High frequency of an otherwise rare phenotype in a small and isolated tiger population

Sagar, Vinay; Kaelin, Christopher B.; Natesh, Meghana; Reddy, P. Anuradha; Mohapatra, Rajesh Kumar; Chhattani, Himanshu; Thatte, Prachi; Vaidyanathan, Srinivas; Biswas, Suvankar; Bhatt, Supriya; Paul, Shashi; Jhala, Y. V.; Verma, Mayank; Pandav, Bivash; Mondol, Samrat; Barsh, Gregory S.; Swain, Debabrata; Ramakrishnan, Uma

doi:10.1073/pnas.2025273118

Cited by 23 publications

(23 citation statements)

References 106 publications

(156 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1 A and B ). We compared our estimates for zoo individuals with their known pedigree values to authenticate these results and found that estimates of recent inbreeding indeed correspond with pedigree values ( 51 ) ( SI Appendix , Table 1 ). Overall, the long ROH of

10 Mb, signifying inbreeding due to ancestors as recent as three generations ago, are rare in large populations but frequent in the small–isolated population.…”

Section: Resultsmentioning

confidence: 69%

“…We collected tissue from tranquilized or dead tigers from several tiger reserves (14 protected areas across India); zoo individuals from Sagar et al. ( 51 ) were also analyzed ( Fig. 5 and SI Appendix , Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

“…4) From Nandankanan Zoo, Odisha, India, Sagar et al. ( 51 ) obtained five blood samples from inbred individuals, and these genomes were used as a control to test our methods. The pedigree-based inbreeding coefficients of these individuals vary from 0.21 ( n = 1) to 0.26 ( n = 1) and 0.28 ( n = 3) ( SI Appendix , Table 1 ).…”

Section: Methodsmentioning

confidence: 99%

“… Sample locations and populations. The numbers represent the protected area where, in the northwestern population, 1 is Ranthambore Tiger Reserve ( n = 11), 2 is Sariska Tiger Reserve ( n = 7); in the southern India population, 3 is Bandipur Tiger Reserve ( n = 3), 4 is Wayanad Wildlife Sanctuary ( n = 6), 12 is Nagarhole Tiger Reserve ( n = 2), 5 is Periyar Tiger Reserve ( n = 1); in the central cluster, 6 is Kanha Tiger Reserve ( n = 9), 7 is Corbett Tiger Reserve ( n = 2), 8 is Lalgarh Range ( n = 1), 10 is Sunderban Tiger Reserve ( n = 2), 11 is Bor Tiger Reserve ( n = 1), 13 is Chitwan National Park ( n = 1), 14 is Chandrapur ( n = 1); in the northeastern population, 9 is Kaziranga Tiger Reserve ( n = 4); and Zoo ( 51 ) is Nanadankanan Zoo ( n = 5). …”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Khan

Patel

Shukla

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

123

116

View full text Add to dashboard Cite

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small–isolated and two large–connected populations in India. As expected, the small–isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large–connected (FROH = 0.35 and FROH = 0.46) populations. The small–isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small–isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small–isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small–isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

show abstract

10 Mb, signifying inbreeding due to ancestors as recent as three generations ago, are rare in large populations but frequent in the small–isolated population.…”

Section: Resultsmentioning

confidence: 69%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Khan

Patel

Shukla

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

123

116

View full text Add to dashboard Cite

show abstract

“…Thus, individuals in the fragmented forest could also be darker due to inbreeding and/or low genetic diversity. Rare (often melanic) pigmentation phenotypes can arise in other taxa due to increased inbreeding (Larison et al, 2021) or population bottlenecks (Sagar et al, 2021). Although previous work indicates identical mitochondrial haplotypes in groups sampled across Tsinjoarivo, mitochondrial DNA may not always accurately estimate relatedness between individuals or populations (Guschanski et al, 2013; Mayor et al, 2004; Meyer et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Melanism in a wild sifaka population: Darker where cold and fragmented

Tapanes

Kamilar

Nukala

et al. 2022

Preprint

View full text Add to dashboard Cite

Pigmentation is one of the most striking examples of diversity in the natural world. Mainly, pelage (hair/fur) pigmentation provides a substrate for selection (i.e., crypsis, signaling, thermoregulation) and is capable of rapid change. Thus, this trait may be the one potential early signal of adaptation (or maladaptation) in wild primate populations. However, most of our hypotheses on the forces responsible for primate pelage pigmentation are based solely on macro-evolutionary studies. Here, we characterize pelage color and pattern variation within a population of wild primates, diademed sifakas (Propithecus diadema), exhibiting striking diversity in coloration (melanic to tri-colored). Our approach jointly assesses climate and pelage variation across the region. We score pelage using a semi-quantitative methodology. We then test if pelage variation is associated with climatic or demographic factors (i.e., sex-class, age-class) across the Tsinjoarivo forest, Madagascar. We find darker bodies and less complex faces occur in colder and more fragmented forests. We explore three hypotheses that may explain this phenotypic pattern: isolation by distance, an environmental gradient, or unique local adaptation. Importantly, each scenario signals the need for enhanced conservation of diademed sifakas in the Tsinjoarivo forest. More studies on primate pigmentation in wild populations will be needed to contextualize if this pattern is exceptional or typical. It is likely that in other primate populations pigmentation may also foretell of adaptation or environmental mismatch.

show abstract

Heterozygosity is low where rare color variants in wild carnivores prevail

Tensen,

Fischer

2024

Ecology and Evolution

View full text Add to dashboard Cite

Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color‐variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average AR was 4.18, HO = 0.59, and HE = 0.66, and FIS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non‐variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.

show abstract

High frequency of an otherwise rare phenotype in a small and isolated tiger population

Cited by 23 publications

References 106 publications

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Melanism in a wild sifaka population: Darker where cold and fragmented

Heterozygosity is low where rare color variants in wild carnivores prevail

Contact Info

Product

Resources

About