Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

Yaakop, Salmah; Ibrahim, Nazlina; Shariff, S.; Zain, Badrul Munir Md.

doi:10.1080/00305316.2015.1081421

Cited by 8 publications

(7 citation statements)

References 55 publications

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“…However, factors other than clock parameters can affect evolutionary rates. Published estimates of when C. capitata last shared a common ancestor with Bactrocera include 24.9 MYA (Yaakop et al, ; no confidence intervals reported), 83 MYA (95% HPD: 64–103 MYA; Nardi et al, ) and 110.9 MYA [95% confidence interval (CI): 131.4–91.2 MYA] (Krosch et al, ). 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 (), as opposed to calibration using maximum fossil ages.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…; Yaakop et al . ), as the distantly related (tribe, supergenus) C . capitata did not separate well from B .…”

Section: Discussionmentioning

confidence: 99%

“…Our study further demonstrates that, in spite of the significant overlap, tephritid antennal responses were also divergent. Interestingly, this did not follow relatedness Yaakop et al 2015), as the distantly related (tribe, supergenus) C. capitata did not separate well from B. dorsalis and B. zonata (Fig. S10), whereas Z. cucurbitae's olfactory responses (same subgenus as B. dorsalis and B. zonata) were the most distant of the four.…”

Section: Sharedness Phylogenetic Relatedness and Pre-adaptive Bridgementioning

confidence: 98%

“…S10), whereas Z. cucurbitae's olfactory responses (same subgenus as B. dorsalis and B. zonata) were the most distant of the four. Z. cucurbitae has both significantly gained and lost the detection of volatiles, which is possibly linked to the fact that Z. cucurbitae is ecologically distinct and prefers herbaceous cucurbits Yaakop et al 2015), whereas C. capitata ecologically strongly overlaps with B. dorsalis and B. zonata. Ecological niche may thus override phylogenetic relatedness in olfactory tuning.…”

Section: Sharedness Phylogenetic Relatedness and Pre-adaptive Bridgementioning

confidence: 99%

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Translating olfactomes into attractants: shared volatiles provide attractive bridges for polyphagy in fruit flies

et al. 2018

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Tephritid flies are serious fruit pests. Despite clear niche differences, many species show considerable overlap in fruit preferences, of which we here analysed the olfactory correlate. Using the volatiles of four unrelated fruit species, antennal responses were quantified to construct a fruit‐odour response database for four tephritid species. Although responses were distinct with a significant niche‐correlated bias, the analyses show that the probability of detection of a volatile strongly increased with its sharedness across fruits. This also held for the unrelated fruit fly Drosophila melanogaster (DoOR repository‐based analyses). We conjectured that shared volatiles signify ‘host’ to the fly ‘nose’ and induce attraction. Indeed, blends of volatiles shared by fruit and detected by all four species were very attractive for tephritid species, more than fruits. Quantitative whole antennal recordings en lieu of, or complementing bottom‐up molecular neurogenetic approaches, enables comparative olfactomics in non‐model species, and facilitate interpretation of olfaction in evolutionary, ecological, and applied contexts.

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“…Our results also revealed that the split between Zeugodacus+Bactrocera and C. capitata occurred less than 20 million years ago. Previously published works proposed that C. capitata and Bactrocera diverged around 24.9 mya (no confidence intervals reported, (Yaakop et al, 2015)), 83 mya (95% height posterior density: 64-103 mya; (Nardi et al, 2010)), 110.9 mya (95% confidence interval: 91.2-131.4 mya; (Krosch et al, 2012)). The difference in the estimates could be due to several factors such as the type of molecular markers (nuclear or mitochondrial), and to the choice of priors: the clock and demographic model, the calibration points, the calibrating mutation rate, and the number of generations per year assumed.…”

Section: Dating Analysis Suggests Fast and Recent Radiation In Bactroceramentioning

confidence: 94%

The impact of fast radiation on the phylogeny ofBactrocerafruit flies

Valerio

Zadra

Stabelli

et al. 2021

Preprint

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True fruit flies (Tephritidae) include several species that cause extensive damage to agriculture worldwide. Among them, species of the genus Bactrocera are widely studied to understand the traits associated to their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but, to date, molecular phylogenies of Bactrocera are still controversial. Here, we employed a comprehensive genomic dataset to infer a robust backbone phylogeny of eleven representative Bactrocera species and two outgroups. We further provide the first genome scaled inference of their divergence using calibrated relaxed clock. The results of our analyses support a closer relationship of B. dorsalis to B. latifrons than to B. tryoni, in contrast to all mitochondrial-based phylogenies. By comparing different evolutionary models, we show that this incongruence likely derives from the fast and recent radiation of these species that occurred around 2 million years ago, which may be associated with incomplete lineage sorting and possibly (ongoing) hybridization. These results can serve as basis for future comparative analyses and highlight the utility of using large datasets and efficient phylogenetic approaches to study the evolutionary history of species of economic importance.

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Molecular clock analysis on fiveBactroceraspecies flies (Diptera: Tephritidae) based on combination ofCOIandNADHsequences

Cited by 8 publications

References 55 publications

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

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

Translating olfactomes into attractants: shared volatiles provide attractive bridges for polyphagy in fruit flies

The impact of fast radiation on the phylogeny ofBactrocerafruit flies

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