Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”

Kjer, Karl M.; Ware, Jessica L.; Rust, Jes; Wappler, Torsten; Lanfear, Robert; Jermiin, Lars S.; Zhou, Xin; Aspöck, Horst; Aspöck, Horst; Beutel, Rolf G.; Blanke, Alexander; Donath, Alexander; Flouri, Tomáš; Frandsen, Paul B.; Kapli, Paschalia; Kawahara, AY; Letsch, Harald; Mayer, Christoph; McKenna, Duane D.; Meusemann, Karen; Niehuis, Oliver; Peters, Ralph S.; Wiegmann, Brian M.; Yeates, David K.; Reumont, Bjoern M von; Stamatakis, Alexandros; Misof, Bernhard

doi:10.1126/science.aaa7136

Cited by 55 publications

(71 citation statements)

References 6 publications

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“…() where a penalized‐likelihood approach was used to recover the ages of the odonate families. However, the age of the MRCA of odonates is congruent with the analyses performed by Kjer () and Tong et al. (; ~230 mol/L).…”

Section: Resultssupporting

confidence: 87%

“…The ages recovered here for deep nodes are largely incongruent with Letsch et al (2016) where a penalized-likelihood approach was used to recover the ages of the odonate families. However, the age of the MRCA of odonates is congruent with the analyses performed by Kjer (2015) and Tong et al (2015;~230 mol/L). Moreover, the estimated divergence time for the genus Enallagma (Coenagrionidae) is also highly incongruent with Callahan and McPeek (2016) where a sequence divergence rate of 2.3% per million years was used to calibrate the age.…”

Section: The Time-calibrated Phylogeny and Divergence Times Of Odonatsupporting

confidence: 75%

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Environmental filtering along a broad‐scale acidity gradient shapes the structure of odonate communities

et al. 2018

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Historical, evolutionary, and ecological processes jointly shape the structure of communities, and the relative influence of such process may vary from one region to another. Nevertheless, much of community ecology focuses on one or several communities in a given region. To assess the relative importance and the context‐dependency of processes shaping communities, studies in community ecology must be conducted across regions and along broad‐scale environmental gradients. Regionally, historical colonization and extinction events, as well as diversification, can influence community structure by shaping the pool of potential community members (i.e., the regional species pool). Locally, a suite of deterministic and stochastic processes can influence community structure. We constructed a large time‐calibrated phylogenetic tree for North American odonates and used analyses of phylogenetic community structure with explicit species pool definitions to assess the predominant processes structuring assemblages along a north–south environmental gradient spanning two biomes and 8° of latitude in eastern Canada. Phylogenetic analyses of 39 lentic (i.e., lake) odonate communities revealed that co‐occurring species were on average more closely related than expected by chance, but only in the temperate biome. In addition, site‐to‐site variation in phylogenetic structure across the temperate and boreal biomes was most strongly related to variation in water pH. The most alkaline lakes were in the temperate biome and were also the most phylogenetically clustered, suggesting that water pH acts as a main environmental filter of odonate communities. An alternative explanation was that the recent radiation of damselflies increased the diversity of this group relative to that of dragonflies in the temperate species pool, thereby leaving a signature of clustering in that biome. However, our comparative null model analyses with explicit species pool definitions at least partially ruled out this explanation. Somewhat contrary to previous hypotheses regarding the assembly of odonate communities, our results suggest that stochastic processes alone cannot account for community structure in odonates and that deterministic, niche‐based processes have a strong influence.

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Section: Resultssupporting

confidence: 87%

Section: The Time-calibrated Phylogeny and Divergence Times Of Odonatsupporting

confidence: 75%

Environmental filtering along a broad‐scale acidity gradient shapes the structure of odonate communities

et al. 2018

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“…Our Bayesian phylogeny estimate of 31.21 MYA (95% CI: 41.27-21.16) is earlier than many others due to root prior calibration using the Rhagoletis-Drosophila split estimated by Misof et al (2014), as opposed to calibration using maximum fossil ages. Therefore, assumptions made by Misof et al (2014) will be carried into the age estimates presented here (Kjer et al, 2015;Tong et al, 2015).…”

Section: Phylogenetic Analysis Of Tephritids and The Molecular Clockmentioning

confidence: 99%

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species

Choo

Nguyen

Ward

et al. 2019

Insect Molecular Biology

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Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex‐determining Y‐chromosome thought to be gene poor and repetitive. Here, we report 39 Y‐chromosome scaffolds (~700 kb) from B. tryoni identified using genotype‐by‐sequencing data and whole‐genome resequencing. Male diagnostic PCR assays validated eight Y‐scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y‐gene, referred to as typo‐gyf, is a truncated Y‐chromosome paralogue of X‐chromosome gene gyf (1773 aa). The Y‐chromosome contained ~41 copies of typo‐gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo‐gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo‐gyf evolved within the past 8.02 million years (95% highest posterior density 10.56–5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y‐sequences may provide useful sites for future transgene insertions, and typo‐gyf could act as a Y‐chromosome diagnostic marker for many Bactrocera species, although its function is unknown.

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“…These Carboniferous age fossils preserve some of the highly conserved external morphology seen in extant cockroaches but also possess an external ovipositor, a trait not found in any extant dictyopterans. It has been proposed that these fossils could be ancestral polyneopterans (Kjer et al, 2015), on the stem of Dictyoptera (Tong et al, 2015), or even within Blattodea .…”

Section: Calibrations For Basal Dictyopteramentioning

confidence: 99%

Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

Evangelista

Djernæs

Kohli

2017

Palaeontologia Electronica

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Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”

Cited by 55 publications

References 6 publications

Environmental filtering along a broad‐scale acidity gradient shapes the structure of odonate communities

Environmental filtering along a broad‐scale acidity gradient shapes the structure of odonate communities

Identification of Y‐chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species

Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

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