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Article
Open AccessGenomes of multicellular algal sisters to land plants illuminate signaling network evolution
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferr...
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Article
Open AccessEnvironmental gradients reveal stress hubs pre-dating plant terrestrialization
Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unravel...
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Article
Open AccessAccessible versatility underpins the deep evolution of plant specialized metabolism
The evolution of several hallmark traits of land plants is underpinned by phytochemical innovations. The specialized metabolism of plants can appear like a teeming chaos that has yielded an ungraspable array o...
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Article
Open AccessWidespread occurrence of covalent lysine–cysteine redox switches in proteins
We recently reported the discovery of a lysine–cysteine redox switch in proteins with a covalent nitrogen–oxygen–sulfur (NOS) bridge. Here, a systematic survey of the whole protein structure database discloses...
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Article
Open AccessUnderwater CAM photosynthesis elucidated by Isoetes genome
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation t...
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Article
Open AccessAuthor Correction: A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
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Article
Open AccessA molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and...
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Article
Open AccessGiant lungfish genome elucidates the conquest of land by vertebrates
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ the land and ultimately gave rise to all land vertebrates, including humans1–3. Here we determine the chromosome-qual...
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Protocol
Automated Removal of Non-homologous Sequence Stretches with PREQUAL
Large-scale multigene datasets used in phylogenomics and comparative genomics often contain sequence errors inherited from source genomes and transcriptomes. These errors typically manifest as stretches of non...
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Article
Open AccessA mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)
Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and ev...
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Article
Open AccessEnvironmental temperatures shape thermal physiology as well as diversification and genome-wide substitution rates in lizards
Climatic conditions changing over time and space shape the evolution of organisms at multiple levels, including temperate lizards in the family Lacertidae. Here we reconstruct a dated phylogenetic tree of 262 ...
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Article
Open AccessPhylogenomics uncovers early hybridization and adaptive loci sha** the radiation of Lake Tanganyika cichlid fishes
Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lake...
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Article
Phylotranscriptomic consolidation of the jawed vertebrate timetree
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to a...
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Article
Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth’s Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa
The Magadi tilapia (Alcolapia grahami) is a cichlid fish that inhabits one of the Earth’s most extreme aquatic environments, with high pH (~10), salinity (~60 % of seawater), high temperatures (~40 °C), and fluct...
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Article
Open AccessThe complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis
With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polypla...
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Article
Open AccessThe origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates
Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that mo...
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Article
Open AccessReversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae
Evolutionary novelties often appear by conferring completely new functions to pre-existing structures or by innovating the mechanism through which a particular function is performed. Sound production plays a c...
