Article
Biochemistry & Molecular Biology
Richard Adams, Michael DeGiorgio
Summary: Likelihood-based tests of phylogenetic trees are crucial in modern systematics. While many such tests exist for gene trees, there is a lack of comparable frameworks for testing species tree hypotheses. To address this, we derive likelihood-based approaches for testing species tree topologies using gene tree topologies as input. These tests leverage the statistical procedures of their gene tree-based counterparts and have been demonstrated with simulated and empirical data sets. We also introduce an open-source R package for conducting formal likelihood-based tests of species topologies.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Ecology
Siavash Mirarab, Luay Nakhleh, Tandy Warnow
Summary: Species tree estimation is crucial for biological research, but it faces challenges due to various complex factors. Over the past decade, there has been significant progress in methods and mathematical theory for species tree estimation, although limitations still exist.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 52, 2021
(2021)
Article
Multidisciplinary Sciences
Trevor L. Hewitt, Amanda E. Haponski, Diarmaid O. Foighil
Summary: A study on North American lampsiline mussels reveals a diversity of infection strategies, including mimicry lures and broadcast infection strategies, which show significant specialization and close correlation with host types; the results support the importance of larval resource partitioning in maintaining mussel species diversity.
Article
Evolutionary Biology
Tyler K. Chafin, Marlis R. Douglas, Max R. Bangs, Bradley T. Martin, Steven M. Mussmann, Michael E. Douglas
Summary: Species are crucial for biodiversity conservation, but their delimitation faces challenges. The Gila robusta complex in southwestern North America exemplifies taxonomic controversy due to conflicting morphological and genetic analyses. Through dense sampling and genomic analysis, this study supports the resurrection of three distinct species despite phylogenetic discordance.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Kevin I. Sanchez, Emilce G. Diaz Huesa, Maria F. Breitman, Luciano J. Avila, Jack W. Sites, Mariana Morando
Summary: In this study, we used dense geographic sampling and novel computational analytical approaches to unravel the evolutionary history of the Patagonian lizard clade Liolaemus kingii. By analyzing nuclear and mitochondrial data, we were able to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. Our results showed evidence of mito-nuclear discordance and supported a reticulated history with extensive gene flow and rapid diversification events in the kingii clade. We discussed the implications of our findings for speciation, phylogeography, and taxonomy in the Patagonian region.
SYSTEMATIC BIOLOGY
(2023)
Article
Environmental Sciences
Kevin Labrador, Joseph Dominic Palermo, Altair Agmata, Rachel Ravago-Gotanco, Ma. Josefa Pante
Summary: The study evaluated the genetic structure of Bali sardinella using RADseq and found genetic differentiation between the two regions. Despite high gene flow, environmental heterogeneity plays a role in maintaining adaptive variation.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Plant Sciences
Luiz A. Cauz-Santos, Steven Dodsworth, Rosabelle Samuel, Maarten J. M. Christenhusz, Denise Patel, Taiwo Shittu, Aljaz Jakob, Ovidiu Paun, Mark W. Chase
Summary: This study investigates the species limits, phylogenetic relationships, and divergence times within Nicotiana benthamiana, a commonly used laboratory organism. The study reveals that the previous taxonomic concept of this species actually comprises five genetically distinct species, one of which includes LAB. The study also provides evidence that LAB is closely related to accessions from the Northern Territory and split from their common ancestor much earlier than the other four species in the clade.
Article
Biochemistry & Molecular Biology
Lois Rancilhac, Iker Irisarri, Claudio Angelini, Jan W. Arntzen, Wieslaw Babik, Franky Bossuyt, Sven Kuenzel, Tim Lueddecke, Frank Pasmans, Eugenia Sanchez, David Weisrock, Michael Veith, Ben Wielstra, Sebastian Steinfartz, Michael Hofreiter, Herve Philippe, Miguel Vences
Summary: Hybridization can lead to genealogical signatures in an organism's genome, causing challenges for phylogenetic inference methods. A phylotranscriptomic approach was used to study the evolutionary history of the Salamandridae and test for inter-lineage introgression. The study identified introgression events among different lineages and proposed hypotheses on the evolutionary relationships within the family.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Tingru Mao, Yewei Liu, Mariana M. Vasconcellos, Marcio R. Pie, Gajaba Ellepola, Chenghai Fu, Jian Yang, Madhava Meegaskumbura
Summary: This study used RADseq to investigate the evolution of Sinocyclocheilus fishes in China. The results revealed the evolutionary relationships and mechanisms of troglomorphism in Sinocyclocheilus, showing that this species has evolved multiple derived cave-adapted traits. Six major clades were identified within Sinocyclocheilus, providing valuable insights for future research on the evolution and adaptation of cave life in this fish genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
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
Biotechnology & Applied Microbiology
Caroline Schwaner, Sarah Farhat, Michelle Barbosa, Isabelle Boutet, Arnaud Tanguy, Emmanuelle Pales Espinosa, Bassem Allam
Summary: The increasing concentration of CO2 in the atmosphere is leading to ocean acidification, which has negative impacts on important species like the northern quahog. Research has shown significant changes in gene expression and genetic variations in clams reared under acidified conditions, but the mechanism of their resilience to ocean acidification is still unclear.
MARINE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Elizabeth S. Allman, Hector Banos, John A. Rhodes
Summary: As more genomic-scale datasets are being used for species tree inference, simulators of the multispecies coalescent (MSC) process are necessary to test and evaluate new inference methods. However, the simulators themselves need to be tested to ensure their validity. This study develops methods to check if a collection of gene trees aligns with the MSC model on a given species tree. The tests conducted on well-known simulators reveal flaws in some of the samples, and are implemented in the freely available R package MSCsimtester for easy application by developers and users.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Yu Wang, Yingnan Wang, Xiaoqi Cheng, Yongli Ding, Chongnv Wang, Juha Merila, Baocheng Guo
Summary: New study shows that introgression contributes significantly to the diversification of Pungitius sticklebacks and plays a crucial role in phenotypic convergence. The analysis of genomic data reveals that introgression is more prevalent than previously thought, with asymmetric gene flow and unequal genomic signatures in hybridizing species. Introgression of genetic variants is accompanied by transitions in important diagnostic traits and adaptation in gene regulatory networks, highlighting its importance as a source of adaptive variation. This study provides insight into the long-standing challenges in the taxonomy and systematics of this highly diverse group of fish.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
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
Microbiology
Chelsea L. Murphy, Andriy Sheremet, Peter F. Dun, John R. Spear, Ramunas Stepanauskas, Tanja Woyke, Mostafa S. Elshahed, Noha H. Youssef
Summary: The study conducted a thorough comparative genomic analysis of 108 genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum, revealing their specialization in methylotrophy and identification of an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds. The occurrence of multiple alkane hydroxylases and monooxygenases was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Members of Binatota were found to prefer terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
Article
Biochemistry & Molecular Biology
Sabine Urban, Alexander Nater, Axel Meyer, Claudius F. Kratochwil
Summary: In this study, researchers found that in Lake Malawi, the melanic horizontal stripes in cichlid fish are associated with recent de novo mutations near the agrp2 gene, whereas in Lake Victoria, the stripes are linked to two intronic regions. The haplotypes associated with these traits predate the Lake Victoria radiation and indicate a standing genetic variation driving phenotypic divergence. Both new and ancient allelic variation at the same locus fueled rapid and convergent phenotypic evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Rebekka Hoech, Ralf F. Schneider, Alison Kickuth, Axel Meyer, Joost M. Woltering
Summary: With over 18,000 species, Acanthomorpha fishes form the largest and most diverse radiation of vertebrates, with their evolutionary success attributed to the spiny rays in their fins. By studying the differentiation of fin domains in Astatotilapia burtoni, researchers identified distinct transcription factor signatures and mechanisms such as BMP inhibition and shh secretion that contribute to the establishment of spiny and soft-ray domains. This research suggests a repeated exaptation of developmental programs contributing to the convergent evolution of spiny fin elements in fishes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Nicolas S. M. Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer, Christian R. Voolstra, Oleg Simakov
Summary: This study analyzed 49 animal genomes and discovered the largest gains of synteny in the last common ancestor of bilaterians and cnidarians. Depending on their node of emergence, the novel syntenic blocks exhibit distinct functional compositions and gene density properties. These findings provide insights into the regulatory properties of microsyntenic blocks in animal genomes.
Article
Evolutionary Biology
Mark D. Scherz, Paul Masonick, Axel Meyer, C. Darrin Hulsey
Summary: Whole genome sequences provide important evidence for our understanding of phylogenetic relationships, but they may not be able to resolve the evolutionary history of rapidly radiating lineages. Integrating results from different methods and using phylogenomic approaches can help overcome these challenges.
SYSTEMATIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Andreas Harer, Yipeng Liang, Frederico Henning, Axel Meyer
Summary: This study uncovers the genetic basis of the gold/dark polymorphism in Midas cichlid fish by identifying a transposon insertion in the gene goldentouch.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Sina J. Rometsch, Julian Torres-Dowdall, Gonzalo Machado-Schiaffino, Nidal Karagic, Axel Meyer
Summary: Exaggerated secondary sexual characteristics in males can serve as ornaments for attracting mates and armaments for male-male competition. However, possessing disproportionately large traits can also impose fitness costs on males due to decreased endurance and increased energetic costs during activities like swimming. The trade-offs associated with large secondary sexual characteristics illustrate the constraints imposed by natural selection on the further exaggeration of these traits.
ECOLOGY AND EVOLUTION
(2021)
Article
Ecology
Sabine Urban, Jan Gerwin, C. Darrin Hulsey, Axel Meyer, Claudius F. Kratochwil
Summary: Color patterns are linked to the behavioral and morphological characteristics of animals, and play an important role in antipredatory strategies. This study finds a strong correlation between stripe patterns and body elongation in cichlid fish, indicating that the effectiveness of the stripes as an antipredatory strategy depends on body shape. However, genetic analyses show that stripes and body elongation segregate independently, suggesting that their correlation is maintained by correlational selection rather than genetic linkage. Furthermore, mate preference tests indicate that females do not differentiate between striped and nonstriped males, suggesting that stripes might be less important for species recognition and mate choice.
ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Paul Masonick, Axel Meyer, Christopher Darrin Hulsey
Summary: By analyzing the genomes of Lake Malawi cichlid species, this study found that protein-coding single nucleotide polymorphisms (SNPs) can provide enough phylogenetic information to study the inter- and intra-specific relationships of hypertrophied lip cichlids, although noncoding SNPs provide better support. The study also revealed that hypertrophied lip cichlids have likely evolved independently at least twice in Lake Malawi.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Camila L. Nacif, Claudius F. Kratochwil, Andreas F. Kautt, Alexander Nater, Gonzalo Machado-Schiaffino, Axel Meyer, Frederico Henning
Summary: The evolution and differentiation of sex chromosomes is a significant event in genome evolution, and the repeated evolution and variability of sex-determination mechanisms in fishes make them a suitable model for studying general patterns in evolution. This study used forward-genetics, long-read sequencing, and optical mapping to determine that sex in Midas cichlids is determined by an XY system and identified and assembled the sex-determining region. The study also found that the male-specific region on chromosome 4 contains transposable elements and a Y-specific duplicate of the anti-Mullerian receptor 2 gene, which has evolved as a master sex-determining gene. The duplication of anti-Mullerian genes is a common mechanism for establishing new sex determiners, highlighting the importance of molecular parallelism in the evolution of sex determination.
Article
Biology
Julian Torres-Dowdall, Sina J. Rometsch, Jacobo Reyes Velasco, Gaston Aguilera, Andreas F. Kautt, Guillermo Goyenola, Ana C. Petry, Gabriel C. Depra, Weferson J. da Graca, Axel Meyer
Summary: Phylogenetic comparative studies suggest that the deviation from bilateral symmetry might evolve through genetic assimilation, but the changes in its inheritance are largely unknown. Research on the evolution of genital asymmetry in Anablepidae fish reveals that the bias towards left-sided males has likely evolved independently three times. Breeding experiments show that regardless of their own sidedness, male fish sire more left-sided offspring. This suggests that sidedness may be inherited as a threshold trait with different thresholds across species.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Claudius F. Kratochwil, Andreas F. Kautt, Sina J. Rometsch, Axel Meyer
Summary: High-throughput DNA sequencing technologies have made it easier to sequence entire genomes. Whole-genome resequencing can help identify and describe species that are difficult to discern, but it can be costly and time-consuming. Species-specific markers can be designed based on whole-genome resequencing data, enabling rapid and reliable species identification at a lower cost.
ECOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Claudius F. Kratochwil, Yipeng Liang, Jan Gerwin, Paolo Franchini, Axel Meyer
Summary: This study investigates the differences between striped and nonstriped cichlid fishes in different lineages of Lake Victoria and Lake Malawi. The gene agrp2 is found to be associated with stripe pattern divergence. The study also examines the development of stripe patterns and vertical bar patterns, and suggests that the stripe phenotype may be caused by a combination of subtle transcriptomic differences or cellular changes.
EVOLUTION & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Melisa Olave, Alexander Nater, Andreas F. Kautt, Axel Meyer
Summary: This study presents a rare example of sympatric homoploid hybrid speciation in Midas cichlid fishes from Nicaragua. The hybrid lineage has diverged from its parental species both genomically and phenotypically, and occupies a different trophic niche facilitated by body shape adaptations.
NATURE COMMUNICATIONS
(2022)
Article
Evolutionary Biology
Paul Masonick, Axel Meyer, Christopher Darrin Hulsey
Summary: The genomic loci underlying variation in vertebrate structures like lips are surprisingly predictable. Both adaptive and maladaptive variation in traits such as jaws and teeth can be structured by the same genes in evolutionarily disparate organisms like teleost fishes and mammals. The recurrence of hypertrophied lips in cichlid fish lineages suggests the presence of shared genetic bases and potential insights into the genetic factors influencing human craniofacial anomalies.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Ralf F. Schneider, Helen M. Gunter, Inken Salewski, Joost M. Woltering, Axel Meyer
Summary: Evolutionary novelties can promote ecological specialization and adaptive radiations. Belonoid fishes, such as flying fishes, halfbeaks, and needlefishes, have highly diversified elongated jaw phenotypes. In this study, the development of elongated jaws in a halfbeak and a needlefish was investigated, revealing that these jaws consist of distinct base and extension portions. The growth dynamics of both bases and extensions were described, and the molecular mechanisms underlying the extension outgrowth were deduced.
