Article
Biochemistry & Molecular Biology
Xavier Didelot, Igor Siveroni, Erik M. Volz
Summary: Phylogenetic dating is a powerful method for drawing epidemiological interpretations from pathogen genomic data. However, commonly used relaxed clock models may not be compatible with biological expectations, leading to estimates with low precision and biased confidence intervals. A new additive relaxed clock model has been proposed to address this issue, providing more accurate estimates of evolutionary rates and ancestral dates.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Tomas Flouri, Jun Huang, Xiyun Jiao, Paschalia Kapli, Bruce Rannala, Ziheng Yang
Summary: The multispecies coalescent model provides a natural framework for phylogenetic analysis of genomic data, allowing estimation of species divergence times and ancestral population sizes. Clock violation should be considered, and the relaxed-clock models can extract valuable phylogenetic information from gene-tree branch lengths.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Xia Liu, Zhaoshan Wang, Wei Wang, Qinqin Huang, Yanfei Zeng, Yu Jin, Honglei Li, Shuhui Du, Jianguo Zhang
Summary: This study examines the origin and biogeography of the Populus genus using phylogenetic analysis of chloroplast fragments. The results suggest that the early divergences of the Salicaceae family occurred in Eurasia after the Cretaceous-Paleogene mass extinction, with subsequent spread to other regions. Modern Populus species began to diversify during the early Oligocene, potentially facilitated by climate changes. Populus species from Eurasia colonized North America via the Bering Land Bridges. The present-day distribution of Populus can be explained by differences in extinction rates in different regions. Further research is needed to test these hypotheses. This study highlights the importance of combining phylogenetic analysis and biogeographic interpretations to understand the origin and distribution of biodiversity in temperate plant floras.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Sebastian Kirchhof, Mariana L. Lyra, Ariel Rodriguez, Ivan Ineich, Johannes Mueller, Mark-Oliver Roedel, Jean-Francois Trape, Miguel Vences, Stephane Boissinot
Summary: Climate change greatly impacts the diversity and evolution of the world's biota. Research shows that the Old World lacertid lizard lineages diversified after the Eocene-Oligocene boundary, with a particular focus on the sub-Saharan Acanthodactylus species and their environmental adaptations.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Karolina S. Kohari, Valeria Palma-Onetto, Rudolf H. Scheffrahn, Alexandre Vasconcellos, Eliana M. Cancello, Rafaella G. Santos, Tiago F. Carrijo
Summary: This study investigated the genetic patterns and phylogeographical processes of Nasutitermes kemneri, an endemic termite in the South American diagonal of open formations. The results revealed the presence of two well-differentiated genetic groups, the Northeastern and the Southwestern populations, which diverged around 2.5 million years ago during the Pliocene-Pleistocene boundary. The Northeastern population exhibited complex genetic structure and experienced repetitive retraction-expansion events due to climactic fluctuations during the Quaternary, while the Southwestern population displayed a star-shaped haplotype structure, suggesting its role as a refugia during interglacial periods.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Lukas Pecina, Peter Vd'acny
Summary: In this study, the phylogenetic relationships and divergence times of clevelandellids living in the hindgut of Panesthiinae cockroaches were reconstructed using nuclear and hydrogenosomal rRNA molecules. The results showed that both types of markers supported the monophyletic origin of the family Clevelandellidae and its four genera. Bayesian relaxed molecular clock analyses suggested that the last common ancestor of Clevelandellidae likely emerged during the Late Cretaceous in the Oriental region and its descendants expanded to Australia during the Neogene colonization of their host Panesthiinae cockroaches. The findings also suggested that the LCA of Clevelandellida may have evolved in ectothermic vertebrates, and might have been transmitted to cockroaches through amphibian feces.
Article
Biology
Siti Zulaiha Zolkaply, Thinh Dinh Do, Md Asaduzzaman, Ying Giat Seah, David Hurwood, Peter Mather, Md Moshiur Rahman, Li Lian Wong
Summary: Herbivorous fish, particularly rabbitfish (Siganidae), play a crucial role in coral reef ecosystems by removing algal turfs growing on corals. Our study on eight Siganus species from the South China Sea and meta-analysis of sequences from ten species revealed the impact of paleo-climatic events and changes in natural geographical distributions on the diversification and speciation of the siganid species. The morphological-molecular approach used in this study provides valuable insights into the phylogenetic relationships and demographic histories of rabbitfish species.
Article
Plant Sciences
Shi-Liang Zhou, Chao Xu, Jing Liu, Yan Yu, Ping Wu, Tao Cheng, De-Yuan Hong
Summary: By sequencing nuclear genes and chloroplast regions of all species in the genus Paeonia, this study reveals that Paeoniaceae separated from Saxifragales in the late Cretaceous, diverged into woody and herbaceous clades in the late Oligocene, and dispersed from the Pan-Himalaya to East Asia, North America, Central Asia, and Europe. Multiple glacial cycles in Europe facilitated the hybridization and formation of allotetraploid species. A new taxonomic system with two subgenera and seven sections is suggested based on the phylogeny of Paeonia L.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Weichen Huang, Lin Zhang, J. Travis Columbus, Yi Hu, Yiyong Zhao, Lin Tang, Zhenhua Guo, Wenli Chen, Michael McKain, Madelaine Bartlett, Chien-Hsun Huang, De-Zhu Li, Song Ge, Hong Ma
Summary: Poaceae (the grasses) is a economically important angiosperm family, with a wide global distribution and diverse ecosystems. A comprehensive analysis of genomic and transcriptomic data was conducted to reconstruct the phylogeny of Poaceae, providing strong support for the monophyly of 11 subfamilies and suggesting multiple independent origins of C4 photosynthesis. This study offers valuable resources and insights for evolutionary analyses of the grass family.
Article
Biochemistry & Molecular Biology
Yanli Che, Wenbo Deng, Weijun Li, Jiawei Zhang, Yukihiro Kinjo, Gaku Tokuda, Thomas Bourguignon, Nathan Lo, Zongqing Wang
Summary: This study investigated the phylogenetic relationships and geographical distribution of Cryptocercus, demonstrating the significant roles of both vicariance and dispersal in shaping the distribution and diversity of these woodroaches. The findings supported six major lineages of Cryptocercus with clear geographical patterns, providing evidence for multiple dispersal and vicariance events that occurred over various time periods in the evolutionary history of the genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lisandra Benitez-Alvarez, Laia Leria, Rosa Fernandez, Eduardo Mateos, Younes El Ouanighi, Nard Bennas, Majida El Alami, Mohamed Yacoubi-Khebiza, Houssam Ayt Ougougdal, Marta Riutort
Summary: Using large data sets obtained from transcriptomic data, we investigated the evolutionary history of the genus Dugesia in the Mediterranean region. The results showed that the region's paleogeological history played a significant role in the diversification of the genus. Multiple biogeographic clades were identified, and their internal relationships were analyzed. This study provides insights into the evolution of Dugesia and marks the beginning of the genomic era in phylogenetic studies on Tricladida.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Qiong Yu, Fu-Sheng Yang, Ya-Xing Chen, Hui Wu, Stefanie M. Ickert-Bond, Xiao-Quan Wang
Summary: By reconstructing the transcriptome-based phylogeny of 19 diploid Ephedra species, the evolutionary history of the gymnosperm genus Ephedra was investigated. The results revealed that Ephedra originated from Mediterranean species and split into three clades: American species, E. rhytidosperma, and other Asian species. Reticulate evolution was found to be common in Ephedra, and the genus likely originated in the late Cretaceous along the Tethys coast.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G. Pybus, Aris Katzourakis
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Ronghui Fan, Keyi Tang, Liang Dou, Changkun Fu, Abu ul Hassan Faiz, Xuming Wang, Yufan Wang, Shunde Chen, Shaoying Liu
Summary: In this study, the phylogenetic relationship of the elegant water shrew, Nectogale elegans, was inferred using sequencing of mitochondrial and nuclear genes. The results revealed two species within the genus Nectogale: N. elegans and N. sikhimensis. The split between these two species may be related to the uplift of the Qinghai-Tibet Plateau, which is supported by both molecular and morphological evidence.
ECOLOGY AND EVOLUTION
(2022)
Article
Zoology
Liang Wang, Shuangmei Ding, Stephen L. Cameron, Xin Li, Yue Liu, Gang Yao, Ding Yang
Summary: Vermileonidae is an odd and rarely collected dipteran family, with larvae famous for their unique prey behavior and adults rarely seen. Researchers have sequenced the complete mitochondrial genome of Vermileonidae for the first time, providing insights into its phylogenetic relationships with other flies. By combining mitochondrial genome data with morphology, geographical distribution, and geological history, researchers propose that Vermileonidae originated in India and spread to Africa, the Palaearctic, and the Nearctic through land bridges.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biodiversity Conservation
Catherine R. M. Attard, Jonathan Sandoval-Castillo, Dean M. Gilligan, Peter J. Unmack, Leanne K. Faulks, Luciano B. Beheregaray
Summary: This study demonstrates the application of genomic techniques in detecting hybrid populations of golden perch in the Murray-Darling Basin, southeast Australia, revealing admixture through a genome-wide dataset of 6,862 SNPs. The research suggests that stocking programs may introduce non-endemic ancestry, impacting genetic variation in the wild.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Biodiversity Conservation
Alicia Dalongeville, Erica S. Nielsen, Peter R. Teske, Sophie von Der Heyden
Summary: The study found that temperature variation is a prominent source of intraspecific genetic variation along the South African coastline characterized by high environmental heterogeneity. Genetic diversity differs between bioregions, but does not display higher levels within the core of each species' range when assessed across multiple species.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Ecology
Emily J. Booth, Jonathan Sandoval-Castillo, Catherine R. M. Attard, Dean M. Gilligan, Peter J. Unmack, Luciano B. Beheregaray
Summary: This study reveals the role of aridification in driving the divergence of a migratory freshwater species in Australia during the late Pleistocene. The findings are important for informing the conservation management of aquatic organisms under climate change.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Ecology
Abbie C. Hay, Jonathan Sandoval-Castillo, Georgina M. Cooke, Ning L. Chao, Luciano B. Beheregaray
Summary: This study examines the role of natural selection in the evolutionary divergence of the Amazonian characin fish. The results suggest that variation in turbidity and pH contribute to adaptive divergence, and genes involved in acid-sensitive ion transport pathways and light-sensitive photoreceptor pathways are associated with this variation.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Andrea Bertram, David Fairclough, Jonathan Sandoval-Castillo, Chris Brauer, Anthony Fowler, Maren Wellenreuther, Luciano B. Beheregaray
Summary: The efficacy of fisheries management strategies depends on carrying out stock assessment and management actions at appropriate spatial scales. This study investigated the population genomics of a heavily exploited snapper species along the Australian coastline to understand population structure, connectivity, and the compatibility of current management practices. The results revealed low genetic differentiation and high connectivity across Western Australia, but also identified genetic discontinuities in certain regions, suggesting a need for a review of current spatial management.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Environmental Sciences
Chris J. Brauer, Jonathan Sandoval-Castillo, Katie Gates, Michael P. Hammer, Peter J. Unmack, Louis Bernatchez, Luciano B. Beheregaray
Summary: Under climate change, species without the ability to shift their range rely on genetic variation for adaptation. Genomic vulnerability studies often overlook hybridization as a source of adaptive variation. This study found that hybrid populations of rainbowfish showed reduced vulnerability to climate change compared to pure narrow endemics, highlighting the importance of hybrid populations and adaptive introgression in the evolutionary rescue of species with narrow environmental ranges.
NATURE CLIMATE CHANGE
(2023)
Editorial Material
Geosciences, Multidisciplinary
R. P. Bourman, C. V. Murray-Wallace, C. Wilson, L. Mosley, J. Tibby, D. D. Ryan, E. D. De Carli, A. Tulley, A. P. Belperio, D. Haynes, A. Roberts, C. Westell, E. J. Barnett, S. Dillenburg, L. B. Beheregaray, P. A. Hesp
AUSTRALIAN JOURNAL OF EARTH SCIENCES
(2023)
Article
Ecology
Katie Gates, Jonathan Sandoval-Castillo, Chris J. Brauer, Peter J. Unmack, Martin Laporte, Louis Bernatchez, Luciano B. Beheregaray
Summary: In order to preserve the diversity of ecological and genetic factors in hotspots like tropical rainforests, it is important to understand the forces behind biodiversity. Through studying an Australian rainbowfish, Melanotaenia splendida splendida, across wet tropical regions, we found that environmental gradients and terrain structure strongly influence genetic and morphological variation. While neutral genetic population structure is mostly affected by limited gene flow, ecological variables are equally effective in explaining overall genetic variation and better at explaining body shape variation. The strongest environmental predictors are hydrological and thermal variables, which are correlated with heritable habitat-associated dimorphism in rainbowfish. Climate-associated genetic variation is significantly associated with morphology, supporting the heritability of shape variation. These results highlight the evolved functional differences among localities and emphasize the importance of hydroclimate in early stages of diversification. It is expected that tropical rainforest endemics will need to undergo significant evolutionary responses to mitigate fitness losses caused by climate change.
Article
Fisheries
A. Bertram, J. Bell, C. J. Brauer, A. Fowler, P. Hamer, J. Sandoval-Castillo, J. Stewart, M. Wellenreuther, L. B. Beheregaray
Summary: In southeastern Australia, population genomic differentiation in snapper is concordant with coastal biogeographic boundaries and related to spawning and recruitment dynamics. The current management boundaries align with genetic breaks at bioregional boundaries or local-scale variation. This study highlights the value of population genomic surveys in uncovering stock boundaries and demographic variation related to spawning and recruitment in species with high dispersal potential, and emphasizes the importance of marine biogeography in shaping population structure in commercially important species.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Environmental Sciences
Karl Moy, Jason Schaffer, Michael P. Hammer, Catherine R. M. Attard, Luciano B. Beheregaray, Richard Duncan, Mark Lintermans, Culum Brown, Peter J. Unmack
Summary: The study explores the threat of translocating species on freshwater fish biodiversity and presents a successful case of conserving Running River rainbowfish. By captive-breeding wild fish and translocating them to unoccupied habitats, two populations of Running River rainbowfish were established, but challenges of predation and release timing remain. This provides valuable insights for similar conservation programs involving short-lived fish species.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2023)
Article
Environmental Sciences
Paula M. de Coito, Arsalan Emami-Khoyi, Terry A. Hedderson, Robert J. Toonen, Peter R. Teske, George M. Branch
Summary: Seagrass habitats are declining globally, endangering seagrass-associated animals such as the Critically Endangered limpet Siphonaria compressa. This rare mollusk is found in only two separate lagoons in South Africa and relies on a specific seagrass species for survival. Genetic and morphological analysis revealed that the two populations are distinct subspecies and therefore translocation between them is not recommended as it may worsen the risk of extinction. Conservation measures for each population, such as seagrass bed protection and restoration, should be implemented instead.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2023)
Article
Ecology
Arsalan Emami-Khoyi, Candice M. Jooste, Ryan J. Wasserman, Tatenda Dalu, Morgan J. J. Raath-Kruger, Bettine Jansen van Vuuren, Peter R. Teske
Summary: This study investigated the spatial genetic structure and dispersal history of a calanoid copepod species in temporary wetlands in the Eastern Cape province of South Africa. The wetland populations were highly structured across the landscape and potentially represent cryptic speciation. The dispersal history of these populations was affected by a postulated barrier, which eventually disappeared, allowing the species to spread into coastal regions.
FRESHWATER BIOLOGY
(2023)
Article
Evolutionary Biology
Eleanor A. L. Pratt, Luciano B. Beheregaray, Pedro Fruet, Gabriela Tezanos-Pinto, Kerstin Bilgmann, Nikki Zanardo, Fernando Diaz-Aguirre, Eduardo R. Secchi, Thales R. O. Freitas, Luciana M. Moller
Summary: Climate change has led to major environmental restructuring in the world's oceans, and marine organisms have responded through genomic adaptation. This study investigates the genomic basis of ecotype formation in bottlenose dolphins in the Southern Hemisphere, revealing subspecies-level genomic divergence and lower genomic diversity in inshore lineages. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems have undergone repeated adaptive evolution in these lineages, suggesting parallel evolution of inshore bottlenose dolphins. Understanding the adaptive capacity of local species and populations is crucial amidst changing marine ecosystems.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Ecology
Andrea Barcelo, Jonathan Sandoval-Castillo, Chris J. Brauer, Kerstin Bilgmann, Guido J. Parra, Luciano B. Beheregaray, Luciana M. Moller
Summary: This study conducted a seascape genomics analysis on 214 common dolphins along the southern coast of Australia, and identified five locally-adapted populations with high levels of genomic variation. The study revealed key environmental variables associated with the genomic variation, and suggested that adaptive divergence in common dolphins is related to important metabolic traits.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Sean James Buckley, Chris J. Brauer, Peter J. Unmack, Michael P. Hammer, Luciano B. Beheregaray
Summary: This study analyzed genetic and environmental data of two ecologically similar and largely co-distributed freshwater fishes, the southern and Yarra pygmy perches, to assess their responses to Plio-Pleistocene climatic changes. The results showed significant differences in responses between the two species, with the southern pygmy perch lacking genetic diversity and historical range expansion. Although some co-occurring populations demonstrated concordant demographic histories, idiosyncratic population size changes were found at the range edges of the more spatially restricted species.
BMC ECOLOGY AND EVOLUTION
(2022)
