Using non-invasively collected genetic data to estimate density and population size of tigers in the Bangladesh Sundarbans

Aziz, Md. Abdul; Tollington, Simon; Barlow, Adam; Greenwood, C. J.; Goodrich, John M.; Smith, Olutolani; Shamsuddoha, Mohammad; Islam, Md. Anwarul; Groombridge, Jim J.

doi:10.1016/j.gecco.2017.09.002

Cited by 20 publications

(20 citation statements)

References 47 publications

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“…Non-invasive biological samples (scat and hair of tigers) were collected from different areas of the Sundarbans, with purposive sampling from isolated forest patches separated by the rivers Arpangassia, Sibsa and Passur. Firstly, we intensively sampled four geographically isolated areas of the Sundarbans using 2×2 km sample grids (detail protocol and sampling effort were described in Aziz et al 2017a).…”

Section: Sample Collectionmentioning

confidence: 99%

“…Microsatellite markers (repeated sequence of nucleotides) are commonly used to investigate genetic structure (Mondol et al 2009b;Reddy et al 2012), spatial genetics (Sharma et al 2012), and genetic connectivity between tiger populations (Joshi et al 2013). In this study, we used a panel of 10 microsatellites from a set of 14 optimised polymorphic loci (Aziz et al 2017a), to amplify tiger-authenticated DNA samples (Table S1). Four multiplexes were designed to include the full set of loci.…”

Section: Microsatellite Genotyping and Individual Identificationmentioning

confidence: 99%

“…The Sundarbans mangrove forests shared between Bangladesh and India is one of the six regional Tiger Conservation Landscapes (TCLs) of global priority (Sanderson et al 2006), and supports one of largest populations of Bengal tigers (Barlow 2009;Dey et al 2015;Aziz et al 2017a). However, tigers in the Sundarbans have long been isolated from the nearest TCL (e.g., Similipal Tiger Reserve in West Bengal, India) by approximately 200 km of agricultural lands and human settlements (Sanderson et al 2006), thereby limiting any opportunity of gene flow between populations.…”

Section: Introductionmentioning

confidence: 99%

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Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

Aziz

Smith

Barlow³

et al. 2018

Conserv Genet

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Section: Sample Collectionmentioning

confidence: 99%

Section: Microsatellite Genotyping and Individual Identificationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

Aziz

Smith

Barlow³

et al. 2018

Conserv Genet

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“…Noninvasive genotyping approaches therefore often involve grouping primers into multiple separate smaller multiplexes (e.g. Aziz et al, 2017; Cegelski, Waits, & Anderson, 2003; Wultsch, Waits, & Kelly, 2014). In addition, purification of the PCR products to remove unincorporated primers and non-target sequences is a common step in amplicon sequencing workflows.…”

Section: Introductionmentioning

confidence: 99%

More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

Eriksson

Ruprecht

Levi

2019

Preprint

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5Non-invasive genotyping methods have become key elements of wildlife research over the last 6 two decades, but their widespread adoption is limited by high costs, low success rates, and high 7 error rates. The information lost when genotyping success is low may lead to decreased precision 8 in animal population densities which could misguide conservation and management actions. Single 9 nucleotide polymorphisms (SNPs) provide a promising alternative to traditionally used 10 microsatellites as SNPs allow amplification of shorter DNA fragments, are less prone to 11 genotyping errors, and produce results that are easily shared among laboratories. Here, we outline 12 a detailed protocol for cost-effective and accurate noninvasive SNP genotyping using highly 13 multiplexed amplicon sequencing optimized for degraded DNA. We validated this method for 14 individual identification by genotyping 216 scats, 18 hairs and 15 tissues from coyotes (Canis 15 latrans). Our genotyping success rate for scat samples was 93%, and 100% for hair and tissue, 16 representing a substantial increase compared to previous microsatellite-based studies at a cost of 17 under $5 per PCR replicate (excluding labor). The accuracy of the genotypes was further 18 corroborated in that genotypes from scats matching known, GPS-collared coyotes were always 19 located within the territory of the known individual. We also show that different levels of 20 multiplexing produced similar results, but that PCR product cleanup strategies can have 21 2 substantial effects on genotyping success. By making noninvasive genotyping more affordable, 22 accurate, and efficient, this research may allow for a substantial increase in the use of 23 noninvasive methods to monitor and conserve free-ranging wildlife populations. 24 Keywords 25 Fecal DNA, individual identification, next-generation sequencing, noninvasive samples, single 26 nucleotide polymorphisms, SNP genotyping. 27 28 29 48 rates when using fragmented DNA from noninvasive sources (Morin, Luikart, & Wayne, 2004).49 Unlike microsatellite genotyping, which use size-based allele determination, SNP alleles are 50 provided directly in the DNA sequence, which facilitates automated allele calling and results that 51 are easily shared among laboratories and research groups.52 4 Recent SNP genotyping approaches for noninvasive samples include the Fluidigm 53 Dynamic Array platform (Fluidigm Corp) and the MassARRAY platform from Sequenom. The 54 Fluidigm platform in particular has produced high genotyping success and low error rates for 55 both fecal and hair samples (Kraus et al., 2015; Von Thaden et al., 2017). However, these 56 techniques require specialized equipment often rendering them prohibitively expensive for 57 wildlife research (Andrews, De Barba, Russello, & Waits, 2018; Carroll et al., 2018). A largely 58 unexplored strategy is to amplify many SNPs together in multiplex PCR and sequence them 59 using high-throughput sequencers. Such genotyping by amplicon sequencing (GBAS) is both 60 cost-effective, a...

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“…However, an accurate picture of population trends on the long term is lacking. Non-invasive genetic analyses are suitable tools to provide estimations of demographic parameters necessary to frame conservation plans [10][11][12][13] . The main objectives of the present study were to assess the suitability of non-invasive genetic techniques to study the snow leopard population living in the SESR, and to obtain information on family relationships and movement patterns.…”

Section: Introductionmentioning

confidence: 99%

Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

Rode¹,

Pelletier²,

Fumey

et al. 2019

Preprint

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Snow leopards (Panthera uncia) are a keystone species of Central Asia's high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven microsatellite loci, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals' movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.

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Using non-invasively collected genetic data to estimate density and population size of tigers in the Bangladesh Sundarbans

Cited by 20 publications

References 47 publications

Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

Do rivers influence fine-scale population genetic structure of tigers in the Sundarbans?

More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

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