Hybridization is observed in many eukaryotic lineages and can lead to the formation of polyploid species. The study of hybridization and polyploidization faces challenges both in data generation and in accounting for population-level phenomena such as coalescence processes in phylogenetic analysis. Genus Fragaria is one example of a set of plant taxa in which a range of ploidy levels is observed across species, but phylogenetic origins are unknown.

Abstract The skull of the extinct rhinoceros Stephanorhinus kirchbergensis (Jäger, 1839) was discovered in the Chondon River valley (Arctic Yakutia, Russia) during the summer of 2014. This is the first find of Stephanorhinus above the Arctic Circle, expanding significantly the known geographic range of the genus. 14C dating and geologic evidence indicate that the skull dates to between 48,000 and 70,000 yr, corresponding to Marine Oxygen Isotope Stage 4/3. It is thus among the latest records of this species. To explore the evolutionary and natural history of this relatively unknown animal, we performed morphological, dietary, and genetic analyses. Phylogenetic inference based on a complete mitochondrial genome sequence confirms the systematic placement of Stephanorhinus as most closely related to the extinct woolly rhinoceros, Coelodonta. Food remains in the fossas of the cheek teeth, identified as Larix, Vaccinium, Betula sp., Aulacomnium, and dicotyledonous herbs and grasses, suggest a mixed feeder’s diet. Microwear analysis suggests that, during the last months of its life, this individual fed predominantly on leaves and twigs. The habitat of Stephanorhinus comprised grassland and open woodland that were characterized by moist and cold climate conditions, similar to those in the region today.

Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.

The amphibian disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has contributed to the decline of Chiricahua leopard frogs (Rana chiricahuensis), a federally threatened species native to the Southwestern United States. We characterized immunogenetic variability in R. chiricahuensis by sequencing an expressed Major Histocompatibility Complex (MHC) class IIβ gene across 13 natural populations in Arizona, USA, as well as 283 individuals that were captive reared from two egg masses. We recovered a total of five class IIβ MHC alleles compared to 84 alleles previously characterized in eight natural populations of the Arizona congener R. yavapaiensis, demonstrating reduced MHC diversity in R. chiricahuensis. One allele was fixed in five populations but none of the R. chiricahuensis alleles were closely related to R. yavapaiensis allele Q, which is significantly associated with chytridiomycosis resistance in laboratory trials. Nine of 13 R. chiricahuensis population localities were Bd positive, and bearing allele RachDRB*04 was the best genetic predictor of an individual being infected with Bd. A total of three class IIβ alleles were recovered from captive reared individuals, which were released to two natural population localities followed by recapture surveys to assess MHC-based survival over winter, the time when chytridiomycosis outbreaks are most severe. At one site, all released animals were fixed for a single allele and MHC-based survival could not be assessed. At the second site, fewer than half of the released but all of the recaptured individuals were homozygous for RachDRB*05, indicating that MHC genotype is important in determining Bd survival under natural field conditions. We conclude that the limited MHC variation in R. chiricahuensis is likely the consequence rather than the cause of natural selection favoring alleles that promote survival in the face of Bd. Our study highlights that preserving even low levels of functional genetic variation may be essential for population persistence, and that local disease adaptation may present as a reduction in genetic diversity. These finding also suggest that for populations that have declined due to a specific infectious pathogen, MHC-based genetically-informed reintroduction approaches may enhance species recovery efforts.

Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.

The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified.

The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified.

Recent advances in ancient DNA methodologies have enabled the retrieval of highly degraded DNA from contexts with poor preservation conditions. While paleofeces have previously been shown to contain endogenous DNA of the defecator, the preserved DNA is composed of a mixture of diverse microbial, floral and fungal constituents, with limited DNA from the host. However, in situations where skeletal remains are unavailable, paleofeces can serve as an important alternative genetic source, allowing for the molecular identification of the target species and diet. Here, we describe the extraction of ancient DNA from a paleofecal sample found within Bechan Cave (southeastern Utah, USA). Previous work in the cave has suggested that these remains likely stem from Mammuthus. We used a comprehensive proboscidean bait set which was used to enrich a nearly complete mitochondrial genome (81.6%) at an average coverage depth of 8.1×. Phylogenetic analysis of the derived consensus sequence revealed that the Bechan Cave bolus does indeed derive from Mammuthus, and its sequence falls within Clade 1 (haplogroups F or C), most similar to specimens identified as Mammuthus columbi.