetically based methods in symbionts (Johnson, 2019). ).…”

Section: Expanding Modeling Of Symbiont Extinction (And Coextinction) Ratesmentioning

confidence: 99%

Assessing symbiont extinction risk using cophylogenetic data

Doña

Johnson

2020

Biological Conservation

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Symbionts have a unique mode of life that has attracted the attention of ecologists and evolutionary biologists for centuries. As a result of this attention, these disciplines have produced a mature body of literature on host-symbiont interactions. In contrast, the discipline of symbiont conservation is still in a foundational stage. Here, we aim to integrate methodologies on symbiont coevolutionary biology with the perspective of conservation. We focus on host-symbiont cophylogenies, because they have been widely used to study symbiont diversification history and contain information on symbiont extinction. However, cophylogenetic information has never been used nor adapted to the perspective of conservation. Here, we propose a new statistic, "cophylogenetic extinction rate" (Ec), based on coevolutionary knowledge, that uses data from event-based cophylogenetic analyses, and which could be informative to assess relative symbiont extinction risks. Finally, we propose potential future research to further develop estimation of symbiont extinction risk from cophylogenetic analyses and continue the integration of this existing knowledge of coevolutionary biology and cophylogenetics into future symbiont conservation studies and practices.

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“…From a research perspective, a practical benefit is that parasite genomes are often considerably smaller than those of their vertebrate hosts (de Moya et al, 2021;Kapusta et al, 2017;Zarowiecki & Berriman, 2015). These smaller genomes make approaches that leverage genome sequencing for the collection of population-genomic data from many individuals more cost effective (Johnson, 2019).…”

Section: Introductionmentioning

confidence: 99%

High levels of inbreeding with spatial and host‐associated structure in lice of an endangered freshwater seal

et al. 2022

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Host‐specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among‐host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly‐transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host‐specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among‐host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population‐genetic analyses of the seals themselves.

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Putting the genome in insect phylogenomics

Cited by 22 publications

References 56 publications

Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Assessing symbiont extinction risk using cophylogenetic data

High levels of inbreeding with spatial and host‐associated structure in lice of an endangered freshwater seal

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