Article
Biology
Diana Tataru, Emma C. Wheeler, Kathleen G. Ferris
Summary: Spatially and temporally varying selection can either reinforce or erode divergence between closely related species. In a drought year, strong divergent habitat-mediated selection maintains species divergence, while in an unusually wet year, the relaxation of divergent selection weakens species differences. Therefore, temporally and spatially varying selection may have opposing roles in mediating species boundaries.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Plant Sciences
Zeyu Zheng, Ying Li, Minjie Li, Guiting Li, Xin Du, Hu Hongyin, Mou Yin, Zhiqiang Lu, Xu Zhang, Nawal Shrestha, Jianquan Liu, Yongzhi Yang
Summary: The study sequenced individuals from three closely related Carpinus species and found low genetic diversity and small population size in Carpinus tibetana, while Carpinus monbeigiana and Carpinus mollicoma diverged around 1.2 million years ago with bidirectional gene flow. Highly diverged genes related to thermoregulation, plant development, and stress response were identified, highlighting adaptations to their habitats. The study also revealed a significant population decline and vulnerability in Carpinus tibetana. The genomic resource generated will aid in future speciation research.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Elinor Jax, Paolo Franchini, Vaishnovi Sekar, Jente Ottenburghs, Daniel Monne Parera, Roman T. Kellenberger, Katharine E. Magor, Inge Mueller, Martin Wikelski, Robert H. S. Kraus
Summary: Animal species differ in their ability to fight off infections. We conducted a study using genomics to investigate the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus. We found that specific genes involved in the immune response play crucial roles and may contribute to differences in susceptibility and resistance to infectious diseases in wild birds. These findings enhance our understanding of host-pathogen interactions and provide new insights into potential drug targets.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Forestry
Zirui Liu, Chengjie Gao, Jin Li, Yingchun Miao, Kai Cui
Summary: This study assessed the phenotypic diversity of Pinus yunnanensis natural populations, revealing abundant variations within and among populations. Temperature was found to be the most important factor affecting the diameter of breast height. Cluster analysis showed that populations were not strictly clustered according to geographic distance. The Lufeng population had noticeable advantages in multiple traits, while the Yongren population showed the worst performance. Eleven superior families were successfully selected using a comprehensive scoring method and principal component analysis.
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
Biochemistry & Molecular Biology
Dongying Xie, Pohao Ye, Yiming Ma, Yongbin Li, Xiao Liu, Peter Sarkies, Zhongying Zhao
Summary: Different modes of reproduction have significant impact on genome composition. This study investigates the gene regulation in hybrid embryos resulting from crosses between Caenorhabditis briggsae and its outcrossing sister species Caenorhabditis nigoni. The results show that gene regulation plays a crucial role during hybridization, and the regulation of C. nigoni genome is more stable compared to C. briggsae. These findings provide insights into how selfing species maintain genomic identity despite genetic exchanges with closely related outcrossing species.
Article
Biochemistry & Molecular Biology
Beatriz Mello, Qiqing Tao, Jose Barba-Montoya, Sudhir Kumar
Summary: Simultaneous molecular dating of population and species divergences is crucial in various biological investigations, and methods such as Bayesian relaxed clock and non-Bayesian RelTime are commonly used. The study indicates that Bayesian approach generally provides accurate molecular date estimates for datasets containing both population and species variations, while RelTime shows similar performance in terms of computational efficiency.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Matthew Wascher, Laura S. Kubatko
Summary: This article investigates the effect of selection on regions of the genome on the accuracy of species-level phylogenetic inference. By using mathematical approximation, it is shown that direct selection has minimal impact on the distribution of gene genealogies, suggesting that many coalescent-based methods are robust to selection. However, selection biases the estimation of speciation times, causing underestimation.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Juba Nait Saada, Zoi Tsangalidou, Miriam Stricker, Pier Francesco Palamara
Summary: Accurate inference of the time to the most recent common ancestor (TMRCA) and allele ages is crucial in population genetic analyses. A likelihood-free method, CoalNN, using a convolutional neural network, predicts pairwise TMRCA and allele ages from sequencing or SNP array data. CoalNN is trained through simulation, adapts to varying parameters using transfer learning, and performs better than model-based approaches. It was applied to analyze 2,504 samples from 26 populations, inferring the age of about 80 million variants. The method captures population variations and identifies variants predicted to be pathogenic, highlighting the effectiveness of simulation-trained models in large genomic datasets.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Marius Roesti, Jeffrey S. Groh, Stephanie A. Blain, Magnus Huss, Peter Rassias, Daniel I. Bolnick, Yoel E. Stuart, Catherine L. Peichel, Dolph Schluter
Summary: Species competing for resources commonly share predators. However, the effects of shared predation are still not well understood. In this study, we compared antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that are all exposed to a trout predator. Our findings show that there is divergence in antipredator traits between the species, with stickleback exhibiting increased antipredator adaptations in sympatry and sculpin exhibiting decreased adaptations. The changes in feeding morphology, diet, and habitat use were primarily driven by stickleback evolution. These results suggest that asymmetric ecological character displacement indirectly influenced the vulnerability of stickleback and sculpin to shared predation, leading to divergence in antipredator traits between sympatric species.
Article
Plant Sciences
Jing Chen, Yujian Guo, Xinwen Hu, Kaibing Zhou
Summary: This study compared chloroplast genome sequences of 13 different oil-tea camellia samples to identify an undetermined species from Hainan Province. The findings indicate that chloroplast genome sequences can be used for species identification and phylogenetic analysis of oil-tea camellia.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Amy L. Dapper, Garett P. Slater, Katherynne Shores, Brock A. Harpur
Summary: Many animal species exhibit haplodiploidy, where fertilized eggs develop into diploid females and unfertilized eggs develop into haploid males. Sex-specific reproductive genes, shared within the same genome but experiencing selection in different ploidal environments, are of particular interest in studying evolutionary genomic patterns in haplodiploid species. Theoretical expectations suggest that reproductive genes evolve more rapidly than constitutively expressed genes in haplodiploid genomes.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Toman Barsbai, Dieter Lukas, Andreas Pondorfer
Summary: Research has shown that human populations and nonhuman mammal and bird species living in the same environment exhibit high levels of similarity in their behaviors, suggesting that local conditions may select for similar behaviors.
Editorial Material
Biochemistry & Molecular Biology
Jenn Coughlan
Summary: As hybridization is found to be common in nature, understanding how natural selection affects hybrids is now more important for speciation. A study in PLOS Biology uses threespine stickleback to identify a genomic marker of ecological incompatibilities.
Article
Multidisciplinary Sciences
F. He, K. A. Steige, V Kovacova, U. Goebel, M. Bouzid, P. D. Keightley, A. Beyer, J. de Meaux
Summary: The study suggests that gene expression differences in response to dehydration stress are influenced by genetic regulation, with the direction of plasticity affecting the effects of gene variants. Evolution of gene expression in Arabidopsis lyrata tends to amplify stress response, while in Arabidopsis halleri it tends to mitigate stress response.
NATURE COMMUNICATIONS
(2021)
Article
Ecology
Melisa Olave, Luciano J. Avila, Jack W. Sites, Mariana Morando
JOURNAL OF BIOGEOGRAPHY
(2020)
Article
Biochemistry & Molecular Biology
Martin M. Femenias, Luciano J. Avila, Jack W. Sites, Mariana Morando
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2020)
Article
Zoology
Paula C. Escudero, Maria A. Gonzalez Marin, Mariana Morando, Luciano J. Avila
JOURNAL OF HERPETOLOGY
(2020)
Article
Ecology
Shai Meiri, Luciano Avila, Aaron M. Bauer, David G. Chapple, Indraneil Das, Tiffany M. Doan, Paul Doughty, Ryan Ellis, Lee Grismer, Fred Kraus, Mariana Morando, Paul Oliver, Daniel Pincheira-Donoso, Marco Antonio Ribeiro-Junior, Glenn Shea, Omar Torres-Carvajal, Alex Slavenko, Uri Roll
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2020)
Article
Biochemistry & Molecular Biology
Mariana Morando, Melisa Olave, Luciano J. Avila, Jack W. Sites, Adam D. Leache
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2020)
Correction
Biochemistry & Molecular Biology
Mariana Morando, Melisa Olave, Luciano J. Avila, Jack W. Sites, Adam D. Leache
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Zoology
Luciano Javier Avila, Juan Esteban Vrdoljak, Cintia Debora Medina, Juan Garcia Massini, Cristian Hernan Fulvio Perez, Jack W. Sites, Mariana Morando
Summary: The newly described species Liolaemus galactostictos sp. nov. stands out from other members of its group due to its black dorsal coloration pattern, unique to this species. Found only in its type locality on the Velasco Mountains in Argentina, this strictly saxicolous, viviparous lizard feeds on insects.
Article
Zoology
Benjamin Michael Marshall, Paul Freed, Laurie J. Vitt, Pedro Bernardo, Gernot Vogel, Sebastian Lotzkat, Michael Franzen, Jakob Hallermann, Richard D. Sage, Brian Bush, Marcelo Ribeiro Duarte, Luciano Javier Avila, David Jandzik, Boris Klusmeyer, Brad Maryan, Jiri Hosek, Peter Uetz
Article
Biochemistry & Molecular Biology
Kevin I. Sanchez, Luciano J. Avila, Jack W. Sites, Mariana Morando
Summary: Recent advances in conceptual and methodological approaches have allowed for more comprehensive studies on species delimitation, particularly in cases with recent divergence times and large effective population sizes. The study on Liolaemus kingii group in Patagonia revealed the importance of using multiple lines of evidence to accurately determine species boundaries and minimize potential errors in classification. The findings suggest that this group can serve as a model system for studying diversification and hybridization in nature, influenced by past climatic changes and generalist morphologies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Zoology
M. Victoria Brizio, Facundo Cabezas-Cartes, Jimena B. Fernandez, Rodrigo Gomez Ales, Luciano J. Avila
Summary: The study reveals that the critically endangered Anelo Sand Dunes Lizard is currently not under environmental stress, but thermoregulates below its preferred body temperature to avoid overheating. An increase in environmental temperature due to global warming will strongly impact their thermal safety margins, increasing their vulnerability.
CANADIAN JOURNAL OF ZOOLOGY
(2021)
Article
Evolutionary Biology
Damien Esquerre, J. Scott Keogh, Diego Demangel, Mariana Morando, Luciano J. Avila, Jack W. Sites, Francisco Ferri-Yanez, Adam D. Leache, Alfaro Michael
Summary: Understanding the reasons behind the heterogeneity among gene trees can improve the accuracy of species trees. This study examines the phylogenomics of a group of South American lizards and finds high levels of discordance between different types of DNA sequences, which can be attributed to extensive incomplete lineage sorting and introgression. These findings shed light on the historical processes that have influenced the evolution of these lizards in the context of Andean orogeny and glacial cycles.
SYSTEMATIC BIOLOGY
(2022)
Article
Ecology
Jared A. Grummer, Luciano J. Avila, Mariana M. Morando, Adam D. Leache
Summary: This study compared three hybrid zones between four species in the Liolaemus fitzingerii group of lizards, confirming sharp species boundaries and geographically localized hybrid zones. The analysis found differences in performance between mitochondrial and nuclear DNA in terms of clines, highlighting the need for further investigation into hybrid zones as hard species boundaries or promoters of speciation.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Martin M. Femenias, Juan C. Santos, Jack W. Sites, Luciano J. Avila, Mariana Morando
Summary: Motivation: Transposable elements (TEs) play a significant role in genomes and their study is hindered by identification and quantification difficulties. In this study, a new pipeline called ExplorATE was developed to quantify active TEs in both model and non-model organisms. ExplorATE achieved better estimates of non-co-transcribed TEs and consumed less execution time compared to other alignment-based or mapping-based software.
Article
Multidisciplinary Sciences
Neil Cox, Bruce E. Young, Philip Bowles, Miguel Fernandez, Julie Marin, Giovanni Rapacciuolo, Monika Bohm, Thomas M. Brooks, S. Blair Hedges, Craig Hilton-Taylor, Michael Hoffmann, Richard K. B. Jenkins, Marcelo F. Tognelli, Graham J. Alexander, Allen Allison, Natalia B. Ananjeva, Mark Auliya, Luciano Javier Avila, David G. Chapple, Diego F. Cisneros-Heredia, Harold G. Cogger, Guarino R. Colli, Anslem de Silva, Carla C. Eisemberg, Johannes Els, Ansel Fong G., Tandora D. Grant, Rodney A. Hitchmough, Djoko T. Iskandar, Noriko Kidera, Marcio Martins, Shai Meiri, Nicola J. Mitchell, Sanjay Molur, Cristiano de C. Nogueira, Juan Carlos Ortiz, Johannes Penner, Anders G. J. Rhodin, Gilson A. Rivas, Mark-Oliver Rodel, Uri Roll, Kate L. Sanders, Georgina Santos-Barrera, Glenn M. Shea, Stephen Spawls, Bryan L. Stuart, Krystal A. Tolley, Jean-Francois Trape, Marcela A. Vidal, Philipp Wagner, Bryan P. Wallace, Yan Xie
Summary: Global assessments have shown that 40.7% of amphibians, 25.4% of mammals, and 13.6% of birds are threatened with extinction, but reptiles have been excluded from these assessments. This study provides a comprehensive extinction-risk assessment for reptiles and finds that at least 21.1% of species are threatened, with similar major threats as other tetrapods. Reptiles in forests are more threatened than those in arid habitats. Threatened reptiles tend to be isolated from other threatened tetrapods.
Article
Ecology
Danielle L. Edwards, Luciano J. Avila, Lorena Martinez, Jack W. Sites, Mariana Morando
Summary: This study investigates the relationship between environmental and phenotypic evolution in the lizard genus Liolaemus. The results suggest that body shape in Liolaemus species has rapidly evolved and is correlated with the occupation of different structural habitats, indicating adaptation for maximal locomotory performance in these environments.
ECOLOGY AND EVOLUTION
(2022)
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)
