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Mistakes in a landmark paper that reported the first orangutan genomes might have implications for breeding programmes.Credit: Fiona Rogers/Nature Picture Library

Susie the Sumatran orangutan was a genetic pioneer — the first of her species to have her genome fully sequenced. Her genetic library, and that of ten other orangutans, appeared in a landmark paper in Nature in 20111 that has underpinned hundreds of subsequent studies.But in August, researchers revealed that eight of the sequences in this paper had mistakenly been assigned to the wrong orangutans2. Nature issued a correction from the authors of the original paper3.The scale of the errors sparked ire on social media, and some scientists have warned that the mistakes could have repercussions for orangutan breeding programmes. “Well that’s a bit of a f&£k up orang-utan genome researchers — only mildly embarrassing guys and girls”, tweeted Michael Sweet, a molecular ecologist at the University of Derby, UK.
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It’s not clear how these swapped identities have affected orangutan research. But researchers involved in the new analysis believe the discovery might highlight how issues in the scientific community — including the pressure to publish and a reliance on peer review to catch mistakes — could allow such errors to slip into the scientific record.“I think there are errors like this in many, many published papers,” says Graham Banes, an evolutionary biologist formerly at the University of Wisconsin–Madison who led the reanalysis of the 2011 paper. “In some ways, we’re lucky that this was just orangutans. What if this was a biomedical paper and people were developing therapies based on published data?”“It’s fairly easy for these things to occur,” adds Robert Fulton, a genomic scientist at Washington University School of Medicine in St Louis, Missouri, who was part of the team behind the original paper and is a co-author on the reanalysis. “What’s important is that that the data are now correct.” Devin Locke, who led the preparation of the 2011 paper and was formerly a colleague of Fulton’s at Washington University, did not respond to questions about the work.Hybrid headacheDetailed ‘reference’ genomes, such as those published in the 2011 Nature paper, are a key tool for biologists. In 2017, Banes and his team were using the genomes to study what happens when different species of orangutan interbreed, a process called hybridization.They noticed that the names given to some of the samples didn’t match the animals’ reported sex. For example, the 2011 paper reported that an orangutan named Dolly was male. But according to the orangutan studbook — a record of orangutans living in zoos — Dolly was female. Even stranger, Banes found that some of the genomes marked as male lacked a Y chromosome. “There was just this series of things that didn’t make sense,” he recalls.
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Banes and his colleagues eventually found that the 2011 paper had misidentified all but two of the orangutan genomes. Some mistakes seem to be the result of typos. In one case, a sample from a male orangutan was given an ID number that actually corresponded to a sample from an African pig in a tissue repository. Other samples seem to have had their identities swapped during laboratory work. The 2011 study helped to pin down when Bornean and Sumatran orangutans split into separate species, and compared their genomes with those of other primates. These conclusions are largely uncompromised by the mix-up. But Banes says that the errors could have implications for other research, including his own.Banes uses genetic data to provide zoos with recommendations about their captive breeding programmes. Zoos try to avoid crossbreeding orangutan species, partly to mimic wild populations and also because hybrids can suffer high rates of miscarriage and birth defects, says Banes. While re-examining the samples from the 2011 paper, the team realized that one of the sequences thought to be Sumatran (Pongo abelii) was actually Tapanuli (Pongo tapanuliensis), a third species of orangutan that was only described in 20174.Unfortunately, the 2011 paper had wrongly assigned the Tapanuli genome to Baldy, a male orangutan, rather than its actual owner, a female orangutan named Bubbles (both are now dead). Banes says that his team came “perilously close” to announcing in a paper that Baldy was Tapanuli.Although Baldy has no living descendants, Bubbles has several offspring at zoos around the world, all of which are Sumatran–Tapanuli hybrids. Zookeepers will now have to decide whether to stop breeding Bubbles’ descendants to avoid further hybridization, says Vincent Nijman, an anthropologist at Oxford Brookes University, UK.‘Bigger concerns’However, Nijman also argues that the errors will have little effect on orangutan conservation as a whole. Zoos often bill their animals as a back-up for endangered species, but conservationists are much more focused on the thousands of orangutans in the wild that are threatened by deforestation. “I think we have bigger concerns than some mixed-up samples,” says Erik Meijaard, a conservation scientist at Borneo Futures, a conservation consultancy company based in Bandar Seri Begawan, Brunei.
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Michael Krützen, an evolutionary geneticist at the University of Zurich in Switzerland, agrees that although the errors are “annoying”, their impact on downstream research is probably minimal. However, he says that the problems might be an example of how academia’s publish-or-perish environment could lead to “sloppy” work, as researchers race to publish their work in high-tier journals.Banes agrees that this kind of pressure — along with an over-reliance on a peer-review system that does not offer its volunteer reviewers tangible financial or professional benefits — could lead to errors slipping into published manuscripts.A spokesperson for Nature declined to comment on why the errors in the 2011 paper were not caught by peer review, citing concerns about confidentiality. (Nature’s news team is editorially independent of its academic publishing operation). “However, we would like to stress that we take our responsibility to maintain the accuracy of the scientific record very seriously,” they wrote in an e-mail. “If issues are raised about any paper we have published, we will look into them carefully and update the literature where appropriate.”Banes says that it’s important not to blame individual scientists for such errors, not least because it could discourage efforts to correct mistakes in future. “I think any scientist could have made these mistakes,” he says. “But if we all jump out and say, ‘oh my god, how could they have been so stupid?’, no one is ever going to correct anything. That shame is detrimental to science.” More

Sequencing and assembly of the H. schachtii genomeWe measured (Supplemental Fig. 1), sequenced (BioProject PRJNA722882), and assembled the genome of H. schachtii (population Bonn) using a combination of flow cytometry, Pacific Biosciences sequencing, and Illumina sequencing. H. schachtii has the largest genome (160–170 Mb) of any cyst nematode measured/sequenced to date (Supplementary Table 1). It was sequenced to 192-fold coverage using Pacific Biosciences sequencing (fragment n50 of 16 kb), and 144-fold coverage using Illumina sequencing (150 bp Paired-end reads). The final, polished, contamination-free (Supplemental Fig. 2), assembly (v1.2) included ~179 Mbp contained within 395 scaffolds: 90% of the sequence is contained on scaffolds longer than 281,463 bp (n = 154). The assembly is a largely complete haploid representation of the diploid genome, as evidenced by core eukaryotic genes being largely present, complete and single copy (CEGMA 93.15% complete with an average of 1.12 copies each, and BUSCO (Eukaryota odb9) 79% complete with 8.2% duplicated—Supplementary Table 2). Over three million variants were phased into haplotypes (2029 blocks, N50 239.5 kb, covering 94.7% of the reference) which can be used to predict true protein variants (Supplementary data 1), and 601 larger structural variants were identified (Supplementary data 2).The trans-kingdom, lifestage-specific, transcriptomes of H. schachtii and A. thaliana provide a holistic view of parasitismWe devised a sampling procedure to cover all major life stages/transitions of the parasitic life cycle to generate a simultaneous, chronological, and comprehensive picture of nematode gene expression, and infection-site-specific plant gene expression patterns. We sampled cysts and pre-infective second-stage juveniles (J2s), as well as infected segments of A. thaliana root and uninfected adjacent control segments of root at 10 hours post infection (hpi – migratory J2s, pre-establishment of the feeding site), 48 hpi (post establishment of the feeding site), 12 days post infection females (dpi – virgin), 12 dpi males (differentiated, pre-emergence, most if not all stopped feeding), and 24 dpi females (post mating), each in biological triplicate (Fig. 1A). We generated approximately nine billion pairs of 150 bp strand-specific RNAseq reads (Supplementary data 3) covering each stage in biological triplicate (for the parasite and the host): in the early stages of infection we generated over 400 million reads per replicate, to provide sufficient coverage of each kingdom.Fig. 1: Trans-kingdom, lifestage-specific, transcriptome of H. schachtii and A. thaliana.A Schematic representation of the life cycle of H. schachtii infecting A. thaliana, highlighting the 7 stages sampled in this study. For each stage, the average number of trimmed RNAseq read pairs per replicate is shown, with the proportion of reads mapping to either parasite or host in parentheses. B Principle components 1 and 2 for H. schachtii and A. thaliana expression data are plotted. Arrows indicate progression through the life cycle/real-time. Hours post infection (hpi), days post infection (dpi).Full size imageStrand-specific RNAseq reads originating from host and parasite were deconvoluted by mapping to their respective genome assemblies (H. schachtii v.1.2 and TAIR10). For the parasite, ~500 million Illumina RNAseq read pairs uniquely mapping to the H. schachtii genome were used to generate a set of 26,739 gene annotations (32,624 transcripts – detailed further in the next section), ~77% of which have good evidence of transcription in at least one lifestage (≥10 reads in at least one rep). Similarly for the host, ~2.8 billion Illumina RNAseq read pairs uniquely mapping to the A. thaliana genome show that ~77% of the 32,548 gene models have good evidence of transcription in at least one stage (≥10 reads in at least one rep, even though we only sampled roots). A principal component analysis of the host and parasite gene expression data offers several insights into the parasitic process. Principle component 1 (60% of the variance) and 2 (19% of the variance) of the parasite recapitulate the life cycle in PCA space (Fig. 1B). The 12 dpi female transcriptome is more similar to the 24 dpi female transcriptome than to the 12 dpi male transcriptome. Principle components 1 (75% of the variance) and 2 (10% of the variance) of the host show that the greatest difference between infected and uninfected plant tissue is at the early time points (10 hpi), and that the transcriptomes of infected and uninfected plant material converge over time, possibly due to systemic effects of infection. A 12 dpi male syncytium transcriptome is roughly intermediate between a control root transcriptome and a 12 dpi female syncytium transcriptome. Given that at this stage most if not all of the males will have ceased feeding, this could be due to inadequate formation of the feeding site, or regression of the tissue. In any case, by comparing both principal component analyses, we can see that what is a relatively small difference in the transcriptomes of the feeding sites of males and females is amplified to a relatively large difference in the transcriptomes of the males and females themselves (Fig. 1B).The consequences, and possible causes, of large-scale segmental duplication in the Heterodera lineageTo understand the evolutionary origin(s) of the relatively large number of genes in H. schachtii in particular, and Heterodera spp. in general, we analysed the abundance and categories of gene duplication in the predicted exome. Compared to a related cyst nematode, Globodera pallida (derived using comparable methodology and of comparable contiguity) the exomes of H. schachtii and H. glycines are characterised by a relatively smaller proportion of single-copy genes (as classified by MCSanX toolkit17, and a relatively greater proportion of segmental duplications (at least five co-linear genes with no >25 genes between them), with relatively similar proportions of dispersed duplications (two similar genes with >20 other genes between them), proximal duplications (two similar genes with  +0.5 or  More