This paper reports the results of an in-depth analysis of the frozen remains of a woolly mammoth (Mammuthus primigenius) named Zhenya, which has been dated to 48,000 cal BP. The carcass, found near the mouth of the Yenisey River in eastern Siberia, was a juvenile male whose ontogenetic age at death was 8–10 AEY. Its reconstructed live height at the shoulders (pSH 227.4 cm) was the equal of some adult female woolly mammoths and extant elephants. The large stature and a flaked off tusk tip that matches breaks on tusks of male African elephants are indirect indications that this mammoth most likely had reached sexual maturity, had been expelled from its maternal herd, and had been in at least one fight with another male. The mammoth’s bones were relatively healthy, although some had minor lesions. Rudimentary upper second molars (M2/m2) were present, but no lower second molars were found in the alveoli, and the left tusk had never developed. Despite the abnormal development of the upper and lower second molars, the cheek teeth which were in wear (Dp4/dp4 and M1/m1) showed normal function without any indications of developmental delay. The completed growth of the light-colored dentin bands on the tusk strongly suggests the Fall of the year was the season of death. This season is also supported by accumulated fat in the upper parts of the torso, indicative of physiological preparation for the winter ahead. The few minor traces of carnivore scavenging, the little disturbed condition of the carcass, and the absence of bone modifications made by human actions, along with the social status of this young male animal, are interpreted here as highly probable evidence that the Zhenya Mammoth died from unrecoverable injuries inflicted during a bull-to-bull fight. The mineralogical analysis of site sediments revealed that the mammoth’s burial in situ took place in the Yenisey River valley seasonally inundated by the river, which together with Fall’s freezing temperatures protected the carcass from scavengers. An analysis of ancient DNA provides strong support for Zhenya’s mitochondrial lineage within the deeply diverging clade III haplogroup B.

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.

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.