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Conservation Genetics the Institute’S Researchers Develop Methods and Tools in Conservation Genetics, and Apply These to Inform the Conservation of Threatened Species

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Main image: bumblebee family lineage survival historical and current effective population size For further information, contact Jinliang Wang: is enhanced in high-quality landscapes. Inset left: of Hainan gibbons [email protected] IMPACT AREAS microsatellite data are used to investigate the Conservation genetics The Institute’s researchers develop methods and tools in conservation genetics, and apply these to inform the conservation of threatened species. enetic diversity influences the these methods to investigate the historical health and long-term survival of and current effective population size of populations, with decreased genetic Hainan gibbons (Nomascus hainanus) from Gdiversity associated with reduced fitness microsatellite data (Bryant et al. 2016). and adaptability to changing environments. Conservation genetics provides the theory Inferring population structure and methods to estimate historical and Individuals of a species may not constitute current genetic diversity and to predict a genetically homogeneous population. the future distribution of genetic diversity Instead, they are usually clustered into in populations and species. This crucial different populations due to patchy information informs conservation strategy geographic distribution and a limited ability in order to minimise risk of extinction in to disperse. Inferring population structure by threatened species. delineating the number and distribution of populations and by measuring the genetic Estimating effective differentiation among populations helps population size us to understand the current distribution Threatened species usually have small and of genetic diversity. declining population sizes, and genetic Institute research has shown that the diversity is lost due to genetic stochasticity. most appropriate statistic for quantifying The rate of loss of genetic diversity is genetic differentiation is Fst (a measure determined by the effective population of genetic differentiation between size (Ne) of the species, which is affected by populations). However, Fst can underestimate factors including the total population size differentiation when calculated from highly (N), variance in reproduction and sex ratio. polymorphic microsatellite data. We have For wild populations, Ne can be dramatically shown for the first time the circumstances smaller than N, especially for when microsatellites give species with extremely locus-dependent and unbalanced sex ratio underestimates of Fst, and high reproductive such as high mutation dominance. rate and low migration Therefore, it rate. We have since is essential to developed a measure the Ne correlation analysis of a population to detect such for conservation circumstances management. We from genotype data have developed (Wang 2015). methods to estimate We have also used Ne from genetic marker a Bayesian clustering data (most recently Wang method (Structure) to 2016a), and produced user- make individual assignments friendly computer software called Colony, to populations from multi-locus genotype which is available on the Institute website for data, most recently to investigate the use by conservation genetics practitioners. population structures of grey squirrels Thousands of downloads of the Colony (Sciurus carolinensis) (Signorile et al. 2016). software have been recorded over the past A new study showed that Structure is easily 12 months and new Institute research used misused when sampling is unbalanced, 20 ZSL Science Review 2016-17 zsl.org zsl.org ZSL Science Review 2016-17 21 Below left: Institute genotyping methods were used to estimate the effective population size of cheetahs IMPACT AREAS using scats detected by trained dogs and could yield biased results when the Non-invasive genotyping alleviates some of default parameter values of the software these difficulties by obtaining DNA by indirect References were adopted (Wang 2017). Our research sampling of a specimen. This does not require Becker, MS, Durant, SM, Garner, TWJ, Bosch, has provided alternative parameter values, handling (or even the presence of) the animal, Watson, FGR, Parker, J and Fisher, MC which yield more accurate population as DNA can be extracted from small quantities M, Gottelli, D, M’soka, J, (2016) Climate forcing structure inferences in both simulated and of hair, feathers, scales or scats, which can Droge, E, Nyirenda, M, of an emerging real datasets. be genotyped by polymerase chain reaction. Schuette, P, Dunkley, S pathogenic fungus We have applied this technique to a range and Brummer, R (2017) across a montane Relatedness and of species, enabling ecological, evolutionary Using dogs to find multihost community. relationship ascertainment and conservation genetics studies of species cats: detection dogs Philosophical Knowing the genetic relatedness among that could not have been studied otherwise. as a survey method for Transactions of the individuals is essential for investigating However, data quality can be problematic wide-ranging cheetah. Royal Society 371: breeding behaviour, inbreeding and because the quality and quantity of DNA Journal of Zoology 201505454 inbreeding depression, social structure, from non-invasive samples is often low and 302: 184-192 and population demographics and genotyping errors are common. An important Signorile, AL, Lurz, connectivity. Traditionally, relatedness is application of non-invasive genotyping, Brekke, P, Ewen, JG, PWW, Wang, J, Reuman, calculated from pedigrees (eg Brekke et al. estimating population census size by Clucas, G and Santure, DC and Carbone, 2015). However, pedigree data are rarely the genetic capture-recapture model, is AW (2015) Determinants C (2016) Mixture or available in wild populations. particularly vulnerable to genotyping errors. of male floating mosaic? Genetic We have proposed advanced behaviour and floater patterns in UK grey likelihood methods for identifying reproduction in a squirrels support a individuals from multi-locus threatened population human-mediated genotypes obtained from non- of the hihi (Notiomystis ‘long-jump’ invasion invasive samples, accounting for cincta). Evolutionary mechanism. Diversity genotyping errors and missing Applications 8: 796-806 and Distributions data (Wang 2016b). Our methods 22: 566-577 have recently been used to Bryant, JV, Gottelli, estimate the density and effective D, Zeng, X, Hong, X, Wang, J (2015) Does Gst population size of cheetahs using Chan, BPL, Fellowes, underestimate genetic scats detected by trained dogs JR, Zhang, Y, Luo, J, differentiation from (Becker et al. 2017). Durrant, C, Geissmann, marker data? Molecular T and Chatterjee, Ecology 24: 3546-3558 Disease emergence HJ (2016) Assessing Infectious diseases can threaten current genetic status Wang, J (2016a) A populations, species and entire of the Hainan gibbon comparison of single- communities of wildlife, and the using historical sample estimators of consequences of disease can and demographic effective population be exacerbated when genetic baselines: implications sizes from genetic diversity of wildlife populations for conservation marker data. Molecular is low. Wildlife hosts of pathogens management of species Ecology 25: 4692-4711 can respond to the emergence of extreme rarity. of disease through selection, Molecular Ecology 25: Wang, J (2016b) To facilitate studies of wild populations, we and we have used population genetics to 3540-3556 Individual identification developed methods to estimate relationship detect both natural and sexual selection in from genetic marker and relatedness from genetic marker data, diseased populations. Carvell, C, Bourke, AF, data: developments producing a computer program called We have shown how the genetic Dreier, S, Freeman, SN, and accuracy Coancestry. Our studies, among many others, interactions between host and pathogen are Hulmes, S, Jordan, WC, comparisons of have used these methods to assess inbreeding strongly regulated by environmental variation Redhead, JW, Sumner, methods. Molecular and inbreeding depression in diverse species, caused by climate change (Clare et al. 2016), S, Wang, J and Heard, Ecology Resources and were most recently used to investigate and we now need to examine how genes are MS (2017) Bumblebee 16: 163-175 the survival and reproduction of bumblebee expressed under these different conditions. family lineage survival (Bombus spp.) queens (Carvell et al. 2017). Hosts cannot fend off pathogens with a single is enhanced in high- Wang, J (2017) The molecular toolkit, so we will continue to quality landscapes. computer program Conservation genetics by unpick the complexities of host immune Nature 543: 547-549 STRUCTURE for non-invasive genotyping gene expression. assigning individuals Threatened species are often difficult to Clare, FC, Halder, JB, to populations: easy sample for genetics studies. Some animals Daniel, O, Bielby, J, to use but easier to To download Colony, visit zsl.org/ are dangerous, such as large carnivores, or Semenov, MA, Jombart, misuse. Molecular science/software/colony – and for difficult to access, such as marine mammals, T, Loyau, A, Schmeller, Ecology Resources. Coancestry, visit zsl.org/science/ while some others are elusive, such as okapis DS, Cunningham, doi:10.1111/1755- software/coancestry (Okapia johnstoni). AA, Rowcliffe, JM, 0998.12650 22 ZSL Science Review 2016-17 zsl.org.
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