The genome of<i>Drosophila innubila</i>reveals lineage-specific patterns of selection in immune genes

Hill, Tom; Koseva, Boryana; Unckless, Robert L.

doi:10.1101/383877

Cited by 16 publications

(43 citation statements)

References 93 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study we combined recent genomic and transcriptomic resources to test whether termite ecology, in particular exposure to pathogens, might affect the evolution of immune genes. Surprisingly, and in contrast to studies from Drosophila Sackton et al 2007;Hill et al, 2019) we could not find evidence for positive selection on the immune genes for eight termite species. We extended our analyses, employing recent tests to explicitly assess relaxed selection , revealing 62 cases of significantly relaxed selection in IGs.…”

Section: Discussioncontrasting

confidence: 99%

“…Thus, more studies are warranted that test selection on such multi-copy genes. However, orthology is difficult to infer for multi-copy genes making the restriction to SCOs a standard procedure (e.g., Pauli et al, 2016;Dowling et al, 2016;Mitterboeck et al, 2017;Ran et al, 2018;Brandt et al, 2019;Hill et al, 2019). Thus, we restricted our analysis to single-copy orthologs because orthology is a basic assumption of the current methods that identify selection in a powerful phylogenetic framework (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…A significant P-value means that at least one codon in the foreground branch has experienced an episode of positive selection. The high sensitivity of the method compared to tests from alternative packages (see e.g., Enard et al, 2016;Ebel et al, 2017;Venkat et al, 2018;Hill et al, 2019) and the option to define the foreground branches according to our research question made it perfectly suited for our study.…”

Section: Inferring Positive Selection and Selection Intensitymentioning

confidence: 99%

See 2 more Smart Citations

No evidence for immune-gene specific signals of selection in termites

Meusemann

Korb

Schughart

et al. 2019

Preprint

View full text Add to dashboard Cite

It has been hypothesized that selection pressure from pathogens plays an important role in shaping social evolution. Social behaviour, in particular brood care, is associated with pathogen pressure in wood-dwelling “lower” termites. Yet, generally pathogen pressure is low in wood-dwelling termite species that never leave the nest except for the mating flight. In comparison, pathogen pressure is higher in species that leave the nest to forage, and thus constantly encounter a diversity of microbes from their environment. We hypothesized that such differences in pathogen pressure are also reflected by differences in the intensity of natural selection on immune genes. We tested this hypothesis in a phylogenetic framework, analyzing rates of non-synonymous and synonymous substitutions on single-copy immune genes. Therefore, we leveraged recent genomic and transcriptomic data from eight termite species, representing wood-dwelling and foraging species as well as 14 additional species spanning the winged insects (Pterygota). Our results provide no evidence for a role of pathogen pressure in selection intensity on single-copy immune genes. Instead, we found evidence for a genome-wide pattern of relaxed selection in termites.Life Science Identifiers (as available Zoobank)Ephemera danica:urn:lsid:zoobank.org:act:06633F75-4809-4BB3-BDCB-6270795368D5Coptotermes sp.urn:lsid:zoobank.org:pub:D6724B7F-F27A-47DC-A4FC-12859ECA0C71Blattella germanica:rn:lsid:zoobank.org:pub:1EA126BA-E9D2-4AA6-8202-26BA5B09B8ADLocusta migratoriaurn:lsid:zoobank.org:pub:D792A09E-844A-412A-BFCA-5293F8388F8CPeriplaneta americana (Blatta americana):urn:lsid:zoobank.org:act:95113A55-4C6D-4DC7-A0E5-620BACADFFE5Apis mellifera:urn:lsid:zoobank.org:act:9082C709-6347-4768-A0DC-27DC44400CB2Bombyx mori (Phalæna (Bombyx) mori)urn:lsid:zoobank.org:act:215466E3-E77F-46E9-8097-372837D7A375Drosophila melanogaster:urn:lsid:zoobank.org:act:5B39F0AA-270D-4AA8-B9A3-C36A3A265910

show abstract

Section: Discussioncontrasting

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Inferring Positive Selection and Selection Intensitymentioning

confidence: 99%

See 1 more Smart Citation

No evidence for immune-gene specific signals of selection in termites

Meusemann

Korb

Schughart

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Sample filtering, mapping and alignment 445We removed adapter sequences using Scythe (BUFFALO 2018), trimmed all data using cutadapt to remove 446 barcodes(MARTIN 2011) and removed low quality sequences using Sickle (parameters: -t sanger -q 20 -l 447 50) (JOSHI AND FASS 2011). We masked the D. innubila reference genome, using D. innubila TE sequences 448 generated previously and RepeatMasker (parameters: -s -gccalc -gff -lib customLibrary) (SMIT AND 449HUBLEY 2013HUBLEY -2015HILL et al 2019). We then mapped the short reads to the masked D. innubila genome450 using BWA MEM (LI AND DURBIN 2009), and sorted and indexed using SAMTools (LI et al 2009).…”

mentioning

confidence: 99%

Adaptation, ancestral variation and gene flow in a ‘Sky Island’Drosophilaspecies

Hill

Unckless

2020

Preprint

Self Cite

View full text Add to dashboard Cite

1Over time, populations of species can expand, contract, and become isolated, creating subpopulations that 2 can adapt to local conditions. Understanding how species adapt following these changes is of great interest, 3 especially as the current climate crisis has caused range shifts for many species. Here, we characterize how 4 Drosophila innubila came to inhabit and adapt to its current range: mountain forests in southwestern USA 5 separated by large expanses of desert. Using population genomic data from more than 300 wild-caught 6 individuals, we examine four distinct populations to determine their population history in these mountain-7 forests, looking for signatures of local adaptation to establish a genomic model for this spatially-distributed 8 system with a well understood ecology. We find D. innubila spread northwards during the previous 9 glaciation period (30-100 KYA), and has recently expanded even further (0.2-2 KYA). Surprisingly, D. 10 innubila shows little evidence of population structure, though consistent with a recent migration, we find 11 signatures of a population contraction following this migration, and signatures of recent local adaptation 12 and selective sweeps in cuticle development and antifungal immunity. However, we find little support for 13 recurrent selection in these genes suggesting recent local adaptation. In contrast, we find evidence of 14 recurrent positive selection in the Toll-signaling system and the Toll-regulated antimicrobial peptides. 15 65 evolutionary change and this is particularly interesting regarding the coevolution with pathogens (DYER 66 AND JAENIKE 2005; UNCKLESS 2011a). We also wanted to understand how D. innubila adapt to their local 67

show abstract

“…When examined within the different pathways, there is evidence for different signatures of adaptation between Drosophila species. Rapid evolution in immune genes seems to be specifically to the viruses they face (DUXBURY et al 2019;HILL et al 2019) or in response to other ecological pressures (HANSON et al 2019). The evolution of immune genes in Caenorhabditis species is less studied and recurrent positive selection appears to be much less pronounced (PUJOL et al 2008;SCHULENBURG et al 2008;DIERKING et al 2016).…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis ofCaenorhabditisandDrosophilatranscriptional changes in response to pathogen infection

Unckless

Lansdon

Ackley

2020

Preprint

Self Cite

View full text Add to dashboard Cite

We analyzed transcriptomic data from C. elegans and D. melanogaster to compare the expression of orthologous pairs of genes in response to bacterial pathogens. Our results indicated that only a handful of genes that are orthologous between species are differentially expressed in response to pathogens, but that the pattern of expression was different when comparing one-to-one orthologs versus those that are restricted to one of the two organisms.These results suggest that, although broad patterns of susceptibility to bacterial pathogens are conserved, the regulatory framework by which the organisms fight pathogens is less well conserved. Further our results suggest a more complete analysis of the evolutionary changes in organismal responses to pathogens is required.Immune divergence in invertebrates 3 | P a g e Abstract Drosophila melanogaster and Caenorhabditis elegans are well-used invertebrate models for studying the innate immune system. The organisms are susceptible to bacterial pathogens that include Pseudomonas species, (entomophilia -Drosophila) or (aeruginosa -Caenorhabditis), E. faecalis and P. rettgeri, which are or are related to human pathogens. Further, the consequences of exposure to these pathogens, in terms of organismal survival, are roughly equivalent when compared. That is, worms and flies are more susceptible to infection by Pseudomonas than E. faecalis, whereas organismal survival on E. faecalis and P. rettgeri are roughly the same in both. To better understand how these organisms are coordinating their responses to these bacterial pathogens we examined transcriptomes in infected animals. We grouped our analysis based on protein orthology. Of the 3611 pairs analyzed, we found genes whose responses were conserved across the different species at a higher than expected rate for two of the three pathogens. Interestingly within the animals, genes with 1:1 orthologs between species behaved differently. Such genes were more likely to be expressed in D. melanogaster, and less likely to be expressed in C. elegans. From this analysis we found that the gene nucleobindin (nucb-1/NUCB1 in C. elegans and D. melanogaster, respectively) was upregulated in both species in response to Gram negative bacteria. We used RNAi to knock down nucb-1 and found the treated animals were more susceptible to infection by the Gram negative pathogen P. rettgeri than controls. These results provide insight into some of the conserved mechanisms of pathogen defense, but also suggest that these divergent organisms have evolved specific means to orchestrate the defense against pathogens.Immune divergence in invertebrates 4 | P a g e

show abstract

The genome ofDrosophila innubilareveals lineage-specific patterns of selection in immune genes

Cited by 16 publications

References 93 publications

No evidence for immune-gene specific signals of selection in termites

No evidence for immune-gene specific signals of selection in termites

Adaptation, ancestral variation and gene flow in a ‘Sky Island’Drosophilaspecies

A comparative analysis ofCaenorhabditisandDrosophilatranscriptional changes in response to pathogen infection

Contact Info

Product

Resources

About