Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type specimens (which contain only heavily degraded DNA or have lost important diagnostic characters), inappropriately chosen type specimens (e.g. juveniles without diagnostic characters) or poorly documented type specimens (with unprecise, incorrect, or missing locality data). Thanks to modern sequencing technologies it is now possible to overcome many such extrinsic factors by sequencing DNA from name-bearing type specimens of uncertain assignment and assigning these to known genetic lineages. Here, we apply this approach to frogs of the Mantidactylus ambreensis complex, which was recently shown to consist of two genetic lineages supported by concordant differentiation in mitochondrial and nuclear genes. These lineages co-occur on the Montagne dʼAmbre Massif in northern Madagascar but appear to have diverged in allopatry. We use a recently published bait set based on three mitochondrial markers from all known Malagasy frog lineages to capture DNA sequences from the 127-year-old holotype of Mantidactylus ambreensis Mocquard, 1895. With the obtained sequences we are able to assign the name M. ambreensis to the lowland lineage, which is rather widespread in the rainforests of northern Madagascar, leaving the microendemic high-elevation lineage on Montagne d’Ambre in north Madagascar in need of description. We describe this species as Mantidactylus ambony sp. nov., differing from M. ambreensis in call parameters and a smaller body size. Thus, using target enrichment to obtain DNA sequence data from this old specimen, we were able to resolve the extrinsic (nomenclatural) hindrances to taxonomic resolution of this complex. We discuss the broad-scale versatility of this ‘barcode fishing’ approach, which can draw on the enormous success of global DNA barcoding initiatives to quickly and efficiently assign type specimens to lineages.

The southern boundary of prehispanic farming in South America occurs in central Mendoza Province, Argentina at approximately 34 degrees south latitude. Archaeological evidence of farming includes the recovery of macrobotanical remains of cultigens and isotopic chemistry of human bone. Since the 1990s, archaeologists have also hypothesized that the llama (Lama glama), a domesticated South American camelid, was also herded near the southern boundary of prehispanic farming. The remains of a wild congeneric camelid, the guanaco (Lama guanicoe), however, are common in archaeological sites throughout Mendoza Province. It is difficult to distinguish bones of the domestic llama from wild guanaco in terms of osteological morphology, and therefore, claims that llama were in geographic areas where guanaco were also present based on osteometric analysis alone remain equivocal. A recent study, for example, claimed that twenty-five percent of the camelid remains from the high elevation Andes site of Laguna del Diamante S4 were identified based on osteometric evidence as domestic llama, but guanaco are also a likely candidate since the two species overlap in size. We test the hypothesis that domesticated camelids occurred in prehispanic, southern Mendoza through analysis of ancient DNA. We generated whole mitochondrial genome datasets from 41 samples from southern Mendoza late Holocene archaeological sites, located between 450 and 3400 meters above sea level (masl). All camelid samples from those sites were identified as guanaco; thus, we have no evidence to support the hypothesis that the domestic llama occurred in prehispanic southern Mendoza.

The impacts of invasive species on biodiversity may be mitigated or exacerbated by abiotic environmental changes. Invasive plants can restructure soil fungal communities with important implications for native biodiversity and nutrient cycling, yet fungal responses to invasion may depend on numerous anthropogenic stressors. In this study, we experimentally invaded a long-term soil warming and simulated nitrogen deposition experiment with the widespread invasive plant Alliaria petiolata (garlic mustard) and tested the responses of soil fungal communities to invasion, abiotic factors, and their interaction. We focused on the phytotoxic garlic mustard because it suppresses native mycorrhizae across forests of North America. We found that invasion in combination with warming, but not under ambient conditions or elevated nitrogen, significantly reduced soil fungal biomass and ectomycorrhizal relative abundances and increased relative abundances of general soil saprotrophs and fungal genes encoding for hydrolytic enzymes. These results suggest that warming potentially exacerbates fungal responses to plant invasion. Soils collected from uninvaded and invaded plots across eight forests spanning a 4 °C temperature gradient further demonstrated that the magnitude of fungal responses to invasion was positively correlated with mean annual temperature. Our study is one of the first empirical tests to show that the impacts of invasion on fungal communities depends on additional anthropogenic pressures and were greater in concert with warming than under elevated nitrogen or ambient conditions.

Abstract. Bees of the tribes Biastini, Neolarrini, and Townsendiellini are cleptoparasites in the subfamily Nomadinae (Hymenoptera, Apidae) and parasitize solit

Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and color pattern. Chromodoris, a genus of colorful and toxic nudibranch in the Indo-Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome-wide data can help improve phylogenetic resolution and provide important insights about evolutionary history. Here, we employ a transcriptome-based exon capture approach to resolve Chromodoris phylogeny with data from 2,925 exons and 1,630 genes, derived from 15 nudibranch transcriptomes. We show that some previously identified mimics instead show mitonuclear discordance, likely deriving from introgression or mitochondrial capture, but we confirm one “pure” mimic in Western Australia. Sister–species relationships and species-level entities were recovered with high support in both concatenated maximum likelihood (ML) and summary coalescent phylogenies, but the ML topologies were highly variable while the coalescent topologies were consistent across datasets. Our work also demonstrates the broad phylogenetic utility of 149 genes that were previously identified from eupulmonate gastropods. This study is one of the first to (a) demonstrate the efficacy of exon capture for recovering relationships among recently radiated invertebrate taxa, (b) employ genome-wide nuclear markers to test mimicry hypotheses in nudibranchs and (c) provide evidence for introgression and mitochondrial capture in nudibranchs.

The Near East and the Caucasus are commonly regarded as the original domestication centres of Vitis vinifera (grapevine), and the region continues to be home to a high diversity of wild and cultivated grapevines, particularly within Georgia. The earliest chemical evidence for wine making was recorded in Georgian Neolithic sites (6000–5800 bc) and grape pips, possibly of the domesticated morphotype, have been reported from several sites of about the same period. We performed geometric morphometric and palaeogenomic investigations of grape pip samples in order to identify the appearance of domesticated grapevine and explore the changes in cultivated diversity in relation to modern varieties. We systematically investigated charred and uncharred grape pip samples from Georgian archaeological sites. Their chronology was thoroughly assessed by direct radiocarbon dating. More than 500 grape pips from 14 sites from the Middle Bronze Age to modern times were selected for geometric morphometric studies. The shapes of the ancient pips were compared to hundreds of modern wild individuals and cultivated varieties. Degraded DNA was isolated from three pips from two sites, converted to Illumina libraries, sequenced at approximately 10,000 single nucleotide polymorphism (SNP) sites, and compared to a large public database of grapevine diversity. The most ancient pip dates from the Middle Bronze Age (1900–1500 cal bc) and the domesticated morphotype is identified from ca. 1000 bc onwards. A great diversity of domesticated shapes was regularly seen in the samples. Most are close to modern cultivars from the Caucasian, southwest Asian and Balkan areas, which suggests that the modern local vine diversity is deeply rooted in early viticulture. DNA was successfully recovered from historic pips and genome-wide analyses found close parental relationships to modern Georgian cultivars.

Plague continued to afflict Europe for more than five centuries after the Black Death. Yet, by the 17th century, the dynamics of plague had changed, leading to its slow decline in Western Europe over the subsequent 200 y, a period for which only one genome was previously available. Using a multidisciplinary approach, combining genomic and historical data, we assembled Y. pestis genomes from nine individuals covering four Eurasian sites and placed them into an historical context within the established phylogeny. CHE1 (Chechnya, Russia, 18th century) is now the latest Second Plague Pandemic genome and the first non-European sample in the post-Black Death lineage. Its placement in the phylogeny and our synthesis point toward the existence of an extra-European reservoir feeding plague into Western Europe in multiple waves. By considering socioeconomic, ecological, and climatic factors we highlight the importance of a noneurocentric approach for the discussion on Second Plague Pandemic dynamics in Europe.

Replacement of local crops with alternative varieties adapted to future conditions may improve food security under climate change. Here the authors apply landscape genomics and ensemble climate modelling to pearl millet in West Africa, supporting the potential of transfrontier assisted seed exchange.