Shyam Gopalakrishnan's research while affiliated with Globe Institute of Technology and other places

Publications (77)

Preprint
The contrast between the tiger's (Panthera tigris) 2-3 My age and extant tigers' coalescence approximately 110,000 years ago suggests an ancient demographic bottleneck. Here we collected over 60 extinct specimens across mainland Asia and generated whole genome sequences from a 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8x coverage), 1...
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Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbar...
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The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day do...
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Retracing pathways of historical species introductions is fundamental to understanding the factors involved in the successful colonization and spread, centuries after a species’ establishment in an introduced range. Numerous plants have been introduced to regions outside their native ranges both intentionally and accidentally by European voyagers a...
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Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched f...
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Snake venoms represent a danger to human health, but also a gold mine of bioactive proteins that can be harnessed for drug discovery purposes. The evolution of snakes and their venom has been studied for decades, particularly via traditional morphological and basic genetic methods alongside venom proteomics. However, while the field of genomics has...
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Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.¹,² Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed...
Preprint
While invasive species are a key driver of the global biodiversity crisis, the drivers of invasiveness remain debated. To investigate the genomic basis of invasiveness in plants, we use the invasive weed Ambrosia artemisiifolia , introduced to Europe in the late 19 th century, resequencing 655 ragweed genomes, including 308 herbarium specimens coll...
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Background: Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional efects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions i...
Preprint
The Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7 . Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9 , until human persecutions led them to extinction 1–7 . There...
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We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.
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The Seychelles Magpie-Robin Copsychus sechellarum is an IUCN Red-List Endangered species endemic to the Seychelles, whose population was reduced to eight individuals on a single island in the 1960s. Translocations from the remaining population to four additional islands have been an integral factor in their recovery, but the potential genetic conse...
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The Sardinian dhole (Cynotherium sardous) was an iconic and unique canid species that was endemic to Sardinia and Corsica until it became extinct at the end of the Late Pleistocene. Given its peculiar dental morphology, small body size, and high level of endemism, several extant canids have been proposed as possible relatives of the Sardinian dhole...
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Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Nor...
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Background Animal protein production is increasingly looking towards microbiome associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria based pro- and synbiotic feed additives on microbiome associated functions i...
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Full-text available
Genomes of high latitude killer whales harbour signatures of post-glacial founding and expansion. Here, we investigate whether reduced efficacy of selection increased mutation load in founder populations, or whether recessive deleterious mutations exposed to selection in homozygous genotypes were purged. Comparing the accumulation of synonymous and...
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Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identif...
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Significance Although today the rainforest is continuous in Central Africa, the scarce fossil record suggests that arid conditions during the ice ages might have reduced tree density. However, the vast majority of the fossil pollen cores preserved in Tropical Africa are too young to inform about this period. Investigating whether the climate change...
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Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros...
Preprint
Full-text available
Background Animal protein production is increasingly looking towards microbiome associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria based pro- and synbiotic feed additives on microbiome associated functions i...
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Full-text available
Several Arctic marine mammal species are predicted to be negatively impacted by rapid sea ice loss associated with ongoing ocean warming. However, consequences for Arctic whales remain uncertain. To investigate how Arctic whales responded to past climatic fluctuations, we analyzed 206 mitochondrial genomes from beluga whales (Delphinapterus leucas)...
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Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America¹, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our res...
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1. Despite widespread recognition of its great promise to aid decision‐making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise during PCR amplification, sequencing, and library generation. We present a co‐designed wet‐lab and bioinformatic workflow for metabarcoding bulk sa...
Preprint
Full-text available
The Sardinian dhole (Cynotherium sardous) was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhol...
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Full-text available
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predati...
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The fungal pathogen Neonectria neomacrospora is of increasing concern in Europe where, within the last decade, it has caused substantial damage to forest stands and ornamental trees of the genus Abies (Mill.). Using whole-genome sequencing of a comprehensive collection of isolates, we show the extent of three major clades within N. neomacrospora ,...
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The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better...
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The dingo is Australia’s iconic top-order predator and arrived on the continent between 5,000-8,000 years ago. To provide an unbiased insight into its evolutionary affiliations and biological interactions, we coupled long-read DNA sequencing with a multiplatform scaffolding approach to produce an ab initio genome assembly of the desert dingo (85X c...
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Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome...
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Biodiversity monitoring projects using environmental DNA techniques are becoming increasingly widespread. However, these techniques depend heavily on the quality and richness of the available DNA reference database against which the DNA sequences are queried. To create a comprehensive DNA sequence database for future DNA‐based biodiversity assessme...
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There is growing interest in the application of sustainable agricultural methods to minimize the environmental impact of farming and thus aiding quantification of the actual benefit that such approaches may confer. We applied DNA metabarcoding with the aim of exploring how the diversity of fungi and arthropods were affected by different agricultura...
Preprint
Full-text available
1. Despite widespread recognition of its great promise to aid decision-making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise during PCR amplification, sequencing, and library generation. We present a co-designed wet-lab and bioinformatic workflow for metabarcoding bulk sa...
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Full-text available
From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bi-directional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions, by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requi...
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Sled dog arctic adaptations go far back Dogs have been used for sledding in the Arctic as far back as ∼9500 years ago. However, the relationships among the earliest sled dogs, other dog populations, and wolves are unknown. Sinding et al. sequenced an ancient sled dog, 10 modern sled dogs, and an ancient wolf and analyzed their genetic relationships...
Preprint
https://authorea.com/users/337132/articles/462777-travel-tales-of-a-worldwide-weed-genomic-signatures-reveal-colonial-trade-routes-and-prior-adaptation-are-key-to-the-success-of-plantago-major
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Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species D. praecox and C. mauritanicum appear in the fossil record ∼5.2 million years ago (Ma), by 4 Ma both were still mixed feeders, a...
Preprint
Full-text available
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR)...
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Full-text available
Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions ( Panthera leo spelaea ), 12 historic lions ( Panthera leo leo/Panthera leo melanochaita ) that lived between the...
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The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine ma...
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The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and...
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Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these...
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The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack...
Preprint
The rainforests of Tropical Africa have fluctuated over time. Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that more arid conditions might have significantly reduced the density of trees during the Ice Ages. Our aim was to investigate whet...
Preprint
From 1500 to 1900, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britain's abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the South Atlantic served as...
Preprint
Full-text available
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack...
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In 1990, a skull from a morphologically unusual Monodontid was found in West Greenland and collected for the Natural History Museum of Denmark, University of Copenhagen. From its intermediate morphology, the skull was hypothesized to be a beluga/narwhal hybrid. If confirmed, the specimen would, to our knowledge, represent the sole evidence of hybri...
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The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300–2700 BCE) exis...
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The application of DNA sequencing‐based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological qu...
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We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous "chewing gum" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,858-5,661 cal. BP (GrM-13305; 5,007+/-11). We sequenced the genome to an average depth-of-coverage of 2.3x and find that the individual who chewed...
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North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the exta...
Data
Table showing the catalog number, species information, average genomic sequencing coverage, identified genetic clusters, location and date of sample collection, and the publication associated with the publicly available data.
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The evolutionary history of the wolf-like canids of the genus Canis has been heavily debated, especially regarding the number of distinct species and their relationships at the population and species level [1–6]. We assembled a dataset of 48 resequenced genomes spanning all members of the genus Canis except the black-backed and side-striped jackals...
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Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from Nor...
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In recent years, the availability of reduced representation library (RRL) methods has catalyzed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thous...
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Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source popu...
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Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co‐amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing pop...
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The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered fr...
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The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary n...