Abstract Understanding how historical and contemporary processes lead to genetic differentiation among populations is a fundamental goal of evolutionary and conservation biology. This study focuses on Galaxias maculatus, a widely distributed fish exhibiting diadromous and freshwater resident forms. We examine the genetic differentiation among resident populations from the Manso River System, a trans-Andean system which thus went through drainage reversal following the Last Glacial Maximum (LGM), and resident and diadromous populations from the connected Puelo River that drains into the Pacific Ocean. Single nucleotide polymorphic (SNP) markers revealed that resident populations from the Manso River System are genetically distinguishable from the diadromous and resident populations from the Puelo River. This suggests that G. maculatus from the Manso River System likely colonized the area from a glacial refugium east of the Andes and did not expand downstream during drainage reversal, whereas the populations from the Puelo River colonized the area from glacial refugia west of the Andes. The populations from the Manso River exhibited lower genetic diversity than the Puelo River populations. Galaxias maculatus resident populations in Patagonia are decreasing due to anthropogenic factors. The Manso River System resident populations are susceptible to these factors and may show further decreases in genetic diversity.

Significance The controversy over the taxonomic identity of the eggs exploited by Australia’s first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless “mihirung” Genyornis and a large megapode Progura , had proven impossible using morphological and geochemical methods. Ancient DNA sequencing remains inconclusive because of the age and burial temperature of the eggshell. In contrast, ancient protein sequences recovered from the eggshell enabled estimation of the evolutionary affinity between the egg and a range of extant taxa. The eggs are those of a Galloanseres (a group that includes extinct Dromornithidae, as well as extant landfowl and waterfowl), Genyornis , and not of the megapode (Megapodiidae, crown Galliformes). , The realization that ancient biomolecules are preserved in “fossil” samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia’s indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [ Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis . Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis . When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.

Odontobutis potamophilus is a popular food fish in China, distributed mainly in the middle and lower reaches of the Yangtze River, where it is a famous delicacy and a newly focused species for aquaculture. The wild populations of O. potamophilus are facing the problem of overfishing and habitat degradation. Therefore, it is very necessary to investigate and protect the wild populations of O. potamophilus . In this study, 72 fish were sampled from 18 different sites over its distribution range. Nuclear sequence data of 4,267 loci were collected using a gene-capture method. Phylogenetic reconstruction revealed that there were three major clades: Oujiang clade (OJ), Qiantang and lower Yangtze clade (QY), and middle Yangtze clade (MY). The discriminant analysis of principal components (DAPC) and a STRUCTURE analysis confirmed that there are three major groups within O. potamophilus . A fastsimcoal2 analysis corroborated the population history and suggested that there was discernible gene flow among these three groups, especially between QY and MY. Estimated pairwise F ST suggested that Linhai (LH) and Shexian (SX) populations were the most divergent pair ( F ST = 0.7077). Taking the nucleotide diversity, population divergence, and admixture status altogether into consideration, we recommend that the LH, Gaoyou (GY) and Chaohu (CH) populations could be protected as the preferred resource for breeding projects. According to the results of genetic analyses, all populations of O. potamophilus should be protected due to low genetic diversity.

Herpes simplex virus (HSV) causes chronic infection in the human host, characterized by self-limited episodes of mucosal shedding and lesional disease, with latent infection of neuronal ganglia. The epidemiology of genital herpes has undergone a significant transformation over the past two decades, with the emergence of HSV-1 as a leading cause of first-episode genital herpes in many countries. Though dsDNA viruses are not expected to mutate quickly, it is not yet known to what degree the HSV-1 viral population in a natural host adapts over time, or how often viral population variants are transmitted between hosts. This study provides a comparative genomics analysis for 33 temporally-sampled oral and genital HSV-1 genomes derived from five adult sexual transmission pairs. We found that transmission pairs harbored consensus-level viral genomes with near-complete conservation of nucleotide identity. Examination of within-host minor variants in the viral population revealed both shared and unique patterns of genetic diversity between partners, and between anatomical niches. Additionally, genetic drift was detected from spatiotemporally separated samples in as little as three days. These data expand our prior understanding of the complex interaction between HSV-1 genomics and population dynamics after transmission to new infected persons.

Abstract Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking noncoding regions, gene tree/species tree methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic, edaphic, and morphological diversity in the group. We found that the combination of exons and flanking noncoding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple evolutionary origins of bee pollination from ancestral hawkmoth pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively reconstruct the recalcitrant history of a rapid radiation. [Gypsum endemism; Oenothera sect. Calylophus; Onagraceae; phylogenomics; pollinator shift; recent radiation; target enrichment.]

Premise Accurate species delimitation is essential for evolutionary biology, conservation, and biodiversity management. We studied species delimitation in North American pinyon pines, Pinus subsection Cembroides, a natural group with high levels of incomplete lineage sorting. Methods We used coalescent-based methods and multivariate analyses of low-copy number nuclear genes and nearly complete high-copy number plastomes generated with the Hyb-Seq method. The three coalescent-based species delimitation methods evaluated were the Generalized Mixed Yule Coalescent (GMYC), Poisson Tree Process (PTP), and Trinomial Distribution of Triplets (Tr2). We also measured admixture in populations with possible introgression. Results Our results show inconsistencies among GMYC, PTP, and Tr2. The single-locus based GMYC analysis of plastid DNA recovered a higher number of species (up to 24 entities, including singleton lineages and clusters) than PTP and the multi-locus coalescent approach. The PTP analysis identified 10 species whereas Tr2 recovered 13, which agreed closely with taxonomic treatments. Conclusions We found that PTP and GMYC identified species with low levels of ILS and high morphological divergence (P. maximartinezii, P. pinceana, and P. rzedowskii). However, GMYC method oversplit species by identification of more divergent samples as singletons. Moreover, both PTP and GMYC were incapable of identifying some species that are readily identified morphologically. We suggest that the divergence times between lineages within North American pinyon pines are so disparate that GMYC results are unreliable. Results of the Tr2 method coincided well with previous delimitations based on morphology, DNA, geography, and secondary chemistry.

The Scirtidae Fleming, 1821 has been identified as one of the earliest diverging groups of Polyphagan beetles and is particularly speciose in Australia. However, very little is known about the origin of the Australian scirtids and there is a need for a robust, well-supported phylogeny to guide the genus and species descriptions and understand the relationships among taxa. In this study we carried out a phylogenetic analysis of the Australian Scirtinae Fleming, 1821, using DNA sequence data from ultraconserved elements (UCEs) and included representative taxa from New Zealand, New Caledonia, South America, South Africa and Eurasia in the analysis. Bayesian analyses of a concatenated dataset from 79 taxa recovered four major Southern Hemisphere groupings and two Australian–Eurasian groupings. The Veronatus group mainly consisted of genera from New Zealand, with the three Australian representatives only distantly related to each other. Relaxed molecular clock analyses, using the estimated age of the crown node of the Polyphaga for calibration, support a Gondwanan history for four of the groups of Australian Scirtinae and a northern origin for two groups. Our results highlight the value of commercially available UCEs for resolving the phylogenetic history of ancient groups of Coleoptera.