@article {160477, title = {Conservation: Sequencing and saving the Saola?}, journal = {Curr Biol}, volume = {35}, year = {2025}, month = {2025 Sep 22}, pages = {R878-R880}, abstract = {

The Critically Endangered Saola is a unique and cryptic Asian member of the cattle family. A new study analyses its genome, identifying evolutionary affinities, genetic variation and a possible path for conservation through captive breeding. But saving the Saola from extinction will require much more.

}, keywords = {Animals, Cattle, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genome}, issn = {1879-0445}, doi = {10.1016/j.cub.2025.07.086}, author = {Ramakrishnan, Uma} } @article {161128, title = {Exceedingly low genetic diversity in snow leopards due to persistently small population size.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Oct 14}, pages = {e2502584122}, abstract = {

Snow leopards () serve as an umbrella species whose conservation benefits their high-elevation Asian habitat. Their numbers are believed to be in decline due to numerous anthropogenic threats; however, their conservation is hindered by numerous knowledge gaps. In particular, the dearth of genetic data, unique among all big cat species, hinders a full understanding of their population structure, historical population size, and current levels of genetic diversity. Here, we use whole-genome sequencing data for 41 snow leopards (37 newly sequenced) to offer insights into these unresolved aspects of snow leopard biology. Among our samples, we find evidence of a primary genetic divide between the northern and southern part of the range around the Dzungarian Basin-as previously identified using landscape models and fecal microsatellite markers-and a secondary divide south of Kyrgyzstan around the Taklamakan Desert. Most noteworthy, we find that snow leopards have the lowest genetic diversity of any big cat species, likely due to a persistently small population size throughout their evolutionary history rather than recent inbreeding. We also find that snow leopards have significantly less highly deleterious homozygous load compared to numerous species, suggesting effective purging during their evolutionary history at small population sizes. Without a large population size or ample standing genetic variation to help buffer them from any forthcoming anthropogenic challenges, snow leopard persistence may be more tenuous than currently appreciated.

}, keywords = {Animals, Conservation of Natural Resources, Ecosystem, Felidae, Genetic Variation, Microsatellite Repeats, Panthera, Population Density}, issn = {1091-6490}, doi = {10.1073/pnas.2502584122}, author = {Solari, Katherine A and Morgan, Simon and Poyarkov, Andrey D and Weckworth, Byron and Samelius, Gustaf and Sharma, Koustubh and Ostrowski, Stephane and Ramakrishnan, Uma and Kubanychbekov, Zairbek and Kachel, Shannon and Johansson, {\"O}rjan and Lkhagvajav, Purevjav and Hemmingmoore, Heather and Alexandrov, Dmitry Y and Bayaraa, Munkhtsog and Grachev, Alexey and Korablev, Miroslav P and Hernandez-Blanco, Jose A and Munkhtsog, Bariushaa and Rosenbaum, Barry and Rozhnov, Viatcheslav V and Madad Rajabi, Ali and Noori, Hafizullah and Suryawanshi, Kulbhushansingh R and Armstrong, Ellie E and Petrov, Dmitri A} } @article {152147, title = {Genetic load.}, journal = {Curr Biol}, volume = {34}, year = {2024}, month = {2024 Dec 16}, pages = {R1216-R1220}, abstract = {

We tend to assume that all genetic variation is good: the higher the variation in a population, the more diverse its gene pool, the more secure its future. Unfortunately, the relationship between genetic variation and survival of a population or a species is more complex. Some genetic variants are advantageous, increasing the survival and reproductive output of an individual, while others may be neutral now (but potentially advantageous in the future), and finally, some genetic variants are disadvantageous. All organisms carry a burden of disadvantageous genetic variants, called {\textquoteright}genetic load{\textquoteright}. This genetic load can lead to diseases or morphological abnormalities and reduce survival or reproduction. Although genetic load has been studied for decades, recent technological advances now enable a more detailed understanding of its characteristics and potential consequences in wild species.

}, keywords = {Animals, Genetic Load, Genetic Variation, Reproduction}, issn = {1879-0445}, doi = {10.1016/j.cub.2024.11.004}, author = {Grossen, Christine and Ramakrishnan, Uma} } @article {152146, title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).}, journal = {Mol Biol Rep}, volume = {52}, year = {2024}, month = {2024 Dec 17}, pages = {55}, abstract = {

BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.

METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97\% and 21.50\%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu{\textquoteright}s Fs test and Tajima{\textquoteright}s D test. Morphometric analysis based on seven characters is also carried out.

CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.

}, keywords = {Animals, Australia, Bayes Theorem, DNA Barcoding, Taxonomic, DNA, Mitochondrial, Gene Flow, Genetic Variation, Haplotypes, India, Insect Vectors, Mitochondria, Phylogeny, Thysanoptera}, issn = {1573-4978}, doi = {10.1007/s11033-024-10108-4}, author = {Singha, Devkant and Patidar, Abhishek and Pal, Shash and Tyagi, Kaomud and Kumar, Vikas} } @article {149377, title = {Unraveling the genomic diversity and admixture history of captive tigers in the United States.}, journal = {Proc Natl Acad Sci U S A}, volume = {121}, year = {2024}, month = {2024 Sep 24}, pages = {e2402924121}, abstract = {

Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated genomic diversity housed in captive populations. For tigers (), captive individuals vastly outnumber those in the wild, but their diversity remains largely unexplored. Privately owned captive tiger populations have remained an enigma in the conservation community, with some believing that these individuals are severely inbred, while others believe they may be a source of now-extinct diversity. Here, we present a large-scale genetic study of the private (non-zoo) captive tiger population in the United States, also known as "Generic" tigers. We find that the Generic tiger population has an admixture fingerprint comprising all six extant wild tiger subspecies. Of the 138 Generic individuals sequenced for the purpose of this study, no individual had ancestry from only one subspecies. We show that the Generic tiger population has a comparable amount of genetic diversity relative to most wild subspecies, few private variants, and fewer deleterious mutations. We observe inbreeding coefficients similar to wild populations, although there are some individuals within both the Generic and wild populations that are substantially inbred. Additionally, we develop a reference panel for tigers that can be used with imputation to accurately distinguish individuals and assign ancestry with ultralow coverage (0.25{\texttimes}) data. By providing a cost-effective alternative to whole-genome sequencing (WGS), the reference panel provides a resource to assist in tiger conservation efforts for both ex- and in situ populations.

}, keywords = {Animals, Animals, Zoo, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genome, Genomics, Phylogeny, Tigers, United States}, issn = {1091-6490}, doi = {10.1073/pnas.2402924121}, author = {Armstrong, Ellie E and Mooney, Jazlyn A and Solari, Katherine A and Kim, Bernard Y and Barsh, Gregory S and Grant, Victoria B and Greenbaum, Gili and Kaelin, Christopher B and Panchenko, Katya and Pickrell, Joseph K and Rosenberg, Noah and Ryder, Oliver A and Yokoyama, Tsuya and Ramakrishnan, Uma and Petrov, Dmitri A and Hadly, Elizabeth A} } @article {109678, title = {How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India.}, journal = {Philos Trans R Soc Lond B Biol Sci}, volume = {377}, year = {2022}, month = {2022 Jun 06}, pages = {20200418}, abstract = {

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60-70\% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue {\textquoteright}Celebrating 50 years since Lewontin{\textquoteright}s apportionment of human diversity{\textquoteright}.

}, keywords = {Animals, Conservation of Natural Resources, Endangered Species, Genetic Variation, Genetics, Population, India, Prospective Studies, Tigers}, issn = {1471-2970}, doi = {10.1098/rstb.2020.0418}, author = {Aylward, Megan and Sagar, Vinay and Natesh, Meghana and Ramakrishnan, Uma} } @article {25260, title = {Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes.}, journal = {J Hered}, volume = {108}, year = {2017}, month = {2017 06 01}, pages = {349-360}, abstract = {

The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species{\textquoteright} distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).

}, keywords = {Animals, Asia, Southeastern, Biological Evolution, Cytochromes b, DNA, Mitochondrial, Felidae, Genetic Variation, Genetics, Population, Genome, Mitochondrial, Haplotypes, Phylogeography, Sequence Analysis, DNA}, issn = {1465-7333}, doi = {10.1093/jhered/esx017}, author = {Patel, Riddhi P and Wutke, Saskia and Lenz, Dorina and Mukherjee, Shomita and Ramakrishnan, Uma and Veron, G{\'e}raldine and Fickel, J{\"o}rns and Wilting, Andreas and F{\"o}rster, Daniel W} } @article {910, title = {Commensalism facilitates gene flow in mountains: a comparison between two Rattus species.}, journal = {Heredity (Edinb)}, volume = {115}, year = {2015}, month = {2015 Sep}, pages = {253-61}, abstract = {

Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20-640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.

}, keywords = {Animal Distribution, Animals, Cluster Analysis, DNA, Mitochondrial, Ecosystem, Gene Flow, Genetic Variation, Genetics, Population, Geography, India, Microsatellite Repeats, Molecular Sequence Data, Rats, Sequence Analysis, DNA, Sympatry}, issn = {1365-2540}, doi = {10.1038/hdy.2015.34}, author = {Varudkar, A and Ramakrishnan, U} } @article {1001, title = {Islands within islands: two montane palaeo-endemic birds impacted by recent anthropogenic fragmentation.}, journal = {Mol Ecol}, volume = {24}, year = {2015}, month = {2015 Jul}, pages = {3572-84}, abstract = {

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky-island-endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (D(PS)) was higher relative to historic differentiation (F(ST)) in anthropogenic fragments, despite the species{\textquoteright} ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high D(PS)/F(ST) values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky-island systems.

}, keywords = {Animal Distribution, Animals, Computer Simulation, Conservation of Natural Resources, Ecosystem, Gene Flow, Genetic Variation, Genetics, Population, Geography, India, Microsatellite Repeats, Passeriformes, Phylogeography, Sequence Analysis, DNA}, issn = {1365-294X}, doi = {10.1111/mec.13266}, author = {Robin, V V and Gupta, Pooja and Thatte, Prachi and Ramakrishnan, Uma} } @article {127108, title = {Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.}, journal = {BMC Genomics}, volume = {15}, year = {2014}, month = {2014 Dec 02}, pages = {1049}, abstract = {

BACKGROUND: Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved.

RESULTS: We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors.

CONCLUSIONS: Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show that rapid evolution and likely loss of expression of miR168 isoforms in tobacco is related to the insertion of MITE-like transposons between miRNA and miRNA* sequences, a possible mechanism showing how miRNAs are lost in few plant lineages even though other close relatives have abundantly expressing miRNAs.

}, keywords = {Argonaute Proteins, Base Sequence, Binding Sites, Disease Resistance, Gene Dosage, Gene Expression Regulation, Plant, Genetic Variation, Genotype, Host-Pathogen Interactions, MicroRNAs, Molecular Sequence Data, Nucleic Acid Conformation, Plants, RNA Precursors, RNA, Messenger, RNA, Plant, Sequence Alignment, Species Specificity}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-1049}, author = {Jagtap, Soham and Shivaprasad, Padubidri V} }