The origin of domestic dogs is poorly understood 1–15, with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum 6, 9, 10, 14, 16 conflicting with genetic ...estimates of a more recent divergence between dogs and worldwide wolf populations 13, 15, 17–19. Here, we present a draft genome sequence from a 35,000-year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.
Display omitted
•An ancient Siberian wolf yields a first draft genome sequence of a Pleistocene carnivore•The 35,000-year-old wolf genome allowed recalibration of the lupine mutation rate•Dog ancestors diverged from modern wolf ancestors at least 27,000 years ago•Ancient Siberian wolves contributed to the ancestry of high-latitude dog breeds
Skoglund et al. recovered the genome sequence of a 35,000-year-old Siberian wolf. Calibration of the molecular clock suggests that the ancestors of modern dogs formed a distinct lineage prior to the peak of the last ice age. Siberian huskies and other northern dog breeds trace a part of their ancestry to the ancient Siberian wolf population.
Genomic approaches have the potential to play a pivotal role in conservation, both to detect threats to species and populations and to restore biodiversity through actions. We here separate these ...approaches into two subdisciplines, vulnerability and restoration genomics, and discuss current applications, outstanding questions, and future potential.
Genomic approaches have the potential to play a pivotal role in conservation, both to detect threats to species and populations and to restore biodiversity through actions. van der Valk and Dalén here separate these approaches into two subdisciplines, vulnerability and restoration genomics, and discuss current applications, outstanding questions, and future potential.
Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected ...to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome‐wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1–2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune‐related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.
The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results ...in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.
Climate change in the past has led to significant changes in species' distributions. However, how individual species respond to climate change depends largely on their adaptations and environmental ...tolerances. In the Quaternary, temperate-adapted taxa are in general confined to refugia during glacials while cold-adapted taxa are in refugia during interglacials. In the Northern Hemisphere, evidence appears to be mounting that in addition to traditional southern refugia for temperate species, cryptic refugia existed in the North during glacials. Equivalent cryptic southern refugia, to the south of the more conventional high-latitude polar refugia, exist in montane areas during periods of warm climate, such as the current interglacial. There is also a continental/oceanic longitudinal gradient, which should be included in a more complete consideration of the interaction between species ranges and climates. Overall, it seems clear that there is large variation in both the size of refugia and the duration during which species are confined to them. This has implications for the role of refugia in the evolution of species and their genetic diversity.
Eradication genomics-lessons for parasite control Cotton, James A; Berriman, Matthew; Dalén, Love ...
Science (American Association for the Advancement of Science),
07/2018, Volume:
361, Issue:
6398
Journal Article
Peer reviewed
Genomic surveillance could help achieve targets for the elimination of tropical diseases
Large-scale programs are seeking to control or eliminate infectious diseases with the greatest impact on ...global health. Many of these efforts target the neglected tropical diseases (NTDs) that disproportionately affect the lives of the poor. Often the aim is to eradicate the causative pathogens. The idea—inspired by the success of smallpox eradication in the 1960s and 1970s—is that a large-scale, but time-limited, effort could eliminate a disease for all successive generations, resulting in an enormous payoff both financially and in improved health. Here, we discuss the value of genomic approaches to support disease eradication efforts, particularly by analogy with how conservation genomics is supporting efforts to prevent extinctions.
Many endangered species have experienced severe population declines within the last centuries 1, 2. However, despite concerns about negative fitness effects resulting from increased genetic drift and ...inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines 3–7. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer’s and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer’s gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.
•Gorilla genomes from museum samples enabled measurement of temporal genomic erosion•Genetic diversity declined and inbreeding increased in Grauer’s gorillas•The frequency of deleterious mutations increased significantly in Grauer’s gorillas•No temporal changes in genomic parameters were observed in the mountain gorilla
Van der Valk et al. investigate the genomic consequences of recent population decline using 100-year-old museum specimens. They find a reduction in genetic diversity, increase in inbreeding, and increase in deleterious mutations in the critically endangered Grauer’s gorillas.
Many species have undergone dramatic population size declines over the past centuries. Although stochastic genetic processes during and after such declines are thought to elevate the risk of ...extinction, comparative analyses of genomic data from several endangered species suggest little concordance between genome-wide diversity and current population sizes. This is likely because species-specific life-history traits and ancient bottlenecks overshadow the genetic effect of recent demographic declines. Therefore, we advocate that temporal sampling of genomic data provides a more accurate approach to quantify genetic threats in endangered species. Specifically, genomic data from predecline museum specimens will provide valuable baseline data that enable accurate estimation of recent decreases in genome-wide diversity, increases in inbreeding levels, and accumulation of deleterious genetic variation.
The small population size of many endangered species makes them vulnerable to genetic threats, such as inbreeding depression, loss of genetic variation, and accumulation of deleterious mutations
Present-day genome-wide diversity is a poor predictor of population size and conservation status in endangered species, making interspecific comparisons of genomic data inadequate indicators of extinction risk.
Historical specimens in museum collections include samples that pre-date the demographic declines that have occurred in recent centuries and, thus, can provide baseline levels of diversity, inbreeding, and genetic load.
Temporal genomic indices based on comparisons of historical and present-day samples are powerful tools to estimate genomic erosion, and could be integrated with other IUCN Red List criteria to assess threat levels in endangered species.
Population bottlenecks can have dramatic consequences for the health and long‐term survival of a species. Understanding of historic population size and standing genetic variation prior to a ...contraction allows estimating the impact of a bottleneck on the species' genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10–20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high‐quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the prebottleneck diversity with several highly differentiated mitochondrial lineages having coexisted historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1–2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long‐term population fluctuations from the emergence of a species through its near extinction up to the recent past.
PDF
