Biogeographic patterns in the Southern Hemisphere have largely been attributed to vicariant processes, but recent studies have challenged some of the classic examples of this paradigm. The parasitoid wasp subfamily Labeninae has been hypothesized to have a Gondwanan origin, but the lack of divergence dating analysis and the discovery of a putative labenine fossil in Europe pose a challenge to that idea. Here we used a combination of phylogenomics, divergence dating and event-based biogeographical inference to test whether Gondwanan vicariance may explain the distribution patterns of Labeninae. Data from genomic ultraconserved elements were used to infer the phylogeny of Labeninae with 54 species from 9 genera and a broad selection of 99 outgroup taxa. Total-evidence divergence dating places the origin of Labeninae at around 146 mya, which is consistent with a Gondwanan origin but predates the full separation of Africa and South America. The results suggest a path for biotic exchange between South America and Australia potentially through Antarctica, until at least 49 million years ago. Total-evidence analysis places the fossil Trigonator macrocheirus Spasojevic et al. firmly inside crown-group Labeninae, suggesting that labenine distribution range at some point during the Eocene surpassed the boundaries of Gondwanaland. Biogeographic inference also indicates that North American groups represent more recent range expansions that nonetheless occurred before the formation of the Isthmus of Panama land bridge. These conclusions point to a more complex scenario than previously expected for Labeninae biogeography.

Whole genome sequencing has opened the doors to Investigative genetic genealogy (IGG) analysis of challenging forensic samples that are not suitable for microarray genotyping. These samples still do not typically achieve high enough coverage for direct genotype calling, therefore a pipeline for imputation from low coverage sequencing data was evaluated using data from the 1000 Genomes Project. This pipeline generated results suitable for IGG down to 0.25X coverage. Additionally, forensic samples from a variety of tissue types and input amounts were f sequenced and successfully uploaded to genetic genealogy databases after imputation.

Variation in breeding systems between species of the same taxonomic group complicates the consistent application of species concepts, and perhaps even the logically consistent circumscription of species. Several genera of arid-zone ephemerals in the Angianthus clade (Asteraceae: Gnaphalieae: Gnaphaliinae) contain both outcrossing and non-outcrossing species. The latter are recognised by producing an order of magnitude fewer pollen grains per anther and an often reduced number of corolla lobes, and they are frequently more widespread than are the former. In its current taxonomy, the genus Pogonolepis comprises an otherwise morphologically indistinguishable pair of one outcrossing and one non-outcrossing species. I generated sequence capture data to test the genetic segregation of P. stricta and P. muelleriana and the utility of sequence capture data for species circumscription and diagnostics. Phylogenetic analysis showed the two species to form two specimen clades, supporting the current taxonomy. Contrary to expectations, non-outcrossing P. muelleriana exhibited lower gene concordance, in line with values expected from recombination, as well as higher heterozygosity than its outcrossing sister species. More research on the breeding system and population structure of the two species may be required to explain these results.

The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.

Hybrid capture with baits has proven to be a rich source of genetic data for many genera. The depth of information provided allows resolution of rapid radiations and of deep phylogenetic patterns. Retrieved data can also be used for population genetic studies and analysis of functional genetic diversity. To gain a better understanding of the evolutionary patterns across this large, diverse and fascinating genus through phylogenetics, population genetics and sequence analysis, we have designed and tested a set of 1239 baits covering low copy number and functionally annotated genes involved in shade adaptation and development and genetically linked to key traits. We demonstrate successful recovery of sequence data from species across Begonia and from fresh, silica-dried and older herbarium material.

Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.1, 2, 3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage’s evolutionary history,4 subsequent shifts in a species’ behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.5, 6, 7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.8,9 Our analyses show that, similar to hummingbirds10 and songbirds,4 the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.