Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

Kieran, Troy J.; Gordon, Eric R. L.; Forthman, Michael; Hoey-Chamberlain, Rochelle; Kimball, Rebecca T.; Faircloth, Brant C.; Weirauch, Christiane; Glenn, Travis C.

doi:10.1016/j.ympev.2018.10.026

Cited by 57 publications

(71 citation statements)

References 39 publications

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“…This subfamily has traditionally been recognized by the sulcate tibiae (shared with Coreinae), a much smaller head relative to the pronotum, and the hind tibia with an apical spine. To our knowledge, all studies that have examined Meropachyinae have proposed a close relationship with the Coreinae (Li, , ; Schaefer, ; Štys, ), with Li (, ) and Kieran et al () providing evidence for a paraphyletic Coreinae, as we corroborated here. The following apomorphies were optimized for the Coreinae + Meropachyinae clade: preclypeus and mandibular plates strongly declivent from the base of the antennae (4‐1; supermatrix tree), ocelli present but not on a small tubercle (7‐1; ACCTRAN), tibiae dorsally sulcate (14‐1), and hamus branching off proximal Cu vein semi‐perpendicularly (18‐1; supermatrix tree).…”

Section: Discussionsupporting

confidence: 88%

“…Pseudophloeinae were always sister to the Alydinae with high support. The Coreinae were paraphyletic with respect to Meropachyinae, with all relationships within this clade highly supported and congruent with Kieran et al (2019); Nematopodini were paraphyletic with respect to Meropachyinae, while Mictini and Acanthocephalini were both monophyletic. Thus, even with | 527 FORTHMAN eT Al.…”

Section: Phylogenetic Inference Of Coreoideamentioning

confidence: 81%

“…Because there is a lack of consensus on the sister group of Coreoidea (Henry, 1997;Hua et al, 2008;Valero et al, 2017;Weirauch, Schuh, Cassis, & Wheeler, 2018), we included several representatives of the superfamilies Lygaeoidea and Pyrrhocoroidea and a species of Pentatomidae as an outgroup. Data for nine coreid taxa, as well as the Pentatomidae and Lygaeoidea, were taken from Kieran et al (2019).…”

Section: Taxon Samplingmentioning

confidence: 99%

“…of genomic loci are highly conserved among divergent taxa (Faircloth, Branstetter, White, & Brady, 2015;Faircloth et al, 2012), and sequence capture based on baits that target the conserved regions also captures more variable flanking nucleotides. Recently, UCE probes for the Order Hemiptera were designed (Faircloth, 2017) and empirically shown (Kieran et al, 2019) to resolve deep and relatively shallower relationships with high support. The study by Kieran et al (2019) included nine species of Coreidae from two subfamilies, which recovered a paraphyletic Coreinae with respect to Meropachyinae.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

2019

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Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.

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Section: Discussionsupporting

confidence: 88%

Section: Phylogenetic Inference Of Coreoideamentioning

confidence: 81%

Section: Taxon Samplingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

2019

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“…UCEs são uma nova classe de marcadores genéticos recentemente descobertos que correspondem a uma região específica do genoma, foram primeiramente observados em humanos (Bejerano et al, 2007) e rapidamente identificados em outros animais (Stephen et al, 2008;Faircloth et al, 2012), suas funções permanecem pouco compreendias, provavelmente estão relacionados com regulação e desenvolvimento (Sandelin et al, 2004;Woolfe et al, 2005). Atualmente, sabe-se que os UCEs são regiões do genoma compartilhadas entre táxons muito distantes evolutivamente, e por isso já foram utilizados para resolver as relações filogenéticas entre aves basais (McCormack et al, 2013a;Hosner et al, 2016), mamíferos (McCormack et al, 2012 e peixes Chakrabarty et al, 2017;Alda et al, 2018), para determinar a posição filogenética das tartarugas entre os répteis , e recentemente também apresentou bons resultados para resolver a filogenia de grupos de invertebrados (Branstetter et al, 2017;Campillo et al, 2018;Kieran et al, 2019). Apesar dos UCEs serem altamente conservados entre táxons distantemente relacionados, suas regiões adjacentes abrigam uma grande fonte de variação Harvey et al, 2017), o que aumenta o sinal filogenético em diferentes níveis temporais, aumentando a resolução dos nós das árvores obtidas McCormack et al, 2012;Hosner et al, 2015).…”

Section: A Filogeografia Comparada E O Sequenciamento De Próxima Geraunclassified

Biogeografia e filogeografia comparada das aves do Centro de Endemismo Pernambuco utilizando Elementos Ultra Conservados (UCEs)

Bocalini¹

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The Pernambuco Centre of Endemism (PCE) is the Atlantic Forest (AF) region most affected by deforestation and fragmentation. The biogeographical relationships among the PCE, the Southern AF and Amazonia (AM) have not been addressed comprehensively in recent studies. Processes that contribute to the origin of the Neotropical biodiversity can occur through different models of diversification such as the forest refugia and riverine barriers and both can be tested with the PCE birds. Furthermore, connections between Amazonia and AF would have been hypothesized to have affected the composition of the PCE based on the species' elevational distribution. Furthermore, connections between AM and AF could have an important role on the PCE diversification process with a putatively altitudinal related origin. Here, we conducted a comparative phylogenomic study of 7 bird taxa endemic to the PCE to clarify its biogeographic history and to detail the historical connections between AM and PCE using the sequencing of ultraconserved elements (UCEs) and one mitochondrial gene. We sequenced ND2 gene and extracted SNPs from approximately 5,000 UCEs and used it to reconstruct phylogenetic relationship among populations, describe population structure and to test alternative demographic scenarios. Mitochondrial DNA and UCEs SNPs analyses presented a congruent pattern in general, in which PCE populations are closely related to Southern AF, an origin not related to elevational range, in some taxa the PCE population is not even an independent evolutionary lineage. Demographic history demonstrated that all taxa presented a pattern of divergence with gene flow, the PCE population likely originated from Amazonia throughout multiple connections within Pliocene and Pleistocene, afterwards this population expanded southwards and colonized the region on the South of Rio São Francisco, subsequent migrations after divergence were present in all taxa and among all regions resulting on secondary contact. Pleistocene climatic changes were the major responsible for the generation of the AF biodiversity and for promoting connections between AM and AF, nevertheless, the divergence and migration patterns we recovered are generally idiosyncratic, demonstrating that differences in the ecological traits of each species may be a decisive factor in their evolutionary history.The origin of PCE bird community has been a prolonged process instead of simultaneous event and multiple connections with Amazonia together with the various Pleistocene climatic oscillations contributed to the formation of its present-day diversity.

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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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Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

Cited by 57 publications

References 39 publications

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

Biogeografia e filogeografia comparada das aves do Centro de Endemismo Pernambuco utilizando Elementos Ultra Conservados (UCEs)

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

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