Mitochondrial SNP markers to monitor evolutionary lineage ancestry in Apis mellifera mellifera conservation programs

The European dark honey bee, Apis mellifera mellifera , is threatened inmost of its native range, in part, due to introgressive hybridization with bees from the highly divergent C-lineage, mainly Apis mellifera carnica and Apis mellifera ligustica (De la Rúa et al. 2009; Pinto et al. 2014). Yet, the maintenance of locally adapted genetic diversity is critical for the population long-term survival and sustainability (De la Rúa et al. 2009; Meixner 2010). The growing awareness that genetic diversity is important for sustainable beekeeping led to implementation of different conservation and breeding programs throughout Europe, which are in need of reliable and costefficient molecular tools to accurately monitor Clineage introgression into A. m. mellifera (De la Rúa et al. 2009; Henriques et al. 2018a, b; Meixner 2010). The large mating flight distances and the polyandrous mating system make it challenging to preserve honey bee subspecies in an open conservation area where intruders can fly in (Neumann et al. 1999). It is therefore necessary to regularly control the genetic ancestry of new or superseded colonies.This work was financed by FEDER (Fundo Europeu de Desenvolvimento Regional) through the program COMPETE 2020–POCI (Programa Operacional para a Competitividade e Internacionalização) and by Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871). Melanie Parejo was supported by a mobility fellowship awarded from the Swiss National Science Foundation (SNSF).info:eu-repo/semantics/publishedVersio

Genomes shed light on the evolution of Begonia, a mega‐diverse genus

Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with ~2,000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana, and B. peltatifolia), and whole genome shot-gun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22,059 - 23,444 protein-coding genes. Synteny analysis revealed a lineage specific whole-genome duplication (WGD) that occurred just before the diversification of the Begonia. Functional enrichment of gene families retained after WGD highlight the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade-adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade

Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot

Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots

Introgression of mitochondrial DNA among lineages in a hybridogenetic ant

We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica. This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Phylogeny and topological incongruence in the Rubioideae (Rubiaceae)

The work with this thesis has focused on evolutionary relationships in the Rubioideae, the most species-rich subfamily of the large and diverse coffee family (Rubiaceae). Despite considerable efforts during the last decades, uncertainty regarding several relationships in this group has remained, either as a result of unconvincing statistic support, incongruent results, or insufficient taxon sampling. Here, sequence data were obtained using both traditional and recently developed molecular methods, substantially expanding the amount of sequence data available for phylogenetic analysis within Rubioideae. Leveraging considerable amounts of data from a comprehensive sample of taxa showed to be highly effective in resolving phylogenetic relationships in the group, including its most recalcitrant parts. The results indicated that nuclear gene tree discordance at short internodes were frequently consistent with high levels of incomplete lineage sorting (ILS) owing to rapid diversification in the group. This finding may explain why some relationships have been notoriously difficult to resolve. Furthermore, while the results from coalescent simulations indicated that ILS alone can explain most of the observed cytonuclear incongruence, plastome introgression may be the more likely explanation in at least one case. Within Rubioideae the tribe Anthospermeae was studied in more detail. The phylogenetic analyses of this tribe revealed several cases and types of topological incongruence. Nevertheless, the deepest splits of the Anthospermeae phylogeny were congruent among analyses, but partly inconsistent with the traditional subtribal delimitation of the tribe. The infratribal classification of Anthospermeae was therefore partly updated. Unusual plastome features were also found within Anthospermeae, comprising large inversions and (putative) mitochondrial-to-plastome DNA transfer. With few other exceptions, plastomes across the Rubioideae tend to be highly conserved and typically conform to the canonical structure, gene content, and gene order of the majority of flowering plants