Article
Biochemistry & Molecular Biology
Pengcheng Wang, John T. Burley, Yang Liu, Jiang Chang, De Chen, Qi Lu, Shou-Hsien Li, Xuming Zhou, Scott Edwards, Zhengwang Zhang
Summary: This study analyzed genomic data of three isolated populations of Brown eared pheasant in China, showing low genome-wide diversity and declining effective population size. The comparison with a closely related species revealed detrimental genetic consequences in the Brown eared pheasant genomes, indicating a potential risk of deleterious mutations in wild populations undergoing long-term decline. This comprehensive conservation genomic analysis could help improve conservation planning for threatened species and promote population recovery.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Jack J. Windig, Ina Hulsegge
Summary: Small populations can suffer from high inbreeding rates and associated genetic issues. The Retriever and Pointer software have been developed to assess inbreeding levels and simulate the effects of genetic management measures. These tools can be used for genetic management of various captive populations and have potential applications in education.
Article
Ecology
Eugenio Lopez-Cortegano, Eulalia Moreno, Aurora Garcia-Dorado
Summary: Inbreeding depression threatens small populations but genetic purging can reduce its effects, as shown in this study on captive breeding programs of endangered ungulates. Purging was found to be effective in smaller populations with lower effective population sizes, while larger populations showed slower purging effects. The study suggests a balance between management strategies and purging for long-term benefits.
Article
Biodiversity Conservation
Ningxin Gu, Guoling Chen, Jia Yang, Chenqing Zheng, Xiaohui Gao, Leyang Yuan, Siyu Wang, Zhongyong Fan, Yiwei Lu, Gang Song, Shuihua Chen, Yang Liu
Summary: The Chinese Crested Tern is one of the most endangered seabird species in the world, with lower genetic diversity and signals of post-bottleneck population expansion observed. The study also found introgression between Chinese Crested Tern and Great Crested Tern.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Agriculture, Dairy & Animal Science
Hsiao-Mei Liang, Kuo-Tai Yang, Yu-Tzu Cheng, Shen-Chang Chang, Cheng-Yung Lin, Ming-Yang Tsai, Der-Yuh Lin, Kuo-Hsiang Hung
Summary: This study investigated the genetic diversity and structure of Formosan sambar deer in Taiwan using microsatellites. The results showed low genetic diversity in captive populations, likely due to inbreeding and bottleneck effects. Two distinct genetic groups were found within the captive populations, but no significant population genetic structure was observed among the captive populations in Taiwan. Introducing new genetic material from the wild can help mitigate the impact of inbreeding and enhance genetic diversity.
Article
Biochemistry & Molecular Biology
Christen M. Bossu, Marina Rodriguez, Christine Rayne, Debra A. Chromczak, Philip G. Higgins, Lynne A. Trulio, Kristen C. Ruegg
Summary: The accelerating loss of global biodiversity is worsened by habitat fragmentation and inbreeding in small populations. To address this issue, conservation practitioners often use assisted breeding programs to increase genetic diversity in declining populations. This study demonstrates the value of genomic approaches in enhancing genetic diversity through assisted breeding efforts, focusing on a highly inbred population of Western burrowing owls. The findings highlight the importance of genomic tools in preserving the adaptive potential of small, inbred populations at risk of further decline.
Article
Genetics & Heredity
Christopher A. Cockerill, Malin Hasselgren, Nicolas Dussex, Love Dalen, Johanna von Seth, Anders Angerbjorn, Johan F. Wallen, Arild Landa, Nina E. Eide, Oystein Flagstad, Dorothee Ehrich, Aleksandr Sokolov, Natalya Sokolova, Karin Noren
Summary: Accelerating climate change is causing severe habitat fragmentation in the Arctic, which is threatening the persistence of cold-adapted species. The Scandinavian arctic fox population is highly fragmented and its future survival depends on the northernmost subpopulations to maintain connectivity with the Siberian population. Analysis of arctic fox genomes revealed increasing signs of genome erosion from Siberia to northern Sweden, indicating a stepping-stone model of population connectivity. Inbreeding and the presence of deleterious mutations were more common in the northern Fennoscandian population, while Siberia had more heterozygous mutations. Understanding the genomic consequences of population fragmentation is crucial for conservation efforts in the face of global warming.
Article
Biochemistry & Molecular Biology
Charles Christian Riis Hansen, Aki Jarl Laruson, Jacob Agerbo Rasmussen, Jesus Adrian Chimal Ballesteros, Mikkel-Holger S. Sinding, Gunnar T. T. Hallgrimsson, Menja von Schmalensee, Robert A. A. Stefansson, Kristinn Haukur Skarphedinsson, Aili Lage Labansen, Madis Leivits, Christian Sonne, Rune Dietz, Kim Skelmose, David Boertmann, Igor Eulaers, Michael D. D. Martin, Agnar S. S. Helgason, M. Thomas P. Gilbert, Snaebjorn Palsson
Summary: Divergence in white-tailed eagle populations across Europe and the North-East Atlantic is observed, with the greatest differentiation between island and mainland populations. The island populations have a common ancestry from a mainland population and show signs of inbreeding and little genetic variation. Temporal differences also indicate persistent regional populations despite potential admixture. These patterns may have been shaped by historical events such as glaciation, colonization, human expansion, and persecution.
Article
Multidisciplinary Sciences
Johanna von Seth, Nicolas Dussex, David Diez-del-Molino, Tom van der Valk, Verena E. Kutschera, Marcin Kierczak, Cynthia C. Steiner, Shanlin Liu, M. Thomas P. Gilbert, Mikkel-Holger S. Sinding, Stefan Prost, Katerina Guschanski, Senthilvel K. S. S. Nathan, Selina Brace, Yvonne L. Chan, Christopher W. Wheat, Pontus Skoglund, Oliver A. Ryder, Benoit Goossens, Anders Gotherstrom, Love Dalen
Summary: Highly endangered species like the Sumatran rhinoceros are facing threats from inbreeding which could lead to higher risk of extinction for small, isolated populations. The presence of genetic burden and inbreeding in rhinoceros populations suggest that assisted gene flow among different populations may be needed in the future to reduce the risk of inbreeding depression.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Anastasia Klimova, Jesus Neftali Gutierrez-Rivera, Victor Sanchez-Sotomayor, Joseph Ivan Hoffman
Summary: Endangered species with small population sizes are at risk of genetic erosion, which can have negative effects on their long-term survival. This study investigates the genetic diversity of the captive Peninsular pronghorn population and reveals a decline in heterozygosity and an increase in inbreeding. The research also reconstructs the recent demographic history of the species and highlights the potential for genetically informed management to contribute to conservation outcomes.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Yasmin Foster, Ludovic Dutoit, Stefanie Grosser, Nicolas Dussex, Brodie J. Foster, Ken G. Dodds, Rudiger Brauning, Tracey Van Stijn, Fiona Robertson, John C. McEwan, Jeanne M. E. Jacobs, Bruce C. Robertson
Summary: Events of inbreeding are inevitable in critically endangered species due to reduced population sizes and unique life-history traits, leading to declines in fitness and increased risk of extinction. Investigating levels of inbreeding in a critically endangered flightless parrot, the kakapo, researchers found correlations between measures of inbreeding and significant differences among descendants of the two founding populations.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Shangchen Yang, Tianming Lan, Yi Zhang, Qing Wang, Haimeng Li, Nicolas Dussex, Sunil Kumar Sahu, Minhui Shi, Mengyuan Hu, Yixin Zhu, Jun Cao, Lirong Liu, Jianqing Lin, Qiu-Hong Wan, Huan Liu, Sheng-Guo Fang
Summary: The Chinese alligator, one of the most endangered crocodiles in the world, has seen a continuous decline and low genetic diversity. The study revealed the presence of at least three genetically distinct populations, including an American population which represents genetic diversity no longer found in the wild. The effective population size of all three populations has been decreasing over the past 20,000 years.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Agriculture, Dairy & Animal Science
Daniele Salvi
Summary: Information on endangered species populations in remote areas is limited, hindering conservation efforts. A climbing expedition on La Canna sea stack, led by an alpine guide, provided valuable data on the critically endangered Aeolian wall lizard. The results showed a small population size with limited genetic diversity and the detrimental effects of inbreeding depression.
Article
Biochemistry & Molecular Biology
Malin Hasselgren, Nicolas Dussex, Johanna von Seth, Anders Angerbjorn, Remi-Andre Olsen, Love Dalen, Karin Noren
Summary: The study revealed higher genetic diversity in immigrant descendants compared to natives, but the genetic rescue effect did not persist through subsequent generations. Additionally, foxes with lower levels of inbreeding had a higher likelihood of surviving to one year of age.
Article
Biochemistry & Molecular Biology
Diana A. Robledo-Ruiz, Alexandra Pavlova, Rohan H. Clarke, Michael J. L. Magrath, Bruce Quin, Katherine A. Harrisson, Han Ming Gan, Gabriel W. Low, Paul Sunnucks
Summary: The article presents an analytical framework for evaluating the efficacy of breeding management strategies for wild populations, showing that the proposed strategies did not significantly improve genetic quality or reduce inbreeding in the critically endangered helmeted honeyeater population. The results demonstrate the usefulness of the analytical framework for testing different in situ breeding strategies and making evidence-based management decisions.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Samarth Mathur, J. Andrew DeWoody
Summary: Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity to respond to ecological stressors. Our study on Montezuma quail populations shows that even in small populations, highly deleterious mutations can be effectively purged due to drift, but the genetic load is elevated in small populations due to inbreeding and a higher frequency of slightly deleterious mutations.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Zoology
Anna Bruniche-Olsen, John W. Bickham, Celine A. Godard-Codding, Vladimir A. Brykov, Kenneth F. Kellner, Jorge Urban, J. Andrew DeWoody
Summary: Environmental changes and commercial whaling have significantly reduced whale populations, including gray whales in the North Pacific. However, genetic signals of recent population declines have not been detected despite sustained habitat loss and a commercial whaling bottleneck. Large haplotype sharing between gray whales in Russian and Mexican waters suggests limited population structure.
JOURNAL OF MAMMALOGY
(2021)
Article
Biochemistry & Molecular Biology
J. Andrew DeWoody, Avril M. Harder, Samarth Mathur, Janna R. Willoughby
Summary: The importance of genetic diversity in conservation biology cannot be overstated, as it is closely tied to evolutionary fitness and crucial for conservation efforts. In the Anthropocene, responsible management should prioritize the conservation of ecosystems, communities, populations, individuals, and their underlying genetic diversity.
Article
Biochemistry & Molecular Biology
Andrew N. Black, Janna R. Willoughby, Anna Bruniche-Olsen, Brian L. Pierce, J. Andrew DeWoody
Summary: Researchers developed a draft reference genome of the White Sands pupfish to study its evolution and conservation. They compared genomic divergence and transposable element profiles between species, finding lower genome-wide heterozygosity in the White Sands pupfish compared to other related species, possibly due to its isolation and limited habitat.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biodiversity Conservation
Rian Bylsma, Danielle K. Walkup, Toby J. Hibbitts, Wade A. Ryberg, Andrew N. Black, J. Andrew DeWoody
Summary: This study aimed to evaluate genetic structure and genomic differentiation between the two putative subspecies of the Western Massasauga rattlesnake. The results showed minimal genetic divergence between subspecies and genetic structure oriented more along a geographic axis. Therefore, formal protection of the Desert Massasauga subspecies is not supported.
CONSERVATION GENETICS
(2022)
Article
Evolutionary Biology
Avril M. Harder, Kimberly K. O. Walden, Nicholas J. Marra, Janna R. Willoughby
Summary: Kangaroo rats, particularly those in the Dipodomys genus, are facing population declines and habitat fragmentation. The assembly and annotation of a reference genome for the bannertailed kangaroo rat provides a valuable resource for studying population genomics and adaptation to extreme environments. This research contributes to the understanding of the impacts of habitat degradation and has implications for conservation efforts.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Andrew J. Mularo, Ximena E. Bernal, J. Andrew DeWoody
Summary: Drastic reductions in population size can reduce additive genetic variance and adaptive potential, but for some traits, genetic variance may increase after a population reduction. Non-additive genetic effects can impact the additive variance contributed by alleles that influence phenotypic expression and fitness.
JOURNAL OF HEREDITY
(2022)
Review
Ecology
Gina F. Lamka, Avril M. Harder, Mekala Sundaram, Tonia S. Schwartz, Mark R. Christie, J. Andrew DeWoody, Janna R. Willoughby
Summary: This review provides an overview of the current state of ecological epigenetics research and discusses the integration of epigenetics into ecology. The study found that current research has primarily focused on summarizing epigenome characteristics and has limited taxonomic and ecosystem coverage. It suggests future research should focus on nucleotide-level differences in the epigenome and incorporate behavior and stress data.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
Elizabeth Buttermore, Stormy Chamberlain, Jannine Cody, Gregory Costain, Louis Dang, Andrew DeWoody, Yssa DeWoody, Kira Dies, Evan Eichler, Santhosh Girirajan, Marie Gramm, Alycia Halladay, Dennis Lal, Matthew Lalli, Tess Levy, Glennis Logsdon, Daniel Lowenstein, Heather Mefford, Jennifer Mulle, Alysson Muotri, Melissa Murphy, Eduardo Perez Palma, Stefan Pinter, Rebecca Pollak, Ryan Purcell, Rodney Samaco, Bina Shah, Karun Singh, Joyce So, Maria Sundberg, Surabi Veeraragavan, Vanessa Vogel-Farley, Anthony Wynshaw-Boris
Summary: Neurodevelopmental CNVs/SVs should be approached as a class of disorders based on shared mechanisms and pathways to identify common etiologic mechanisms and therapies. Collaboration between scientists, clinicians, and patients is crucial to expedite therapeutic outcomes.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Letter
Multidisciplinary Sciences
J. Andrew DeWoody, Jong Yoon Jeon, John W. Bickham, Erangi J. Heenkenda, Safia Janjua, Gina F. Lamka, Andrew J. Mularo, Andrew Black, Anna Bruniche-Olsen, Janna R. Willoughby
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yanzhu Ji, Shaohong Feng, Lei Wu, Qi Fang, Anna Bruniche-Olsen, J. Andrew DeWoody, Yalin Cheng, Dezhi Zhang, Yan Hao, Gang Song, Yanhua Qu, Alexander Suh, Guojie Zhang, Shannon J. Hackett, Fumin Lei
Summary: This study investigates the impact of generation time and body mass on genomic attributes in birds and finds correlations between these traits and orthologous microsatellite length, TE length, and DNA deletions. The effects are more pronounced in nonpasserine birds.
Article
Evolutionary Biology
Andrew N. Black, Kristin J. Bondo, Andrew Mularo, Alvaro Hernandez, Yachi Yu, Carleigh M. Stein, Andy Gregory, Kent A. Fricke, Jeff Prendergast, Dan Sullins, David Haukos, Michael Whitson, Blake Grisham, Zach Lowe, J. Andrew DeWoody
Summary: The Lesser Prairie-Chicken (LEPC) is a famous North American prairie grouse known for its beautiful breeding displays. However, its population has drastically declined due to climate and human activities, leading to its disappearance across its historical range. This led to the listing of two distinct population segments (DPSs) as threatened or endangered. A new annotated reference genome from a LEPC sample from the southern DPS was generated, providing valuable resources for evolutionary and conservation genetic research in prairie grouse.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Avril M. Harder, Mekala Sundaram, Lana L. Narine, Janna R. Willoughby
Summary: The increasing availability of satellite imagery has allowed for forward-looking studies on the impact of climate change on wild population dynamics, as well as retrospective analysis using historical data. This study used 167 Landsat-5 TM images to identify environmental drivers of fitness and population size in a well-studied population of banner-tailed kangaroo rats. The results revealed contrasting effects of surface temperature on individual fitness and population size, highlighting the importance of remotely sensed data in ecological studies.
ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Samarth Mathur, John M. Tomecek, Luis A. Tarango-Arambula, Robert M. Perez, J. Andrew DeWoody
Summary: Small populations of Montezuma Quail are vulnerable to genetic load and drift, reducing fitness and adaptive potential. Through analysis of 66 whole genomes, we found that Montezuma Quail are evolving like a ring species, with Texas populations remaining small but stable and Arizona populations contracting for thousands of years. Most deleterious mutations are young and segregating privately in each population, with a greater number in the larger population. Our study emphasizes the importance of evolutionary history, demographic changes, genetic load, and adaptive potential in wild populations.