@article {78173, title = {Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?}, journal = {Ecol Evol}, volume = {10}, year = {2020}, month = {05/2020}, pages = {4583-4594}, abstract = {

Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25\%-98\% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype-phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome-wide data from such samples, and (c) evaluate the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population.We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.Whole genome sequencing methods resulted in between 25\%-98\% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long-term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual-based genetics of elusive endangered species in the wild.

}, doi = {10.1002/ece3.6157}, author = {Khan, A and Patel, K and Bhattacharjee, S and Sharma, S and Chugani, AN and Sivaraman, K and Hosawad, V and Sahu,YK and Reddy, GV and Ramakrishnan, U} } @article {77440, title = {Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape}, journal = {DIVERSITY AND DISTRIBUTIONS}, volume = {26}, year = {2020}, month = {03/2020}, pages = {299-314}, abstract = {

Aim: Maintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on genetic structure in four widespread species-jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris).

Location: Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land use types.

Methods: Microsatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on genetic structure was inferred using a multimodel landscape resistance optimization approach.

Results: All four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on gene flow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables-land use, human population density, density of linear features and roads-impacted the study species differently. Although land use was found to be an important variable explaining genetic structure for all four species, the amount of variation explained, and the optimum spatial resolution and the resistance values of different land use classes varied.

Main conclusions: As expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

}, doi = {10.1111/ddi.13022}, author = {Thatte, P and Chandramouli, A and Tyagi, A and Patel, K and Baro, P and Chhattani, H and Ramakrishnan, U} } @article {71094, title = {Human footprint differentially impacts genetic connectivity of four wide-ranging mammals in a fragmented landscape}, journal = {Diversity and Distribution}, year = {2019}, month = {12/2019}, abstract = {

Aim

Maintaining connectivity is critical for long-term persistence of wild carnivores in landscapes fragmented due to anthropogenic activity. We examined spatial genetic structure and the impact of landscape features on genetic structure in four widespread species{\textemdash}jungle cat (Felis chaus), leopard (Panthera pardus), sloth bear (Melursus ursinus) and tiger (Panthera tigris).

Location

Our study was carried out in the central Indian landscape, a stronghold in terms of distribution and abundance of large mammals. The landscape comprises fragmented forests embedded in a heterogeneous matrix of multiple land use types.

Methods

Microsatellite data from non-invasively sampled individuals (90 jungle cats, 82 leopards, 104 sloth bears and 117 tigers) were used to investigate genetic differentiation. Impact of landscape features on genetic structure was inferred using a multimodel landscape resistance optimization approach.

Results

All four study species revealed significant isolation by distance (IBD). The correlation between genetic and geographic distance was significant only over a short distance for jungle cat, followed by longer distances for sloth bear, leopard and tiger. Overall, human footprint had a high negative impact on gene flow in tigers, followed by leopards, sloth bears and the least on jungle cats. Individual landscape variables{\textemdash}land use, human population density, density of linear features and roads{\textemdash}impacted the study species differently. Although land use was found to be an important variable explaining genetic structure for all four species, the amount of variation explained, and the optimum spatial resolution and the resistance values of different land use classes varied.

Main conclusions

As expected from theory, but rarely demonstrated using empirical data, the pattern of spatial autocorrelation of genetic variation scaled with dispersal ability and density of the study species. Landscape genetic analyses revealed species-specific impact of landscape features and provided insights into interactions between species biology and landscape structure. Our results emphasize the need for incorporating functional connectivity data from multiple species for landscape-level conservation planning.

}, doi = {10.1111/ddi.13022}, author = {Thatte, P and Chandramouli, A and Tyagi, A and Patel, K and Baro, B and Chhattani, H and Ramakrishnan, U} }