Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants.

BACKGROUND: Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi. RESULTS: Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins. CONCLUSIONS: There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

A Reference Genome Assembly of American Bison, Bison bison bison.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes.

Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the "bush at the top" of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.

Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes.

The Southern Ocean around Antarctica is among the most rapidly warming regions on Earth, but has experienced episodic climate change during the past 40 million years. It remains unclear how ancient periods of climate change have shaped Antarctic biodiversity. The origin of antifreeze glycoproteins (AFGPs) in Antarctic notothenioid fishes has become a classic example of how the evolution of a key innovation in response to climate change can drive adaptive radiation. By using a time-calibrated molecular phylogeny of notothenioids and reconstructed paleoclimate, we demonstrate that the origin of AFGP occurred between 42 and 22 Ma, which includes a period of global cooling approximately 35 Ma. However, the most species-rich lineages diversified and evolved significant ecological differences at least 10 million years after the origin of AFGPs, during a second cooling event in the Late Miocene (11.6-5.3 Ma). This pattern indicates that AFGP was not the sole trigger of the notothenioid adaptive radiation. Instead, the bulk of the species richness and ecological diversity originated during the Late Miocene and into the Early Pliocene, a time coincident with the origin of polar conditions and increased ice activity in the Southern Ocean. Our results challenge the current understanding of the evolution of Antarctic notothenioids suggesting that the ecological opportunity that underlies this adaptive radiation is not linked to a single trait, but rather to a combination of freeze avoidance offered by AFGPs and subsequent exploitation of new habitats and open niches created by increased glacial and ice sheet activity.

Resolution of ray-finned fish phylogeny and timing of diversification.

Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major ray-finned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three long-standing problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."

The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond.

The perciform group Labroidei includes approximately 2600 species and comprises some of the most diverse and successful lineages of teleost fishes. Composed of four major clades, Cichlidae, Labridae (wrasses, parrotfishes, and weed whitings), Pomacentridae (damselfishes), and Embiotocidae (surfperches); labroids have been an icon for studies of biodiversity, adaptive radiation, and sexual selection. The success and diversification of labroids have been largely attributed to the presence of a major innovation in the pharyngeal jaw apparatus, pharyngognathy, which is hypothesized to increase feeding capacity and versatility. We present results of large-scale phylogenetic analyses and a survey of pharyngeal jaw functional morphology that allow us to examine the evolution of pharyngognathy in a historical context. Phylogenetic analyses were based on a sample of 188 acanthomorph (spiny-rayed fish) species, primarily percomorphs (perch-like fishes), and DNA sequence data collected from 10 nuclear loci that have been previously used to resolve higher level ray-finned fish relationships. Phylogenies inferred from this dataset using maximum likelihood, Bayesian, and species tree analyses indicate polyphyly of the traditional Labroidei and clearly separate Labridae from the remainder of the traditional labroid lineages (Cichlidae, Embiotocidae, and Pomacentridae). These three "chromide" families grouped within a newly discovered clade of 40 families and more than 4800 species (>27% of percomorphs and >16% of all ray-finned fishes), which we name Ovalentaria for its characteristic demersal, adhesive eggs with chorionic filaments. This fantastically diverse clade includes some of the most species-rich lineages of marine and freshwater fishes, including all representatives of the Cichlidae, Embiotocidae, Pomacentridae, Ambassidae, Gobiesocidae, Grammatidae, Mugilidae, Opistognathidae, Pholidichthyidae, Plesiopidae (including Notograptus), Polycentridae, Pseudochromidae, Atherinomorpha, and Blennioidei. Beyond the discovery of Ovalentaria, this study provides a surprising, but well-supported, hypothesis for a convict-blenny (Pholidichthys) sister group to the charismatic cichlids and new insights into the evolution of pharyngognathy. Bayesian stochastic mapping ancestral state reconstructions indicate that pharyngognathy has evolved at least six times in percomorphs, including four separate origins in members of the former Labroidei, one origin in the Centrogenyidae, and one origin within Beloniformes. Our analyses indicate that all pharyngognathous fishes have a mechanically efficient biting mechanism enabled by the muscular sling and a single lower jaw element. However, a major distinction exists between Labridae, which lacks the widespread, generalized percomorph pharyngeal biting mechanism, and all other pharyngognathous clades, which possess this generalized biting mechanism in addition to pharyngognathy. Our results reveal a remarkable history of pharyngognathy: far from a single origin, it appears to have evolved at least six times, and its status as a major evolutionary innovation is reinforced by it being a synapomorphy for several independent major radiations, including some of the most species rich and ecologically diverse percomorph clades of coral reef and tropical freshwater fishes, Labridae and Cichlidae. [Acanthomorpha; Beloniformes; Centrogenyidae; key innovation; Labroidei; Ovalentaria; pharyngeal jaws; Perciformes.].

Nuclear gene-inferred phylogenies resolve the relationships of the enigmatic Pygmy Sunfishes, Elassoma (Teleostei: Percomorpha).

Elassoma, the Pygmy Sunfishes, has long proven difficult to classify among the more than 15,000 species of percomorph fishes. Hypotheses dating to the 19th Century include Elassoma in Centrarchidae or in the monogeneric Elassomatidae, and more recent phylogenetic hypotheses have classified Elassoma in Smegmamorpha that also contained Synbranchiformes, Mugiliformes, Gasterosteiformes, and Atherinomorpha. No published phylogenetic analysis of morphological or molecular data has supported the monophyly of Smegmamorpha, or a consistent resolution of Elassoma relationships. In this study, we investigated the phylogenetic relationships of Elassoma and test the monophyly of Smegmamorpha with a nucleotide dataset comprising 10 protein-coding nuclear genes sampled from 65 percomorph species. Maximum likelihood analyses of each individual gene and the concatenated 10 genes all result in strong support for a clade composed of Elassoma and Centrarchidae, and no analysis supports monophyly of Smegmamorpha. Based on these results, a rank-free phylogenetic definition of Centrarchidae is presented that includes Elassoma, and the continued recognition of Smegmamorpha is discouraged. We discuss the implications of these phylogenetic analyses for relationships of several other percomorph lineages, including Kyphosidae, Terapontidae, Kuhliidae, Cheilodactylidae, Percichthyidae, Howellidae, Enoplosidae, Sinipercidae, and Cirrhitidae.

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.

Response to selection for parasitism of a suboptimal, low-preference host in an aphid parasitoid.

Risks of postintroduction evolution in insects introduced to control invasive pests have been discussed for some time, but little is known about responses to selection or genetic architectures of host adaptation and thus about the likelihood or rapidity of evolutionary shifts. We report here results on the response to selection and genetic architecture of parasitism of a suboptimal, low-preference host species by an aphid parasitoid, Aphelinus rhamni, a candidate for introduction against the soy bean aphid, Aphis glycines. We selected A. rhamni for increased parasitism of Rhopalsiphum padi by rearing the parasitoid on this aphid for three generations. We measured parasitism of R. padi at generations 2 and 3, and at generation 3, we crossed and backcrossed parasitoids from the populations reared on R. padi with those from populations reared on Aphis glycines and compared parasitism of both R. padi and Aphis glycines among F 1 and backcross females. Aphelinus rhamni responded rapidly to selection for parasitism of R. padi. Selection for R. padi parasitism reduced parasitism of Aphis glycines, the original host of A. rhamni. However, parasitism of R. padi did not increase from generation 2 to generation 3 of selection, suggesting reduced variance available for selection, which was indeed found. We tested the associations between 184 single nucleotide polymorphisms (SNP) and increased parasitism of R. padi and found 28 SNP loci, some of which were associated with increased and others with decreased parasitism of R. padi. We assembled and annotated the A. rhamni genome, mapped all SNP loci to contigs and tested whether genes on contigs with SNP loci associated with parasitism were enriched for candidate genes or gene functions. We identified 80 genes on these contigs that mapped to 1.2 Mb of the 483 Mb genome of A. rhamni but found little enrichment of candidate genes or gene functions.

Counties not countries: Variation in host specificity among populations of an aphid parasitoid.

Parasitic wasps are among the most species-rich groups on Earth. A major cause of this diversity may be local adaptation to host species. However, little is known about variation in host specificity among populations within parasitoid species. Not only is such knowledge important for understanding host-driven speciation, but because parasitoids often control pest insects and narrow host ranges are critical for the safety of biological control introductions, understanding variation in specificity and how it arises are crucial applications in evolutionary biology. Here, we report experiments on variation in host specificity among 16 populations of an aphid parasitoid, Aphelinus certus. We addressed several questions about local adaptation: Do parasitoid populations differ in host ranges or in levels of parasitism of aphid species within their host range? Are differences in parasitism among parasitoid populations related to geographical distance, suggesting clinal variation in abundances of aphid species? Or do nearby parasitoid populations differ in host use, as would be expected if differences in aphid abundances, and thus selection, were mosaic? Are differences in parasitism among parasitoid populations related to genetic distances among them? To answer these questions, we measured parasitism of a taxonomically diverse group of aphid species in laboratory experiments. Host range was the same for all the parasitoid populations, but levels of parasitism varied among aphid species, suggesting adaptation to locally abundant aphids. Differences in host specificity did not correlate with geographical distances among parasitoid populations, suggesting that local adaption is mosaic rather than clinal, with a spatial scale of less than 50 kilometers. We sequenced and assembled the genome of A. certus, made reduced-representation libraries for each population, analyzed for single nucleotide polymorphisms, and used these polymorphisms to estimate genetic differentiation among populations. Differences in host specificity correlated with genetic distances among the parasitoid populations.

Variation in genome size and karyotype among closely related aphid parasitoids (Hymenoptera, Aphelinidae).

Genome sizes were measured and determined for the karyotypes of nine species of aphid parasitoids in the genus Aphelinus Dalman,1820. Large differences in genome size and karyotype were found between Aphelinus species, which is surprising given the similarity in their morphology and life history. Genome sizes estimated from flow cytometry were larger for species in the Aphelinus mali (Haldeman, 1851) complex than those for the species in the Aphelinus daucicola Kurdjumov, 1913 and Aphelinus varipes (Förster,1841) complexes. Haploid karyotypes of the Aphelinus daucicola and Aphelinus mali complexes comprised five metacentric chromosomes of similar size, whereas those of the Aphelinus varipes complex had four chromosomes, including a larger and a smaller metacentric chromosome and two small acrocentric chromosomes or a large metacentric and three smaller acrocentric chromosomes. Total lengths of female haploid chromosome sets correlated with genome sizes estimated from flow cytometry. Phylogenetic analysis of karyotypic variation revealed a chromosomal fusion together with pericentric inversions in the common ancestor of the Aphelinus varipes complex and further pericentric inversions in the clade comprising Aphelinus kurdjumovi Mercet, 1930 and Aphelinus hordei Kurdjumov, 1913. Fluorescence in situ hybridization with a 28S ribosomal DNA probe revealed a single site on chromosomes of the haploid karyotype of Aphelinus coreae Hopper & Woolley, 2012. The differences in genome size and total chromosome length between species complexes matched the phylogenetic divergence between them.

Divergence in skeletal mass and bone morphology in antarctic notothenioid fishes.

Although notothenioid fishes lack swim bladders, some species live temporarily or permanently in the water column. Given its relatively high density, skeletal mass is a key determinant of buoyancy. Notothenioids have reduced skeletal ossification, but there is little quantitative data on the phylogenetic distribution of this trait. We obtained dry skeletal masses for 54 specimens representing 20 species from six notothenioid families. Although comparative data are sparse, notothenioid skeletons comprise a smaller percentage of body mass, <3.5%, than those of three non-notothenioid perciforms. With relatively high skeletal mass, the non-Antarctic Bovichtus diacanthus is similar in skeletal mass to some non-notothenioids. Eleginops maclovinus, the non-Antarctic sister group of the Antarctic clade, has a relatively light skeleton (<2% of body mass) similar to many species in the Antarctic clade. Low skeletal mass is therefore a synapomorphy shared by Eleginops plus the Antarctic clade. We provide gross, histological, and micro-CT documentation of the structure and location of bone and cartilage in skulls, pectoral girdles, and vertebrae, with emphasis on the bovichtid B. diacanthus, the eleginopsid E. maclovinus, and the channichthyid Chaenodraco wilsoni. In Eleginops and the Antarctic clade, most bone is spongy and most species have persisting cartilage in the skull and appendicular skeleton. We also measured the relative size of the notochordal canal in adult vertebral centra of 38 species representing all eight families. There is considerable interspecific variation in this pedomorphic trait and all species show an ontogenetic reduction in the relative size of the canal. However, large persisting canals are present in adults of the Antarctic clade, especially in the nototheniids Pleuragramma and Aethotaxis and in a number of bathydraconid and channichthyid genera.

Divergence in skeletal mass and bone morphology in antarctic notothenioid fishes.

Cover illustration. Notothenioid fishes lack swim bladders, but species live temporarily or permanently in the water column. Without swim bladder, skeletal mass becomes a key determinant of buoyancy. In this issue of the Journal of Morphology, Joseph Eastman and coauthors (pp. 841-861 10.1002/jmor.20258) quantify the degree of skeletal ossification in notothenioid fish and discuss it in phylogenetic context. The cover image shows a volume rendered micro-CT image showing extensive bone in the adult skeleton of the non-Antarctic notothenioid Bovichtus diacanthus from Tristan da Cunha. Tissue density is mapped in false color on a spectrum ranging from less dense (cool colors) to more dense (warm colors). Bone is considerably more extensive in B. diacanthus than in Antarctic notothenioids.

Scanning electron microscopic analysis of spontaneous and UV-induced abnormal segment patterns in Chironomus samoensis (Diptera, Chironomidae).

The embryonic body pattern of Chironomus samoensis, as well as other chironomids, can be altered dramatically by irradiating their eggs with ultraviolet light (UV). Anterior UV irradiation leads to the formation of double abdomen embryos whose anterior segments are replaced by posterior segments with reversed polarity. Most double abdomens are symmetrical showing a mirror image duplication of the posterior six or seven segments. However, in some cases the anterior end of the double abdomen is shorter, and comprises fewer segments, than its posterior counterpart. These asymmetries range from moderate to extreme. They involve the juxtaposition, at the plane of polarity reversal, of disparate segments. The same range of symmetrical and asymmetrical double abdomens is also formed spontaneously in an apparently mutant strain of C. samoensis. There are striking similarities between this natural variant and the Drosophila melanogaster mutant bicaudal which are also discussed with respect to models of embryonic pattern formation.