Article
Biochemistry & Molecular Biology
Jun Huang, Yuttapong Thawornwattana, Tomas Flouri, James Mallet, Ziheng Yang
Summary: Genomic sequence data are valuable for studying species divergence and gene flow. However, when the model of gene flow is misspecified, estimation bias and interpretation issues may arise. Despite this, the simple introgression model can still be useful for extracting information about between-species gene flow and divergence.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Forestry
Bartosz Labiszak, Witold Wachowiak
Summary: This study investigates the role of hybridization and introgression in the evolutionary history of closely related pine taxa. The results indicate the significant impact of interspecific gene flow in the divergence of species and reveal asymmetrical migration patterns between different pine species. The study provides insights into the role of reticulation evolution in maintaining species integrity in forest trees.
Article
Biochemistry & Molecular Biology
Yuttapong Thawornwattana, Jun Huang, Tomas Flouri, James Mallet, Ziheng Yang
Summary: Genomic data provide valuable information for studying species divergence and gene flow between species, including the direction, timing, and strength of gene flow. However, inferring the direction of gene flow is challenging due to similar patterns generated by gene flow in opposite directions. This study uses likelihood-based methods and simulation to investigate the information about the direction of gene flow present in genomic sequence data. The results show that it is easier to infer gene flow from a small population to a large one and from outgroup species to ingroup species than in the opposite direction, and a longer time of separate evolution between divergence and introgression makes gene flow inference easier.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Green & Sustainable Science & Technology
Georgios A. Gkafas, Joanne Sarantopoulou, Chrysoula Apostologamvrou, Chryssanthi Antoniadou, Athanasios Exadactylos, Georgios Fleris, Dimitris Vafidis
Summary: By analyzing RAD sequencing data, this study found strong evidence of admixture between two congeneric holothurians, Holothuria (Holothuria) tubulosa and Holothuria (Roweothuria) poli, living in sympatry in the Hellenic Seas. The populations of the two species diverged around 13.5 thousand years ago, just after the Last Glacial Maximum, indicating a role for admixture upon secondary contact and supporting the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
Review
Biochemistry & Molecular Biology
Zachary B. Hancock, Emma S. Lehmberg, Heath Blackmon
Summary: In this article, we review the evidence for how continuous spatial structure can impact phylogenetic inference. Using complex continuous-space demographic models, we illustrate the impact of spatial structure on gene tree stoichiometry, topological and branch-length variance, network estimation, and species delimitation. We conclude by suggesting how researchers can identify spatial structure in phylogenetic datasets.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
David A. Rasmussen, Niklaus J. Grunwald
Summary: Phylogeography combines geographic information with phylogenetic and population genomic approaches to infer the evolutionary history of a species or population in a geographic context. It is particularly useful for understanding the emergence, spread, and evolution of plant pathogens. Phylogeography can provide insights into questions about the origin, native status, and frequency of introductions of pathogens.
Article
Plant Sciences
David Wickell, Jacob Landis, Elizabeth Zimmer, Fay-Wei Li
Summary: Isoetes appalachiana is a common allopolyploid species, formed from multiple phylogenetic origins. Hybridization is unidirectional, with I. engelmannii consistently being the maternal progenitor. Polyploid lineages are genetically isolated and rarely experience gene flow between geographically distinct populations.
Article
Biochemistry & Molecular Biology
Arthur Weyna, Lucille Bourouina, Nicolas Galtier, Jonathan Romiguier
Summary: Hybridization plays a central role in evolutionary processes such as speciation or adaptation, but its prevalence and distribution across different species remains largely unknown. In this study, a new statistical method is developed and implemented to detect F1 hybrids from single-individual genome sequencing data. The method is applied to sequencing data from over 1,500 species of arthropods, revealing the highest number of candidate F1 hybrids in Hymenoptera, particularly ants, suggesting a higher rate of recent hybridization in these groups. The prevalence of F1 hybrids is found to be heterogeneously distributed across ant taxa, with specific ecological and life-history traits being associated with many candidates. This study demonstrates the potential of large-scale genomic comparative studies in uncovering the determinants of first-generation hybridization across different taxa.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Edward A. Myers
Summary: The study reveals widespread introgression in the western rattlesnake species group, leading to gene flow confounding phylogenetic relationships. Different topologies were observed between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, with introgression events predominantly restricted to geographically co-occurring species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Genetics & Heredity
Kathryn M. Everson, Mariah E. Donohue, David W. Weisrock
Summary: In recent years, it has been recognized that interspecific gene flow is common across different species. The lemurs of the genus Eulemur in Madagascar provide a unique opportunity to explore the effects of gene flow and reticulation on species boundaries. Analyses of mitochondrial and nuclear datasets reveal that not all recognized species in the genus Eulemur are monophyletic, and suggest the presence of ancient reticulations. These findings demonstrate the prominent role of hybridization in the genus Eulemur and highlight the need for greater taxonomic attention and conservation efforts.
Article
Biochemistry & Molecular Biology
Michael San Jose, Camiel Doorenweerd, Scott Geib, Norman Barr, Julian R. Dupuis, Luc Leblanc, Angela Kauwe, Kimberley Y. Morris, Daniel Rubinoff
Summary: With the increasing availability of genomic data, the definition of species boundaries and relationships is becoming more ambiguous, possibly due to the neglect of gene flow. This study compared the results of phylogenetic and coalescent approaches, and found incongruence between species relationships. The importance of testing for gene flow, even when using high statistical support methods, was highlighted.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Virology
Anthony Lam, Sebastian Duchene
Summary: Phylodynamic inference is crucial in understanding the transmission dynamics of viral outbreaks, with estimating the molecular evolutionary rate being an essential first step. The birth-death model outperforms the coalescent exponential model in estimating epidemiological parameters when faced with low diversity sequence data, while the coalescent model requires additional samples and sequence variability for accurate estimates. This was supported by empirical data analyses of SARS-CoV-2 outbreaks in Australia and New Zealand, emphasizing the importance of considering the birth-death model for future viral outbreak investigations with low sequence diversity.
Article
Biochemistry & Molecular Biology
Jun Chen, Yan-Fei Zeng, Da-Yong Zhang
Summary: This study investigated the historical divergence and hybridization in two closely related Chinese oak species, revealing that the Northeastern China Liaodong Oak originated from the Mongolian Oak, not from the Northwest-Northern China Liaodong Oak. It also found that asymmetrical hybridization and introgression, likely facilitated by pollen flow, promoted the dispersal of the Northeastern China Liaodong Oak to the Northeastern region.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Oksana V. Vernygora, Erin O. Campbell, Nick Grishin, Felix A. H. Sperling, Julian R. Dupuis
Summary: Divergence times are crucial for understanding evolutionary hypotheses, but conflicting age estimates across studies undermine their validity. By analyzing genomic data of tiger swallowtail butterflies, we found significant variations in divergence age estimates among different analytical approaches. Our study enhances the understanding of divergence time estimation and sheds light on the biases in age estimation analyses.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Xiyun Jiao, Ziheng Yang
Summary: This study demonstrates that in the presence of cross-species gene flow, individuals of the same species may not necessarily be more genetically similar to each other than to individuals of another species. The research highlights the significant impact that gene flow can have on genetic history and suggests a novel approach for detecting reproductive barriers and defining species boundaries.
SYSTEMATIC BIOLOGY
(2021)
