Ancestral Lineage Research Articles

Conservation of Ancient Genetic Pathways for Intracellular Persistence Among Animal Pathogenic Bordetellae.

Animal and human pathogens of the genus Bordetella are not commonly considered to be intracellular pathogens, although members of the closely related classical bordetellae are known to enter and persist within macrophages in vitro and have anecdotally been reported to be intracellular in clinical samples. B. bronchiseptica, the species closest to the ancestral lineage of the classical bordetellae, infects a wide range of mammals but is known to have an alternate life cycle, persisting, replicating and disseminating with amoeba. These observations give rise to the hypothesis that the ability for intracellular survival has an ancestral origin and is common among animal-pathogenic and environmental Bordetella species. Here we analyzed the survival of B. bronchiseptica and defined its transcriptional response to internalization by murine macrophage-like cell line RAW 264.7. Although the majority of the bacteria were killed and digested by the macrophages, a consistent fraction survived and persisted inside the phagocytes. Internalization prompted the activation of a prominent stress response characterized by upregulation of genes involved in DNA repair, oxidative stress response, pH homeostasis, chaperone functions, and activation of specific metabolic pathways. Cross species genome comparisons revealed that most of these upregulated genes are highly conserved among both the classical and non-classical Bordetella species. The diverse Bordetella species also shared the ability to survive inside RAW 264.7 cells, with the single exception being the bird pathogen B. avium, which has lost several of those genes. Knock-out mutations in genes expressed intracellularly resulted in decreased persistence inside the phagocytic cells, emphasizing the importance of these genes in this environment. These data show that the ability to persist inside macrophage-like RAW 264.7 cells is shared among nearly all Bordetella species, suggesting that resisting phagocytes may be an ancient mechanism that precedes speciation in the genus and may have facilitated the adaptation of Bordetella species from environmental bacteria to mammalian respiratory pathogens.

Stratified reconstruction of ancestral Escherichia coli diversification

BackgroundPhylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies.ResultsPhylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed.ConclusionsA staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.

Extensive host-switching of avian feather lice following the Cretaceous-Paleogene mass extinction event

Nearly all lineages of birds host parasitic feather lice. Based on recent phylogenomic studies, the three major lineages of modern birds diverged from each other before the Cretaceous-Paleogene (K-Pg) mass extinction event. In contrast, studies of the phylogeny of feather lice on birds, indicate that these parasites diversified largely after this event. However, these studies were unable to reconstruct the ancestral avian host lineage for feather lice. Here we use genome sequences of a broad diversity of lice to reconstruct a phylogeny based on 1,075 genes. By comparing this louse evolutionary tree to the avian host tree, we show that feather lice began diversifying on the common ancestor of waterfowl and landfowl, then radiated onto other avian lineages by extensive host-switching. Dating analyses and cophylogenetic comparisons revealed that two of three lineages of birds that diverged before the K-Pg boundary acquired their feather lice after this event via host-switching.

Craniometric variation and ancestry estimation in two contemporary Caribbean populations

Ancestry estimation of skeletonized remains by forensic anthropologists is conducted through comparative means, and a lack of population-specific data results in possible misclassifications. This is especially germane to individuals of Latin American ancestry. Generally, each country in Latin America can trace their ancestral lineage through three main parental groups: Indigenous, European, and African. However, grouping all Latin American individuals under the broad “Hispanic” category ignores the specific genetic contributions from each parental group, which is variable and dependent on the population histories and sociocultural dynamics of each country. This study analyzes the craniometric ancestry of Hispaniola (the Dominican Republic and Haiti) using 190 cranial Computed Tomography (CT) scans (f=103; m=87), along with the island’s history, to explore similarities and differences between the two groups. MANOVA results indicate that 53.6% and 71.4% of the 28 cranial measurements differ between the ancestries and sexes, respectively; and intraobserver error analyses demonstrate that 85.7% of measurements from CT scans are good-excellent in reliability. Further, a total of 12 canonical discriminant function analyses produced cross-validated classification accuracies of 73.7–78.6% for females, 71.8–87.5% for males, and 72.0–77.8% for pooled sex. This study demonstrates that, despite sharing a small island, Dominican and Haitian individuals can be differentiated with a fair amount of statistical certainty, which is possible due to complex socio-cultural, -political, and -demographic factors that have produced and maintained genetic heterogeneity. Moreover, the discriminant functions provided here can be used by the international forensic science community to identify individuals living on Hispaniola.

Profiling of 17 Y-STR loci in Mazandaran and Gilan provinces of Iran

Background/aimThe Y-chromosome mainly consists of heterochromatin regions that have a father-to-son inheritance. Short tandem repeat polymorphic (STRP) markers distributed all over the chromosome provide the opportunity for investigations in forensic medicine and ancestral lineage studies. Due to the existence of wide varieties of geographical and ethnic groups in Iran, studying Y-STRP markers is necessary for further applications. Here we investigated the provinces of Mazandaran and Gilan for the first time.Materials and methodsSamples included 119 and 90 unrelated males from Mazandaran and Gilan, respectively. Using a PCR amplification kit, 17 Y-STRP markers were amplified and genotyping was conducted by capillary electrophoresis. Allele frequency, haplotype diversity (HD), and haplotype discrimination capacity (DC) were calculated. The populations were compared together and to neighboring countries including Afghanistan and Azerbaijan by FST index.ResultsA total of 204 unique haplotypes were observed. No uniqueness was observed between the two provinces. HD was 0.9993 and 0.9998 in Mazandaran and Gilan, respectively. DC was 0.9666 and 0.9888 for Mazandaran and Gilan, respectively. DYS385b and DYS391 had the most and least polymorphic content in both provinces, respectively. There was not a significant difference between these two provinces (FST = 0.0006 and P = 0.00) and neighboring countries.ConclusionThe results highlight the effectiveness of these Y-STRP markers for male discrimination in the north of Iran. Using additional markers along with extended sample size would provide a better opportunity for removing matched haplotypes and introducing the best polymorphic markers in this specific population.

Distribution and evolution of the serine/aspartate racemase family in plants

Previous studies have shown that several d-amino acids are widely present in plants, and serine racemase (SerR), which synthesizes d-serine in vivo, has already been identified from three plant species. However, the full picture of the d-amino acid synthesis pathway in plants is not well understood. To clarify the distribution of amino acid racemases in plants, we have cloned, expressed and characterized eight SerR homologous genes from five plant species, including green alga. These SerR homologs exhibited racemase activity towards serine or aspartate and were identified on the basis of their maximum activity as SerR or aspartate racemase (AspR). The plant AspR gene is identified for the first time from Medicago truncatula, Manihot esculenta, Solanum lycopersicum, Sphagnum girgensohnii and Spirogyra pratensis. In addition to the AspR gene, three SerR genes are identified in the former three species. Phylogenetic tree analysis showed that SerR and AspR are widely distributed in plants and form a serine/aspartate racemase family cluster. The catalytic efficiency (kcat/Km) of plant AspRs was more than 100 times higher than that of plant SerRs, suggesting that d-aspartate, as well as d-serine, can be synthesized in vivo by AspR. The amino acid sequence alignment and comparison of the chromosomal gene arrangement have revealed that plant AspR genes independently evolved from SerR in each ancestral lineage of plant species by gene duplication and acquisition of two serine residues at position 150 to 152.

Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations.

The transition from land to water in whales and dolphins (cetaceans) was accompanied by remarkable adaptations. To reveal genomic changes that occurred during this transition, we screened for protein-coding genes that were inactivated in the ancestral cetacean lineage. We found 85 gene losses. Some of these were likely beneficial for cetaceans, for example, by reducing the risk of thrombus formation during diving (F12 and KLKB1), erroneous DNA damage repair (POLM), and oxidative stress-induced lung inflammation (MAP3K19). Additional gene losses may reflect other diving-related adaptations, such as enhanced vasoconstriction during the diving response (mediated by SLC6A18) and altered pulmonary surfactant composition (SEC14L3), while loss of SLC4A9 relates to a reduced need for saliva. Last, loss of melatonin synthesis and receptor genes (AANAT, ASMT, and MTNR1A/B) may have been a precondition for adopting unihemispheric sleep. Our findings suggest that some genes lost in ancestral cetaceans were likely involved in adapting to a fully aquatic lifestyle.

Xylocythere sarrazinae, a new cytherurid ostracod (Crustacea) from a hydrothermal vent field on the Juan de Fuca Ridge, northeast Pacific Ocean, and its phylogenetic position within Cytheroidea

This paper described Xylocythere sarrazinae sp. nov. (Ostracoda: Cytheroidea: Cytheruridae: Eucytherurinae), collected at 2196 m depth from the Grotto hydrothermal edifice (Main Endeavor Field, Juan de Fuca Ridge) in the northeastern Pacific Ocean. This new species was found living in association with Ridgeia piscesae tubeworm assemblages. It is the second representative of Xylocythere described from such vents. Xylocythere sarrazinae sp. nov. is easily distinguished from the seven described species of Xylocythere by the surface ornamentations of its carapace, with the most similar species to it being Xylocythere pointillissima Maddocks & Steineck, 1987. However, Xylocythere sarrazinae sp. nov can be distinguished from X. pointillissima based on the following characters: having a subsquare basal capsule outline, a spatulate upper ramus, a flattened distal lobe of the male copulatory organ, and having 15 maxillula branchial plate setae. We found that one specimen of this new species had multiple spherical objects associated with the internal openings of its pore clusters. These objects were quite similar in shape to that of chemoautotrophic bacteria, which were previously reported from the outer surfaces of pore clusters in other Xylocythere species. Finally, we provided a preliminary phylogenetic analysis of this new species based on 18S rRNA gene sequences to determine the phylogenetic position of the subfamily Eucytherurinae within the superfamily Cytheroidea. This analysis revealed that Xylocythere (Eucytherurinae) may be the most ancestral lineage among the Cytheruridae and identified paraphyletic relationships among the three subfamilies within Cytheruridae. This result supported certain previous studies’ conclusions based on morphology and fossil records.

The role of floral oils in the evolution of apid bees (Hymenoptera: Apidae)

AbstractMost bees collect pollen and nectar for their larvae, while some also collect other resources. We investigated the evolution of floral oil-collecting behaviour in the Apidae and the evolutionary effects of floral oils on host brood cells for cuckoo bees. Focusing on apid bee phylogeny, we reconstructed the evolution of floral oil collection by females, use of floral oils in cell construction and the inclusion of oils in provisioning immatures. Ancestral character reconstruction demonstrates that floral oil-collecting behaviour arose four times independently. We also found that in cuckoo bees, parasitization of oil-collecting bees arose three times (including one secondary return) in Apidae. Except for Ctenoplectrina, oil cuckoo bees are all closely related to each other, forming an independent clade within the Nomadinae. Analysis of evolutionary transition rates indicates that there is a greater tendency for switching from an oil-collecting host to a non-oil-collecting host than the reverse. In apid bees, evolutionary transition rates are higher for switching to cuckoo behaviour from an ancestral lineage in which females collect floral oils than from other pollen-collecting lineages. We conclude that adaptation to oil collection is advantageous for pollen-collecting bees, and that the origin of oil cuckoo bees from non-oil cuckoo bees is constrained.

Loss of developmental diapause as prerequisite for social evolution in bees.

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs have been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction (ASR) of the ecological and evolutionary factors associated with diapause phase. We find that social lifestyle, latitude and voltinism are significant predictors of the life stage in which diapause occurs. ASR revealed that the most recent common ancestor of all bees likely exhibited developmental diapause and shifts to adult, reproductive, or no diapause have occurred in the ancestors of lineages in which social behaviour has evolved. These results provide fresh insight regarding the role of diapause as a prerequisite for the evolution of sociality in bees.

Maternal phylogeographic patterns and coalescent times of Arabidopsis thaliana based on chloroplast DNA analyses.

Arabidopsis thaliana, one of the most important model plants, has played an essential role in every biological field including evolutionary biology. Recent population genomic studies have gradually clarified the origin and evolution of this species. Nevertheless, incongruent patterns among gene trees based on cytogenetic data have highlighted the importance of understanding the life history evolution and landscape biogeography of extant A. thaliana populations. Here, we focus on the maternally inherited chloroplast genome in A. thaliana and carry out phylogeographic analyses and coalescent time estimations. The maternal lineage of A. thaliana originated in the European to West and Central Asian regions in the Early Pleistocene. Relicts, the ancient lineages suggested by population genomic data, are not ancestral maternal lineages, but are derived from the European population. Part of the European population then dispersed eastward and spread to the Indian region, and finally extended to the Yangtze River region. The branching patterns and evolutionary time scales of the maternal genealogy are significantly different from those estimated from analyses of autosomal genes, and these cannot be explained by incomplete lineage sorting of the ancestral polymorphisms during the coalescent process due to large differences in the evolutionary time scale involved.

Diverse origin of Plasmodium falciparum in northwest Ecuador

BackgroundEcuador plans to eliminate malaria by 2020, and the country has already seen a decrease in the number of cases from more than 100,000 in 2000 to only 618 in 2015. Around 30% of malaria infections in Ecuador are caused by Plasmodium falciparum. Most malaria population genetics studies performed in Latin America, especially in the Pacific Coast, indicate a high clonality and a clear structure of P. falciparum populations. It was shown that an outbreak of P. falciparum in northwest Ecuador was the result of a clonal expansion of parasites circulating at low levels in the country or re-invading Ecuador from neighbouring territories. However, general characteristics of P. falciparum circulating in the northwest coast of Ecuador have not been determined. The main goal of this study was to genetically characterize the population structure of P. falciparum in coastal Ecuadorian localities bordering with Colombia.MethodsMolecular investigation of 41 samples collected from 2013 to 2016 in San Lorenzo County, northwest Ecuador was performed using seven neutral microsatellite markers.ResultsThe genetic population structure of P. falciparum in northwest Ecuador is clearly defined as three different genetic groups previously reported in Ecuador, Peru and Colombia.ConclusionsThe limited number of P. falciparum clonal types that are circulating in northwest Ecuador, are related to ancestral parasite clonal lineages reported in the Pacific Coast. These parasites could be a product of migration from neighbouring regions or residual clonal types circulating in the country in low proportions. Studies of the genetic characterization of P. falciparum in eliminating areas help determine the possible origin of parasites in order to create strategies to prevent the entrance of new lineages and achieve local elimination of malaria.

The speciation and hybridization history of the genus Salmonella

Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella , an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander’s group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.

Intraspecific Diversity of Fission Yeast Mitochondrial Genomes.

The fission yeast Schizosaccharomyces pombe is an important model organism, but its natural diversity and evolutionary history remain under-studied. In particular, the population genomics of the S. pombe mitochondrial genome (mitogenome) has not been thoroughly investigated. Here, we assembled the complete circular-mapping mitogenomes of 192 S. pombe isolates de novo, and found that these mitogenomes belong to 69 nonidentical sequence types ranging from 17,618 to 26,910 bp in length. Using the assembled mitogenomes, we identified 20 errors in the reference mitogenome and discovered two previously unknown mitochondrial introns. Analyzing sequence diversity of these 69 types of mitogenomes revealed two highly distinct clades, with only three mitogenomes exhibiting signs of inter-clade recombination. This diversity pattern suggests that currently available S. pombe isolates descend from two long-separated ancestral lineages. This conclusion is corroborated by the diversity pattern of the recombination-repressed K-region located between donor mating-type loci mat2 and mat3 in the nuclear genome. We estimated that the two ancestral S. pombe lineages diverged about 31 million generations ago. These findings shed new light on the evolution of S. pombe and the data sets generated in this study will facilitate future research on genome evolution.

Lacking catalase, a protistan parasite draws on its photosynthetic ancestry to complete an antioxidant repertoire with ascorbate peroxidase

BackgroundAntioxidative enzymes contribute to a parasite’s ability to counteract the host’s intracellular killing mechanisms. The facultative intracellular oyster parasite, Perkinsus marinus, a sister taxon to dinoflagellates and apicomplexans, is responsible for mortalities of oysters along the Atlantic coast of North America. Parasite trophozoites enter molluscan hemocytes by subverting the phagocytic response while inhibiting the typical respiratory burst. Because P. marinus lacks catalase, the mechanism(s) by which the parasite evade the toxic effects of hydrogen peroxide had remained unclear. We previously found that P. marinus displays an ascorbate-dependent peroxidase (APX) activity typical of photosynthetic eukaryotes. Like other alveolates, the evolutionary history of P. marinus includes multiple endosymbiotic events. The discovery of APX in P. marinus raised the questions: From which ancestral lineage is this APX derived, and what role does it play in the parasite’s life history?ResultsPurification of P. marinus cytosolic APX activity identified a 32 kDa protein. Amplification of parasite cDNA with oligonucleotides corresponding to peptides of the purified protein revealed two putative APX-encoding genes, designated PmAPX1 and PmAPX2. The predicted proteins are 93% identical, and PmAPX2 carries a 30 amino acid N-terminal extension relative to PmAPX1. The P. marinus APX proteins are similar to predicted APX proteins of dinoflagellates, and they more closely resemble chloroplastic than cytosolic APX enzymes of plants. Immunofluorescence for PmAPX1 and PmAPX2 shows that PmAPX1 is cytoplasmic, while PmAPX2 is localized to the periphery of the central vacuole. Three-dimensional modeling of the predicted proteins shows pronounced differences in surface charge of PmAPX1 and PmAPX2 in the vicinity of the aperture that provides access to the heme and active site.ConclusionsPmAPX1 and PmAPX2 phylogenetic analysis suggests that they are derived from a plant ancestor. Plant ancestry is further supported by the presence of ascorbate synthesis genes in the P. marinus genome that are similar to those in plants. The localizations and 3D structures of the two APX isoforms suggest that APX fulfills multiple functions in P. marinus within two compartments. The possible role of APX in free-living and parasitic stages of the life history of P. marinus is discussed.

Admixture between Ancient Lineages, Selection, and the Formation of Sympatric Stickleback Species-Pairs.

Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data have revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic reanalysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping, and genome-wide single-nucleotide polymorphism data, we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead, we reveal a complex colonization history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.

Whole-genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China.

Ten indigenous chicken breeds were originally distributed in Jiangxi Province, China, and they define a critical component of Chinese chicken genetic resources. We have investigated the population genetics of seven Jiangxi chicken breeds using 600K chicken BeadChip SNP data. To provide a genome-wide perspective for the population structure of all 10 Jiangxi chicken breeds, we herein genotyped 78additional individuals from the seven breeds and 63 chickens from three uninvestigated breeds-Yugan Black (YG), Nancheng Black (NC) and Wanzai Yellow using 55K chicken SNP arrays. We then explored merged data of 17101 SNPs from 235 individuals to infer the population structure of the 10 breeds. We showed that NC and YG are two regional populations of the same breed, as individuals from the two populations clustered together to form a branch separate from the other breeds in the neighbor-joining tree, they always grouped together in multidimensional principal component analyses and they displayed an identical pattern of ancestral lineage composition. Hence, NC and YG should be considered a single breed in the state-supported conservation scheme. Moreover, we conducted a genome scan for signatures of selection for black plumage. bayescan and hapflk analyses of two contrasting groups (three black-feathered breeds vs. six non-black-feathered breeds) consistently detected 25 putative regions under selection. Nine pigmentation- associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2) reside within these regions, and these genes are interesting candidates for black plumage and provide a starting point for further identification of causative mutations for black feathers in chicken.

Discovery of All Three Types in Cartilaginous Fishes Enables Phylogenetic Resolution of the Origins and Evolution of Interferons.

Interferons orchestrate host antiviral responses in jawed vertebrates. They are categorized into three classes; IFN1 and IFN3 are the primary antiviral cytokine lineages, while IFN2 responds to a broader variety of pathogens. The evolutionary relationships within and between these three classes have proven difficult to resolve. Here, we reassess interferon evolution, considering key phylogenetic pitfalls including taxon sampling, alignment quality, model adequacy, and outgroup choice. We reveal that cartilaginous fishes, and hence the jawed vertebrate ancestor, possess(ed) orthologs of all three interferon classes. We show that IFN3 groups sister to IFN1, resolve the origins of the human IFN3 lineages, and find that intronless IFN3s emerged at least three times. IFN2 genes are highly conserved, except for IFN-γ-rel, which we confirm resulted from a teleost-specific duplication. Our analyses show that IFN1 phylogeny is highly sensitive to phylogenetic error. By accounting for this, we describe a new backbone IFN1 phylogeny that implies several IFN1 genes existed in the jawed vertebrate ancestor. One of these is represented by the intronless IFN1s of tetrapods, including mammalian-like repertoires of reptile IFN1s and a subset of amphibian IFN1s, in addition to newly-identified intron-containing shark IFN1 genes. IFN-f, previously only found in teleosts, likely represents another ancestral jawed vertebrate IFN1 family member, suggesting the current classification of fish IFN1s into two groups based on the number of cysteines may need revision. The providence of the remaining fish IFN1s and the coelacanth IFN1s proved difficult to resolve, but they may also be ancestral jawed vertebrate IFN1 lineages. Finally, a large group of amphibian-specific IFN1s falls sister to all other IFN1s and was likely also present in the jawed vertebrate ancestor. Our results verify that intronless IFN1s have evolved multiple times in amphibians and indicate that no one-to-one orthology exists between mammal and reptile IFN1s. Our data also imply that diversification of the multiple IFN1s present in the jawed vertebrate ancestor has occurred through a rapid birth-death process, consistent with functional maintenance over a 450-million-year host-pathogen arms race. In summary, this study reveals a new model of interferon evolution important to our understanding of jawed vertebrate antiviral immunity.

An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids

The phylum Cyanobacteria includes free-living bacteria and plastids, the descendants of cyanobacteria that were engulfed by the ancestral lineage of the major photosynthetic eukaryotic group Archaeplastida. Endosymbiotic events that followed this primary endosymbiosis spread plastids across diverse eukaryotic groups. The remnants of the ancestral cyanobacterial genome present in all modern plastids, enable the placement of plastids within Cyanobacteria using sequence-based phylogenetic analyses. To date, such phylogenetic studies have produced conflicting results and two competing hypotheses: (1) plastids diverge relatively recently in cyanobacterial evolution and are most closely related to nitrogen-fixing cyanobacteria, or (2) plastids diverge early in the evolutionary history of cyanobacteria, before the divergence of most cyanobacterial lineages. Here, we use phylogenetic analysis of ribosomal proteins from an expanded data set of cyanobacterial and representative plastid genomes to infer a deep placement for the divergence of the plastid ancestor lineage. We recover plastids as sister to Gloeomargarita and show that the group diverges from other cyanobacterial groups before Pseudanabaena, a previously unreported placement. The tree topologies and phylogenetic distances in our study have implications for future molecular clock studies that aim to model accurate divergence times, especially with respect to groups containing fossil calibrations. The newly sequenced cyanobacterial groups included here will also enable the use of novel cyanobacterial microfossil calibrations.

East Asian origins of European holly oaks (Quercus section Ilex Loudon) via the Tibet‐Himalaya

AbstractAimMany subtropical organisms exhibit an East Asian‐Tethyan disjunction, a distribution split between East Asia and the Mediterranean. The underlying mechanisms and timing have remained unclear to date. The evolutionary history of Quercus section Ilex Loudon, a representative East Asian‐Tethyan disjunct lineage with a rich and widespread fossil record, was investigated to understand the key drivers of this disjunction.LocationEurasia.MethodsThe phylogeny of Quercus section Ilex was reconstructed using RAD‐seq. Divergence times were estimated based on three fossil calibrations. Ancestral range and niche were reconstructed on the calibrated tree to infer the timing of transitions in geographic distributions and niche. Convergence in ecological space was estimated by fitting alternative multiple‐regime Ornstein‐Uhlenbeck models. Leaf shape affinities among extant and fossil taxa of section Ilex were assessed using geometric morphometric approaches.ResultsSix clades were well resolved in section Ilex. Ancestral range reconstruction and divergence time dating suggest a wide distribution along the East Tethys seaway, with initial divergence at the mid‐Eocene, and all six clades originating before the Miocene. The section dispersed from East Asia to the Mediterranean at the Eocene‐Oligocene boundary. A shift toward higher elevations was detected in the Himalayan clade during the middle or late Miocene. European fossil lineages during the early Miocene differ in leaf morphology from later lineages, which we infer to be a consequence of adaptive differentiation or species turnover.Main conclusionsQuercus section Ilex was widespread along the East Tethys seaway from the middle Eocene onward. The European holly oaks originated from an East Asian ancestral lineage that dispersed to Europe via the Tibet‐Himalaya corridor in the Oligocene. Lowlands along the margins of the Himalayas and through an Oligocene Tibetan valley served as the dispersal route(s) for these species. Changing climates drove Miocene extinction and local adaptation of European lineages.