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How to clone a mammoth : the science of de-extinction
\"Could extinct species like mammoths and passenger pigeons be brought back to life? The science says yes. In [this book], Beth Shapiro, evolutionary biologist and pioneer in 'ancient DNA' research, walks readers through the astonishing and controversial process of de-extinction. From deciding which species should be restored, to sequencing their genomes, to anticipating how revived populations might be overseen in the wild, Shapiro vividly explores the extraordinary cutting-edge science that is being used--today--to resurrect the past\"--Amazon.com.
Book
Ancient DNA : the making of a celebrity science
The untold story of the rise of the new scientific field of ancient DNA research, and how Jurassic Park and popular media influenced its development Ancient DNA research—the recovery of genetic material from long-dead organisms—is a discipline that developed from science fiction into a reality between the 1980s and today. Drawing on scientific, historical, and archival material, as well as original interviews with more than fifty researchers worldwide, Elizabeth Jones explores the field's formation and explains its relationship with the media by examining its close connection to de-extinction, the science and technology of resurrecting extinct species. She reveals how the search for DNA from fossils flourished under the influence of intense press and public interest, particularly as this new line of research coincided with the book and movie Jurassic Park. Ancient DNA is the first account to trace the historical and sociological interplay between science and celebrity in the rise of this new research field. In the process, Jones argues that ancient DNA research is more than a public-facing science: it is a celebrity science.
eBook
De-extinction : the science of bringing lost species back to life
In the twenty-first century, because of climate change and other human activities, many animal species have become extinct, and many others are at risk of extinction. Once they are gone, we cannot bring them back or can we?
Book
Dense sampling of bird diversity increases power of comparative genomics
Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confdently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specifc variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will ofer new perspectives on evolutionary processes in cross-species comparative analyses and assist in eforts to conserve species.
Journal Article
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa
1
. However, the irreversible post-mortem degradation
2
of ancient DNA has so far limited its recovery—outside permafrost areas—to specimens that are not older than approximately 0.5 million years (Myr)
3
. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I
4
, and suggested the presence of protein residues in fossils of the Cretaceous period
5
—although with limited phylogenetic use
6
. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch
7
–
9
, using the proteome of dental enamel from a
Stephanorhinus
tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)
10
. Molecular phylogenetic analyses place this
Stephanorhinus
as a sister group to the clade formed by the woolly rhinoceros (
Coelodonta antiquitatis
) and Merck’s rhinoceros (
Stephanorhinus kirchbergensis
). We show that
Coelodonta
evolved from an early
Stephanorhinus
lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus
Stephanorhinus
is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates
11
, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
Palaeoproteomic analysis of dental enamel from an Early Pleistocene
Stephanorhinus
resolves the phylogeny of Eurasian Rhinocerotidae, by enabling the reconstruction of molecular evolution beyond the limits of ancient DNA preservation.
Journal Article
Grey wolf genomic history reveals a dual ancestry of dogs
Abstract 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 dog lineage ( Canis familiaris ) lived 1–8 . Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.
Journal Article
Conservation genetics as a management tool
About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201–204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
Journal Article
The inflated significance of neutral genetic diversity in conservation genetics
The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.
Journal Article
An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern
Background
Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted.
Results
Here we used microsatellite and SNP data generated from Gunnison sage-grouse (
Centrocercus minimus
) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (
H
O
,
H
E
,
F
IS
,
A
R
) and differentiation (
F
ST
,
G
ST
,
D
Jost
). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for
H
E
,
F
IS
,
A
R
, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data.
Conclusion
We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.
Journal Article
Genetic Restoration of the Florida Panther
The rediscovery of remnant Florida panthers (Puma concolor coryi) in southern Florida swamplands prompted a program to protect and stabilize the population. In 1995, conservation managers translocated eight female pumas (P. c. stanleyana) from Texas to increase depleted genetic diversity, improve population numbers, and reverse indications of inbreeding depression. We have assessed the demographic, population-genetic, and biomedical consequences of this restoration experiment and show that panther numbers increased threefold, genetic heterozygosity doubled, survival and fitness measures improved, and inbreeding correlates declined significantly. Although these results are encouraging, continued habitat loss, persistent inbreeding, infectious agents, and possible habitat saturation pose new dilemmas. This intensive management program illustrates the challenges of maintaining populations of large predators worldwide.
Journal Article