Article
Ecology
David R. R. Breininger, Eric D. D. Stolen, Geoffrey M. M. Carter, Stephanie A. A. Legare, William V. V. Payne, Daniel J. J. Breininger, James E. E. Lyon, Chris D. D. Schumann, Danny K. K. Hunt
Summary: Fecundity is a crucial aspect in evolutionary and ecological theory and applications, and it can be influenced by various environmental factors. This study on Florida scrub-jays found that habitat quality, presence/absence of nonbreeders, population density, breeder experience, and rainfall all play a role in fecundity. Strong territories and the proportion of strong territories in the overall population were identified as important factors for breeding pairs' fecundity. Understanding the impact of low-quality habitats on population recovery and sustainability is crucial.
ECOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Steven D. Leavitt, Ann DeBolt, Ethan McQuhae, Jessica L. Allen
Summary: The Florida Perforate Cladonia (FPC), a federally endangered species, remains imperiled in isolated populations in the Florida scrub. Reference genomes of threatened and endangered species like FPC provide crucial insights into genomic diversity and adaptations. In this study, the first draft nuclear and mitochondrial genomes were assembled for FPC, and genetic diversity within and among populations in southeastern Florida was assessed. The genomic resources generated here are important for informed conservation efforts for the FPC.
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
Ecology
Young Ha Suh, Reed Bowman, John W. Fitzpatrick
Summary: This study investigates the formation of groups by unrelated members in animal societies, using the Florida scrub-jay as a case study. The researchers focus on the dispersal behavior of subordinates and compare the adaptive benefits of joining unrelated groups as helpers versus remaining home and dispersing only to breed. They find that staging dispersers, who join unrelated groups, tend to leave at a younger age and move greater distances compared to direct dispersers. The study also reveals sexual asymmetry in dispersal patterns, with staging appearing as an alternative strategy for female helpers and a less optimal choice for males. The findings highlight the plasticity of dispersal behavior in response to social and environmental conditions and contribute to our understanding of non-kin-based social groups.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Ecology
David R. Breininger, Geoffrey M. Carter, Stephanie A. Legare, William Payne, Eric D. Stolen, Daniel J. Breininger, James E. Lyon
Summary: Adult nonbreeders play important roles in the stability and conservation of many species, even though their functional roles are often underestimated. They can buffer breeding population sizes and help raise new generations of offspring, but can also have negative effects when present in high numbers. Long-term studies are useful for understanding the relationships among nonbreeder population parameters.
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
Biodiversity Conservation
Karl E. Miller, Colin P. Shea
Summary: The study found that regenerating clearcut stands 3-10 years post-harvest in Ocala National Forest provide optimal habitat conditions for Florida scrub-jays, with the highest number of family groups and juveniles occurring in stands 6.5 and 7.4 years post-harvest, respectively. This suggests that managers can increase Florida scrub-jay populations in Ocala NF by focusing on habitat within 3-10 years post-harvest.
ENDANGERED SPECIES RESEARCH
(2021)
Article
Biodiversity Conservation
Phoebe A. Burns, Kevin C. Rowe, Marissa L. Parrott, Emily Roycroft
Summary: Modern sequencing approaches, especially museum genomics, have allowed for the reconstruction of population decline and extinction by integrating genomic data from collections across decades. Understanding species declines is crucial for conservation and genetic management, particularly in Australia where European invasion has led to the highest rate of mammal extinction. Using historical museum specimens and tissue collections, researchers generated genomic data from extinct and surviving populations of the endangered Australian Pookila. The study revealed significant loss of genetic diversity and highlighted the vulnerability of small remnant populations to extinction.
BIOLOGICAL CONSERVATION
(2023)
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
Environmental Sciences
Karen L. Neely, Cynthia L. Lewis, Kathleen S. Lunz, Lystina Kabay
Summary: The study revealed that the pillar coral population in Florida has been reproductively extinct for decades, with severe losses. Long-term chronic stressors have been affecting the population's recovery, while back-to-back years of coral bleaching and thermally-exacerbated diseases led to a sharp decline in population numbers.
FRONTIERS IN MARINE SCIENCE
(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
Ecology
Elizabeth A. McHuron, Lisanne Aerts, Glenn Gailey, Olga Sychenko, Daniel P. Costa, Marc Mangel, Lisa K. Schwarz
Summary: Acoustic disturbance poses a growing conservation concern for wildlife populations, with Stochastic Dynamic Programming providing a framework to quantify and predict the impacts of disturbance. Using the western gray whale as a case study, the model showed how disturbance affects survival probabilities and spatial distribution, particularly in energy-rich feeding areas. Disturbance had unequally distributed impacts on individuals, highlighting the importance of assessing who, where, and when disturbance occurs for large capital breeders.
ECOLOGICAL APPLICATIONS
(2021)
Article
Evolutionary Biology
Binia De Cahsan, Michael V. Westbury, Sofia Paraskevopoulou, Hauke Drews, Moritz Ott, Guenter Gollmann, Ralph Tiedemann
Summary: Range margin populations are vulnerable to rapid environmental change, and gene flow may be crucial for their survival. Translocations are proposed to increase genetic diversity but carry the risk of losing locally adapted alleles. A study on European fire-bellied toads in Germany found signs of introgression from southern populations, with introgressed alleles possibly providing adaptive advantages. This research highlights the complex genetic consequences of translocations on range margin populations.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Pengcheng Wang, Rong Hou, Yang Wu, Zhengwang Zhang, Pinjia Que, Peng Chen
Summary: Global biodiversity is under serious threat, and the genomic consequences of recent rapid population declines of wild organisms are poorly understood. In this study, the whole genome of the critically endangered Yellow-breasted Bunting was assembled and annotated, revealing that populations experiencing recent rapid decline have different genomic statuses compared to populations with long-term declines.
Article
Multidisciplinary Sciences
Lidia Escoda, Oliver Hawlitschek, Jorge Gonzalez-Esteban, Jose Castresana
Summary: Recently, populations with very low genetic diversity have been found, some of which can persist in the long term, while others may face extinction. This study focuses on the Iberian desman population, which exhibits extremely low heterozygosity values and high levels of inbreeding. Some individuals in the population appear to be genetically identical, posing challenges for genetic identification and parentage analysis. However, characterizing these genetically impoverished populations and improving genomic methodologies for their study are crucial for scientific and conservation purposes.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yasir H. Ahmed-Braimah, Mariana F. Wolfner, Andrew G. Clark
Summary: This study reveals differences in postmating responses between different Drosophila species, suggesting that variations in male genotypes may have immunogenic effects on females.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Iskander Said, Michael P. McGurk, Andrew G. Clark, Daniel A. Barbash
Summary: Competition between transposable elements (TEs) may lead to the emergence of new variants, with hosts preferentially producing antisense piRNAs to silence these emerging variants.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Manisha Munasinghe, Benjamin C. Haller, Andrew G. Clark
Summary: In this study, the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population were investigated using computer simulations. Disrupting these interactions resulted in less-fit males, but the strength of these interactions was not enough to drive population isolation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Matthew Metzloff, Emily Yang, Sumit Dhole, Andrew G. Clark, Philipp W. Messer, Jackson Champer
Summary: Our study demonstrates the construction of a tethered drive system in Drosophila, utilizing a locally confined CRISPR Toxin-Antidote Recessive Embryo (TARE) drive to support modification and suppression homing drives. Each drive was able to bias inheritance in its favor, and the TARE drive was shown to spread only when released above a threshold frequency in experimental cage populations. After the TARE drive had established in the population, it facilitated the spread of a subsequently released split homing modification drive (to all individuals in the cage) and of a homing suppression drive (to its equilibrium frequency).
Article
Evolutionary Biology
Tram N. Nguyen, Nancy Chen, Elissa J. Cosgrove, Reed Bowman, John W. Fitzpatrick, Andrew G. Clark
Summary: Understanding the genomic consequences of population decline is crucial for predicting species' vulnerability to global change. This study compared the genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations of Florida scrub jays that have experienced different demographic trajectories. The results showed that the population decline led to decreased heterozygosity and increased inbreeding in the declining population, while the stable population did not show significant changes. This study highlights the divergence in genetic characteristics caused by local population decline despite ongoing gene flow.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Rebecca G. Cheek, Brenna R. Forester, Patricia E. Salerno, Daryl R. Trumbo, Kathryn M. Langin, Nancy Chen, T. Scott Sillett, Scott A. Morrison, Cameron K. Ghalambor, W. Chris Funk
Summary: This study investigated the genetic divergence mechanism of a bird species endemic to a small island. The island scrub-jay on Santa Cruz Island showed genetic differentiation related to habitat type and bill length. Neutral landscape genomic analyses revealed that the genetic differentiation was primarily influenced by geographic distance and habitat composition. Putatively adaptive loci associated with habitat type were identified using multivariate redundancy analysis. Genome-wide association analyses revealed the polygenic basis of bill length variation. These findings support the hypothesis that divergent selection can lead to adaptive divergence at microgeographic scales in the presence of ongoing gene flow.
Article
Neurosciences
You Chen, Andrew G. Clark, Haiyuan Yu
Summary: This article presents a fine-mapping approach called RefMap, which integrates functional genomics with GWAS summary statistics to prioritize causal variants for amyotrophic lateral sclerosis.
Article
Multidisciplinary Sciences
Felicia N. New, Benjamin R. Baer, Andrew G. Clark, Martin T. Wells, Ilana L. Brito
Summary: This study examines the interactions between host genetics and gut microbiome by analyzing the gut microbiomes and human variants of 250 individuals. The findings reveal associations between host genetics and microbiome-related metabolic traits, disorders, and certain cancers. The study also identifies common and rare microbial functions that are associated with host genetics.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Emily Yang, Matthew Metzloff, Anna M. Langmueller, Xuejiao Xu, Andrew G. Clark, Philipp W. Messer, Jackson Champer
Summary: Gene drives are engineered alleles that can bias inheritance and spread throughout a population. This study constructed a homing suppression drive in Drosophila melanogaster using multiplexed gRNAs to inhibit the formation of resistance alleles, reaching a moderate equilibrium frequency in cage populations but with a fitness cost preventing elimination. The results demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Yiqin Wang, Xiaoxian Guo, Xiumei Hong, Guoying Wang, Colleen Pearson, Barry Zuckerman, Andrew G. Clark, Kimberly O. O'Brien, Xiaobin Wang, Zhenglong Gu
Summary: This study investigates the role of mitochondrial genome (mtDNA) in autism spectrum disorder (ASD) risk, and finds that mutations in mtDNA are associated with increased ASD risk in children, and the heteroplasmies in parents have different effects in ASD children.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Dawn S. Chen, Andrew G. Clark, Mariana F. Wolfner
Summary: In a study on Drosophila, researchers found that inhibiting the activity of Tdc2 neurons in females resulted in a higher proportion of offspring from the first male. This suggests that octopaminergic/tyraminergic signaling plays a role in biased sperm usage in multiply-mated females, and highlights a new role for the female nervous system in postcopulatory sexual selection.
Article
Biology
Anna M. Langmueller, Jackson Champer, Sandra Lapinska, Lin Xie, Matthew Metzloff, Samuel E. Champer, Jingxian Liu, Yineng Xu, Jie Du, Andrew G. Clark, Philipp W. Messer
Summary: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a highly efficient genome editing technology with a wide range of potential applications. However, integrating CRISPR/Cas9 into an organism's genome may have harmful effects on transgenic individuals, particularly in the case of gene drives that aim to alter the genetics of entire populations. This study assesses the fitness effects of CRISPR/Cas9 expression in Drosophila melanogaster populations, and finds that a high-fidelity version of Cas9 performs well in terms of drive conversion efficiency. These findings have implications for the design of gene drives and other applications involving genomic integration of CRISPR endonucleases.
Article
Biochemistry & Molecular Biology
Wenqi Cao, Kory C. Douglas, Paul B. Samollow, John L. VandeBerg, Xu Wang, Andrew G. Clark
Summary: Genomic imprinting is a phenomenon that plays important roles in many biological processes, and is only observed in therian mammals. A study investigated the imprinting pattern in marsupials using unbiased RNA-seq studies, discovering and validating 13 imprinted genes, including nine novel imprinted genes. Differential methylation and clustering were observed at marsupial-specific imprinted genes, revealing common mechanisms in the epigenetic regulation of marsupial imprinting.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Sofie Y. N. Delbare, Sara Venkatraman, Kate Scuderi, Martin T. Wells, Mariana F. Wolfner, Sumanta Basu, Andrew G. Clark
Summary: This study used high-resolution time series RNA-sequencing data to explore the genetic architecture of female's response to SP in Drosophila melanogaster. The results showed that SP not only triggers the transcriptional switch in females after mating, but also affects metabolic gene regulatory network and neuronal gene regulatory network, especially the disruption of female's circadian rhythm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Jullien M. Flynn, Kevin B. Hu, Andrew G. Clark
Summary: This study discovered chromosome fusion and fission events in a strain of D. virilis, leading to genome instability. One substrain with an X-autosome fusion had a 20x higher nondisjunction rate and another substrain with higher satellite DNA had an overall higher DNA breakage rate. These findings suggest a potential role of satellite DNA abundance in genome instability. The establishment of a novel system with four different karyotypes provides a valuable tool for future studies on genome instability, centromere function, and sex chromosome evolution.