Common Ancestor Research Articles

Origin and evolution of the blue light receptor cryptochromes (CRY1/2) in aquatic angiosperms.

Cryptochromes (CRYs), which are responsible for sensing blue light in plants, play a critical role in regulating blue light signals and circadian rhythms. However, their functions extend beyond light detection, as they also aid plants in adapting to stress and potentially other regulatory mechanisms. Aquatic angiosperms, which independently evolved from various angiosperm lineages, have developed specific adaptations to unique light qualities and environmental stressors found in aquatic habitats compared to terrestrial ones. It was hypothesized that the sequences and regulatory networks of angiosperm CRY1/2 underwent adaptive evolution in different aquatic angiosperm lineages. To test this hypothesis, we compiled comprehensive datasets consisting of 55 green plant genomes (including 37 angiosperm genomes), 80 angiosperm transcriptomes, and 4 angiosperm expression networks. Through comparative analysis, we found that CRY1 originated from a common ancestor of seed plants, whereas CRY2 originated from a common ancestor of land plants. In angiosperms, the CRY1/2 sequences of aquatic lineages exhibited positive selection, and the conserved valine-proline (VP) motif of CRY2 showed a convergent loss in two aquatic species. Co-expressed genes associated with blue light receptors (CRY) showed adaptations to aquatic environments, specifically in relation to flooding and osmotic stress. These discoveries shed light on the adaptive evolution of CRY1/2, encompassing their origins, sequences, and regulatory networks. Furthermore, these results provide valuable insights for investigating the uncharacterized functions and regulatory pathways of CRY and offer potential targets for enhancing growth and adaptation in agricultural plants.

Neural crest lineage in the protovertebrate model Ciona.

Neural crest cells are multipotent progenitors that produce defining features of vertebrates such as the 'new head'1. Here we use the tunicate, Ciona, to explore the evolutionary origins of neural crest since this invertebrate chordate is among the closest living relatives of vertebrates2-4. Previous studies identified two potential neural crest cell types in Ciona, sensory pigment cells and bipolar tail neurons5,6. Recent findings suggest that bipolartail neurons are homologous to cranial sensory ganglia rather than derivatives of neural crest7,8. Here we show that the pigment cell lineage also produces neural progenitor cells that form regions of the juvenile nervous system following metamorphosis. Neural progenitors are also a major derivative of neural crest in vertebrates, suggesting that the last common ancestor of tunicates and vertebrates contained a multipotent progenitor population at the neural plate border. It would therefore appear that a key property of neural crest, multipotentiality, preceded the emergence of vertebrates.

Speciation and diversification of the Bupleurum (Apiaceae) in East Asia.

Bupleurum, belonging to the Apiaceae, is widely distributed across the Eurasian continent. The origin and species diversification of Bupleurum in East Asia, remain incompletely resolved due to the limited samples in previous studies. To address these issues, we have reconstructed a robust phylogenetic framework for Bupleurum in East Asia based on the ITS and three plastid genes. Our phylogenetic analysis confirms the monophyly of Bupleurum with strong support. Both ITS and chloroplast dataset divided the Bupleurum in East Asia into East Asia Group I and East Asia Group II in this study. The divergence time and ancestral area reconstruction of ITS dataset indicated that the Bupleurum originated in the Mediterranean basin and its adjacent areas around 50.33 Ma. subg. Penninervia and subg. Bupleurum diverged at about 44.35 Ma, which may be related to the collision of India with the Eurasian continent. Both East Asia Group I and East Asia Group II originated from a common ancestor in the Mediterranean, East Asia Group I divergence around 12.95 Ma; East Asia Group II divergence around 13.32 Ma. The character reconstruction showed that the morphological characters and altitude distribution analyzed in this study exhibit a scattered distribution in East Asian Group I and East Asian Group II. Additionally, diversification rate analysis shows that the East Asian Group I and East Asian Group II exhibited no significant shifts in diversification rates in the evolutionary history according to ITS and combined dataset. Both molecular and morphological data supports that East Asian Bupleurum is a museum taxon, meaning that the species diversity of East Asian Bupleurum has gradually accumulated over time.

Expression and functional divergence of a type-A response regulator paralog pair formed by dispersed duplication during Populus deltoides evolution

Gene duplication and divergence are essential to plant evolution. The Arabidopsis type-A response regulator (ARR) family, negative regulators in cytokinin signaling, exemplifies gene expansion and differential retention. Despite extensive research, the understanding of type-A RR homologs in woody plants remains limited. In this study, the evolution history of type-A RR gene families across four rosids and one monocot has been comprehensively investigated. Focusing on Populus deltoides, a unique pair of dispersed duplicates, PdRR8 and PdFERR, is identified, and their duplication is estimated to have occurred in the common ancestor of the four rosids. The duplication remnants corresponding to PdRR8 have been retained in all rosids but the counterpart of PdFERR has been lost. In poplar, PdRR8 shows the highest expression levels in leaves, while PdFERR is specifically expressed in female floral buds. Among various external stimuli, cold strongly represses PdRR8 promoter activity, whereas 6-BA markedly inhibits that of PdFERR. Overexpression of PdRR8 in the Arabidopsis arr16arr17 double-mutant fully complements the reduced hydrotropic response. In contrast, PdFERR fails to rescue the hydrotropic defects of the mutant. Results of evolutionary, expression and functional analyses indicate that PdRR8, rather than PdFERR, is the true ortholog of the ARR16-ARR17 paralogs. Though PdRR8 and PdFERR originate from a common ancestral gene and evolve under strong negative selection, these two dispersed duplicates have exhibited differential expression and some degree of functional divergence.

Chromosome-level genome assembly of the cosmopolitan diatom Skeletonema costatum provides insights into ecological adaptation

The cosmopolitan diatom species Skeletonema costatum is an ecologically important dominant phytoplankton frequently found in the coastal estuarine and marine waters, and often causes harmful algae blooms. Despite of its critical ecological importance, chromosome-level genome assemble is still unavailable, hindering in-depth understanding of their evolution and environmental adaption. Here, we report a chromosome-level genome assembly for the marine diatom species S. costatum. The assembled genome size was 136.49 Mb, with a contig N50 of 302 Kb and 95.30 % of the reads anchored into 23 pseudo-chromosomes with a scaffold N50 of 6.19 Mb. A total of 28,321 protein-coding genes were predicted, with 86.03 % being functional annotated. The BUSCO assessment of genome assembly and genome annotation were both above 90 %. Phylogenetic analysis showed the expected topology, with S. costatum and its closely related species S. marinoi diverged from their common ancestor around 22.6 million years ago. The genome size of S. costatum is comparatively larger than those of its closely related diatoms, due mostly to its higher transposable element contents and larger number of proteincoding genes. Collinearity analysis revealed strong collinearity between S. costatum and other Skeletonema with most chromosomes showing clear one-to-one correspondences. A larger family of nine copies of the cryptochrome genes that function as blue light photoreceptors were identified in S. costatum, which could contribute its ecological success. The availability of the high-quality chromosome-level genome assembly for S. costatum represents a valuable resource that may facilitate comparative genomics for revealing important ecological clues and gene families, and future genetics and environmental studies among Skeletonema species.

Genetic structure and common ancestry expose the dingo-dog hybrid myth

Abstract The evolutionary history of canids has been shown to be complex, with hybridization and domestication confounding our understanding of speciation among various canid lineages. The dingo is a recent canid lineage that was completely isolated from other canids for over 5000 years on the Australian mainland, but the introduction of domestic dogs in 1788 has placed doubt on its independence, with recent studies highlighting hybridization between dingoes and domestic dogs. Using genomic single nucleotide polymorphism data from 434 Australian canid samples, we explicitly test for introgression between closely related canid groups and dingoes. We found no evidence of introgression between dingoes and domestic dogs and show that previous work has likely mischaracterized shared ancestral genetic variation as evidence for hybridization. Further, New Guinea Singing Dogs are the only canid group that significantly shared genetic variation with dingoes, which fits with our understanding of previous phylogenetic analyses. Despite more recent sympatric distributions with dogs, dingoes have likely maintained their independence since their arrival in Australia, even in areas with high lethal control, indicating that their evolutionary trajectory is currently being conserved. The future conservation of the dingo lineage will require policies that promote coexistence pathways between humans and dingoes that protect rangeland systems and the dingoes’ evolutionary future.

Exploring Fish Parvalbumins through Allergen Names and Gene Identities

Parvalbumins are the main source of food allergies in fish meat, with each fish possessing multiple different parvalbumins. The naming convention of these allergens in terms of allergen codes (numbers) is species-specific. Allergen codes for parvalbumin isoallergens and allergen variants are based on sequence identities relative to the first parvalbumin allergen discovered in that particular species. This means that parvalbumins with similar allergen codes, such as catfish Pan h 1.0201 and redfish Seb m 1.0201, are not necessarily the most similar proteins, or encoded by the same gene. Here, we aim to elucidate the molecular basis of parvalbumins. We explain the complicated genetics of fish parvalbumins in an accessible manner for fish allergen researchers. Teleost or modern bony fish, which include most commercial fish species, have varying numbers of up to 22 parvalbumin genes. All have derived from ten parvalbumin genes in their common ancestor. We have named these ten genes “parvalbumin 1-to-10” (PVALB1-to-PVALB10), building on earlier nomenclature established for zebrafish. For duplicated genes, we use variant names such as, for example, “PVALB2A and PVALB2B”. As illustrative examples of our gene identification system, we systematically analyze all parvalbumin genes in two common allergy-inducing species in Japan: red seabream (Pagrus major) and chum salmon (Oncorhynchus keta). We also provide gene identifications for known parvalbumin allergens in various fish species.

Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes.

Deuterostomes are one major group of bilaterians composed by hemichordates and echinoderms (collectively called Ambulacraria) and chordates. Comparative studies between these groups can provide valuable insights into the nature of the last common ancestor of deuterostomes and that of bilaterians. Indirect development of hemichordates, with larval phases similar to echinoderms and an adult body plan with an anteroposterior polarity like chordates and other bilaterians, makes them a suitable model for studying the molecular basis of development among deuterostomes. However, a comprehensive, quantitative catalogue of gene expression and chromatin dynamics in hemichordates is still lacking. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordate Ptychodera flava. We observed that P. flava development is underpinned by a biphasic transcriptional program probably controlled by distinct genetic networks. Comparisons with other bilaterian species revealed similar transcriptional and regulatory dynamics during hemichordate gastrulation, cephalochordate neurulation and elongation stages of annelids. By means of regulatory networks analysis and functional validations by transgenesis experiments in echinoderms, we propose that gastrulation is the stage of highest molecular resemblance in deuterostomes and that much of the molecular basis of deuterostome development was probably present in the bilaterian last common ancestor.

Universal dynamical function behind all genetic codes: [formula omitted]-adic attractor dynamical model

The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers Z2. This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function B such that the dynamical functions for all known genetic codes can be obtained from B by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by B. We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from B through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.

Long-term genomic surveillance reveals the circulation of clinically significant Salmonella in lymph nodes and beef trimmings from slaughter cattle from a Mexican feedlot.

This longitudinal study characterized Salmonella circulating in lymph nodes (LN, n = 800) and beef trimmings (n = 745) from slaughter cattle from a Mexican feedlot. During two years, LN and beef trimming samples were collected 72-96 h post-slaughter, and we obtained 77 isolates of the serovars Anatum (n = 23), Reading (n = 22), Typhimurium (n = 10), London (n = 9), Kentucky (n = 6), Fresno (n = 4), Give, Muenster, and monophasic 1,4,[5],12:i- (n = 1 each). These isolates were subjected to whole genome sequencing, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, reconstruction of their ancestral isolation sources through evolutionary analysis, and virulence profiling. Although LN and beef trimmings were not mixed, evolutionary analysis estimated that the common ancestor of all study isolates was likely of LN origin. Moreover, isolates from both sources were highly clonal (0-21 SNP distance), highlighting the complexity of Salmonella transmission dynamics. The pathogen persisted across cattle cohorts, as shown by clonality between isolates collected in different years (1-20 SNP distance). Major virulence genes were highly conserved (97-100% identity to the reference sequences) and most isolates carried a conserved version of pathogenicity islands 1-5, 9, 11, and 12. Typhimurium strains carried the Salmonella plasmid virulence operon (spvRABCD), and a Muenster isolate carried the st313td gene, both of which are associated with invasive phenotypes. Most isolates (49/77) were genetically similar (1-43 SNPs) to strains involved in human salmonellosis, highlighting their public health significance. Further research is needed on Salmonella transmission dynamics in cattle and the mechanisms determining subclinical infection and persistence in farm environments.

Translation of Mutant Repetitive Genomic Sequences in Hirsutella sinensis and Changes in the Secondary Structures and Functional Specifications of the Encoded Proteins.

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2-17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect-fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution.

Evolutionary origins of the lysosome-related organelle sorting machinery reveal ancient homology in post-endosome trafficking pathways

The major organelles of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (~1.5 billion years ago). Their acquisitions were defining milestones during eukaryogenesis. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct interorganelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of additional, distinct cellular compartments, infer ancestral states predating LECA, and explore the process of eukaryogenesis itself. Here, we undertake a molecular evolutionary analysis (including providing a transcriptome of the jakobid flagellate Reclinomonas americana), exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles (LROs), the Biogenesis of LRO Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery is present across the eukaryotic tree of life and was likely in place prior to LECA, making it an underappreciated facet of eukaryotic cellular organisation. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1 and MON1 proteins, and an unexpected relationship with the "homotypic fusion and vacuole protein sorting" (HOPS) and "Class C core vacuole/endosomal tethering" (CORVET) complexes), offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LROs biogenesis machinery from before the LECA to current eukaryotic diversity, integrating it into the larger mechanistic framework describing endomembrane evolution.

A Pleistocene Biogeography in Miniature: The Small‐Scale Evolutionary History of Podarcis lusitanicus (Squamata, Lacertidae)

ABSTRACTAimRecent literature is unveiling more complex responses of biodiversity to Pleistocenic climatic oscillations than those derived from initial models based solely on southern glacial macrorefugia. Here, we zoom in to delve into the genetic diversity and population structure of Podarcis lusitanicus, a lizard species native to the north‐western Iberian Peninsula.LocationNorth‐western Iberian Peninsula.TaxonPodarcis lusitanicus.MethodsUtilising a comprehensive multilocus approach, we explored the species' phylogeography and demographic history at a very fine spatial scale and timeframe. Concurrently, we evaluated both current and historical habitat suitability for the species, linking it to the observed demographic trends. We examined DNA sequences from two mitochondrial (cytb and ND4) and three nuclear genes (ACM4, MC1R and PDC) in 230 specimens collected from 21 populations spanning most of the species' distribution range.ResultsOur findings corroborate cytonuclear discordances in Podarcis, with nuclear genes failing to identify the mitochondrial clades in P. lusitanicus. Despite its separation from other Podarcis species approximately 4 million years ago, its diversification occurred much more recently, around 0.4 million years ago, resulting in three monophyletic lineages that are geographically coherent. This pattern suggests that some lineages of P. lusitanicus might have gone extinct after the split from the common ancestor. Pleistocene climatic oscillations profoundly influenced the demographic history of the species. During warmer periods, such as the Last Interglacial, populations expanded and came into secondary contact, whereas during the Last Glacial Maximum, populations contracted and became isolated in multiple micro‐refugia. The subsequent Mid‐Holocene warming facilitated population recovery, range expansion and lineage admixture.Main ConclusionsThis study underscores the intricate interplay between isolation and dispersal at a microscale, driven by Pleistocene climatic fluctuations, which have profoundly shaped the genetic structure and diversity of Iberian terrestrial biodiversity and may remain overlooked by biogeographic studies at coarser scales.

Re-appraising the evidence for the source, regulation and function of p53-family isoforms.

The p53 family of proteins evolved from a common ancestor into three separate genes encoding proteins that act as transcription factors with distinct cellular roles. Isoforms of each member that lack specific regions or domains are suggested to result from alternative transcription start sites, alternative splicing or alternative translation initiation, and have the potential to exponentially increase the functional repertoire of each gene. However, evidence supporting the presence of individual protein variants at functional levels is often limited and is inferred by mRNA detection using highly sensitive amplification techniques. We provide a critical appraisal of the current evidence for the origins, expression, functions and regulation of p53-family isoforms. We conclude that despite the wealth of publications, several putative isoforms remain poorly established. Future research with improved technical approaches and the generation of isoform-specific protein detection reagents is required to establish the physiological relevance of p53-family isoforms in health and disease. In addition, our analyses suggest that p53-family variants evolved partly through convergent rather than divergent evolution from the ancestral gene.

Gyrodactylus serrai n. sp. (Gyrodactylidae), from the Near-Threatened Clanwilliam Sawfin, Cheilobarbus serra (Peters) (Cyprinidae, Smilogastrinae), in the Cape Fold Ecoregion, South Africa

A new species of Gyrodactylus is described from the gills of the near-threatened Clanwilliam sawfin, Cheilobarbus serra (Smiliogastrinae) collected from the Matjies River, Cape Fold Ecoregion, Western Cape Province, South Africa. Morphometry and morphology of the haptoral hard parts (hamuli, bars and marginal hooks) of Gyrodactylus serrain. sp. differ from the other known species of the genus in the smaller size of hamuli and the shape and size of marginal hooks. Furthermore, ITS rDNA for the new species is unique among available Gyrodactylus spp. data in GenBank. Based on the uncorrected p-distances, G. serrain. sp. is genetically most closely related to Gyrodactylus moroccensis Rahmouni, 2023 and Gyrodactylus pseudomoroccensis Rahmouni, 2023 from two species of Luciobarbus (Barbinae) from northern Africa, with interspecific divergence of 8.7% and 8.8%, respectively. The presence of a median ridge in the terminal part of the ventral bar membrane at G. serrain. sp. most probably represents a morphological link to the North African Gyrodactylus spp. that suggests a morphogenetic association across the African continent as a result of ancient waterways that facilitated the dispersion of cyprinids and their parasite fauna or an independent evolution event retaining similarities from a common ancestor. The description of Gyrodactylus serrain. sp. represents only the second species of Gyrodactylus described from an endemic South African cyprinid host, underscoring the need for focused research on this group of fishes to provide a sound understanding of the parasitic communities of these highly threatened and poorly studied hosts.

On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution

Obviously, the discussion of different factors that could have contributed to the origin of life and evolution is clear speculation, since there is no way of checking the validity of most of the related hypotheses in practice, as the corresponding events not only already happened, but took place in a very distant past. However, there are a few undisputable facts that are present at the moment, such as the existence of a wide variety of living forms and the abundant presence of intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) in all living forms. Since it seems that the currently existing living forms originated from a common ancestor, their variety is a result of evolution. Therefore, one could ask a logical question of what role(s) the structureless and highly dynamic but vastly abundant and multifunctional IDPs/IDRs might have in evolution. This study represents an attempt to consider various ideas pertaining to the potential roles of protein intrinsic disorder in the origin of life and evolution.

Transcriptomic dynamics of ABA response in Brassica napus guard cells

Drought has a significant, negative impact on crop production; and these effects are poised to increase with climate change. Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). Because plants lose the majority of their water through stomatal pores on aerial surfaces of plants, stomatal closure is one of the rapid responses mediated by ABA to reduce transpirational water loss. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. However, guard cell transcriptomes have not been analyzed in agronomically valuable crops such as a major oilseed crop, rapeseed. In this study, we investigated the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus and conducted comparison analysis with the transcriptomes of A. thaliana. We discovered changes in gene expression indicating alterations in a host of physiological processes, including stomatal movement, metabolic reprogramming, and light responses. Our results suggest the existence of both immediate and delayed responses to ABA in Brassica guard cells. Furthermore, the transcription factors and regulatory networks mediating these responses are compared to those identified in Arabidopsis. Our results imply the continuing evolution of ABA responses in Brassica since its divergence from a common ancestor, involving both protein-coding and non-coding nucleotide sequences. Together, our results will provide a basis for developing strategies for molecular manipulation of drought tolerance in crop plants.

Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head

To shed light on the enigmatic origin of the vertebrate head, our study employs an integrated approach that combines single-cell transcriptomics, perturbations in signaling pathways, and cis-regulatory analysis in amphioxus. As a representative of a basal lineage within the chordate phylum, amphioxus retains many characteristics thought to have been present in the common chordate ancestor. Through cell type characterization, we identify the presence of prechordal plate-like, pre-migratory, and migratory neural crest-like cell populations in the developing amphioxus embryo. Functional analysis establishes conserved roles of the Nodal and Hedgehog signaling pathways in prechordal plate-like populations, and of the Wnt signaling pathway in neural crest-like populations’ development. Furthermore, our trans-species transgenic experiments highlight similarities in the regulatory environments that drive neural crest-like and prechordal plate-like developmental programs in both vertebrates and amphioxus. Our findings provide evidence that the key features of vertebrate head development can be traced back to the common ancestor of all chordates.

Intricate Evolution of Multifunctional Lipoxygenase in Red Algae.

Lipoxygenases (LOXs) from lower organisms have substrate flexibility and function versatility in fatty acid oxidation, but it is not clear how these LOXs acquired the ability to execute multiple functions within only one catalytic domain. This work studied a multifunctional LOX from red alga Pyropia haitanensis (PhLOX) which combined hydroperoxidelyase (HPL) and allene oxide synthase (AOS) activity in its active pocket. Molecular docking and site-directed mutagenesis revealed that Phe642 and Phe826 jointly regulated the double peroxidation of fatty acid, Gln777 and Asn575 were essential to the AOS function, and the HPL activity was improved when Asn575, Gln777, or Phe826 was replaced by leucine. Phylogenetic analysis indicated that Asn575 and Phe826 were unique amino acid sites in the separated clades clustered with PhLOX, whereas Phe642 and Gln777 were conserved in plant or animal LOXs. The N-terminal START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) domain of PhLOX was another key variable, as the absence of this domain disrupted the versatility of PhLOX. Moreover, the functions of two homologous LOXs from marine bacterium Shewanella violacea and red alga Chondrus crispus were examined. The HPL activity of PhLOX appeared to be inherited from a common ancestor, and the AOS function was likely acquired through mutations in some key residues in the active pocket. Taken together, our results suggested that some LOXs from red algae attained their versatility by amalgamating functional domains of ancestral origin and unique amino acid mutations.

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex.

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.