Article
Biochemistry & Molecular Biology
Karel Janko, Oldrich Bartos, Jan Koci, Jan Roslein, Edita Jankova Drdova, Jan Kotusz, Jan Eisner, Martin Mokrejs, Eva Stefkova-Kasparova
Summary: Hybridization and genome duplication are crucial for animal and plant evolution, but they can lead to changes in subgenomes of hybrids and polyploids. This study found that asexual hybrids have stable genomes at the chromosome level but experience gradual loss of heterozygosity at the gene level due to allelic deletions and conversions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Tomasz S. S. Gaczorek, Marzena Marszalek, Katarzyna Dudek, Jan W. W. Arntzen, Ben Wielstra, Wieslaw Babik
Summary: This study provides evidence for the prevalence of MHC gene introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.
Article
Plant Sciences
Carolina Osuna-Mascaro, Rafael Rubio de Casas, Jose M. Gomez, Joao Loureiro, Silvia Castro, Jacob B. Landis, Robin Hopkins, Francisco Perfectti
Summary: This study analyzed the evolution of Erysimum species from the South of the Iberian Peninsula and found that hybridization played a significant role in their evolution, especially in species with purple and yellow flowers. These results demonstrate the importance of hybridization for plant diversification, which should be considered in studies of plant evolution.
Article
Ecology
Kyle E. McElroy, Laura Bankers, Deanna Soper, Gery Hehman, Jeffrey L. Boore, John M. Logsdon, Maurine Neiman
Summary: The question of why sexual reproduction is common despite the higher efficiency and lower cost of asexual reproduction remains unanswered. Comparisons between sexual and asexual taxa help to understand the genetic structure underlying asexuality and the mechanisms behind transitions and maintenance. Transcriptome sequencing was used to compare ovarian gene expression patterns between sexual and asexual individuals of Potamopyrgus antipodarum, a snail species with frequent transitions to asexuality. Population history was found to be a major factor influencing gene expression variation, potentially more influential than reproductive mode. A smaller set of genes with consistent expression differences between sexual and asexual individuals across genetic backgrounds provides a starting point for further exploration on the role of gene expression in the transition to asexual reproduction.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Entomology
Zhi-Chao Yan, Guang-Yuan Qi, Tian-Yi Yao, Yuan-Xi Li
Summary: Despite its substantial costs, sexual reproduction dominates in animals. One popular explanation for the paradox of sex is that asexual reproduction is more likely to accumulate deleterious mutations than sexual reproduction. To test this hypothesis, we compared the mitogenomes of two asexual wasp strains, Trichogramma cacoeciae and T. pretiosum, to their sexual relatives. These two asexual strains represent two different transition mechanisms in Trichogramma from sexual to asexual reproduction. We sequenced and assembled complete mitochondrial genomes of asexual T. cacoeciae and T. pretiosum. Compared to four sexual relatives, we found no evidence of higher mutation accumulation in asexual Trichogramma mitogenomes than in their sexual relatives. We also did not detect any relaxed selection in asexual Trichogramma mitogenomes. In contrast, the intensified selection was detected in Nad1 and Nad4 of the asexual T. pretiosum mitogenome, suggesting more purifying selection. In summary, no higher mitochondrial mutation accumulation was detected in these two asexual Trichogramma strains. This study provides a basis for further investigating mitochondrial evolution and asexual reproduction in Trichogramma.
Article
Multidisciplinary Sciences
Muriel Gros-Balthazard, Jonathan M. Flowers, Khaled M. Hazzouri, Sylvie Ferrand, Frederique Aberlenc, Sarah Sallon, Michael D. Purugganan
Summary: Researchers recovered seven date palm seeds from archaeological sites in the Southern Levant, dating from the fourth century BCE to the second century CE, which were germinated to yield viable plants. Whole-genome sequencing of these ancient samples showed genetic relationships between the ancient Judean date palms and modern West Asian and North African date palm varieties. These findings provide insights into crop evolution and the introgression of genetic features from the Cretan palm Phoenix theophrasti into modern North African date palm populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Kara M. Million, Amrita Bhattacharya, Zoe M. Dinges, Sarah Montgomery, Eries Smith, Curtis M. Lively
Summary: Research suggests that clonal populations of the New Zealand freshwater snail maintain high levels of single-nucleotide polymorphism (SNP) diversity and DNA content variation even without sexual reproduction. Laboratory experiments also reveal differences in pathogen susceptibility among distinct clonal genotypes.
JOURNAL OF HEREDITY
(2021)
Article
Biochemistry & Molecular Biology
Sibelle T. Vilaca, Francesco Maroso, Paulo Lara, Benoit de Thoisy, Damien Chevallier, Larissa Souza Arantes, Fabricio R. Santos, Giorgio Bertorelle, Camila J. Mazzoni
Summary: Hybridization and introgression patterns in the Brazilian sea turtle population were investigated using RAD-Seq markers, mitogenomes, and satellite telemetry. The study found that all adult hybrids were first generation (F1) and most displayed loggerhead migratory behavior. Paternal leakage and different proportions of mitochondria from maternal and paternal species were also detected.
Review
Biology
Jeannie Mounger, Malika L. Ainouche, Oliver Bossdorf, Armand Cave-Radet, Bo Li, Madalin Parepa, Armel Salmon, Ji Yang, Christina L. Richards
Summary: This paper reviews the processes that contribute to the success of invasive species, highlighting the role of epigenetic and non-genetic mechanisms in creating trait variation within and among invasive populations. These mechanisms, such as exposure to environmental stress, hybridization, and whole-genome duplication, can lead to gene expression re-programming and epigenetic changes that contribute to phenotypic variation or novelty.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Andrea M. Quattrini, Karen E. Snyder, Risa Purow-Ruderman, Isabela G. L. Seiblitz, Johnson Hoang, Natasha Floerke, Nina I. Ramos, Herman H. Wirshing, Estefania Rodriguez, Catherine S. McFadden
Summary: Mitochondrial-nuclear discordance is commonly observed in phylogenetic reconstructions, and this study examines such discordance in Anthozoa using a large and comparable dataset. Results show pervasive discordance between mitochondrial and nuclear datasets, likely caused by introgressive hybridization and unique properties of mitochondrial genomes. The study highlights the caution needed when using mitochondrial genomes in analyses and adds to the understanding of anthozoan evolution.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Kyle E. McElroy, Stefan Mueller, Dunja Lamatsch, Laura Bankers, Peter D. Fields, Joseph R. Jalinsky, Joel Sharbrough, Jeffrey L. Boore, John M. Jr Jr Logsdon, Maurine Neiman
Summary: The study reveals that asexual reproduction in the New Zealand freshwater snail leads to significant changes in the important gene family rDNA, with asexual individuals harboring more rDNA-histone copies, potentially associated with functional consequences related to the loss of sexual reproduction.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Andrew W. Wood, Thomas F. Duda Jr
Summary: This study evaluated whether hybridization and introgression have impacted the evolutionary history of a subgenus of Conidae (Virroconus). The findings indicate that these mechanisms may have contributed to the adaptive radiation of Conidae by generating novel gene combinations and facilitating exploitation of distinct niches. Introgression of mitochondrial and nuclear gene regions was identified among Virroconus species, suggesting a complex interplay of genetic exchange in their evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Jessie A. Pelosi, W. Brad Barbazuk, Emily B. Sessa
Summary: The research investigates the genomic consequences of asexual reproduction in ferns. The study finds that Vittaria appalachiana, a gametophyte-only fern, exhibits certain distinct genomic features in terms of nucleotide expression compared to sexually reproducing species. The results provide new directions for further research on the genomic effects of asexual reproduction in gametophyte-only plants.
INTERNATIONAL JOURNAL OF PLANT SCIENCES
(2023)
Article
Multidisciplinary Sciences
Rusly Rosazlina, Niels Jacobsen, Marian Orgaard, Ahmad Sofiman Othman
Summary: Natural hybridization in Cryptocoryne from Peninsular Malaysia was studied using DNA sequencing data, identifying the parents of the putative hybrids as Cryptocoryne xpurpurea nothovar. purpurea. DNA analysis confirmed the hybrid status of these plants through an additive ITS sequence pattern from two parental species. Bidirectional hybridization was observed with identical sequences from both parental species, suggesting that each was the maternal parent in different accessions.
Article
Multidisciplinary Sciences
Ricardo Gonzalez Munoz, Daniel Lauretta, Maria Cielo Bazterrica, Francisco Alejandro Puente Tapia, Agustin Garese, Gregorio Bigatti, Pablo E. Penchaszadeh, Betina Lomovasky, Fabian H. Acuna
Summary: This study confirmed the presence of D. lineata in Argentina using both morphological and molecular tools, and found that the analyzed specimens were sterile, indicating the absence of sexual reproduction in the studied localities. Continued monitoring is crucial to assess the potential establishment of sexual reproduction, expansion of distribution range, or disappearance of D. lineata populations along the Argentine coast.
Article
Ecology
Andrew Dopheide, Leah K. Tooman, Stefanie Grosser, Barbara Agabiti, Birgit Rhode, Dong Xie, Mark I. Stevens, Nicola Nelson, Thomas R. Buckley, Alexei J. Drummond, Richard D. Newcomb
ECOLOGICAL APPLICATIONS
(2019)
Article
Ecology
Shelley S. Langton-Myers, Gregory I. Holwell, Thomas R. Buckley
JOURNAL OF EVOLUTIONARY BIOLOGY
(2019)
Article
Ecology
Thomas R. Buckley, Nathan P. Lord, Ana Ramon-Laca, Julia S. Allwood, Richard A. B. Leschen
JOURNAL OF BIOGEOGRAPHY
(2020)
Article
Ecology
Sarah N. Inwood, Gemma M. McLaughlin, Thomas R. Buckley, Murray P. Cox, Kim M. Handley, Tammy E. Steeves, Timothy J. Strabala, Rebecca McDougal, Peter K. Dearden
NEW ZEALAND JOURNAL OF ECOLOGY
(2020)
Letter
Plant Sciences
Jerry A. Cooper, Duckchul Park
Article
Evolutionary Biology
Sarah Bank, Thomas R. Buckley, Thies H. Buscher, Joachim Bresseel, Jerome Constant, Mayk De Haan, Daniel Dittmar, Holger Drager, Rafhiah S. Kahar, Albert Kang, Bruno Kneubuhler, Shelley S. Langton-Myers, Sven Bradler
Summary: Stick and leaf insects are large terrestrial herbivorous arthropods known for disguising themselves as plant parts. Their evolutionary history is shaped by convergent evolution and adaptive radiations, leading to morphological and ecological diversity among different lineages.
SYSTEMATIC ENTOMOLOGY
(2021)
Article
Evolutionary Biology
Chen Wu, Victoria G. Twort, Richard D. Newcomb, Thomas R. Buckley
Summary: The study found several meiotic genes duplicated in the New Zealand geographic parthenogenetic stick insect, some of which are rare or unique compared to other arthropods. These genes may play important roles in the evolution of reproductive mode.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Ann M. McCartney, Elena Hilario, Seung-Sub Choi, Joseph Guhlin, Jessica M. Prebble, Gary Houliston, Thomas R. Buckley, David Chagne
Summary: By utilizing data with varying coverage and read lengths for long read assembly, more contiguous and gene-complete genome assemblies can be achieved. It is important to develop assembly workflows based on the volume and read length of sequencing data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Mycology
Danny Haelewaters, Duckchul Park, Peter R. Johnston
Summary: Cyttaria is a unique genus that parasitizes trees in Nothofagus and Lophozonia in southern South America, Australia, and New Zealand. Genetic analysis shows that Cyttaria has an isolated position near the base of Helotiales, with a weak relationship with Polydesmia pruinosa and Chlorociboriaceae. The order Cyttariales is proposed to be a synonym of Helotiales. Nothofagus and Lophozonia in southern South America, Australia, and New Zealand. Genetic analysis shows that Cyttaria has an isolated position near the base of Helotiales, with a weak relationship with Polydesmia pruinosa and Chlorociboriaceae. The order Cyttariales is proposed to be a synonym of Helotiales.
MYCOLOGICAL PROGRESS
(2021)
Article
Ecology
Talia Brav-Cubitt, Richard A. B. Leschen, Andrew J. Veale, Thomas R. Buckley
Summary: This study found that urban reserves have the potential to retain high biodiversity, but populations within them may have reduced genetic diversity and be genetically differentiated due to urbanisation. The research also showed that differentiation can occur even within continuous forest, indicating the influence of urbanisation and other landscape factors on gene flow between populations.
NEW ZEALAND JOURNAL OF ECOLOGY
(2022)
Article
Plant Sciences
Peter R. Johnston, Duckchul Park
Summary: Fungi in the class Leotiomycetes are ecologically diverse, and many species of Hymenotorrendiella are specialized to certain hosts due to an endophytic phase in their life cycle. The biology of wood-inhabiting species is still unknown, but they are found in different regions and closely related to each other. The leaf-inhabiting H. communis has an interesting life cycle where it infects living leaves and later fruits on dead leaves.
NEW ZEALAND JOURNAL OF BOTANY
(2023)
Review
Multidisciplinary Sciences
Thomas R. Buckley, Robert J. B. Hoare, Richard A. B. Leschen
Summary: New Zealand alpine environments are home to a diverse range of insect species, with different adaptations to survive in the alpine zone. The genetic basis of these adaptations is being studied.
JOURNAL OF THE ROYAL SOCIETY OF NEW ZEALAND
(2024)
Article
Biochemistry & Molecular Biology
Andrew Dopheide, Talia Brav-Cubitt, Anastasija Podolyan, Richard A. B. Leschen, Darren Ward, Thomas R. Buckley, Manpreet K. Dhami
Summary: The lack of locally relevant DNA reference databases limits the potential for DNA-based biodiversity monitoring. This study demonstrates a sensitive and efficient method for generating DNA barcodes from invertebrate specimens, providing a foundation for DNA-based assessments and monitoring of biodiversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Editorial Material
Multidisciplinary Sciences
Graham P. Wallis, Thomas R. Buckley
JOURNAL OF THE ROYAL SOCIETY OF NEW ZEALAND
(2024)
Article
Zoology
Robert J. B. Hoare, Brian H. Patrick, Thomas R. Buckley, Talia Brav-Cubitt
Summary: This study reviews the endemic Notoreas perornata complex in New Zealand. The larvae of this species feed on Pimelea spp. in fragmented and threatened shrubland habitats. Allopatric populations differ in size and wing pattern, but not in genitalia. The mitochondrial DNA gene tree shows rapid recent divergence without diagnosable lineages. Based on the results, Notoreas simplex is considered synonymous with N. perornata, and N. perornata is considered a highly diverse but monotypic species. Conservation recommendations are made for 10 populations or groups of populations that show signs of subspecific divergence based on morphology and/or DNA data.
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)