Genes

Editorial

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2 pages, 153 KiB

Open AccessEditorial

Conservation Genetics and Genomics

by Michael Russello, George Amato, Robert DeSalle and Michael Knapp

Genes 2020, 11(3), 318; https://doi.org/10.3390/genes11030318 - 17 Mar 2020

Cited by 9 | Viewed by 3516

Abstract

For more than thirty years, methods and theories from evolutionary biology, phylogenetics, population genetics and molecular biology have been used by conservation biologists to better understand threats to endangered species due to anthropogenic changes [...] Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

Research

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17 pages, 2470 KiB

Open AccessArticle

Population Genomics and Structure of the Critically Endangered Mariana Crow (Corvus kubaryi)

by Nandadevi Cortes-Rodriguez, Michael G. Campana, Lainie Berry, Sarah Faegre, Scott R. Derrickson, Renee Robinette Ha, Rebecca B. Dikow, Christian Rutz and Robert C. Fleischer

Genes 2019, 10(3), 187; https://doi.org/10.3390/genes10030187 - 1 Mar 2019

Cited by 11 | Viewed by 5900

Abstract

The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined [...] Read more.

The Mariana Crow, or Åga (Corvus kubaryi), is a critically endangered species (IUCN -International Union for Conservation of Nature), endemic to the islands of Guam and Rota in the Mariana Archipelago. It is locally extinct on Guam, and numbers have declined dramatically on Rota to a historical low of less than 55 breeding pairs throughout the island in 2013. Because of its extirpation on Guam and population decline on Rota, it is of critical importance to assess the genetic variation among individuals to assist ongoing recovery efforts. We conducted a population genomics analysis comparing the Guam and Rota populations and studied the genetic structure of the Rota population. We used blood samples from five birds from Guam and 78 birds from Rota. We identified 145,552 candidate single nucleotide variants (SNVs) from a genome sequence of an individual from Rota and selected a subset of these to develop an oligonucleotide in-solution capture assay. The Guam and Rota populations were genetically differentiated from each other. Crow populations sampled broadly across their range on Rota showed significant genetic structuring – a surprising result given the small size of this island and the good flight capabilities of the species. Knowledge of its genetic structure will help improve management strategies to help with its recovery. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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9 pages, 3036 KiB

Open AccessArticle

Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand

by Zhenhua Dang, Patricia A. McLenachan, Peter J. Lockhart, Nick Waipara, Orhan Er, Christy Reynolds and Dan Blanchon

Genes 2019, 10(2), 106; https://doi.org/10.3390/genes10020106 - 31 Jan 2019

Cited by 5 | Viewed by 4318

Abstract

Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in [...] Read more.

Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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17 pages, 1433 KiB

Open AccessArticle

Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation

by Sofiia Kolchanova, Sergei Kliver, Aleksei Komissarov, Pavel Dobrinin, Gaik Tamazian, Kirill Grigorev, Walter W. Wolfsberger, Audrey J. Majeske, Jafet Velez-Valentin, Ricardo Valentin de la Rosa, Joanne R. Paul-Murphy, David Sanchez-Migallon Guzman, Michael H. Court, Juan L. Rodriguez-Flores, Juan Carlos Martínez-Cruzado and Taras K. Oleksyk

Genes 2019, 10(1), 54; https://doi.org/10.3390/genes10010054 - 16 Jan 2019

Cited by 8 | Viewed by 12803

Abstract

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds [...] Read more.

Islands have been used as model systems for studies of speciation and extinction since Darwin published his observations about finches found on the Galapagos. Amazon parrots inhabiting the Greater Antillean Islands represent a fascinating model of species diversification. Unfortunately, many of these birds are threatened as a result of human activity and some, like the Puerto Rican parrot, are now critically endangered. In this study we used a combination of de novo and reference-assisted assembly methods, integrating it with information obtained from related genomes to perform genome reconstruction of three amazon species. First, we used whole genome sequencing data to generate a new de novo genome assembly for the Puerto Rican parrot (Amazona vittata). We then improved the obtained assembly using transcriptome data from Amazona ventralis and used the resulting sequences as a reference to assemble the genomes Hispaniolan (A. ventralis) and Cuban (Amazona leucocephala) parrots. Finally, we, annotated genes and repetitive elements, estimated genome sizes and current levels of heterozygosity, built models of demographic history and provided interpretation of our findings in the context of parrot evolution in the Caribbean. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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15 pages, 1737 KiB

Open AccessArticle

Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

by Dehuai Luo, Yanping Li, Qingyuan Zhao, Lianpeng Zhao, Arne Ludwig and Zuogang Peng

Genes 2019, 10(1), 38; https://doi.org/10.3390/genes10010038 - 10 Jan 2019

Cited by 24 | Viewed by 7341

Abstract

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This [...] Read more.

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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19 pages, 1986 KiB

Open AccessArticle

Reference Genomes from Distantly Related Species Can Be Used for Discovery of Single Nucleotide Polymorphisms to Inform Conservation Management

by Stephanie J. Galla, Natalie J. Forsdick, Liz Brown, Marc P. Hoeppner, Michael Knapp, Richard F. Maloney, Roger Moraga, Anna W. Santure and Tammy E. Steeves

Genes 2019, 10(1), 9; https://doi.org/10.3390/genes10010009 - 22 Dec 2018

Cited by 48 | Viewed by 10118

Abstract

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely [...] Read more.

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-quality reference genomes for single nucleotide polymorphism (SNP) discovery using the critically endangered kakī/black stilt (Himantopus novaezelandiae) and four Charadriiform reference genomes as proof of concept. We compare diversity estimates (i.e., nucleotide diversity, individual heterozygosity, and relatedness) based on kakī SNPs discovered from genotyping-by-sequencing and whole genome resequencing reads mapped to conordinal (killdeer, Charadrius vociferus), confamilial (pied avocet, Recurvirostra avosetta), congeneric (pied stilt, Himantopus himantopus) and conspecific reference genomes. Results indicate that diversity estimates calculated from SNPs discovered using closely related reference genomes correlate significantly with estimates calculated from SNPs discovered using a conspecific genome. Congeneric and confamilial references provide higher correlations and more similar measures of nucleotide diversity, individual heterozygosity, and relatedness. While conspecific genomes may be necessary to address other questions in conservation, SNP discovery using high-quality reference genomes of closely related species is a cost-effective approach for estimating diversity measures in threatened species. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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12 pages, 2389 KiB

Open AccessArticle

Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast

by Elizabeth Heppenheimer, Kristin E. Brzeski, Ron Wooten, William Waddell, Linda Y. Rutledge, Michael J. Chamberlain, Daniel R. Stahler, Joseph W. Hinton and Bridgett M. VonHoldt

Genes 2018, 9(12), 618; https://doi.org/10.3390/genes9120618 - 10 Dec 2018

Cited by 23 | Viewed by 22370

Abstract

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red [...] Read more.

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7000 single nucleotide polymorphisms (SNPs) in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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18 pages, 1508 KiB

Open AccessArticle

Population Genomic Analysis of North American Eastern Wolves (Canis lycaon) Supports Their Conservation Priority Status

by Elizabeth Heppenheimer, Ryan J. Harrigan, Linda Y. Rutledge, Klaus-Peter Koepfli, Alexandra L. DeCandia, Kristin E. Brzeski, John F. Benson, Tyler Wheeldon, Brent R. Patterson, Roland Kays, Paul A. Hohenlohe and Bridgett M. Von Holdt

Genes 2018, 9(12), 606; https://doi.org/10.3390/genes9120606 - 4 Dec 2018

Cited by 27 | Viewed by 11759

Abstract

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover [...] Read more.

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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15 pages, 1526 KiB

Open AccessArticle

What Is the Giant Wall Gecko Having for Dinner? Conservation Genetics for Guiding Reserve Management in Cabo Verde

by Catarina Jesus Pinho, Bárbara Santos, Vanessa A. Mata, Mariana Seguro, Maria M. Romeiras, Ricardo Jorge Lopes and Raquel Vasconcelos

Genes 2018, 9(12), 599; https://doi.org/10.3390/genes9120599 - 3 Dec 2018

Cited by 24 | Viewed by 7193

Abstract

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall [...] Read more.

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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19 pages, 1945 KiB

Open AccessArticle

Population Connectivity and Traces of Mitochondrial Introgression in New Zealand Black-Billed Gulls (Larus bulleri)

by Claudia Mischler, Andrew Veale, Tracey Van Stijn, Rudiger Brauning, John C. McEwan, Richard Maloney and Bruce C. Robertson

Genes 2018, 9(11), 544; https://doi.org/10.3390/genes9110544 - 9 Nov 2018

Cited by 7 | Viewed by 5126

Abstract

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although [...] Read more.

Black-billed gulls (Larus bulleri) are endemic to New Zealand and are suspected to be undergoing substantial population declines. They primarily breed on open gravel beds in braided rivers of the South Island—a habitat that is diminishing and becoming increasingly modified. Although management of this species is increasing, little has been published on their movements and demographics. In this study, both mitochondrial DNA (mtDNA) control region domain I and nuclear single nucleotide polymorphisms (SNPs) were examined to help understand the connectivity and population structure of black-billed gulls across the country and to help inform management decisions. Mitochondrial DNA showed no population structure, with high haplotype and low nucleotide diversity, and analyses highlighted mitochondrial introgression with the closely related red-billed gulls (Larus novaehollandiae scopulinus). Nuclear DNA analyses, however, identified two groups, with Rotorua birds in the North Island being distinct from the rest of New Zealand, and isolation-by-distance evident across the South Island populations. Gene flow primarily occurs between nearby colonies with a stepwise movement across the landscape. The importance from a genetic perspective of the more isolated North Island birds (1.6% of total population) needs to be further evaluated. From our results, we infer that the South Island black-billed gull management should focus on maintaining several populations within each region rather than focusing on single specific colonies or river catchments. Future study is needed to investigate the genetic structure of populations at the northern limit of the species’ range, and identify the mechanisms behind, and extent of, the hybridisation between red-billed and black-billed gulls. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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18 pages, 1267 KiB

Open AccessFeature PaperArticle

A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaiiʻs Last Remaining Crow Species

by Jolene T. Sutton, Martin Helmkampf, Cynthia C. Steiner, M. Renee Bellinger, Jonas Korlach, Richard Hall, Primo Baybayan, Jill Muehling, Jenny Gu, Sarah Kingan, Bryce M. Masuda and Oliver A. Ryder

Genes 2018, 9(8), 393; https://doi.org/10.3390/genes9080393 - 1 Aug 2018

Cited by 18 | Viewed by 9330

Abstract

Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the [...] Read more.

Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world’s most endangered bird species, the ʻAlalā (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawaiʻi, the ʻAlalā survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the ʻAlalā genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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14 pages, 2700 KiB

Open AccessArticle

Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity

by Nicolas Dussex, Johanna Von Seth, Bruce C. Robertson and Love Dalén

Genes 2018, 9(4), 220; https://doi.org/10.3390/genes9040220 - 19 Apr 2018

Cited by 27 | Viewed by 8387

Abstract

Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute [...] Read more.

Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kākāpō (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kākāpō contributed to a rapid loss of genetic diversity following severe population declines. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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9 pages, 591 KiB

Open AccessArticle

Genome Sequence of the Freshwater Yangtze Finless Porpoise

by Yuan Yuan, Peijun Zhang, Kun Wang, Mingzhong Liu, Jing Li, Jinsong Zheng, Ding Wang, Wenjie Xu, Mingli Lin, Lijun Dong, Chenglong Zhu, Qiang Qiu and Songhai Li

Genes 2018, 9(4), 213; https://doi.org/10.3390/genes9040213 - 16 Apr 2018

Cited by 15 | Viewed by 7033

Abstract

The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina [...] Read more.

The Yangtze finless porpoise (Neophocaena asiaeorientalis ssp. asiaeorientalis) is a subspecies of the narrow-ridged finless porpoise (N. asiaeorientalis). In total, 714.28 gigabases (Gb) of raw reads were generated by whole-genome sequencing of the Yangtze finless porpoise, using an Illumina HiSeq 2000 platform. After filtering the low-quality and duplicated reads, we assembled a draft genome of 2.22 Gb, with contig N50 and scaffold N50 values of 46.69 kilobases (kb) and 1.71 megabases (Mb), respectively. We identified 887.63 Mb of repetitive sequences and predicted 18,479 protein-coding genes in the assembled genome. The phylogenetic tree showed a relationship between the Yangtze finless porpoise and the Yangtze River dolphin, which diverged approximately 20.84 million years ago. In comparisons with the genomes of 10 other mammals, we detected 44 species-specific gene families, 164 expanded gene families, and 313 positively selected genes in the Yangtze finless porpoise genome. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information under BioProject accession number PRJNA433603. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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Review

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33 pages, 1447 KiB

Open AccessReview

De-Extinction

by Ben Jacob Novak

Genes 2018, 9(11), 548; https://doi.org/10.3390/genes9110548 - 13 Nov 2018

Cited by 40 | Viewed by 52124

Abstract

De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In [...] Read more.

De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In 2016, a special committee of the International Union for the Conservation of Nature (IUCN) published a set of guidelines for de-extinction practice, establishing the first detailed description of de-extinction; yet incoherencies in published literature persist. There are even several problems with the IUCN definition. Here I present a comprehensive definition of de-extinction practice and rationale that expounds and reconciles the biological and ecological inconsistencies in the IUCN definition. This new definition brings together the practices of reintroduction and ecological replacement with de-extinction efforts that employ breeding strategies to recover unique extinct phenotypes into a single “de-extinction” discipline. An accurate understanding of de-extinction and biotechnology segregates the restoration of certain species into a new classification of endangerment, removing them from the purview of de-extinction and into the arena of species’ recovery. I term these species as “evolutionarily torpid species”; a term to apply to species falsely considered extinct, which in fact persist in the form of cryopreserved tissues and cultured cells. For the first time in published literature, all currently active de-extinction breeding programs are reviewed and their progress presented. Lastly, I review and scrutinize various topics pertaining to de-extinction in light of the growing body of peer-reviewed literature published since de-extinction breeding programs gained public attention in 2013. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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20 pages, 928 KiB

Open AccessPerspective

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

by Clare I.M. Adams, Michael Knapp, Neil J. Gemmell, Gert-Jan Jeunen, Michael Bunce, Miles D. Lamare and Helen R. Taylor

Genes 2019, 10(3), 192; https://doi.org/10.3390/genes10030192 - 1 Mar 2019

Cited by 135 | Viewed by 20524

Abstract

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to [...] Read more.

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit. Full article

(This article belongs to the Special Issue Conservation Genetics and Genomics)

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