Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from ten specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets, and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different datasets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. SNP calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous SNP calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

The octocoral genus Chrysogorgia Duchassaing & Michelotti, 1864 contains about 80 nominal species that are ecologically important components of benthic communities. A review of morphological variation within Chrysogorgia identified nine groups that may represent distinct lineages; which would help clarify their taxonomy and guide genus revision. Here, we applied a recently developed universal target enrichment bait method for octocoral exons and ultraconserved elements (UCEs) on 96 specimens varying in morphology, collection ages and DNA quality and quantity to determine whether there was genetic support for morphologically defined groups within Chrysogorgia. Following Illumina sequencing and SPAdes assembly we recovered 1682 of 1700 targeted exon loci and 1333 of 1340 targeted UCE loci. Loci recovery per sample was highly variable and significantly correlated with time since specimen collection (2-60 years) and DNA quantity and quality. Phylogenetically informative sites in UCE and exon loci ranged from 34.75 – 36.10% for 50% and 75% taxon-occupancy matrices, respectively. Maximum likelihood analyses recovered highly resolved trees with topologies supporting the recognition of 11 candidate genera, nine of which are novel. Our results also demonstrate that this target-enrichment approach can be applied to degraded museum specimens of up to 60 years old. This study shows that an integrative approach consisting of molecular and morphological methods is essential in a proper revision of Chrysogorgiath taxonomy and regional diversity of these ecologically important corals.

The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group’s genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison, gen. nov. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly delimited groups. Eighteen new species are described: Bavia nessagyna, Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I. sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus), M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P. bakau, P. kohi, P. mandai, and Stagetillus irri, all sp. nov., with taxonomic authority W. Maddison. The distinctions between baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established: Bavia maurerae (Freudenschuss & Seiter, 2016), Indopadilla annamita (Simon, 1903), I. kahariana (Prószyński & Deeleman-Reinhold, 2013), I. sonsorol (Berry, Beatty & Prószyński, 1997), I. suhartoi (Prószyński & Deeleman-Reinhold, 2013), Maripanthus menghaiensis (Cao & Li, 2016), M. smedleyi (Reimoser, 1929), Nungia hatamensis (Thorell, 1881), N. modesta (Keyserling, 1883), N. papakula (Strand, 1911), N. xiaolonghaensis (Cao & Li, 2016), Padillothorax casteti (Simon, 1900), P. exilis (Cao & Li, 2016), P. flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillus banda (Strand, 1911), all comb. nov. One combination is restored, Bavia capistrata (C. L. Koch, 1846). Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes, emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic–pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.

Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

Modified-live herpesvirus vaccines are widely used in humans and animals, but field strains can emerge that have a higher virulence and break vaccinal protection. Since the introduction of the first vaccine in the 1970s, Marek’s disease virus overcame the vaccine barrier by the acquisition of numerous genomic mutations. However, the evolutionary adaptations in the herpesvirus genome responsible for the vaccine breaks have remained elusive. Here, we demonstrate that point mutations in the multifunctional meq gene acquired during evolution can significantly alter virulence. Defined mutations found in highly virulent strains also allowed the virus to overcome innate cellular responses and vaccinal protection. Concomitantly, the adaptations in meq enhanced virus shedding into the environment, likely providing a selective advantage for the virus. Our study provides the first experimental evidence that few point mutations in a single herpesviral gene result in drastically increased virulence, enhanced shedding, and escape from vaccinal protection.

William Adams (Miura Anjin) was an English navigator who sailed with a Dutch trading fleet to the far East and landed in Japan in 1600. He became a vassal under the Shogun, Tokugawa Ieyasu, was bestowed with a title, lands and swords, and became the first SAMURAI from England. “Miura” comes from the name of the territory given to him and “Anjin” means “pilot”. He lived out the rest of his life in Japan and died in Hirado, Nagasaki Prefecture, in 1620, where he was reportedly laid to rest. Shortly after his death, graveyards designated for foreigners were destroyed during a period of Christian repression, but Miura Anjin’s bones were supposedly taken, protected, and reburied. Archaeological investigations in 1931 uncovered human skeletal remains and it was proposed that they were those of Miura Anjin. However, this could not be confirmed from the evidence at the time and the remains were reburied. In 2017, excavations found skeletal remains matching the description of those reinterred in 1931. We analyzed these remains from various aspects, including genetic background, dietary habits, and burial style, utilizing modern scientific techniques to investigate whether they do indeed belong to the first English SAMURAI.

Genetic analyses are an important contribution to wildlife reintroductions, particularly in the modern context of extirpations and ecological destruction. To address the complex historical ecology of the sea otter (Enhydra lutris) and its failed 1970s reintroduction to coastal Oregon, we compared mitochondrial genomes of pre-extirpation Oregon sea otters to extant and historical populations across the range. We sequenced, to our knowledge, the first complete ancient mitogenomes from archaeological Oregon sea otter dentine and historical sea otter dental calculus. Archaeological Oregon sea otters (n = 20) represent 10 haplotypes, which cluster with haplotypes from Alaska, Washington and British Columbia, and exhibit a clear division from California haplotypes. Our results suggest that extant northern populations are appropriate for future reintroduction efforts. This project demonstrates the feasibility of mitogenome capture and sequencing from non-human dental calculus and the diverse applications of ancient DNA analyses to pressing ecological and conservation topics and the management of at-risk/extirpated species.

Detailed paleoecological evidence from Arctic Alaska’s past megafauna can help reconstruct paleoenvironmental conditions and can illustrate ecological adaptation to varying environments. We examined a rare, largely articulated and almost complete skeleton of a steppe bison (Bison priscus) recently unearthed in Northern Alaska. We used a multi-proxy paleoecological approach to reconstruct the past ecology of an individual representing a key ancient taxon. Radiocarbon dating of horn keratin revealed that the specimen has a finite radiocarbon age ∼46,000 ± 1000 cal yr BP, very close to the limit of radiocarbon dating. We also employed Bayesian age modeling of the mitochondrial genome, which estimated an age of ∼33,000–87,000 cal yr BP. Our taphonomic investigations show that the bison was scavenged post-mortem and infested by blowflies before burial. Stable carbon and oxygen isotope (δ13C and δ15N) analyses of sequentially sampled horn keratin reveal a seasonal cycle; furthermore, high δ15N values during its first few years of life are consistent with patterns observed in modern bison that undertook dispersal. We compared sequential analyses of tooth enamel for strontium isotope ratios (87Sr/86Sr) to a spatial model of 87Sr/86Sr values providing evidence for dispersal across the landscape. Synthesis of the paleoecological findings indicates the specimen lived during interstadial conditions. Our multi-proxy, paleoecological approach, combining light and heavy isotope ratios along with genetic information, adds to the broader understanding of ancient bison ecology during the Late Pleistocene, indicating that ancient bison adopted different degrees of paleo-mobility according to the prevailing paleoecological conditions and climate.