Article
Multidisciplinary Sciences
Sandor Csosz, Ana C. Loss, Brian L. Fisher
Summary: The study assessed the diversity of Malagasy Aphaenogaster fauna using multiple lines of evidence including quantitative morphometric, qualitative morphological, and DNA sequence data. Five species were identified, three of which are new to science.
Article
Evolutionary Biology
James D. Boyko, Jeremy M. Beaulieu
Summary: The correlation between two categorical characters is often spurious, especially when it is based on a single replicate deep in time. This problem of false correlation can be solved by using the hidden Markov model (HMM) framework, which includes a statistical solution to the issue of single unreplicated evolutionary events. By developing a multirate independent model within the HMM framework, support for correlation can be drastically reduced, providing a practical solution for model misspecification and improving comparative methods in biology.
SYSTEMATIC BIOLOGY
(2023)
Article
Zoology
Enrico Schifani, Antonio Alicata
Summary: The ant genus Aphaenogaster is highly diverse in the West-Palearctic region, but its taxonomy poses challenges in several groups. The existence of redundant valid taxa without clear identities complicates specimen identification and biodiversity databases. Through literature review and study of material, taxonomic changes are proposed that will reduce the gap between nomenclature and actual understanding of species diversity.
Article
Evolutionary Biology
Odile Maliet, Helene Morlon
Summary: Diversification rates vary across species due to environmental conditions and species-specific features. A new inference technique is presented here that reduces computation time by using data augmentation, allowing for the estimation of posterior distribution of tree with extinct and unsampled lineages as well as associated diversification rates. Simulation results demonstrate the statistical performance of this approach, which is applied to the study of bird radiation.
SYSTEMATIC BIOLOGY
(2022)
Article
Genetics & Heredity
Xin-Yu Luo, Ru-Yi Yin, Xiang-Qin Huang, Yi Luo, Zhao-Min Zhou
Summary: In this study, the mitochondrial genome of Aphaenogaster japonica was reported, and it was found that the Stenammini and Myrmicini groups may not form a robust monophyletic group.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Multidisciplinary Sciences
Yi-Tian Fu, Renfu Shao, Guo-Hua Suleman, Wei Wang, Hui-Mei Wang, Guo-Hua Liu
Summary: We sequenced the mt genomes of two lice species and found that they share seven minichromosomes with the same gene content and arrangement. Our analysis revealed numerous inter-minichromosomal recombination events, as well as gene duplication, degeneration, deletion, and translocation. The hotspots for inter-minichromosomal recombination were identified as upstream regions of cox3 and nad2 genes. These findings provide important insights into mt genome evolution in metazoans.
Article
Biochemistry & Molecular Biology
Sudhir Kumar, Qiqing Tao, Alessandra P. Lamarca, Koichiro Tamura
Summary: Repeated runs of the same program can generate different molecular phylogenies from identical data sets under the same analytical conditions. This lack of reproducibility casts a long shadow on downstream research employing these phylogenies. However, our findings show that alternative phylogenies reconstruct evolutionary relationships with comparable accuracy and have similar log-likelihoods to the true tree. Computational irreproducibility plays a minor role in molecular phylogenetics, as the relationship between irreproducibility and inaccuracy is due to their common dependence on the amount of phylogenetic information in the data.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Entomology
Sebastian Salata, Celal Karaman, Kadri Kiran, Lech Borowiec
Summary: Members of the Aphaenogaster splendida group were reviewed, with 12 species recognized including three new species. Status restoration and rank elevation were also observed for some species. Detailed descriptions, measurements, habitat preferences, and activities of all 12 species were provided. Keys to workers and known gynes, as well as photographs of all species and their known castes, were presented.
Review
Ecology
Helene Morlon, Stephane Robin, Florian Hartig
Summary: The reliability of using birth-death processes to analyze the diversification and extinction dynamics of the past based on phylogenies of extant species is regularly questioned. However, when combined with appropriate prior hypotheses and regularization techniques, extant phylogenies can still provide important information about past diversification dynamics.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Mark Pagel, Ciara O'Donovan, Andrew Meade
Summary: Macroevolution poses challenges to evolutionary theory due to abrupt changes and long stagnation periods. This study introduces a statistical model that considers directional changes and evolvability changes to account for this uneven evolutionary landscape. In mammals, both processes independently contribute to macroevolution, with increased evolvability being more common than reduced evolutionary potentials. Large or sudden phenotypic changes can be statistically explained as biased random walks, bridging the gap between macroevolution and gradualist microevolution. This study emphasizes the importance of considering multiple evolutionary processes simultaneously.
NATURE COMMUNICATIONS
(2022)
Article
Evolutionary Biology
Jeremy Andreoletti, Antoine Zwaans, Rachel C. M. Warnock, Gabriel Aguirre-Fernandez, Joelle Barido-Sottani, Ankit Gupta, Tanja Stadler, Marc Manceau
Summary: Phylodynamic models aim to infer phylogenetic relationships, model parameters, and the number of lineages over time based on molecular sequence data. Recent developments include the integration of molecular and morphological data in a unified Bayesian inference framework, as well as new methodological developments in incorporating occurrence data and estimating lineage numbers. This research has practical applications in epidemiology and macroevolution, and has the potential to bridge the gap between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Robert J. Warren II, Antoine Guiguet, Chloe Mokadam, John F. Tooker, Andrew R. Deans
Summary: This study found that ants disperse oak galls of certain cynipid wasp species in a similar manner to how they disperse seeds with elaiosomes. The ants retrieve the galls, attracted by specific appendages called kapellos. The chemical composition and morphology of the appendages on seeds and galls are similar. The results suggest a convergence in ant-mediated dispersal between myrmecochorous seeds and oak galls, and challenge established assumptions in ant-plant research.
AMERICAN NATURALIST
(2022)
Article
Multidisciplinary Sciences
Jeffrey J. Quinn, Matthew G. Jones, Ross A. Okimoto, Shigeki Nanjo, Michelle M. Chan, Nir Yosef, Trever G. Bivona, Jonathan S. Weissman
Summary: This study used a Cas9-based lineage tracer to track the development and metastasis of lung cancer cells in a mouse model over months, revealing heterogeneity in metastatic capacity and genetic differences that drive invasiveness. The study also uncovered some genes driving metastasis and an unexpected suppressive role of KRT17 in metastasis.
Article
Biochemistry & Molecular Biology
Stilianos Louca, Matthew W. Pennell
Summary: Time-calibrated phylogenies of extant species are commonly used in estimating historical speciation and extinction rates, but controversy exists due to zero inflation in extinction estimates. A novel explanation is provided based on the discovery of alternative congruent diversification scenarios, which may result in estimators converging to scenarios with negative extinction rates. This mechanism explains the zero inflation of extinction rate estimates without detectable model violations, potentially resolving a long-standing mystery in phylogenetics.
Article
Plant Sciences
Min Zhang, Yi-Wei Tang, Ying Xu, Takahiro Yonezawa, Yang Shao, Yu-Guo Wang, Zhi-Ping Song, Ji Yang, Wen-Ju Zhang
Summary: A high level of rDNA polymorphism exists universally in the genus Camellia, with functional rDNA being relatively conserved. Sequence variations mainly come from rRNA pseudogenes and GC-rich regions in the genome, indicating a mixture of concerted and birth-and-death evolution in Camellia.
Article
Entomology
S. Pita, P. Lorite, A. Cuadrado, Y. Panzera, J. De Oliveira, K. C. C. Alevi, J. A. Rosa, S. P. C. Freitas, A. Gomez-Palacio, A. Solari, C. Monroy, P. L. Dorn, M. Cabrera-Bravo, F. Panzera
Summary: The subfamily Triatominae, which includes more than 150 blood-sucking species, has stable chromosome numbers. Research has shown that the mobility of rDNA clusters has been common in the evolutionary history of this group, potentially affecting genetic recombination and species diversification.
MEDICAL AND VETERINARY ENTOMOLOGY
(2022)
Article
Ecology
Eugenia E. Montiel, Pablo Mora, Jose M. Rico-Porras, Teresa Palomeque, Pedro Lorite
Summary: The red palm weevil, known for its harmful effects on palm trees, has limited genetic information available. This study presents the characterization and chromosomal location of satellite DNA in the red palm weevil, and suggests a potential role of these satellite DNA sequences in the development of the species.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Areli Ruiz-Mena, Pablo Mora, Eugenia E. Montiel, Teresa Palomeque, Pedro Lorite
Summary: The ant species T. ibericum from the Iberian Peninsula may form supercolonies, potentially invasive and pest species. The complete mitogenome of T. ibericum was analyzed, revealing gene rearrangements unique to Tapinoma species and potentially phylogenetically informative. Phylogenetic analysis supported the monophyletic nature of the genus Tapinoma within the Dolichoderinae subfamily.
Article
Genetics & Heredity
Pablo Mora, Eugenia E. Montiel, Teresa Palomeque, Pedro Lorite
Summary: In this study, the complete mitochondrial genome of the blister beetle Hycleus scutellatus is reported. The phylogenetic analysis suggests that Hycleus species are closely related to the genus Mylabris. This study provides a new resource for future evolutionary analyses of blister beetles within the family Meloidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Multidisciplinary Sciences
Martina Hejnickova, Martina Dalikova, Magda Zrzava, Frantisek Marec, Pedro Lorite, Eugenia E. Montiel
Summary: Comparative genomic hybridization and FISH revealed significant variation in the composition of the W chromosome in Peribatodes rhomboidaria, with an abundance of mobile elements. Bioinformatic analysis and FISH mapping confirmed the enrichment of ten putative W chromosome-enriched repeats, mainly LTR and LINE mobile elements. This study provides evidence that mobile elements are driving the differentiation of the W chromosome in Lepidoptera.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Pablo Mora, Sebastian Pita, Eugenia E. E. Montiel, Jose M. Rico-Porras, Teresa Palomeque, Francisco Panzera, Pedro Lorite
Summary: The genome of Triatoma delpontei, a species within Heteroptera, is two to three times larger than other Heteroptera genomes. An analysis of repetitive DNA sequences revealed that satellite DNA makes up more than half of the T. delpontei genome. These satellite DNA sequences have played a significant role in the evolution of Triatominae genomes.
Article
Entomology
O. Sanllorente, A. Lenoir, E. Perdereau, F. Ruano, F. M. Azcarate, M. Silvestre, P. Lorite, A. Tinaut
Summary: Social parasites rely on chemical cues to invade and coexist with hosts. Most ants that are obligate social parasites can parasitize several host species with different levels of chemical similarity. However, there are exceptions, such as Rossomyrmex minuchae, which can only parasitize a single host species. A recent discovery of a new R. minuchae population showed local adaptation to a different host species, P. nasuta, and genetic differences from other populations, indicating historical genetic isolation and potential speciation.
Article
Biochemistry & Molecular Biology
Diogo C. Cabral-de-Mello, Pablo Mora, Jose M. Rico-Porras, Ana B. S. M. Ferretti, Teresa Palomeque, Pedro Lorite
Summary: This study provides insights into the abundance and distribution of satellite DNA in heteropterans, particularly in the male genome, challenging the traditional belief that euchromatin is not enriched with satDNAs.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Camille Cornet, Pablo Mora, Hannah Augustijnen, Petr Nguyen, Marcial Escudero, Kay Lucek
Summary: Repetitive elements can cause large-scale chromosomal rearrangements, potentially promoting reproductive isolation and speciation. The role of repetitive elements in holocentric organisms and their association with karyotype changes in Erebia butterflies and Carex sedges were investigated at both micro- and macro-evolutionary scales. The results suggest that repetitive elements are associated with population differentiation and chromosomal rearrangements in holocentric clades, playing a role in adaptation and species diversification.
Article
Entomology
Francisco Panzera, Angeles Cuadrado, Pablo Mora, Teresa Palomeque, Pedro Lorite, Sebastian Pita
Summary: This study analyzed the distribution of microsatellites in the holocentric chromosomes of Triatominae, which are vectors of Chagas disease. The results showed that there are differences in microsatellite distribution between Triatomini and Rhodniini species, with higher abundance and diversity in Triatomini. Additionally, a high abundance of GATA repeats was found in the Y chromosome of all Triatomini species, suggesting it is an ancestral trait specific to Triatomini.
Article
Biochemistry & Molecular Biology
Anna Volenikova, Karolina Luksikova, Pablo Mora, Tomas Pavlica, Marie Altmanova, Jana Stundlova, Sarka Pelikanova, Sergey A. Simanovsky, Marek Jankasek, Martin Reichard, Petr Nguyen, Alexandr Sember
Summary: Satellite DNA is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. Through studying satDNA in African annual killifishes of the genus Nothobranchius, we found that repeats associated with (peri)centromeric regions evolve rapidly and exhibit different evolutionary trends in two clades.
CHROMOSOME RESEARCH
(2023)
