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Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases J. Hered. (IF 3.1) Pub Date : 2024-03-07 Ricardo Perez-Enriquez, Oscar E Juárez, Pavel Galindo-Torres, Ana Luisa Vargas-Aguilar, Raúl Llera-Herrera
The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world's aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads
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Germline ecology: managed herds, tolerated flocks, and pest control J. Hered. (IF 3.1) Pub Date : 2024-03-06 David Haig
Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. mtDNA and rDNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic
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The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies J. Hered. (IF 3.1) Pub Date : 2024-02-28 Kevin R Bredemeyer, Bridgett M vonHoldt, Nicole M Foley, Isabella Childers, Kristin E Brzeski, William J Murphy
Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding
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Phylogeographic analyses of an endemic Neotropical fox (Lycalopex vetulus) reveal evidence of hybridization with a different canid species (L. gymnocercus) J. Hered. (IF 3.1) Pub Date : 2024-02-27 Fabricio Silva Garcez, Ligia Tchaicka, Frederico Gemesio Lemos, Carlos Benhur Kasper, Júlio Cesar Dalponte, Eduardo Eizirik
The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by
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A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia) J. Hered. (IF 3.1) Pub Date : 2024-02-24 Whitney L E Tsai, Merly Escalona, Kimball L Garrett, Ryan S Terrill, Ruta Sahasrabudhe, Oanh Nguyen, Eric Beraut, William Seligmann, Colin W Fairbairn, Ryan J Harrigan, John E McCormack, Michael E Alfaro, Thomas B Smith, Rachael A Bay
The Yellow Warbler (Setophaga petechia) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C
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Conservation genomics of wolves: the global impact of RK Wayne’s research J. Hered. (IF 3.1) Pub Date : 2024-02-20 Marco Musiani, Ettore Randi
RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the U.S.. His influence has been felt in other countries and regions outside the contiguous U.S., where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids
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Patterns of genetic divergence in the Rio Grande cooter (Pseudemys gorzugi), a riverine turtle inhabiting an arid and anthropogenically modified system J. Hered. (IF 3.1) Pub Date : 2024-02-19 Michael W Vandewege, Javier Gutierrez, Drew R Davis, Michael R J Forstner, Ivana Mali
The lower Rio Grande and Pecos River of the southwest United States of America have been heavily modified by human activities, profoundly impacting the integrity of their aquatic wildlife. In this context, we focused our study on the population genomics of the Rio Grande Cooter (Pseudemys gorzugi), a freshwater turtle of increasing conservation concern, residing in these two rivers and their tributaries
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United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals J. Hered. (IF 3.1) Pub Date : 2024-02-17 Hagar K Soliman, Jenn M Coughlan
Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting—parent-of-origin-biased gene expression—is fundamental for
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Differentiated sex chromosomes, karyotype evolution and spontaneous triploidy in carphodactylid geckos J. Hered. (IF 3.1) Pub Date : 2024-02-17 Pensabene Eleonora, Augstenová Barbora, Kratochvíl Lukáš, Rovatsos Michail
Geckos exhibit derived karyotypes without clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic
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Genomic Data Revealed Inbreeding Despite a Geographically Connected Stable Effective Population Size Since the Holocene in the Protected Formosan Long-Arm Scarab Beetle, Cheirotonus formosanus J. Hered. (IF 3.1) Pub Date : 2024-02-16 Jen-Pan Huang, Shu-Ping Wu, Wei-Yun Chen, Guanjie Pham, Yi-Hsiu Kuan
Biodiversity conservation is a top priority in the face of global environmental change, and the practical restoration of biodiversity has emerged as a key objective. Nevertheless, the question of how to effectively contribute to biodiversity restoration and identify suitable systems for such efforts continues to present major challenges. By using genome-wide SNP data, our study revealed that populations
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NewickTreeModifier: a simple web page to prune and modify Newick trees J. Hered. (IF 3.1) Pub Date : 2024-02-02 Lynn Ogoniak, Raphael Steffen, Norbert Grundmann, Ben Stöver, Kai Müller, Jürgen Schmitz
Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier, a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species provided in FASTA, NEXUS, or PHYLIP sequence format with an
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The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species J. Hered. (IF 3.1) Pub Date : 2024-02-01 Alayna Mead, Sorel T Fitz-Gibbon, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork
Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, and grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit
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A chromosome-level genome assembly for the dugong (Dugong dugon) J. Hered. (IF 3.1) Pub Date : 2024-01-21 D Nevé Baker, Linelle Abueg, Merly Escalona, Katherine A Farquharson, Janet M Lanyon, Diana Le Duc, Torsten Schöneberg, Dominic Absolon, Ying Sims, Olivier Fedrigo, Erich D Jarvis, Katherine Belov, Carolyn J Hogg, Beth Shapiro
The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population
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Drift drives the evolution of chromosome number I: The impact of trait transitions on genome evolution in Coleoptera J. Hered. (IF 3.1) Pub Date : 2024-01-05 Heath Blackmon, Michelle M Jonika, James M Alfieri, Jeffery P Demuth
Chromosomal mutations such as fusions and fissions are often thought to be deleterious, especially in heterozygotes (underdominant), and consequently are unlikely to become fixed. Yet, many models of chromosomal speciation ascribe an important role to chromosomal mutations. When the effective population size (Ne) is small, the efficacy of selection is weakened, and the likelihood of fixing underdominant
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Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast J. Hered. (IF 3.1) Pub Date : 2023-12-30 Jorge Alberto Mares-Mayagoitia, Fabiola Lafarga-De la Cruz, Fiorenza Micheli, Pedro Cruz- Hernández, Juan A de-Anda-Montañez, John Hyde, Norma Y Hernández-Saavedra, Paulina Mejía-Ruíz, Vladimir S De Jesús-Bonilla, Carmen E Vargas-Peralta, Fausto Valenzuela- Quiñonez
Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, USA to Baja California Sur, Mexico, exposed to a latitudinal
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Mitogenomic analysis of a late Pleistocene jaguar from North America J. Hered. (IF 3.1) Pub Date : 2023-12-27 Megha Srigyan, Blaine W Schubert, Matthew Bushell, Sarah H D Santos, Henrique Vieira Figueiró, Samuel Sacco, Eduardo Eizirik, Beth Shapiro
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses
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Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction J. Hered. (IF 3.1) Pub Date : 2023-12-26 A de Flamingh, T P Gnoske, A G Rivera-Colón, V A Simeonovski, J C Kerbis Peterhans, N Yamaguchi, K E Witt, J Catchen, A L Roca, R S Malhi
Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the “Cape Flats” in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as “Black-maned lions” and claimed that they were phenotypically distinct
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The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity J. Hered. (IF 3.1) Pub Date : 2023-12-26 Yulin Zhang, Aaron J Stern, Rasmus Nielsen
Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success
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The difficulty of detecting inbreeding depression and its effect on conservation decisions J. Hered. (IF 3.1) Pub Date : 2023-12-23 Sarah R Hoy, Kristin E Brzeski, Leah M Vucetich, Rolf O Peterson, John A Vucetich
Statistical inferences about inbreeding depression are often derived from analyses with low power and a high risk of failing to detect inbreeding depression. That risk is widely appreciated by scientists familiar with the relevant statistical and genetical theory, but may be overlooked and underappreciated by decision-makers. Consequently, there is value in demonstrating this risk using a real example
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Reference genome of Townsend’s big-eared bat, Corynorhinus townsendii J. Hered. (IF 3.1) Pub Date : 2023-12-12 Samantha L R Capel, Natalie M Hamilton, Devaughn Fraser, Merly Escalona, Oanh Nguyen, Samuel Sacco, Ruta Sahasrabudhe, William Seligmann, Juan M Vazquez, Peter H Sudmant, Michael L Morrison, Robert K Wayne, Michael R Buchalski
Townsend's big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North American. Considered a species of conservation concern throughout much of its range, protection efforts would greatly benefit from understanding patterns of population structure, genetic diversity, and local adaptation. To facilitate such research, we present the first de novo genome
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Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex J. Hered. (IF 3.1) Pub Date : 2023-11-28 Nathan A Johnson, Andrew R Henderson, Jess W Jones, Caitlin E Beaver, Steven A Ahlstedt, Gerald R Dinkins, Nathan L Eckert, Mark J Endries, Jeffrey T Garner, John L Harris, Paul D Hartfield, Don W Hubbs, Timothy W Lane, Monte A McGregor, Kendall R Moles, Cheryl L Morrison, Matthew D Wagner, James D Williams, Chase H Smith
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated
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The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils J. Hered. (IF 3.1) Pub Date : 2023-11-21 Magnus Wolf, Carola Greve, Tilman Schell, Axel Janke, Thomas Schmitt, Steffen U Pauls, Horst Aspöck, Ulrike Aspöck
Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies
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A chromosome-level genome assembly for the smoky rubyspot damselfly (Hetaerina titia) J. Hered. (IF 3.1) Pub Date : 2023-11-21 Christophe W Patterson, Erandi Bonillas-Monge, Adrian Brennan, Gregory F Grether, Luis Mendoza-Cuenca, Rachel Tucker, Yesenia M Vega-Sánchez, Jonathan Drury
Smoky rubyspot damselflies (Hetaerina titia Drury, 1773) are one of the most commonly encountered odonates along streams and rivers on both slopes of Central America and the Atlantic drainages in the US and southern Canada. Owing to their highly variable wing pigmentation, they have become a model system for studying sexual selection and interspecific behavioural interference. Here, we sequence and
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Repeated patterns of reptile diversification in Western North America supported by the Northern Alligator Lizard (Elgaria coerulea) J. Hered. (IF 3.1) Pub Date : 2023-11-20 Adam D Leaché, Hayden R Davis, Chris R Feldman, Matthew K Fujita, Sonal Singhal
Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard
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Large variance in inbreeding within the Iberian wolf population J. Hered. (IF 3.1) Pub Date : 2023-11-13 Isabel Salado, Michaela Preick, Natividad Lupiáñez-Corpas, Alberto Fernández-Gil, Carles Vilà, Michael Hofreiter, Jennifer A Leonard
The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300-350 packs and then stabilized. In contrast to many current European wolf populations
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Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer’s Pochard (Aythya baeri) in North America J. Hered. (IF 3.1) Pub Date : 2023-11-08 Asako Y Chaille, Robert C Lacy, Andrea S Putnam, Jamie L Toste, Aryn P Wilder, Jamie A Ivy
The application of molecular tools to population management can improve the long-term genetic viability of ex situ populations. In this study, we aimed to understand the implications of integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer’s pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for
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Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages J. Hered. (IF 3.1) Pub Date : 2023-10-28 Lauren M Hennelly, Ghulam Sarwar, Hira Fatima, Geraldine Werhahn, Fakhar I Abbas, Abdul M Khan, Tariq Mahmood, Shannon Kachel, Zairbek Kubanychbekov, Muhammad T Waseem, Rubab Zahra Naqvi, Abdul Hamid, Yasir Abbas, Hamera Aisha, Muhammad Waseem, Muhammad Farooq, Benjamin N Sacks
Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best-studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf
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Gut bacterial composition shows sex-specific shifts during breeding season in ex situ managed black-footed ferrets J. Hered. (IF 3.1) Pub Date : 2023-10-26 Alexandra L DeCandia, Laura Adeduro, Piper Thacher, Adrienne Crosier, Paul Marinari, Robyn Bortner, Della Garelle, Travis Livieri, Rachel Santymire, Pierre Comizzoli, Michael Maslanka, Jesús E Maldonado, Klaus-Peter Koepfli, Carly Muletz-Wolz, Sally L Bornbusch
The gut microbiome of mammals engages in a dynamic relationship with the body and contributes to numerous physiological processes integral to overall health. Understanding the factors shaping animal-associated bacterial communities is therefore paramount to the maintenance and management in ex situ wildlife populations. Here, we characterized the gut microbiome of 48 endangered black-footed ferrets
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The genome of the invasive and broadly polyphagous Diaprepes root weevil, Diaprepes abbreviatus (Coleoptera), reveals an arsenal of putative polysaccharide-degrading enzymes J. Hered. (IF 3.1) Pub Date : 2023-10-23 Terrence Sylvester, Richard Adams, Wayne B Hunter, Xuankun Li, Bert Rivera-Marchand, Rongrong Shen, Na Ra Shin, Duane D McKenna
The Diaprepes root weevil (DRW), Diaprepes abbreviatus, is a broadly polyphagous invasive pest of agriculture in the southern United States and the Caribbean. Its genome was sequenced, assembled, and annotated to study genomic correlates of specialized plant feeding and invasiveness and to facilitate the development of new methods for DRW control. The 1.69 Gb D. abbreviatus genome assembly was distributed
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Reduction of genetic diversity in ‘Alalā (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s J. Hered. (IF 3.1) Pub Date : 2023-10-17 Geneviève Blanchet, M Renee Bellinger, Anna M Kearns, Nandadevi Cortes-Rodriguez, Bryce Masuda, Michael G Campana, Christian Rutz, Robert C Fleischer, Jolene T Sutton
Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the ‘Alalā, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low
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Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus) J. Hered. (IF 3.1) Pub Date : 2023-10-14 Natalie Payne, John A Erwin, Joan L Morrison, James F Dwyer, Melanie Culver
We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since
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Ancestry testing of “Old Tom,” a killer whale central to mutualistic interactions with human whalers J. Hered. (IF 3.1) Pub Date : 2023-10-12 Isabella M Reeves, John A Totterdell, Emma L Betty, David M Donnelly, Angela George, Steven Holmes, Luciana Moller, Karen A Stockin, Rebecca Wellard, Charlie White, Andrew D Foote
Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as “Old Tom,” washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to
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Patterns of reproduction and autozygosity distinguish the breeding from non-breeding gray wolves of Yellowstone National Park J. Hered. (IF 3.1) Pub Date : 2023-10-03 Bridgett M vonHoldt, Alexandra L DeCandia, Kira A Cassidy, Erin E Stahler, Janet S Sinsheimer, Douglas W Smith, Daniel R Stahler
For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding
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A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris J. Hered. (IF 3.1) Pub Date : 2023-09-30 Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman
The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here
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Domestication is Associated with Increased Interspecific Hybrid Compatibility in Landfowl (Order: Galliformes) J. Hered. (IF 3.1) Pub Date : 2023-09-27 James M Alfieri, Reina Hingoranee, Giridhar N Athrey, Heath Blackmon
Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among
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A Reference Genome for Ecological Restoration of the Sunflower Sea Star, Pycnopodia helianthoides J. Hered. (IF 3.1) Pub Date : 2023-09-19 Lauren Marie Schiebelhut, Melissa B DeBiasse, Lars Gabriel, Katharina J Hoff, Michael N Dawson
Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric
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A genome assembly of the Yuma myotis bat, Myotis yumanensis J. Hered. (IF 3.1) Pub Date : 2023-09-13 Joseph Curti, Devaughn Fraser, Merly Escalona, Colin W Fairbairn, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, William Seligmann, Peter H Sudmant, Erin Toffelmier, Juan Manuel Vazquez, Robert Wayne, H Bradley Shaffer, Michael R Buchalski
The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of twelve bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these twelve
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A reference genome assembly for the continentally-distributed ring-necked snake, Diadophis punctatus J. Hered. (IF 3.1) Pub Date : 2023-09-08 Erin P Westeen, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Robert N Fisher, Erin Toffelmier, H Bradley Shaffer, Ian J Wang
Snakes in the family Colubridae include over 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose
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Guidelines and quantitative standards for improved cetacean taxonomy using full mitochondrial genomes J. Hered. (IF 3.1) Pub Date : 2023-08-29 Phillip A Morin, Karen K Martien, Aimee R Lang, Brittany L Hancock-Hanser, Victoria L Pease, Kelly M Robertson, Maya Sattler, Elizabeth Slikas, Patricia E Rosel, C Scott Baker, Barbara L Taylor, Frederick I Archer
In many organisms, especially those of conservation concern, traditional lines of evidence for taxonomic delineation, such as morphological data, are often difficult to obtain. In these cases, genetic data are often the only source of information available for taxonomic studies. In particular, population surveys of mitochondrial genomes offer increased resolution and precision in support of taxonomic
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Comparative analyses reveal potential genetic mechanisms for high-altitude adaptation of Schizopygopsis fishes based on the chromosome-level genomes J. Hered. (IF 3.1) Pub Date : 2023-08-29 Chuang Zhou, Zhengrui Hu, Qian Chen, Chao Du, Yi Liu, Zhaobin Song
The schizothoracine fishes, widely distributed in the Qinghai-Tibetan Plateau and its adjacent areas, are considered as ideal models for investigation of high-altitude adaptation. Schizophygopsis are one group of the highly specialized schizothoracine fishes, and the genetic basis for their high-altitude adaptation is poorly understood. In this study, we performed comparative genomics analyses to investigate
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Diversity of mitochondrial DNA in three species of great whales before and after modern whaling J. Hered. (IF 3.1) Pub Date : 2023-08-14 Angela L Sremba, Anthony R Martin, Peter Wilson, Ana Lúcia Cypriano-Souza, Danielle L Buss, Tom Hart, Marcia H Engel, Sandro L Bonatto, Howard Rosenbaum, Tim Collins, Carlos Olavarría, Frederick I Archer, Debbie Steel, Jennifer A Jackson, C Scott Baker
The 20 th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for three great whales in the South Atlantic, the blue, humpback
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Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration in Sceloporus lizards J. Hered. (IF 3.1) Pub Date : 2023-07-27 Christopher D Robinson, Matthew D Hale, Tyler N Wittman, Christian L Cox, Henry B John-Alder, Robert M Cox
Phenotypic sexual dimorphism often involves the hormonal regulation of sex-biased expression for underlying genes. However, it is generally unknown whether the evolution of hormonally mediated sexual dimorphism occurs through upstream changes in tissue sensitivity to hormone signals, downstream changes in responsiveness of target genes, or both. Here, we use comparative transcriptomics to explore these
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A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex J. Hered. (IF 3.1) Pub Date : 2023-07-25 Erin P Westeen, Merly Escalona, Matthew Holding, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ralph Perri, Robert N Fisher, Erin Toffelmier, H Bradley Shaffer, Ian J Wang
Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution
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Sampling affects population genetic inference: a case study of the Allen's (Selasphorus sasin) and rufous hummingbird (Selasphorus rufus) J. Hered. (IF 3.1) Pub Date : 2023-07-17 Brian M Myers, Kevin J Burns, Christopher J Clark, Alan Brelsford
Gene flow can affect evolutionary inference when species are undersampled. Here, we evaluate the effects of gene flow and geographic sampling on demographic inference of two hummingbirds that hybridize, Allen's hummingbird (Selasphorus sasin) and rufous hummingbird (S. rufus). Using whole-genome data and extensive geographic sampling, we find widespread connectivity, with introgression far beyond the
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A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta J. Hered. (IF 3.1) Pub Date : 2023-07-11 Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman
The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part
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A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri) J. Hered. (IF 3.1) Pub Date : 2023-07-03 Phred M Benham, Carla Cicero, Devon A DeRaad, John E McCormack, Robert K Wayne, Merly Escalona, Eric Beraut, Mohan P A Marimuthu, Oanh Nguyen, Michael W Nachman, Rauri C K Bowie
The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a
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A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data J. Hered. (IF 3.1) Pub Date : 2023-06-29 Remy Nguyen, Joshua D Kapp, Samuel Sacco, Steven P Myers, Richard E Green
Several methods exist for detecting genetic relatedness or identity by comparing DNA information. These methods generally require genotype calls, either SNPs or STRs, at the sites used for comparison. For some DNA samples, like those obtained from bone fragments or single rootless hairs, there is often not enough DNA present to generate genotype calls that are accurate and complete enough for these
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Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae) J. Hered. (IF 3.1) Pub Date : 2023-06-22 Guilherme Caeiro-Dias, Megan J Osborne, Hannah M Waterman, Trevor J Krabbenhoft, Thomas F Turner
Sex determination systems and genetic sex differentiation across fishes are highly diverse but are unknown for most Cypriniformes, including Rio Grande silvery minnow (Hybognathus amarus). In this study, we aimed to detect and validate sex-linked markers to infer sex determination system and to demonstrate the utility of combining several methods for sex-linked marker detection in non-model organisms
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Assembly of the largest squamate reference genome to date: the western fence lizard, Sceloporus occidentalis J. Hered. (IF 3.1) Pub Date : 2023-06-19 Anusha P Bishop, Erin P Westeen, Michael L Yuan, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Erin Toffelmier, Robert N Fisher, H Bradley Shaffer, Ian J Wang
Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland
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Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales J. Hered. (IF 3.1) Pub Date : 2023-06-17 Sorel Fitz-Gibbon, Alayna Mead, Scott O’Donnell, Zhi-Zhong Li, Merly Escalona, Eric Beraut, Samuel Sacco, Mohan P A Marimuthu, Oanh Nguyen, Victoria L Sork
Juglans californica, California walnut, is a vulnerable small tree that is locally abundant but restricted to woodland and chaparral habitats of Southern California threatened by urbanization and land use change. This species is the dominant species in a unique woodland ecosystem in California. It is one of two endemic California walnut species (family Juglandaceae). The other species, Northern California
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Chromosome-level reference genome of stinkwort, Dittrichia graveolens (L.) Greuter: a resource for studies on invasion, range expansion, and evolutionary adaptation under global change J. Hered. (IF 3.1) Pub Date : 2023-06-02 Susan L McEvoy, Nicky Lustenhouwer, Miranda K Melen, Oanh Nguyen, Mohan P A Marimuthu, Noravit Chumchim, Eric Beraut, Ingrid M Parker, Rachel S Meyer
Dittrichia graveolens (L.) Greuter, or stinkwort, is a weedy annual plant within the family Asteraceae. The species is recognized for the rapid expansion of both its native and introduced ranges: in Europe, it has expanded its native distribution northward from the Mediterranean basin by nearly 7 degrees latitude since the mid-20th century, while in California and Australia the plant is an invasive
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Genomic Resources for Asian (Elephas maximus) and African Savannah Elephant (Loxodonta africana) Conservation and Health Research J. Hered. (IF 3.1) Pub Date : 2023-05-29 Natalia A Prado, Ellie E Armstrong, Janine L Brown, Shifra Z Goldenberg, Peter Leimgruber, Virginia R Pearson, Jesús E Maldonado, Michael G Campana
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian
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Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii J. Hered. (IF 3.1) Pub Date : 2023-05-17 Jonathan Q Richmond, Jimmy A McGuire, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Samuel Sacco, Eric Beraut, Erin Toffelmier, Robert N Fisher, Ian J Wang, H B Shaffer
Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville’s horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g., cranial horns, dorsoventrally
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Reference genome for the American rubyspot damselfly, Hetaerina americana J. Hered. (IF 3.1) Pub Date : 2023-05-17 Gregory F Grether, Joscha Beninde, Eric Beraut, Noravit Chumchim, Merly Escalona, Zachary G MacDonald, Courtney Miller, Ruta Sahasrabudhe, Andrew M Shedlock, Erin Toffelmier, H Bradley Shaffer
Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus
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No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow) J. Hered. (IF 3.1) Pub Date : 2023-05-11 Rita O Afonso, Francisco Pina-Martins, Vicki Friesen, Zhengxin Sun, Letizia Campioni, Jeremy Madeiros, Mónica C Silva
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950’s the population has been recovering aided by the implementation of an ongoing conservation plan
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Juvenile Idiopathic Epilepsy in Arabian Horses is not a Single Gene Disorder J. Hered. (IF 3.1) Pub Date : 2023-05-05 Julia Ciosek, Abigail Kimes, Tatiana Vinardell, Donald C Miller, Douglas F Antczak, Samantha Brooks
Valued for their temperament, beauty, athletic ability, and exhibition in the show ring, Arabian horses are an important component of the horse industry. Juvenile Idiopathic Epilepsy (JIE), a seizure disorder, is most often reported in Arabian foals from birth to six months of age. Affected foals exhibit tonic-clonic seizures lasting as long as five minutes and risking secondary complications like
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Reference genome of the black rail, Laterallus jamaicensis J. Hered. (IF 3.1) Pub Date : 2023-04-29 Laurie A Hall, Ian J Wang, Merly Escalona, Eric Beraut, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Steven R Beissinger
The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution
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Management of diversity and inbreeding when importing new stock into an inbred population J. Hered. (IF 3.1) Pub Date : 2023-04-29 Brian Kinghorn, Alexander Kinghorn
This article relates to breeding programs that seek to manage genetic diversity. The method maximises a multicomponent objective function, applicable across breeding scenarios. However, this paper focuses on breeding decisions following immigration of ten unrelated individuals into a highly inbred simulated population (F≈0.34). We use Optimal Contribution Selection to maximise retention of genetic
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In Memoriam: Fred M. Utter, a founder of fisheries genetics J. Hered. (IF 3.1) Pub Date : 2023-04-28 Fred W Allendorf, Nils Ryman, Robin S Waples
Fred Utter died in his sleep during the night of 5 March 2023 at the age of 91. In this paper, three friends and colleagues of Fred describe the important role that his genetics research has played in the management and conservation of fish populations.
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Reference genome of the Virginia rail, Rallus limicola J. Hered. (IF 3.1) Pub Date : 2023-04-27 Laurie A Hall, Ian J Wang, Merly Escalona, Eric Beraut, Samuel Sacco, Ruta Sahasrabudhe, Oanh Nguyen, Erin Toffelmier, H Bradley Shaffer, Steven R Beissinger
The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many