Article
Plant Sciences
Concetta Burgarella, Angelique Berger, Sylvain Glemin, Jacques David, Nancy Terrier, Monique Deu, David Pot
Summary: This study focused on Sorghum bicolor and utilized transcriptomic resources to explore the adaptive consequences of the domestication process. Gene expression and nucleotide variability analyses revealed downregulation and reduction of diversity in domesticated sorghum, with functional annotation pointing to metabolic pathways contributing to the sorghum domestication syndrome. The study identified significantly differentially expressed genes and highlighted large rewiring of the transcriptome during the domestication and improvement processes, paving the way for the identification of key domestication genes for breeding purposes.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Engineering, Multidisciplinary
Jiachao Zhang, Rob Knight
Summary: Next-generation sequencing technology has revolutionized our ability to study the taxonomic composition and functions of host-associated microbiota and microbiomes. In the next decade, there will be an increase in human microbiome research projects, particularly those focusing on genomic mutations within the microbiome. This review discusses the coevolution of microbes within a microbiome, the relationship between microbial genomic mutations and metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Furthermore, it explores advancements in methods and algorithms for annotating and analyzing microbial genomic mutations.
Article
Multidisciplinary Sciences
Balint Stewart, Nicole Gruenheit, Amy Baldwin, Rex Chisholm, Daniel Rozen, Adrian Harwood, Jason B. Wolf, Christopher R. L. Thompson
Summary: This study investigates natural variation in predatory performance in the microbial predator Dictyostelium discoideum. The researchers found widespread nontransitive differences among strains in predatory success across different bacterial prey, which can facilitate strain coexistence in multi-prey environments. Furthermore, most mutations had prey-specific effects, highlighting the potential for prey-specific effects to weaken selection and prevent the emergence of an optimal generalist predator.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kavitha Uthanumallian, Cintia Iha, Sonja Repetti, Cheong Xin Chan, Debashish Bhattacharya, Sebastian Duchene, Heroen Verbruggen
Summary: This study investigates the genomic signature of secondary plastid endosymbiosis, revealing an increase in gene loss associated with this process while showing that essential genes for plastid function are retained. The data also demonstrate a temporary relaxation of purifying selection during secondary endosymbiosis, with selection intensity rebounding to pre-endosymbiosis levels afterwards. Independent endosymbiosis events in different lineages highlight evolutionary contexts and the interplay between selection and drift during organellogenesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Parul Johri, Susanne P. Pfeifer, Jeffrey D. Jensen
Summary: Building appropriate baseline models for natural populations helps answer fundamental questions in population genetics and identify candidate loci experiencing rare and episodic forms of selection. A baseline model was developed for a human population of West African ancestry, the Yoruba, taking into account various evolutionary processes. An approximate Bayesian approach was used to infer population growth and distribution of fitness effects, suggesting weak to moderate positive selection that is consistent but difficult to identify if rare.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Parul Johri, Kellen Riall, Hannes Becher, Laurent Excoffier, Brian Charlesworth, Jeffrey D. Jensen
Summary: Current methods for inferring population history assume neutrality, but neglect the effects of direct and background selection. The study shows that background selection can lead to mis-inferences of population growth, especially with increasing strength of purifying selection and density of directly selected sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Lisa Lehnen, Pierre-Loup Jan, Anne-Laure Besnard, Damien Fourcy, Gerald Kerth, Martin Biedermann, Pierrette Nyssen, Wigbert Schorcht, Eric J. Petit, Sebastien J. Puechmaille
Summary: Genetic diversity within species is essential for population and ecosystem persistence and integrity, influenced significantly by factors such as population size and connectivity. This study highlights the importance of historic bottlenecks, contemporary colony size, and connectivity in shaping genetic diversity, with contemporary connectivity having the most profound impact at a large geographic scale. Understanding the relative importance of these factors over time is crucial for effective conservation planning.
Article
Genetics & Heredity
Luther Fort Mbo Nkoulou, Lauriane Archange Tchinda Ninla, David Cros, Guillaume Martin, Zenabou Ndiang, Jordan Houegban, Hermine Bille Ngalle, Joseph Martin Bell, Enoch G. Achigan-Dako
Summary: Banana accessions in West and Central Africa were investigated for genomic selection using phenotyping and genotyping. Population structure and clustering analysis revealed genetic diversity at the molecular level. The AAB genomic group showed the best performance for fruit weight and plant height. The knowledge generated in this study allows the possibility to apply genomic selection in banana.
Review
Agriculture, Dairy & Animal Science
Heike Proehl, Ariel Rodriguez, Jianping Jiang, Bin Wang, Wei Zhu
Summary: Threatened animal species living in small and isolated populations with reduced genetic diversity often have lower fitness. However, there is a scarcity of published studies on this topic, with a focus on only a few species and a high proportion of non-significant results. Increasing research efforts and implementing conservation measures to enhance genetic diversity are important for the maintenance of amphibian and other animal populations.
Article
Ecology
Nicholas M. A. Crouch, David Jablonski
Summary: Understanding the relationship between species richness and genetic diversity is a continuous challenge. This study uses avian functional traits and genetic sequences to investigate whether increasing species richness affects morphological space occupation or decreases genetic diversity. The results suggest that higher species richness does not necessarily lead to morphological space occupation or reduced genetic diversity.
FUNCTIONAL ECOLOGY
(2023)
Article
Plant Sciences
Chedly Kastally, Alina K. Niskanen, Annika Perry, Sonja T. Kujala, Komlan Avia, Sandra Cervantes, Matti Haapanen, Robert Kesalahti, Timo A. Kumpula, Tiina M. Mattila, Dario Ojeda, Jaakko S. Tyrmi, Witold Wachowiak, Stephen Cavers, Katri Karkkainen, Outi Savolainen, Tanja Pyhajarvi
Summary: Pinus sylvestris (Scots pine), the most widespread coniferous tree in Eurasia, has significant economic and ecological importance. A new 50K SNP genotyping array (PiSy50k) was developed to overcome the challenge of its large and repetitive genome for genetic studies and forestry applications. The array performed well in large-scale genotyping and validation, making it a valuable tool for future genetic studies and forestry applications.
Article
Plant Sciences
Jing-Fang Guo, Baosheng Wang, Zhan-Lin Liu, Jian-Feng Mao, Xiao-Ru Wang, Wei Zhao
Summary: This study investigated the biogeographic history of a relict conifer species, Pinus bungeana, in central China. The species exhibited extremely low genetic diversity and strong population structure, indicating long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, while expanding in the east. Local adaptation played a small but significant role in population diversity. Fragmented populations with low genetic diversity make the species highly vulnerable to climate change.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Maria Lucena-Perez, Daniel Kleinman-Ruiz, Elena Marmesat, Alexander P. Saveljev, Krzysztof Schmidt, Jose A. Godoy
Summary: Demographic bottlenecks tend to reduce genetic diversity through genetic drift, but the overall effect varies across the genome due to randomness in drift and local factors like recombination, mutation, and selection. Bottlenecked populations show weaker correlations of genetic diversity with various genomic features compared to nonbottlenecked populations. Additionally, genomic regions under intense purifying selection and the X chromosome may exhibit increased diversity in bottlenecked populations.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Andrea K. Townsend, Melissa L. Jones, Nancy Chen, Caroline Chivily, Casey McAndrews, Anne B. Clark, Kevin J. McGowan, John Eimes
Summary: Infectious diseases can cause population declines in wildlife, leading to changes in genetic diversity. A study on American crows found increased genetic diversity after the emergence of West Nile virus, potentially due to increased immigration. However, inbreeding also appeared to increase in the post-WNV population, which may impact their response to future pathogen risks.
Article
Genetics & Heredity
Chuan Ma, Ruoyang Hu, Cecilia Costa, Jianke Li
Summary: This study sequenced the mitochondrial genomes of genetically selected high royal jelly-producing bees (RJBs) and unselected Italian bees (ITBs). The results showed that RJBs had lower genetic diversity levels and were mainly influenced by genetic drift and purifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Manuel de Pedro, Maria Mayol, Santiago C. Gonzalez-Martinez, Ingrid Regalado, Miquel Riba
Summary: This study investigates the adaptive factors constraining adaptation in Leontodon longirostris, a short-lived species, along an expansion route. The study finds that phenological patterns play a crucial role in shaping adaptive clines for major life-history stage transitions, and the observed genetic load does not seem to hinder adaptation to climatic variability.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Marina de Miguel, Isabel Rodriguez-Quilon, Myriam Heuertz, Agathe Hurel, Delphine Grivet, Juan Pablo Jaramillo-Correa, Giovanni G. Vendramin, Christophe Plomion, Juan Majada, Ricardo Alia, Andrew J. Eckert, Santiago C. Gonzalez-Martinez
Summary: A decade of genetic association studies has shown that complex traits are determined by multiple genetic loci, each with a small effect-size. This study used a multilocus approach to estimate the degree of polygenicity in fitness-related traits of a long-lived plant, maritime pine, and analyzed its variation across environments and years. The results showed a remarkably stable degree of polygenicity across traits, environments, and years, with evidence of local adaptation and negative selection.
Article
Plant Sciences
Nicole Moreira Veto, Dragos Postolache, Frank L. Guzman Escudero, Elia Vajana, Ricardo Burgo Braga, Fabiano Salgueiro, Rogerio Margis, Giovanni G. Vendramin, Andreia C. Turchetto-Zolet
Summary: This study investigates population genetic structure and adaptive genetic diversity in Eugenia uniflora, a tropical tree species. The study finds spatial population structuring and higher genetic diversity in southern populations. It also identifies candidate loci potentially involved in local adaptation.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Forestry
Jelena M. M. Aleksic, Milan Mataruga, Vanja Danicic, Branislav Cvjetkovic, Dordije Milanovic, Giovanni Giuseppe Vendramin, Camilla Avanzi, Andrea Piotti
Summary: Studying the transmission of genetic diversity between generations is crucial for assessing the survival prospects of fragmented forest tree populations. This is especially urgent for rare, endangered species at high risk of extinction and highly susceptible to climate change. In this study, the gene flow patterns of the IUCN red-listed Serbian spruce population were assessed for the first time using parentage analysis. The results showed that fire disturbance triggered natural regeneration and increased pollen immigration. The study provides essential information for the dynamic management and conservation of this rare and endangered species.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Review
Forestry
Alejandra Lorena Goncalves, Maria Victoria Garcia, Maria Eugenia Barrandeguy, Santiago Cesar Gonzalez-Martinez, Myriam Heuertz
Summary: Gene dispersal processes play a significant role in shaping the demographic and microevolutionary dynamics of tree species. This review examines the drivers of gene dispersal, including the mating system, population density, propagule dispersal, and successional stage, and their consequences for gene dispersal in tree species from seasonally dry tropical forests (SDTF). Understanding these determinants can inform management actions for the conservation and restoration of SDTF.
TREE GENETICS & GENOMES
(2022)
Article
Biochemistry & Molecular Biology
Gustavo Giles-Perez, Erika Aguirre-Planter, Luis E. Eguiarte, Juan Pablo Jaramillo-Correa
Summary: Secondary contact of recently diverged species may result in rampant hybridization or reinforced reproductive isolation. This study used genetic data to explore different demographic hypotheses, revealing rapid speciation and asymmetrical gene flow as important factors contributing to reproductive isolation in a fir species complex.
Article
Forestry
Bruno Fady, Edoardo Esposito, Khaled Abulaila, Jelena M. Aleksic, Ricardo Alia, Paraskevi Alizoti, Ecaterina-Nicoleta Apostol, Phil Aravanopoulos, Dalibor Ballian, Magda Bou Dagher Kharrat, Isabel Carrasquinho, Marwan Cheikh Albassatneh, Alexandru-Lucian Curtu, Rakefet David-Schwartz, Giovanbattista de Dato, Bouchra Douaihy, Nicolas-George Homer Eliades, Louis Fresta, Semir Bechir Suheil Gaouar, Malika Hachi Illoul, Vladan Ivetic, Mladen Ivankovic, Gaye Kandemir, Abdelhamid Khaldi, Mohamed Larbi Khouja, Hojka Kraigher, Francois Lefevre, Ilene Mahfoud, Maurizio Marchi, Felipe Perez Martin, Nicolas Picard, Maurizio Sabatti, Hassan Sbay, Caroline Scotti-Saintagne, Darrin T. Stevens, Giovanni Giuseppe Vendramin, Barbara Vinceti, Marjana Westergren
Summary: This review examines the major achievements in forest genetics research in biodiversity-rich countries of the Mediterranean region over the past few decades. The analysis shows that the research is primarily focused on population diversity and differentiation, environmental conditions and stress response, and phylogeography. The study also highlights the increasing contribution of Asia and Africa to the research in the Mediterranean region. Future research priorities include studying poorly known species and populations, utilizing genomic methods, modeling adaptive capacity, and identifying areas of high and low genetic diversity for conservation and restoration.
CURRENT FORESTRY REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Ivan Scotti, Hadrien Lalague, Sylvie Oddou-Muratorio, Caroline Scotti-Saintagne, Rose Ruiz Daniels, Delphine Grivet, Francois Lefevre, Philippe Cubry, Bruno Fady, Santiago C. Gonzalez-Martinez, Anne Roig, Isabelle Lesur-Kupin, Francesca Bagnoli, Vanina Guerin, Christophe Plomion, Philippe Rozenberg, Giovanni G. Vendramin
Summary: Microgeographical adaptation occurs when directional selection persists despite gene flow. This study investigates the patterns of genomic divergence in four European and Mediterranean conifers with different life-history traits and ecological requirements. The results show that selection is strong in all species but affects different loci in each. Within-population diversity at microgeographical scales is likely to be a reservoir of adaptive potential.
Article
Ecology
Juliette Archambeau, Marta Benito Garzon, Marina de Miguel, Benjamin Brachi, Frederic Barraquand, Santiago C. Gonzalez-Martinez
Summary: This study empirically tested the effects of environmental selection and population admixture on genetic variation in maritime pine populations. The results showed that populations experiencing colder winters had lower genetic variation for early height growth, while within-population genetic variation was not influenced by environmental heterogeneity or admixture. These findings provide insights into the adaptive potential of populations to changing environments.
Article
Ecology
Felix Gugerli, Sabine Brodbeck, Bertalan Lendvay, Benjamin Dauphin, Francesca Bagnoli, Willem O. van Der Knaap, Willy Tinner, Maria Hohn, Giovanni G. Vendramin, Cesar Morales-Molino, Christoph Schworer
Summary: The study aimed to understand the historical climate shifts and their impact on Pinus cembra. The research combined genetic structure and palaeoecological findings to identify putative refugia and re-colonisation routes. The results suggest that P. cembra survived the Last Glacial Maximum in southern regions and expanded into its current range during the Late Glacial.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Forestry
Rita Verbylaite, Filippos A. Aravanopoulos, Virgilijus Baliuckas, Ausra Juskauskaite
Summary: The aim of this study was to assess the genetic diversity of protected black alder populations, compare the genetic diversity between maternal and progeny generations, and determine the impact of forest management practices on genetic diversity. The results revealed high genetic diversity in Lithuanian black alder populations, with no significant genetic differences between different generations.
Article
Forestry
Yusuf Kurt, Burcu Cengel, Ercan Velioglu, Santiago C. Gonzalez-Martinez, Delphine Grivet, Nuray Kaya
Summary: The aim of this study was to characterize and compare genetic resources of Aleppo pine and Brutia pine in the Mediterranean Basin. By analyzing 56 populations from eight countries, it was found that the genetic diversity of Brutia pine was slightly higher than that of Aleppo pine. Furthermore, Aleppo pine populations showed clear east-west differentiation, while Brutia pine populations did not exhibit any spatial genetic pattern.
Article
Plant Sciences
Rita Verbylaite, Filippos A. Aravanopoulos, Virgilijus Baliuckas, Ausra Juskauskaite, Dalibor Ballian
Summary: The aim of this study was to assess if a progeny plantation can also serve as an ex situ conservation plantation, using the case study of a Lithuanian progeny trial of Alnus glutinosa. By comparing the genetic diversity and copy number of captured alleles, it was concluded that the progeny plantation can be used as an ex situ collection for the A. glutinosa populations from the first provenance region.
Article
Biochemistry & Molecular Biology
Marjana Westergren, Juliette Archambeau, Marko Bajc, Rok Damjanic, Adelaide Theraroz, Hojka Kraigher, Sylvie Oddou-Muratorio, Santiago C. Gonzalez-Martinez
Summary: This study examined the response of European beech to selection under field conditions. The results showed that larger trees with higher fruit production and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, indicating the impact of late frosts on selection. Compared to other studies, this research found relatively low to moderate heritability and evolvability for most traits. The study suggests that forest tree populations, such as European beech, can locally adapt even at short time scales.
Article
Forestry
Sanna Olsson, Guia Giovannelli, Anne Roig, Ilaria Spanu, Giovanni Giuseppe Vendramin, Bruno Fady
Summary: Using the subsection Pinus as an example, this study explains the issue of weak support in phylogenetic studies of closely related pine species and suggests that popular genetic markers are not recommended for species identification purposes in European pines.
IFOREST-BIOGEOSCIENCES AND FORESTRY
(2022)