The enduring value of reciprocal illumination in the era of insect phylogenomics: a response to Cai <i>et al</i>. (2020)

Gustafson, Grey T.; Miller, Kelly B.; Michat, Mariano C.; Alarie, Yves; Baca, Stephen M.; Balke, Michael; Short, Andrew Edward Z.

doi:10.1111/syen.12471

Cited by 8 publications

(17 citation statements)

References 80 publications

(202 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, review of all major past studies on dytiscoid phylogeny in Gustafson et al . (2021) shows a similar trend in that those with complete dytiscoid taxon sampling and substantial molecular data (>5000 bp or eight gene fragments), outside the primary use of mitochondrial genes, have supported the relationships among Dytiscoidea recovered here. Therefore, we suspect the recovery of Hygrobiidae as sister to the clade [Dytiscidae, (Amphizoidae, Aspidytidae)] in previous studies employing substantial molecular data (i.e.…”

Section: Discussionsupporting

confidence: 74%

“…Nearly all analyses recovered Hygrobiidae as part of a clade comprising Amphizoidae, Aspidytes and Sinaspidytes . This is consistent with previous phylogenetic investigations utilizing considerable amounts of molecular data coupled with complete taxon sampling in terms of representation of dytiscoid families (McKenna et al ., 2015; Toussaint et al ., 2016; Gustafson et al ., 2020; reviewed in Gustafson et al ., 2021). Only our uncurated ASTRAL analysis of the 70% CM recovered Hygrobiidae as sister to Dytiscidae with low support, a relationship supported primarily by investigations utilizing morphological data (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Only our uncurated ASTRAL analysis of the 70% CM recovered Hygrobiidae as sister to Dytiscidae with low support, a relationship supported primarily by investigations utilizing morphological data (e.g. Beutel et al ., 2006, 2020b; reviewed in Gustafson et al ., 2021). Cai et al .…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Integrative phylogenomics reveals a Permian origin of Adephaga beetles

Baca

Gustafson

Alexander

et al. 2021

Systematic Entomology

Self Cite

View full text Add to dashboard Cite

Beetles are arguably the most diverse group of animals on Earth with over 400 000 described species. Yet the timing of main diversification events among these insects remains debated. The use of phylogenomic data generated using next‐generation sequencing recently resolved most recalcitrant phylogenetic relationships across Coleoptera. However, limited taxon sampling for some major clades still prevents the use of important fossil calibrations that could provide more accurate estimates of the timing of lineage diversification events among beetles. Here, we present a new fossil‐based dated framework with a focus on the suborder Adephaga. We rely on an integrative phylogenomic approach using a combination of genomic, ultraconserved element and RNAseq transcriptomic datasets, further revealing the prevalent exonic nature of ultraconserved elements in Coleoptera. We infer a robust phylogenomic tree under various optimality criteria and analytical conditions. Our preferred phylogenetic reconstruction is consistent with those of previous phylogenomic studies in recovering the paraphyly of ‘Hydradephaga’, Gyrinidae as sister to all other Adephaga, the monophyly of Geadephaga and Haliplidae as sister to a monophyletic Dytiscoidea. We further recover strong support for paraphyly of Aspidytidae and the placement of Hygrobiidae as part of a clade comprising Aspidytes, Ribera, Beutel, Balke & Vogler, Sinaspidytes Balke, Beutel & Ribera and Amphizoidae. Using 23 carefully chosen fossil calibrations across Coleoptera, we infer the origin of modern beetles ca. 317 Ma in the mid‐Carboniferous, the divergence between Archostemata and Adephaga ca. 296 Ma in the early Permian, and the crown of Adephaga in the end‐Permian ca. 255 Ma. Importantly, our analyses provide more precise estimates of divergence times for internal splits within Adephaga, including ground beetles, tiger beetles and aquatic adephagan lineages. These results represent a major step forward in our understanding of beetle diversification and will serve as a fundamental framework to unravel the evolutionary history of many clades within Adephaga.

show abstract

Section: Discussionsupporting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Integrative phylogenomics reveals a Permian origin of Adephaga beetles

Baca

Gustafson

Alexander

et al. 2021

Systematic Entomology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Most of the activities of this school are no different from what molecular phylogeneticists simply call molecular dating, which is a widely implemented technique. Some of the recurring controversies engendered by "molecular paleobiologists" have stemmed from overconfidence in the completeness of the fossil record, overconfidence in morphological phylogenies (or specific, arbitrarily selected morphological phylogenies, when competing hypotheses are available), overvaluing morphological and paleontological evidence in the assessment of competing molecular hypotheses, overinterpreting paleontological and morphological data in establishing calibrations in molecular dating; outright misconstruing or misrepresenting the morphological literature to accord with a preferred molecular topology; and consistently ignoring the repeated observation by other research groups that site heterogeneous models (as well as other proposed silver bullets to achieving morphological trees with molecular data) do not actually achieve the desired result across datasets [10,44,[54][55][56][57][58][59]. However, given that morphological hypotheses of relationships predate molecular counterparts by decades or sometimes centuries, "molecular paleobiological" results are often unguardedly accepted by the broader community for their palatability, specifically by those who do not examine the underlying phylogenomic data and analyses or lack the expertise to do so.…”

Section: Figurementioning

confidence: 99%

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

2021

View full text Add to dashboard Cite

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

show abstract

“…8). This combination of efforts gave us the benefits of reciprocal illumination comparing results of analyses of multiple sources of data (Hennig, 1950, 1966; Gustafson et al ., 2021).…”

Section: Introductionmentioning

confidence: 99%

SPECIES DELIMITATION IN NICOTIANA SECT. SUAVEOLENTES (SOLANACEAE): RECIPROCAL ILLUMINATION LEADS TO RECOGNITION OF MANY NEW SPECIES

Chase¹,

Christenhusz²,

Palsson³

et al. 2021

Curtis's Botanical Magazine

View full text Add to dashboard Cite

Summary In this volume of Curtis's Botanical Magazine, we increase the number of species recognised in Nicotiana sect. Suaveolentes to 38, up from the 21 recorded in the Flora of Australia published 39 years ago, but we estimate the final number is likely to exceed 60. We examine the reasons why so many unrecognised species exist. Several Australian and American botanists have previously specialised in Nicotiana but did not detect such diversity. We have carried out many fieldtrips, seen most known species in the wild and have grown these accessions from diverse areas side‐by‐side in cultivation to avoid basing decisions about species characteristics on features heavily influenced by environmental plasticity. In the end, we conclude that it is a mixture of focused and extensive fieldwork and more recent genomic, genetic and karyological studies combined in the process of reciprocal illumination, that has enabled us to describe so many new species. We also briefly focus on the topic of why Nicotiana is so species‐rich in Australia.

show abstract

The enduring value of reciprocal illumination in the era of insect phylogenomics: a response to Cai et al. (2020)

Cited by 8 publications

References 80 publications

Integrative phylogenomics reveals a Permian origin of Adephaga beetles

Integrative phylogenomics reveals a Permian origin of Adephaga beetles

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

SPECIES DELIMITATION IN NICOTIANA SECT. SUAVEOLENTES (SOLANACEAE): RECIPROCAL ILLUMINATION LEADS TO RECOGNITION OF MANY NEW SPECIES

Contact Info

Product

Resources

About