71 documents found, page 1 of 8
The interrelationships of land plants and the nature of the ancestral embryophyte
Puttick, Mark N.; Morris, Jennifer L.; Williams, Tom A.; Cox, C. J.; Edwards, Dianne; Kenrick, Paul; Pressel, Silvia; Wellman, Charles H.The evolutionary emergence of land plant body plans transformed the planet. However, our understanding of this formative episode is mired in the uncertainty associated with the phylogenetic relationships among bryophytes (hornworts, liverworts, and mosses) and tracheophytes (vascular plants). Here we attempt to clarify this problem by analyzing a large transcriptomic dataset with models that allow for compositi...
Optimal data partitioning, multispecies coalescent and Bayesian concordance ana...
Lu, Limin; Cox, C. J.; Mathews, Sarah; Wang, Wei; Wen, Jun; Chen, ZhiduanEvolutionary rate heterogeneity and rapid radiations are common phenomena in organismal evolution and represent major challenges for reconstructing deep-level phylogenies. Here we detected substantial conflicts in and among data sets as well as uncertainty concerning relationships among lineages of Vitaceae from individual gene trees, supernetworks and tree certainty values. Congruent deep-level relationships o...
Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (...
Califano, Gianmaria; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Cox, C. J.; Mata, Leonardo; Costa, RodrigoAs wild fish stocks decline worldwide, land-based fish rearing is likely to be of increasing relevance to feeding future human generations. Little is known about the structure and role of microbial communities in fish aquaculture, particularly at larval developmental stages where the fish microbiome develops and host animals are most susceptible to disease. We employed next-generation sequencing (NGS) of 16S rR...
Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)
Shaw, A. Jonathan; Devos, Nicolas; Liu, Yang; Cox, C. J.; Goffinet, B.; Flatberg, Kjell Ivar; Shaw, BlankaBackground and Aims Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selec...
Multilocus genetic analyses provide insight into speciation and hybridization i...
Martínez-Garrido, Jose; Serrão, Ester; Engelen, Aschwin H.; Cox, C. J.; García-Murillo, Pablo; Gonzalez-Wangueemert, MercedesAquatic plants of the genus Ruppia inhabit some of the most threatened habitats in the world, such as coastal lagoons and inland saline to brackish waters where their meadows play several key roles. The evolutionary history of this genus has been affected by the processes of hybridization, polyploidization, and vicariance, which have resulted in uncertainty regarding the number of species. In the present study,...
Absence of N-terminal acetyltransferase diversification during evolution of euk...
Rathore, Om; Faustino, Alexandra; Prudencio, Pedro; Van Damme, Petra; Cox, C. J.; Martinho, Rui GoncaloProtein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, ...
Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: mole...
Marques, Cátia L.; Fernandez, Ignacio; Viegas, Michael; Cox, C. J.; Martel, Paulo; Rosa, Joana; Cancela, Leonor; Laizé, VincentBMP2, BMP4 and BMP16 form a subfamily of bone morphogenetic proteins acting as pleiotropic growth factors during development and as bone inducers during osteogenesis. BMP16 is the most recent member of this subfamily and basic data regarding protein structure and function, and spatio-temporal gene expression is still scarce. In this work, insights on BMP16 were provided through the comparative analysis of struc...
Increased diversification rates follow shifts to bisexuality in liverworts
Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert; Shaw, Blanka; Patino, Jairo; Desamore, Aurelie; Goffinet, B.; Cox, C. J.; Shaw, A. JonathanShifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). T...
Multiple domestications of asian rice
Civáň, Peter; Craig, Hayley; Cox, C. J.; Brown, Terence A.In their recent Correspondence about our study showingthat there were three origins of Asian rice2, Huang and Han suggest that the methodology that we used to infer multiple domestications was flawed as it did not take account of the strong genetic bottleneck in japonica.
Geographical range in liverworts: does sex really matter?
Laenen, Benjamin; Machac, Antonin; Gradstein, S. Robbert; Shaw, Blanka; Patino, Jairo; Desamore, Aurelie; Goffinet, B.; Cox, C. J.; Shaw, JonathanAimWhy some species exhibit larger geographical ranges than others remains a fundamental, but largely unanswered, question in ecology and biogeography. In plants, a relationship between range size and mating system was proposed over a century ago and subsequently formalized in Baker's Law. Here, we take advantage of the extensive variation in sexual systems of liverworts to test the hypothesis that dioecious sp...