Article
Biochemistry & Molecular Biology
Carolin Dahms, Petri Kemppainen, Linda N. Zanella, Davor Zanella, Antonella Carosi, Juha Merila, Paolo Momigliano
Summary: This study focuses on the genetic differentiation and parallel evolution of three-spined stickleback populations from the Adriatic Sea compared to populations from other regions. The findings suggest that Adriatic populations are highly differentiated, of low genetic diversity and likely stem from multiple independent colonizations during the Pleistocene, despite still showing some degree of genetic parallelism.
Article
Biochemistry & Molecular Biology
Andreas Harer, Daniel Bolnick, Diana J. Rennison
Summary: The study investigated genomic signatures of divergence across populations of threespine stickleback that adapted to benthic or limnetic ecological niches. They found that the magnitude and repeatability of genomic signatures of ecological divergence highly depend on the geographic context, with some candidate regions identified to be important for adaptation to benthic and limnetic niches.
Article
Behavioral Sciences
A. Ramesh, M. M. Domingues, E. J. Stamhuis, T. G. G. Groothuis, F. J. Weissing, M. Nicolaus
Summary: The water management measures in the 1970s in the Netherlands resulted in resident populations of three-spined sticklebacks that can no longer migrate to the sea. Research shows that these resident fish exhibit genetic differentiation in behavior and morphology compared to their migrant counterparts. This suggests that around 50 years of isolation can lead to behaviorally relevant genetic differentiation.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2021)
Article
Limnology
Ben A. Wasserman, Tanya L. Rogers, Stephan B. Munch, Eric P. Palkovacs
Summary: Population abundance fluctuations in interacting species can be influenced by abiotic factors, biotic interactions, or a combination of both. Nonlinear relationships make it difficult to identify the true effects of these drivers. This study used empirical dynamic modeling to investigate the species interaction between two fish species in a fluctuating environment. The results showed that competition was not a significant factor, and both species largely responded independently to abiotic conditions. The study highlights the importance of understanding drivers of population abundance and informing management strategies for endangered species.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Juntao Hu, Rowan D. H. Barrett
Summary: Repeated phenotypic patterns support the role of natural selection. Epigenetic modifications can contribute to parallel adaptation. The role of epigenetic processes during parallel adaptation remains unclear.
Article
Biochemistry & Molecular Biology
Doko-Miles J. Thorburn, Kostas Sagonas, Mahesh Binzer-Panchal, Frederic J. J. Chain, Philine G. D. Feulner, Erich Bornberg-Bauer, Thorsten B. H. Reusch, Irene E. Samonte-Padilla, Manfred Milinski, Tobias L. Lenz, Christophe Eizaguirre
Summary: Genome sequencing is important for understanding genetic basis of adaptation, population structure and epigenetic mechanisms. However, a suitable reference genome is needed for mapping population-level resequencing data. This study compared the use of two different reference genomes for the three-spined stickleback and found that using a local reference genome increased mapping efficiency and genotyping accuracy. The choice of reference genome also had significant impacts on downstream analyses, such as outlier genes and enriched gene functions.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biodiversity Conservation
Jorn P. Scharsack, Bartholomaus Wieczorek, Alexander Schmidt-Drewello, Janine Buescher, Frederik Franke, Andrew Moore, Antoine Branca, Anika Witten, Monika Stoll, Erich Bornberg-Bauer, Susann Wicke, Joachim Kurtz
Summary: Global climate change can influence the interaction between hosts and parasites, with rising temperatures potentially exacerbating host exploitation by parasites. The study showed that warm temperatures enhanced parasite growth and infectivity to final hosts, while hosts exhibited lower body condition and less active immune system at high temperatures. The data suggests that parasite exposure combined with rising temperatures can shift the host's immunometabolism, providing nutrients for parasite growth and suppressing immune defense.
GLOBAL CHANGE BIOLOGY
(2021)
Article
Ecology
Nayade alvarez-Quintero, Alberto Velando, Jose C. Noguera, Sin-Yeon Kim
Summary: The study on three-spined stickleback revealed that changes in reproductive strategies in response to environmental cues can impact offspring's growth and survival. When females experience a late breeding photoperiod, they reduce investment in early clutches, while males increase investment in sexual signals.
ECOLOGY AND EVOLUTION
(2021)
Article
Biology
Agnes Piecyk, Megan A. Hahn, Olivia Roth, Nolwenn M. Dheilly, David C. Heins, Michael A. Bell, Martin Kalbe
Summary: The study revealed geographic differences in defense mechanisms, with qualitative resistance, quantitative resistance and tolerance being important concepts in studies of parasite infections.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yufang Shen, Hui Xia, Zhonghua Tu, Yaxian Zong, Lichun Yang, Huogen Li
Summary: Ecological adaptive differentiation affects species diversity and genetic diversity in forests, with significant niche divergence between L. chinense and L. tulipifera detected. Environmental variables are associated with genetic variation, and 28 adaptive loci provide evidence for local adaptation in Liriodendron. The study highlights the role of heterogeneous environments in shaping genetic structure and driving local adaptation, informing conservation efforts for L. chinense in the future.
Article
Ecology
Sin-Yeon Kim, Nayade Alvarez-Quintero, Neil B. Metcalfe
Summary: The social environment in animal groups plays a crucial role in shaping individual behaviors and life histories. A mismatch between individual and group behavior patterns can have disadvantages, such as nonadaptive behaviors that increase energetic costs. This study manipulated the sociability of juvenile three-spined sticklebacks and found that unsociable groups exhibited bolder collective behaviors during feeding, while individuals in groups with similar sociability gained more mass. Mismatched sociability in a group may confer a growth disadvantage due to the expression of nonadaptive behaviors.
ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Natalie Pilakouta, Shaun S. Killen, Bjarni K. Kristjansson, Skuli Skulason, Jan Lindstrom, Neil B. Metcalfe, Kevin J. Parsons
Summary: Studies have found that organisms' ability to adapt to climate change does not necessarily lead to changes in their temperature preferences. Research shows that fish living in warm environments have similar temperature preferences to those living in cold environments. Thus, preferred temperature may not be a reliable indicator of a species' adaptive potential to a new temperature environment.
ECOLOGY AND EVOLUTION
(2023)
Article
Biology
Ken A. Thompson, Dolph Schluter
Summary: In contrast to ecological speciation, speciation by parallel natural selection has been less studied. This study leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish to investigate the fitness consequences of hybridization in different environments. The results showed heterosis and hybrid breakdown in both ecotypes, with differences observed between pond and aquarium settings.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Quiterie Haenel, Laurent Guerard, Andrew D. C. MacColl, Daniel Berner
Summary: Adaptation to derived habitats can stem from standing genetic variation, with variants favored in new habitats potentially being neutral in ancestral populations. This suggests a potential mechanism for the maintenance of genetic variation that has been underappreciated.
Article
Biology
Louise Cominassi, Kirsten N. Ressel, Allison A. Brooking, Patrick Marbacher, Eleanor C. Ransdell-Green, Kristin M. O'Brien
Summary: This study investigated the changes in metabolic rate and mitochondrial function in response to temperature in threespine stickleback. The results showed that the metabolic rate increased with acclimation temperature and the changes in mitochondrial function in some tissues played a significant role in the changes in metabolic rate.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Ecology
Bohao Fang, Paolo Momigliano, Kimmo K. Kahilainen, Juha Merila
Summary: The study reveals the evolution of whitefish morphs in a Finnish lake, showing clear genetic differentiation between morphs despite current syntopy. Through identification of genetic markers associated with gonad weight variation, they suggest that ecological adaptations in spawning time may contribute to maintaining partial reproductive isolation in whitefish populations.
Article
Biochemistry & Molecular Biology
Xueyun Feng, Juha Merila, Ari Loytynoja
Summary: Introgressive hybridization is an important process in evolution. The analysis of whole-genome sequences of nine-spined sticklebacks in northern Europe revealed a complex pattern of population ancestry. Freshwater isolates provided insights into the past and intermediate states of evolutionary processes.
Article
Evolutionary Biology
Elisavet A. Toli, Anastasios Bounas, Juha Merila, Konstantinos Sotiropoulos
Summary: Phenotypic changes in response to environmental cues allow organisms to adapt and enhance their fitness in a given habitat. The genetic basis of this phenotypic plasticity is largely unknown. In this study, we investigated the genetic and phenotypic divergence among different morphs of a Greek smooth newt population. We found low genetic divergence between morphs and similar levels of gene diversity. Despite high gene flow, we identified candidate genes associated with the different morphs that play functional roles in metabolic processes.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Ecology
Antoine Fraimout, Elisa Paivio, Juha Merila
Summary: The study found that the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks may explain the divergence in complex behaviors between marine and pond populations, and this divergence is parallel. The research also revealed a significant correlation between behavioral differences and responses to reduced predation pressure.
Editorial Material
Multidisciplinary Sciences
Juha Merila
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Zoology
Wei Chen, Hongzhou Chen, Jiahong Liao, Min Tang, Haifen Qin, Zhenkun Zhao, Xueyan Liu, Yanfang Wu, Lichun Jiang, Lixia Zhang, Bohao Fang, Xueyun Feng, Baowei Zhang, Kerry Reid, Juha Merila
Summary: This study reports the genome assembly of Rana kukunoris, a high-altitude-adapted frog, providing valuable resources for studying life history evolution and adaptation to high-altitude environments.
FRONTIERS IN ZOOLOGY
(2023)
Article
Ecology
Mikko Kivikoski, Pasi Rastas, Ari Loeytynoja, Juha Merilae
Summary: Map distance, a measure of the expected number of crossovers between two loci in genetics, is estimated using mapping functions based on observed recombination frequencies. Traditional mapping functions developed when the number of markers was low may underpredict recombination frequencies from map distance in high-density marker data. This study demonstrates that a piecewise function can provide more accurate predictions, highlighting the context-dependent association between map distance and recombination frequency.
Article
Ornithology
Chen-Yang Liu, Juha Merilae, Yang Liu, Lei Lv
Summary: Global climate change has had a widespread impact on the reproductive phenology of many wild organisms. In this study, the relationship between breeding timing and spring temperatures was explored using data from hair-crested drongos in the wild. It was found that low night temperatures delay breeding time, likely due to the physiological constraints on egg-laying caused by the need for thermoregulation. However, the timing of breeding showed no trend over the study period.
JOURNAL OF AVIAN BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yu Wang, Yingnan Wang, Xiaoqi Cheng, Yongli Ding, Chongnv Wang, Juha Merila, Baocheng Guo
Summary: New study shows that introgression contributes significantly to the diversification of Pungitius sticklebacks and plays a crucial role in phenotypic convergence. The analysis of genomic data reveals that introgression is more prevalent than previously thought, with asymmetric gene flow and unequal genomic signatures in hybridizing species. Introgression of genetic variants is accompanied by transitions in important diagnostic traits and adaptation in gene regulatory networks, highlighting its importance as a source of adaptive variation. This study provides insight into the long-standing challenges in the taxonomy and systematics of this highly diverse group of fish.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Mikko Kivikoski, Antoine Fraimout, Pasi Rastas, Ari Loytynoja, Juha Merila
Summary: Crossovers in meiosis play a crucial role in ensuring proper segregation and recombination of chromosomes in sexual reproduction. However, little is known about the heritability and repeatability of crossover rates in the wild. This study examined crossover rate variation in outbred stickleback populations and found that repeatability was moderate, with higher values in females than in males. Due to limitations in sample size and parental relatedness, heritability could not be confidently estimated. Overall, the evolvability of crossover rates appears to be low based on our results and comparisons with previous studies.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Antoine Fraimout, Pasi Rastas, Lei Lv, Juha Merila
Summary: Using experimental cross data and genome-wide identity-by-descent (IBD) relationships, this study finds a significant decrease in offspring survival probability with increasing parental IBD sharing in an outbred marine nine-spined stickleback population, indicating substantial inbreeding load. Interestingly, a positive effect of paternal inbreeding coefficient on offspring survival suggests that certain combinations of parental inbreeding and genetic relatedness among mates may promote offspring survival. These results demonstrate the potential for inbreeding depression in outbred populations and highlight the importance of considering fine-scale genetic relatedness in future studies.
Article
Biochemistry & Molecular Biology
Sunandan Das, Eli Greenbaum, Shai Meiri, Aaron M. Bauer, Frank T. Burbrink, Christopher J. Raxworthy, Jeffrey L. Weinell, Rafe M. Brown, Jonathan Brecko, Olivier S. G. Pauwels, Nirhy Rabibisoa, Achille P. Raselimanana, Juha Merila
Summary: The snake superfamily Elapoidea is a classic example of ancient and rapid radiation. Previous studies have had difficulty resolving the phylogenetic relationships within this highly diverse group. This study sequenced over 4,500 ultraconserved element loci from representative taxa and used multiple methods to infer their phylogeny, resulting in largely congruent and well-supported topologies. Elapoidea originated in the early Eocene and rapidly diversified into major lineages during this epoch.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Review
Ecology
Mi Yoon Chung, Juha Merila, Yuseob Kim, Kangshan Mao, Jordi Lopez-Pujol, Myong Gi Chung
Summary: Increased access to genome-wide data provides new opportunities for plant conservation. However, information on neutral genetic diversity in a small number of marker loci can still be valuable. To bridge the gap between conservation science and practice, conservation practitioners should use population genetic information more efficiently. They can use estimates of genetic differentiation in quantitative traits (Q(ST)) and neutral markers (F(ST)) to capture both adaptive and neutral genetic variations.
ECOLOGY AND EVOLUTION
(2023)
Review
Ecology
Mi Yoon Chung, Juha Merilae, Jialiang Li, Kangshan Mao, Jordi Lopez-Pujol, Yoshihiko Tsumura, Myong Gi Chung
Summary: Genetic diversity is crucial for evolutionary change and the ability of populations to adapt to new environmental conditions. While the importance of incorporating genetic diversity into conservation measures is recognized, the distinction between neutral and adaptive genetic variation has received less attention. This review addresses the utility of neutral genetic variation in ecological and evolutionary inference, as well as conservation strategies for plant populations and species. It also discusses the identification and estimation of adaptive genetic variation and emphasizes the need for a better understanding of its role in climate change adaptation. Until more estimates of adaptive genetic variation are available, conservation researchers and practitioners should continue to utilize neutral genetic variation to develop relevant strategies for rare and endangered plant species.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Chaowei Zhang, Kerry Reid, Arthur F. Sands, Antoine Fraimout, Mikkel Heide Schierup, Juha Merila
Summary: Mutation rate is a critical parameter in population genetics, but accurate estimates for wild organisms are limited. This study estimated mutation rates in two marine populations of nine-spined stickleback using pedigrees, whole-genome resequencing, and a high-quality reference genome. The results showed high levels of parental mosaicism and increased estimated divergence times after recalibration with the mutation rate.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)