Helen R. Taylor

An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

DNA barcoding has become a well‐funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.

Genomics advances the study of inbreeding depression in the wild

Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high‐throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable.

Emerging Technologies to Conserve Biodiversity: Further Opportunities via Genomics. Response to Pimm et al.

In a recent article in TREE [1], Pimm et al. outlined some new technologies that may be used to tackle the global biodiversity crisis, and the issues and questions accompanying these advances. Their focus was on three specific challenges: monitoring individuals and their movements; collecting data on species occurrence and locations; and remote sensing of environmental drivers of biodiversity loss. Here, we broaden that discussion to encompass some of the rapidly evolving genomic technologies that appear likely to play important roles in addressing those same conservation challenges.

Cryptic inbreeding depression in a growing population of a long‐lived species

Genetic effects are often overlooked in endangered species monitoring, and populations showing positive growth are often assumed to be secure. However, the continued reproductive success of a few individuals may mask issues such as inbreeding depression, especially in long‐lived species. Here, we test for inbreeding depression in little spotted kiwi (Apteryx owenii) by comparing a population founded with two birds to one founded with 40 birds, both from the same source population and both showing positive population growth. We used a combination of microsatellite genotypes, nest observations and modelling to examine the consequences of assessing population viability exclusively via population growth. We demonstrate (i) significantly lower hatching success despite significantly higher reproductive effort in the population with two founders; (ii) positive growth in the population with two founders is mainly driven by ongoing chick production of the founding pair; and (iii) a substantial genetic load in the population founded with two birds (10–15 diploid lethal equivalents). Our results illustrate that substantial, cryptic inbreeding depression may still be present when a population is growing, especially in long‐lived species with overlapping generations.

Genetic sex assignment in wild populations using genotyping-by-sequencing data: A statistical threshold approach

Establishing the sex of individuals in wild systems can be challenging and often requires genetic testing. Genotyping-by-sequencing (GBS) and other reduced-representation DNA sequencing (RRS) protocols (e.g., RADseq, ddRAD) have enabled the analysis of genetic data on an unprecedented scale. Here, we present a novel approach for the discovery and statistical validation of sex-specific loci in GBS data sets. We used GBS to genotype 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We retained monomorphic loci as potential sex-specific markers in the locus discovery phase. We then used (i) a sex-specific locus threshold (SSLT) to identify significantly male-specific loci within our data set; and (ii) a significant sex-assignment threshold (SSAT) to confidently assign sex in silico the presence or absence of significantly male-specific loci to individuals in our data set treated as unknowns (98.9% accuracy for females; 95.8% for males, estimated via cross-validation). Furthermore, we assigned sex to 86 individuals of true unknown sex using our SSAT and assessed the effect of SSLT adjustments on these assignments. From 90 verified sex-specific loci, we developed a panel of three sex-specific PCR primers that we used to ascertain sex independently of our GBS data, which we show amplify reliably in at least two other pinniped species. Using monomorphic loci normally discarded from large SNP data sets is an effective way to identify robust sex-linked markers for nonmodel species. Our novel pipeline can be used to identify and statistically validate monomorphic and polymorphic sex-specific markers across a range of species and RRS data sets.

De-extinction needs consultation

To the Editor — De-extinction stands to divert funding away from existing conservation projects. Understandably, the resurrection of extinct species and associated gene-editing approaches face some opposition from conservation practitioners. Bennett et al.1 make some excellent points regarding the potential for de-extinction projects to divert funding from conservation of extant Australasian species. We contend that a further issue for conservation-motivated de-extinction is that many conservation practitioners are opposed to it and partially opposed to the gene editing techniques it relies on. It is widely acknowledged that a gap exists between genetics research and conservation practice2, which could widen with increased use of genomics3. It is therefore vital to understand practitioner attitudes to conservation-driven de-extinction and gene editing. New Zealand (NZ) (a focal country of Bennett et al.1) is, arguably, an ideal testing ground for conservation-driven de-extinction and gene editing. Multiple NZ species have become extinct in the past 150 years (ref. 4), producing far more tractable de-extinction candidates than the much-publicized moa and mammoths. NZ’s main conservation challenge is invasive mammalian predators; radical solutions are needed to hit the country’s goal of being free from introduced predators by 2050 (ref. 5). Finally, many native NZ species have extremely low genetic variation due to human-driven population bottlenecks6. Gene editing could help address these issues, but conservation practitioner support is vital and has not been assessed. We conducted a formal survey of 148 practitioners working in NZ’s governmentrun Department of Conservation (Fig. 1; Supplementary Methods). The majority (62%) of practitioners considered deextinction unfeasible within their lifetime, and only 47% thought it could be a useful conservation tool. The former may suggest a lack of awareness of the extent of research interest and progress in de-extinction techniques (for example, ref. 7). There is confusion generally regarding what de-extinction means; many people do not appreciate that de-extinction actually involves creating a technically feasible proxy (that is, a mammoth-like elephant) rather than an impossible resurrection (that is, an actual mammoth)8. Communication from researchers is key to helping practitioners understand the reality of the de-extinction landscape. As Bennett et al. indicate1, the main concern among practitioners opposed to de-extinction was the diversion of funds from extant species conservation. Those in favour of de-extinction liked the idea of completely restoring an ecosystem, raising questions around what goals we should set for ecosystem restoration in our rapidly changing environment9, and whether extant or extinct ecological replacements would be best to restore ecosystem function. Support for gene editing was mostly to manage invasive species (Fig. 1), thus avoiding the use of toxins, which are the current prevalent tool for invasive mammal control in NZ. Those opposed were worried about leakage into non-target populations or species. Both sides demonstrated awareness of at least some of the risks associated with gene editing (Supplementary Results). Many supporting gene editing in native species felt it was merely an extension of selective breeding. Those opposed were concerned regarding the hubris of playing God (a common feeling towards synthetic biology10) and would rather see a species go extinct than edit genes. Again, better communication between researchers and practitioners will increase preparedness for a technology evolving more rapidly than many realize. However, the concerns around playing God demonstrate that attitudes De-extinction needs consultation

Chick Timer™ software proves an accurate disturbance minimising tool for monitoring hatching success in little spotted kiwi (Apteryx owenii)

Measuring hatching success in birds is important for assessing population viability, but nests are often cryptic and may be abandoned if birds are disturbed during nesting. We evaluated the suitability of Wildtech New Zealand Ltds Chick Timer™ radio telemetry software for monitoring hatching success in little spotted kiwi (Apteryx owenii). The software provided accurate reports of activity levels and times of nest emergence by adult birds. Eighty four per cent of incubation attempts and 70% of first hatching events were detected, with no false indications of incubation or hatching. Our results suggest that this technology will facilitate studies of hatching success in little spotted kiwi and other large birds with cryptic or inaccessible nests. A ground truthing study such as this one, however, is required before full implementation of the software in any species.

Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species

Abstract Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.