Article
Ecology
Ying Zhen, Michel A. K. Dongmo, Ryan J. Harrigan, Kristen Ruegg, Qi Fu, Rachid Hanna, Timothy C. Bonebrake, Thomas B. Smith
Summary: This study investigates the thermal responses of butterflies from different habitats and explores the genetic and plasticity factors that shape these responses. The results show that butterflies from different habitats exhibit differences in phenotypic plasticity, suggesting the influence of genetic and environmental factors. However, there is no distinct population structure between habitats, indicating ongoing gene flow.
Article
Biodiversity Conservation
Xin Wang, Zhixin Zhang, Stefano Mammola, Adeljean L. F. C. Ho, Yanhong Zhang, Geng Qin, Qiang Lin
Summary: The study on the marine species Syngnathus schlegeli in Chinese coastal waters revealed a north-to-south phenotypic gradient and genetic divergence, indicating relative independence of South China Sea populations. High niche differentiation among populations and historical barriers to dispersal were observed, leading to the establishment of three distinct clades in the widely distributed marine pipefish. The research demonstrates that even in a highly connected sea environment, there is potential for ecological specialization.
DIVERSITY AND DISTRIBUTIONS
(2021)
Article
Biochemistry & Molecular Biology
Yangchun Gao, Yiyong Chen, Shiguo Li, Xuena Huang, Juntao Hu, Dan G. Bock, Hugh J. MacIsaac, Aibin Zhan
Summary: Recent studies have shown that adaptation is not only due to selection on DNA sequence-based variation, but also influenced by epigenetic factors. This study examined the genetic and epigenetic mechanisms underlying environmental adaptation in a marine invasive tunicate species. The results revealed clear population differentiation at both the genetic and epigenetic levels, with local environmental variables playing a significant role. Minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. The patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting some autonomy of epigenetic variation. Shared and specific genes and biological pathways associated with environmental factors were identified, indicating complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. These mechanisms may facilitate population persistence under environmental change and successful invasions across novel environments.
Article
Evolutionary Biology
W. Babik, K. Dudek, M. Marszalek, G. Palomar, B. Antunes, S. Sniegula
Summary: The process of urbanization presents significant challenges to organisms, and this study aims to understand the genetic adaptations of damselflies to urban environments. Using genome scanning methods, the researchers identified candidate genetic markers related to urbanization in different geographical regions. Interestingly, genes involved in synapse organization were found to be associated with the adaptive response in the nervous system. This finding highlights the polygenic nature of adaptation to urbanization and mirrors previous studies in different species.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer
Summary: This study sequenced the polyploid genomes of Brettanomyces bruxellensis yeast strains using long-read sequencing strategy, revealing unique polyploidization history and trajectories in different subpopulations. The genomes contain both genetically close and diverged copies, indicating auto- and allopolyploidization events. Loss of heterozygosity events has influenced the structure of these polyploid genomes.
Article
Biochemistry & Molecular Biology
Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leache, Todd A. Castoe, Tereza Jezkova
Summary: This study examined the genetic diversity of a desert lizard, revealing significant genetic differentiation between populations in cold and hot deserts, as well as numerous loci associated with climate. Founders effects were identified in the recently expanded populations, indicating subsets of genetic variation found in southern populations.
Article
Biochemistry & Molecular Biology
Dinarzarde C. Raheem, David J. Gower, Karin Breugelmans, Kithsiri B. Ranawana, Thierry Backeljau
Summary: Based on phylogenetic analyses and ancestral-state reconstructions, this study clarified the systematics and evolution of Sri Lankan Corilla. The results revealed evolutionary relationships and habitat preferences between two sub-groups and several species. The study also demonstrated convergent evolution in shell morphology of lowland lineages.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Ecology
Olivia S. Harringmeyer, Hopi E. Hoekstra
Summary: This study identified 21 large inversion polymorphisms in populations of deer mice, which are widespread and important for patterns of recombination and likely to be involved in local adaptation.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Quiterie Haenel, Krista B. Oke, Telma G. Laurentino, Andrew P. Hendry, Daniel Berner
Summary: This study investigates how ecological divergence leads to strong reproductive isolation between populations in close geographic contact, using whole-genome sequencing of stickleback fish populations adapted to neighboring lake and stream habitats. The findings highlight the efficacy of polygenic selection in maintaining reproductive isolation without physical isolation, emphasizing the importance of studying speciation at fine eco-geographic and genomic scales.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Bridgett M. Vonholdt, Daniel R. Stahler, Kristin E. Brzeski, Marco Musiani, Rolf Peterson, Michael Phillips, John Stephenson, Kent Laudon, Erin Meredith, John A. Vucetich, Jennifer A. Leonard, Robert K. Wayne
Summary: Effective population size estimates are critical for evolutionary predictions and conservation decisions, especially for species with social factors that impact breeding and population size. This study investigated the genomic estimates of effective population size in grey wolf populations in North America, revealing significant genetic structure and historical signatures of predator extermination efforts. The findings highlight the importance of effective population size estimates for grey wolf conservation.
Article
Biochemistry & Molecular Biology
Matthew Barnbrook, Mario Duran-Castillo, Jo Critchley, Yvette Wilson, Alex Twyford, Andrew Hudson
Summary: The study of speciation cases involving parallel adaptations can reveal adaptive characters and their underlying genes. By studying the parallel evolution of alpine morphology in the genus Antirrhinum, it was found that two later diverged sympatric species only differ by around 2% of nuclear loci, but still maintain morphological characters typical of earlier-diverged alpine or lowland lineages and correlate with local landscape features, as expected of ecological adaptations. The morphological differences involve multiple, unlinked genes that can be easily broken up by recombination in hybrids. There is little evidence of post-pollination barriers to gene flow or recombination, suggesting that genetic isolation related to ecological adaptation is important in maintaining character combinations and might have contributed to parallel speciation. Genes involved in the earlier alpine-lowland split were also reused in parallel evolution of alpine species, consistent with introgressive hybridization, and it is speculated that many non-ecological barriers to gene flow might have been purged during the process.
Article
Biochemistry & Molecular Biology
Matthew K. Brachmann, Kevin Parsons, Skuli Skulason, Oscar Gaggiotti, Moira Ferguson
Summary: Sympatric adaptive phenotypic divergence of benthic and pelagic morphs in Icelandic Arctic charr is underlined by genomic differentiation. The divergence histories were reconstructed using coalescent modeling and single nucleotide polymorphisms. Genomic differentiation was characterized by outlier loci and was associated with phenotypic and ecological variation, suggesting a genomic basis for adaptive divergence. Little evidence was found for a parallel genomic basis of differentiation among populations.
Article
Biology
Jennifer Walsh, Shawn M. Billerman, Bronwyn G. Butcher, Vanya G. Rohwer, David P. L. Toews, Vicens Vila-Coury, Irby J. Lovette
Summary: Genome-wide analyses of admixture between two closely related North American oriole species reveal longstanding barriers to reproductive isolation. This study provides insights into the mechanisms that facilitate and inhibit speciation using a hybrid zone between the Baltimore and Bullock's orioles. The findings highlight the complex interactions between pre- and post-mating barriers and the rapid accumulation of barriers between these species.
COMMUNICATIONS BIOLOGY
(2023)
Article
Entomology
Jinyu Li, Longqing Shi, Wei Chen, Yi Mao, Liette Vasseur, Geoff Gurr, Minsheng You, Shijun You
Summary: The study on the tea green leafhopper found that climatic differences play a significant role in the subpopulation differentiation of the leafhopper, which explains the observed increase in outbreak frequency under climate change. This study also demonstrates the usefulness of molecular genetic approaches in studying the effects of environmental heterogeneity on natural population genetic variation.
ENTOMOLOGIA GENERALIS
(2023)
Review
Biology
Eleanor K. O'Brien, Greg M. Walter, Jon Bridle
Summary: Models of local adaptation to spatially varying selection suggest that the interaction between adaptive potential and genetic variation determines the maximum rate of evolution. Our research on rainforest Drosophila and UK butterflies along environmental gradients shows that local adaptation is not consistently observed, genetic variation in fitness may not always be visible to selection in the field, and antagonistic interactions between species can increase the cost of adaptation. However, rapid range expansion can occur when biotic interactions evolve. Future research should investigate how environmental sensitivity of genotypes affects ecological exposure and the probability of evolutionary rescue.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biodiversity Conservation
Sirena Lao, Bruce A. Robertson, Abigail W. Anderson, Robert B. Blair, Joanna W. Eckles, Reed J. Turner, Scott R. Loss
BIOLOGICAL CONSERVATION
(2020)
Article
Entomology
Megan A. Roselli, Samantha M. Cady, Sirena Lao, Bruce H. Noden, Scott R. Loss
JOURNAL OF MEDICAL ENTOMOLOGY
(2020)
Article
Ecology
Scott R. Loss, Sirena Lao, Abigail W. Anderson, Robert B. Blair, Joanna W. Eckles, Reed J. Turner
Article
Evolutionary Biology
Thomas B. Smith, Trevon L. Fuller, Ying Zhen, Virginia Zaunbrecher, Henri A. Thomassen, Kevin Njabo, Nicola M. Anthony, Mary K. Gonder, Wolfgang Buermann, Brenda Larison, Kristen Ruegg, Ryan J. Harrigan
Summary: Preserving biodiversity under rapidly changing climate conditions is challenging. One approach to estimate impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. Understanding future genomic and environmental relationships can help guide management decisions, such as establishing new protected areas where populations might be buffered from high temperatures or major changes in rainfall. In Central Africa, deforestation, mining, and infrastructure development are major anthropogenic threats leading to population declines of rainforest species. The study investigates multiple anthropogenic threats in a Central African rainforest songbird, the little greenbul (Andropadus virens), and suggests that some populations will require significant shifts in adaptive genomic variation to keep pace with predicted climate and land use changes.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Eric C. Anderson
Summary: The study introduces an R package, CKMRpop, for simulating age-structured populations to help understand the foundations of CKMR and assess its feasibility in different scenarios. By simulating output, sampled pairs of individuals related within a user-specified number of generations can be found, providing a basis for CKMR inference.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Diana S. Baetscher, Jessie Beck, Eric C. Anderson, Kristen Ruegg, Andrew M. Ramey, Scott Hatch, Hannah Nevins, Shannon M. Fitzgerald, John Carlos Garza
Summary: Global fisheries cause significant harm to seabirds through unintentional bycatch, particularly in species that form metapopulations. This study used genetic stock identification to assign bycatch Northern Fulmars to specific breeding colonies in Alaska and found disproportionate levels of bycatch from different colonies. The overlap between fisheries and colony-specific foraging areas was lower during the summer breeding season, leading to greater differences in bycatch vulnerability. These findings highlight the importance of genetic stock identification in linking at-sea threats to specific colonies and informing management strategies to reduce bycatch.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Victoria L. Sork, Shawn J. Cokus, Sorel T. Fitz-Gibbon, Aleksey Zimin, Daniela Puiu, Jesse A. Garcia, Paul F. Gugger, Claudia L. Henriquez, Ying Zhen, Kirk E. Lohmueller, Matteo Pellegrini, Steven L. Salzberg
Summary: The genus Quercus, which has diversified into over 450 species, plays dominant roles in ecosystems. This study presents a genome and methylome for a California endemic oak, Quercus lobata, and identifies evolutionary features that contribute to its success. The analysis reveals genetic and phenotypic diversity through duplications of protein-coding genes and methylation patterns associated with transposable elements.
NATURE COMMUNICATIONS
(2022)
Article
Zoology
Chengqi Zhu, Xiaodong Xu, Ying Zhen
Summary: Two new species of the genus Pyrocoelia were described from Mt. Cenwanglaoshan of Guangxi, Southwest China. These new species were distinguished from other known species based on external morphological characters and male genitalia. In addition, the distribution of Pyrocoelia species in China was summarized.
Article
Ornithology
Sirena Lao, Abigail W. Anderson, Robert B. Blair, Joanna W. Eckles, Reed J. Turner, Scott R. Loss
Summary: Weather has a significant impact on collisions between migrating birds and building windows, particularly in spring and fall. Favorable weather for migration increases collisions, such as tailwinds, while impediments to migration, such as changes from fair conditions to headwinds, also increase collisions. Additionally, we found more nuanced weather effects, including the weather conditions 2-3 nights before collisions and multi-day sequences of conditions. Therefore, permanent measures like reducing nighttime lighting and using bird-friendly building design and glass treatments should be prioritized.
ORNITHOLOGICAL APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Adam H. Freedman, Ryan J. Harrigan, Ying Zhen, Alison M. Hamilton, Thomas B. Smith
Summary: Accelerating climate change and habitat loss require the consideration of species' adaptability in biodiversity conservation plans. However, the mechanisms responsible for generating adaptive variation and new species in high-biodiversity biomes like African rainforests are poorly understood. By studying an African rainforest skink, we provide compelling evidence that ecotone speciation driven by ecological divergence is important for African rainforest biodiversity. These findings inform conservation strategies that preserve biodiversity production and maintenance processes.
Article
Multidisciplinary Sciences
Tianyu Wang, Lina Shi, Ying Zhen
Summary: Apocynaceae plants produce toxic cardenolides that can be utilized and confer resistance by herbivores. Omnivorous katydid Pacific Ducetia can feed on cardenolides-rich oleander leaves, showing an unusual case of cardenolide resistance in nonspecialist species.
Article
Ecology
Ying Zhen, Michel A. K. Dongmo, Ryan J. Harrigan, Kristen Ruegg, Qi Fu, Rachid Hanna, Timothy C. Bonebrake, Thomas B. Smith
Summary: This study investigates the thermal responses of butterflies from different habitats and explores the genetic and plasticity factors that shape these responses. The results show that butterflies from different habitats exhibit differences in phenotypic plasticity, suggesting the influence of genetic and environmental factors. However, there is no distinct population structure between habitats, indicating ongoing gene flow.
Article
Biochemistry & Molecular Biology
Matthew G. DeSaix, Eric C. Anderson, Christen M. Bossu, Christine E. Rayne, Teia M. Schweizer, Nicholas J. Bayly, Darshan S. Narang, Julie C. Hagelin, H. Lisle Gibbs, James F. Saracco, Thomas W. Sherry, Michael S. Webster, Thomas B. Smith, Peter P. Marra, Kristen C. Ruegg
Summary: Using low-coverage whole genome sequencing, we identified fine-scale population structure in the American Redstart and assigned individuals accurately to genetically distinct breeding populations. We found population-specific patterns of varying migratory connectivity in the nonbreeding range. Combining migratory connectivity results with demographic analysis, we propose conservation strategies for preserving numbers of individuals and genetic diversity throughout the annual cycle.
Article
Biochemistry & Molecular Biology
Anne K. Beulke, Alicia Abadia-Cardoso, Devon E. Pearse, Laura C. Goetz, Neil F. Thompson, Eric C. Anderson, John Carlos Garza
Summary: This study used genetic pedigree reconstruction to investigate the sex-specific patterns of life history traits and their genetic and environmental underpinnings in anadromous steelhead trout. The results showed that spawn date was highly heritable and had a high genetic correlation across sexes, while age at maturity was also highly heritable with a lower genetic correlation across sexes. Additionally, a migration-associated inversion polymorphism was found to have sex-specific correlations with age at maturity.
Article
Multidisciplinary Sciences
Neil F. Thompson, Eric C. Anderson, Anthony J. Clemento, Matthew A. Campbell, Devon E. Pearse, James W. Hearsey, Andrew P. Kinziger, John Carlos Garza
