The members of the Temnothorax salvini (Forel) species group are rarely collected, arboreally nesting ants of Central American forests. Previously thought to consist of two broadly dispersed species, recent collections have revealed a diversity of specimens that defy the two-species salvini group concept, but these are difficult to distinguish from each other based solely on morphology. I contrast several model-based approaches to species delimitation based on target-enriched genomic data. With molecular data from thousands of ultraconserved elements (UCEs), mitochondrial genome sequences and morphometric data, I use an integrated approach to species delimitation within the salvini group. Morphometric data were analysed using cluster analysis of principal component analysis (PCA) output. I use several popular methods of molecular species delimitation, including bPTP, BPP and STACEY, using a novel approach to filtering UCE data based on posterior predictive checks of nucleotide substitution model adequacy. In addition, I use iBPP to integrate morphometric PCA data and filtered UCE data in a ‘total evidence’ analysis. I use geographical range data for an independent contrast to discriminate among competing species delimitation hypotheses. Furthermore, I investigate the evolutionary timescale and biogeographical history of the group and find that it arose roughly 13 Ma ago in habitats associated with present day mid-to-high elevations of the mountain complex spanning southern Mexico to northern Nicaragua. In addition, dispersal of the salvini group into the Southern Sierra Madre in Mexico, lowland habitats and the southern Central American cordilleras in Costa Rica and Panama subsequent to mountain building in southern Central America 5–8 Ma ago appears to follow a taxon-cycle dynamic, with the lowland-adapted T. aztecus representing the most recent expansion phase. I find that the salvini group, which previously contained two named species, is composed of nine, all of which are morphologically diagnosable a posteriori.

Asteraceae account for 10% of all flowering plant species, and 35-40% of these are in five closely-related tribes that total over 10,000 species. These tribes include Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae, which form one of two enormous clades within Subfamily Asteroideae. We took a phylogenomics approach to resolve evolutionary relationships among these five tribes. We sampled the nuclear and plastid genomes via HybSeq target enrichment and genome skimming, and recovered 74 plastid genes and nearly 1000 nuclear loci, known as Conserved Orthologous Sequences. We tested for conflicting support in both datasets and used network analyses to assess patterns of reticulation to explain the early evolutionary history of this lineage which has experienced whole genome duplications and rapid radiations. We found both concordance and conflicting support in both datasets and documented four ancient hybridization events. Due to the timing of the early radiation of this five-tribe lineage, shortly before the Eocene-Oligocene extinction event (34 MYA), early lineages were likely lost, obscuring some details of their early evolutionary history. This article is protected by copyright. All rights reserved.

Rogadinae are a cosmopolitan, species-rich braconid wasp subfamily whose species are endoparasitoids that attack larvae of a number of lepidopteran families. Members of this subfamily are characterized by pupating within the mummified host larval skin. The subfamily contains six tribes whose relationships have only been partially clarified: Aleiodini, Betylobraconini, Clinocentrini, Rogadini, Stiropiini and Yeliconini. The limits and composition of the closely related subfamilies to the Rogadinae, Hormiinae and Lysiterminae, also remain unclear. Here, we generated ultraconserved element data to reconstruct an almost fully resolved phylogeny for the members of Rogadinae and related subfamilies. Based on our best estimate of phylogeny, we confirm the monophyly of Rogadinae including Betylobraconini, synonymize Xenolobus Fahringer and Bequartia Cameron within the species-rich genus Aleiodes Wesmael (syn.n.) based on DNA, and synonymize Promesocentrus van Achterberg with Pilichremylus Belokobylskij (syn.n.) based on morphology. We also consistently recovered Hormiinae and Lysiterminae as not reciprocally monophyletic, and thus propose to unite their members under Hormiinae. The ancestral host preference for Rogadinae was probably attacking concealed lepidopteran larvae, with the occurrence of at least two main subsequent transitions to attack both concealed and exposed hosts, one within Rogadini and a second within Aleiodini. We highlight the importance of natural history collections as a source for conducting genomic-based studies using techniques that allow to obtain a substantial amount of data from considerably old preserved insect specimens.

Targeted capture of nuclear genes increasingly contributes to unravelling phylogenetic relationships that hitherto remained unresolved because of limitations of traditional Sanger sequencing. In particular, the study of tropical plant families has been compromised because they often rely on highly degraded DNA obtained from herbarium specimens. One such example is the pantropical Ochnaceae, which comprises 33 genera and approximately 550 species, occurring mostly in savannas and moist tropical forests. Here, we developed a set of baits covering about 660,000 bp from 275 nuclear genes used for the targeted enrichment based on all but one genus and more than 250 species. Using this novel dataset, we resolved the phylogenetic backbone of Ochnaceae, including that of Ochninae, and we established new relationships. Most importantly, our findings highlight that the neotropical and palaeotropical taxa of Sauvagesia form independent clades, requiring the re-erection of formerly separate genera. Ouratea and Ochna (both Ochninae), by far the most species-rich genera and represented by 120 and 41 species, respectively, came out as monophyletic. In contrast, the third-most species-rich genus, Campylospermum, is polyphyletic in two distinct clades. Ouratea, the only neotropical genus of Ochninae, was sister to the five palaeotropical genera of this subtribe. The bait kit developed in this study proved to be particularly useful for unravelling relationships within Ochninae, which includes about two-thirds of the species diversity in the family.

The gallopheasants comprise a clade of 22 species including some of the most elaborately plumaged and highly ornamented birds in the world. They also occupy a remarkable breath of environments and habitats, ranging from lowland rainforests to high grasslands and steppes of the Tibetan plateau. Here, we provide the first well-resolved species phylogeny of this charismatic group, inferred from ultraconserved elements, nuclear introns and mitochondrial DNA sequences. Unlike previous studies which found unresolvable relationships and suggested a rapid initial burst of diversification, we identified a well-resolved phylogeny supported in both concatenated and coalescent analytical frameworks, and a steady accrual of lineages through time. Morphological trait reconstructions demonstrated strong phylogenetic signal, not only for highly ornamented males, but also in more cryptically plumaged females. Environmental niche similarly exhibited strong phylogenetic signal. Moreover, evolution of male traits, female traits and environmental niche were all significantly correlated, making it difficult to disentangle their individual roles in gallopheasant diversification.

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia followed by migrations from Africa and Middle East. Remains of these different cultural, genetic and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n=30) and the Comoros (n=3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of the branch 1, closely related to SNP-type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which together with previously published genomes amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers, and suggests a later origin from East Africa, the Middle East or South Asia.

AbstractBackground. Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. Plasma EBV DNA is a validated screening tool

Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analysed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid C. majovskyi evolved at least twice in different regions by autopolyploidy from diploid C. matthioli. The extensive genome size and genetic variation of C. rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

Madagascar’s shrew tenrecs (Mammalia: Tenrecidae; Microgale, Nesogale) represent an excellent system for studying speciation. Most species are endemic to the island’s eastern humid forests, a region renowned for high levels of biodiversity and a high rate of in situ diversification. We set out to understand the speciation dynamics in a clade of recently described taxa: Microgale fotsifotsy and M. soricoides, which have nearly identical distributions in the moist evergreen forest, and M. nasoloi, which occurs in the western dry deciduous forest. A phylogenetic analysis using mitochondrial DNA data recovered two distinct clades of M. fotsifotsy: a south clade that is sister to the broadly sympatric M. soricoides, and a north clade that is sister to the dry-forest and distantly allopatric species M. nasoloi. To better understand this result, we analyzed cranioskeletal measurements and performed demographic analyses using nuclear sequence data from ultraconserved elements. Nuclear data did not support a sister relationship between M. soricoides and the south clade of M. fotsifotsy but did demonstrate introgression between these clades, which likely explains the discordance between nuclear and mitochondrial phylogenies. Demographic analyses also revealed the absence of gene flow between the north and south clades of M. fotsifotsy. Morphometric data revealed several major differences between M. soricoides and M. fotsifotsy, as well as more subtle differences between the two clades of M. fotsifotsy. In light of these results, we treat the southern clade of M. fotsifotsy as a new candidate species. Our findings demonstrate the utility of integrating multiple data types to understand complex speciation histories, and contribute to a growing body of evidence that species diversity on Madagascar is underestimated.

Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.