Article
Multidisciplinary Sciences
Xinfeng Wang, Ziwen He, Zixiao Guo, Ming Yang, Shaohua Xu, Qipian Chen, Shao Shao, Sen Li, Cairong Zhong, Norman C. Duke, Suhua Shi
Summary: In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent study on two closely related mangrove species (Rhizophora mucronata and R. stylosa) found that despite being sympatric, their genomes remained well delineated with only small introgression blocks. These findings suggest that true 'good species' may continue to exchange genes long after speciation, but detecting such exchanges is challenging.
NATIONAL SCIENCE REVIEW
(2022)
Article
Biochemistry & Molecular Biology
Guilherme C. Baiao, Daniela I. Schneider, Wolfgang J. Miller, Lisa Klasson
Summary: Hybridization and introgression of genomic elements contribute to genetic diversity in biological lineages. The mitochondrial evolutionary history of Drosophila paulistorum and the willistoni subgoup was investigated using phylogenetic and comparative analyses. The results show that D. paulistorum has polyphyletic mitochondria, which form two non-sister clades named alpha and beta. It is suggested that both alpha and beta mitochondria were acquired through introgression from unknown fly lineages within the willistoni subgroup.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Aidan W. Short, Matthew A. Streisfeld
Summary: The reuse of old genetic variation can promote rapid diversification in evolutionary radiations. In the Mimulus aurantiacus species complex, there is evidence for ancient and recurrent hybridization. Selection against gene flow can reduce genomic signatures of ancient hybridization.
Article
Ecology
Anthony J. Barley, Tod W. Reeder, Adrian Nieto-Montes de Oca, Charles J. Cole, Robert C. Thomson
Summary: Transitions between sexual and unisexual reproductive modes have significant consequences for the evolutionary trajectories of species. North American whiptail lizards are known to have numerous triploid lineages with no known diploid unisexual ancestors, suggesting alternative mechanisms of triploid formation may be at play. By leveraging genomic, morphological, and karyotypic data, researchers described a new diploid unisexual whiptail and identified it as the likely unisexual progenitor of an extant triploid lineage. The study also resolved patterns of polyploidization within the A. sexlineatus species group and tested predictions about the phenotypic outcomes of hybridization.
AMERICAN NATURALIST
(2021)
Article
Biochemistry & Molecular Biology
Michael V. Westbury, Andrea A. Cabrera, Alba Rey-Iglesia, Binia De Cahsan, David A. Duchene, Stefanie Hartmann, Eline D. Lorenzen
Summary: The study investigates the role of post-divergence gene flow in speciation process in the toothed whale superfamily Delphinoidea. The researchers used a multifaceted approach including phylogenomics, distribution of shared derived alleles, and demographic inference. The findings reveal complex speciation within Delphinoidea, with evidence of ancient interfamilial gene flow events prior to diversification of each family. Contemporary hybridization events do not contribute to parental species' gene pools.
Article
Biochemistry & Molecular Biology
Gregory L. Owens, Marco Todesco, Natalia Bercovich, Jean-Sebastien Legare, Nora Mitchell, Kenneth D. Whitney, Loren H. Rieseberg
Summary: The origins of the texanus subspecies of Helianthus annuus in Texas are likely not from introgression with the local congener H. debilis, but rather from introgression with the sister species H. argophyllus. Genomic differentiation in H. a. texanus is mainly driven by large segregating inversions, some of which show signs of natural selection based on haplotype frequencies.
Article
Biochemistry & Molecular Biology
Axel Jensen, Frances Swift, Dorien de Vries, Robin M. D. Beck, Lukas F. K. Kuderna, Sascha Knauf, Idrissa S. Chuma, Julius D. Keyyu, Andrew C. Kitchener, Kyle Farh, Jeffrey Rogers, Tomas Marques-Bonet, Kate M. Detwiler, Christian Roos, Katerina Guschanski
Summary: Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. This study analyzed whole-genome sequencing data from 22 species of guenons and found rampant gene flow characterized their evolutionary history. Ancient hybridization events were identified across deeply divergent lineages with differences in ecology, morphology, and karyotypes. The study also revealed that genes with immune functions were overrepresented in introgressing regions, suggesting adaptive introgression, while genes involved in pigmentation and morphology may contribute to reproductive isolation. Additionally, it was found that some of the most species-rich guenon clades were of admixed origin.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Kenneth K. Askelson, Garth M. Spellman, Darren Irwin
Summary: Analysis of genomic variation reveals high differentiation among white-breasted nuthatch populations, suggesting the existence of at least three species. It also shows evidence of introgression between a ghost lineage and a current population, contributing to differentiation.
Article
Biochemistry & Molecular Biology
Ivan Prates, Mark N. N. Hutchinson, Sonal Singhal, Craig Moritz, Daniel L. L. Rabosky
Summary: This study investigates the taxonomic intractability in an Australian lizard clade, the Ctenotus inornatus species group, and reveals the challenges in resolving species boundaries due to decoupled genetic and phenotypic breaks, uncertain geographic ranges, and idiosyncratic patterns of introgression. The study highlights the importance of spatial variation in species boundaries and its impact on genetic and phenotypic variation.
Article
Biochemistry & Molecular Biology
Deyan Ge, Zhixin Wen, Anderson Feijo, Andrey Lissovsky, Wei Zhang, Jilong Cheng, Chaochao Yan, Huishang She, Dezhi Zhang, Yalin Cheng, Liang Lu, Xinlai Wu, Danping Mu, Yubo Zhang, Lin Xia, Yanhua Qu, Alfried P. Vogler, Qisen Yang
Summary: Climate-sensitive pikas in the Qinghai-Tibetan Plateau and its vicinity have experienced population reduction due to climate changes and human disturbance, while the plateau pika remains common. By sequencing the whole genomes of six closely related species, we found evidence of ancient introgression, lineage replacement, and bidirectional introgression. The strongest gene flow occurred from the dominant plateau pika to ecologically distinct species in peripheral areas. Our findings highlight the differences in hybridization consequences and the unique role of the Qinghai-Tibetan Plateau in conserving evolutionary processes.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Noora Poikela, Dominik R. Laetsch, Maaria Kankare, Anneli Hoikkala, Konrad Lohse
Summary: Interspecific gene flow is a source of genetic variation, but selection against it strengthens reproductive barriers between species. We used an experimental approach to investigate the role of chromosomal inversions and incompatibility genes in preventing gene flow between Drosophila virilis group species. Our findings suggest that genetic incompatibilities within chromosomal inversions play an important role in speciation.
Article
Biochemistry & Molecular Biology
Mahendra Mariadassou, Marie Suez, Sanbadam Sathyakumar, Alain Vignal, Mariangela Arca, Pierre Nicolas, Thomas Faraut, Diane Esquerre, Masahide Nishibori, Agathe Vieaud, Chih-Feng Chen, Hung Manh Pham, Yannick Roman, Frederic Hospital, Tatiana Zerjal, Xavier Rognon, Michele Tixier-Boichard
Summary: The study used whole genome sequencing to reconstruct the history of the four species in the Gallus genus, revealing discrepancies in phylogeny reconstruction methods and genomic components. It suggested G. gallus may be the earliest lineage instead of G. varius. The importance of carefully selecting and validating samples in phylogenomics was emphasized.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joaquin Ortego, L. Lacey Knowles
Summary: The genomic data confirm a Pleistocene origin of the species complex in the flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula, with multiple analytical approaches revealing limited asymmetric historical hybridization between two taxa. In the divergence in isolation model, rapid evolution of reproductive isolation was observed.
Article
Multidisciplinary Sciences
Carl-Johan Rubin, Erik D. Enbody, Mariya P. Dobreva, Arhat Abzhanov, Brian W. Davis, Sangeet Lamichhaney, Mats Pettersson, Ashley T. Sendell-Price, C. Grace Sprehn, Carlos A. Valle, Karla Vasco, Ola Wallerman, B. Rosemary Grant, Peter R. Grant, Leif Andersson
Summary: Through studying Darwin's finches, it was found that ancestral haplotype blocks play a crucial role in phenotypic evolution and speciation, serving as key determinants of the unusual phenotypic diversity exhibited by these birds.
Article
Biology
Raphael T. F. Coimbra, Sven Winter, Arthur Muneza, Stephanie Fennessy, Moses Otiende, Domnic Mijele, Symon Masiaine, Jenna Stacy-Dawes, Julian Fennessy, Axel Janke
Summary: Through analyzing the genomes of wild giraffes, the study found evidence of historical gene flow between Nubian and reticulated giraffes. However, contemporary gene flow between these two lineages is minimal. The study also observed a decline in effective population sizes of Nubian and reticulated giraffes. Overall, the findings suggest that these three giraffe lineages have maintained their reproductive isolation.
Article
Agronomy
Ivair Valmorbida, Brad S. Coates, Erin W. Hodgson, Molly Ryan, Matthew E. O'Neal
Summary: This study analyzed the relationship between vgsc gene mutations and fitness costs in soybean aphids. The results showed that there was no negative pleotropic effect associated with pyrethroid resistance in the tested clones, and discussed the potential impact on insecticide resistance management and integrated pest management plans.
PEST MANAGEMENT SCIENCE
(2022)
Article
Virology
Sijun Liu, Thomas W. Sappington, Brad S. Coates, Bryony C. Bonning
Summary: A novel toursvirus was identified from pooled genomic data of southern and northern corn rootworm populations in the U.S., with most viral sequences coming from the southern corn rootworm dataset. The study successfully recovered most of the viral genome, with evidence of transposon insertion in viral sequences in the two host species, suggesting potential differences in transmission mechanisms.
Article
Ecology
Johanna Honka, Serena Baini, Jeremy B. Searle, Laura Kvist, Jouni Aspi
Summary: The population of taiga bean geese has halved in recent decades, mainly due to hunting throughout their range. Understanding the genetic population structure and diversity is crucial for management and conservation efforts. Different genetic subpopulations within the species need to be managed separately to prevent extinction, and inbreeding or lack of genetic diversity could pose risks to their adaptation and survival. The study found some genetic structuring in mitochondrial DNA but not in nuclear microsatellite markers, suggesting that the population can be managed as a single unit.
ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Mumtaz Baig, Sameera Farah, Ashwin Atkulwar, Jeremy B. Searle
Summary: This study used a genomic approach to analyze R. rattus in the Indian peninsula and found distinct geographic differentiation within the species in India, as well as signals of admixture between two subpopulations.
Article
Ecology
Jeremy B. Searle, Fernando Pardo-Manuel de Villena
Article
Genetics & Heredity
Dimpal Lata, Brad S. Coates, Kimberly K. O. Walden, Hugh M. Robertson, Nicholas J. Miller
Summary: This study estimated the genome sizes of Diabrotica corn rootworms using flow cytometry and found that the differences in genome size between different subgroups were mainly attributed to variations in the content of transposable elements, providing insights for studying insect-plant interactions.
G3-GENES GENOMES GENETICS
(2022)
Article
Ecology
Andrew P. Morgan, Jonathan J. Hughes, John P. Didion, Wesley J. Jolley, Karl J. Campbell, David W. Threadgill, Francois Bonhomme, Jeremy B. Searle, Fernando Pardo-Manuel De Villena
Summary: House mice, as animals with a commensal relationship with humans, have spread globally and are important model organisms in biomedical research. An analysis of ancestry, population structure, and inbreeding in wild mice revealed that major ancestry components in North America, Australia, etc. are of northern European origin, and inbreeding is prevalent in commensal populations.
Article
Genetics & Heredity
Trevor J. L. Sless, Jeremy B. Searle, Bryan N. Danforth
Summary: Brood parasites, such as Holcopasites calliopsidis, are an important but understudied group within the wider diversity of bees. This study presents the draft assembly of H. calliopsidis, the first brood parasitic species to undergo detailed genomic analysis. It was found that H. calliopsidis has the smallest genome among bees, with no apparent loss of genic content but significant contractions in individual gene families. The discovery of over 12,000 putative genes, with functional annotation for nearly 10,000 of them, provides valuable insights into the genomic basis of brood parasitism.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Laura van Rosmalen, Robin Schepers, Wensi Hao, Anna S. Przybylska-Piech, Jeremy S. Herman, Joanna Stojak, Jan M. Wojcik, Louis van de Zande, Jeremy B. Searle, Roelof A. Hut
Summary: The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in this pathway and its abundance and function can tune sensitivity to the photoperiod. Genetic variations in Tshr were found in Western European vole populations and were significantly correlated with a predicted critical photoperiod (pCPP) for the spring onset of local primary food production. However, this relationship was lacking in Eastern Europe. These findings suggest that Tshr has been targeted by natural selection in Western European voles to optimize the timing of seasonal reproduction.
Article
Biochemistry & Molecular Biology
Yue Yu, Li-Li Huang, Fang-Sen Xue, Erik B. B. Dopman
Summary: Understanding the molecular basis of repeated evolution improves our ability to predict evolution across the tree of life. High-throughput sequencing has enabled comparative genome scans to examine the repeatability of genetic changes driving phenotypic evolution. Asian corn borer and European corn borer show repeatable phenological adaptation to different climates, and circadian rhythm genes play a role in this repeated adaptation. Independent mutational paths and adaptive introgression may contribute to the repeated phenological evolution.
Article
Evolutionary Biology
Alexandra A. Raspopova, Vladimir S. Lebedev, Jeremy B. Searle, Anna A. Bannikova
Summary: In this study, the phylogenetic relationships within the chromosomally variable Sorex araneus species group were reconstructed using nuclear and mitochondrial genes. The results showed a complex evolutionary history with high incidence of reticulation and possible ancient hybridizations. The authentic mitochondrial lineage of the Iberian shrew S. granarius was found to be closely related to S. coronatus, indicating introgression from S. araneus. This study also revealed deeper reticulations for the first time, suggesting hybrid origins for the S. arcticus and S. coronatus lineages.
Article
Zoology
Pablo Colunga-Salas, Tania Marines-Macias, Giovani Hernandez-Canchola, Soraia Barbosa, Cassandra Ramirez, Jeremy B. Searle, Livia Leon-Paniagua
Summary: This study examined the genetic diversity and population structure of two endemic arboreal mice species in Mexican cloud forests. The results showed that both species had low genetic diversity compared to other similar species, and different population structure patterns were observed, potentially due to their different ecological associations. These findings highlight the importance of considering differential ecological associations for the conservation and management of species.
Article
Cell Biology
Thomas J. Firneno Jr, Georgy Semenov, Erik B. Dopman, Scott A. Taylor, Erica L. Larson, Zachariah Gompert
Summary: This study characterizes the relationship between the coupling coefficient and genetic loci across hybrid zones, showing a smooth continuum from high variance and weak coupling to low variance and strong coupling. The results suggest low hybridization rates and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2023)