Evidence of positive selection associated with placental loss in tiger sharks

Swift, Dominic G.; Dunning, Luke T.; Igea, Javier; Brooks, Edward J.; Jones, Catherine S.; Noble, Leslie R.; Ciezarek, Adam; Humble, Emily; Savolainen, Vincent

doi:10.1186/s12862-016-0696-y

Cited by 22 publications

(15 citation statements)

References 73 publications

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“…Since most codon sites are highly conserved to maintain protein function [ 61 ], the site models of PAML, M1a (neutral) vs. M2a (selection) and M7 (beta) vs. M8 (beta & ω ≥ 1), were applied to test whether the positive selection was operating in duplicated SHB ORs (Cluster 2, Figure 2 ), which might be associated with unique olfactorial adaptations [ 59 ]. As in the branch model test, the alignment files of codon sequences were prepared by PAL2NAL [ 58 ] and the same tree topology in Cluster 2 was used in the tree file for PAML.…”

Section: Methodsmentioning

confidence: 99%

Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida)

Liu

Beaurepaire

Rogers

et al. 2020

IJMS

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Olfaction is key to many insects. Odorant receptors (ORs) stand among the key chemosensory receptors mediating the detection of pheromones and kairomones. Small hive beetles (SHBs), Aethina tumida, are parasites of social bee colonies and olfactory cues are especially important for host finding. However, how interactions with their hosts may have shaped the evolution of ORs in the SHB remains poorly understood. Here, for the first time, we analyzed the evolution of SHB ORs through phylogenetic and positive selection analyses. We then tested the expression of selected OR genes in antennae, heads, and abdomens in four groups of adult SHBs: colony odor-experienced/-naive males and females. The results show that SHBs experienced both OR gene losses and duplications, thereby providing a first understanding of the evolution of SHB ORs. Additionally, three candidate ORs potentially involved in host finding and/or chemical communication were identified. Significantly different downregulations of ORs between the abdomens of male and female SHBs exposed to colony odors may reflect that these expression patterns might also reflect other internal events, e.g., oviposition. Altogether, these results provide novel insights into the evolution of SHB ORs and provide a valuable resource for analyzing the function of key genes, e.g., for developing biological control. These results will also help in understanding the chemosensory system in SHBs and other beetles.

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Section: Methodsmentioning

confidence: 99%

Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida)

Liu

Beaurepaire

Rogers

et al. 2020

IJMS

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“…However, the ratio averaged over all sites is unlikely to exceed 1, because positive selection is unlikely to affect all codon sites of a gene (Yang, 2007 ). Also, most codon sites were supposed to be highly conserved to maintain protein function (Swift et al, 2016 ). Therefore, we employed a pair of site models (M7 and M8) to test whether positive selection episodes had affected specific amino acid sites in each gene.…”

Section: Methodsmentioning

confidence: 99%

Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species

Teng

Fan

et al. 2017

Front. Plant Sci.

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Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS). About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins) involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.

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“…This phenomenon may even be desirable, as it allows assessment of mtDNA diversity. After removal of mitochondrial sequences, the reads were mapped against the transcriptome of tiger shark 36 , using the BWA-mem algorithm. This transcriptome includes 179,867 unique contigs greater than200 bp length (average 822 bp, maximum 15,892 bp).…”

Section: Bioinformatics Pipeline and Data Lteringmentioning

confidence: 99%

Retrospective Genomics Suggests the Disappearance of a Tiger Shark (Galeocerdo Cuvier) Population Off South-Eastern Australia

Manuzzi

Jiménez‐Mena

Henriques

et al. 2021

Preprint

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Over the last century, many populations of sharks have been reduced in numbers by overexploitation or attempts to mitigate human-shark interactions. Still, there is a general perception that populations of large ocean predators cover wide areas and therefore their diversity is less susceptible to local anthropogenic disturbance. Here we report retrospective genomic analyses of DNA using archived and contemporary samples of tiger shark (Galeocerdo cuvier) from eastern Australia. Using SNP loci, we documented a significant overall change in genetic composition of tiger sharks born over the last century. The change was most likely due to a shift over time in the relative contribution of two well differentiated, but hitherto cryptic populations. Our data strongly indicate a dramatic shift in relative contribution of the two populations to the overall tiger shark abundance of the east coast of Australia, possibly associated with differences in direct or indirect exploitation rates.

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Evidence of positive selection associated with placental loss in tiger sharks

Cited by 22 publications

References 73 publications

Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida)

Gene Expression and Functional Analyses of Odorant Receptors in Small Hive Beetles (Aethina tumida)

Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species

Retrospective Genomics Suggests the Disappearance of a Tiger Shark (Galeocerdo Cuvier) Population Off South-Eastern Australia

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