Abdelkader Ainouche

This study is the first attempt to inventory and evaluate the taxonomic identification of the Algerian myrmecofauna by integrating traditional morphology with molecular barcoding and phylogenetic approach. Sixty-one specimens of ants belonging to the family Formicidae, collected from different ecosystems in Algeria, were sequenced and barcoded using the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). The DNA barcodes newly generated from this study were compared and analyzed with COX1 homologs available in GenBank databases representing putative conspecific and congeneric relatives of the Algerian ant samples and several others to represent the Formicoid, Poneroid, and Leptanillinae diversity to serve as molecular barcode references and outgroups for phylogenetic analyses. The results confirmed the COX1 gene as an excellent molecular marker at the generic level. They allowed the unambiguous taxonomic assignment of the Algerian specimens surveyed to fourteen Formicoid genera belonging to the Myrmicinae, Formicinae, and Dolichoderinae subfamilies, with abundance of Crematogaster, Tapinoma, Cataglyphis, and Componotus representatives. Such an integrative approach not only provided molecular support to most morphology-based identification but also allowed suggestion of taxonomic assignment or reassignment of some incompletely determined specimens, in accordance with the latest taxonomic revisions (e.g., Plagiolepis schmitzii, Camponotus spissinodis). It also helped to circumscribe some cases which need further investigations to illuminate complex evolutionary relationships and to re-evaluate and refine the taxonomic value of the most relevant diagnostic characters. Moreover, these preliminary data support the previous detection of three additional non-native ants in Algeria. Altogether, these results demonstrate the significant advantages that can be derived from a comprehensive development of such integrative studies for faster and better knowledge and understanding of the myrmecofauna diversity of Africa conserving regional biodiversity. Dataset published through GBIF (DOI: 10.15468/sjtjv2)

Premise: Plant lineages differ markedly in species richness globally, regionally, and locally. Differences in whole‐genome characteristics (WGCs) such as monoploid chromosome number, genome size, and ploidy level may explain differences in global species richness through speciation or global extinction. However, it is unknown whether WGCs drive species richness within lineages also in a recent, postglacial regional flora or in local plant communities through local extinction or colonization and regional species turnover.Methods: We tested for relationships between WGCs and richness of angiosperm families across the Netherlands/Germany/Czechia as a region, and within 193,449 local vegetation plots.Results: Families that are species‐rich across the region have lower ploidy levels and small monoploid chromosomes numbers or both (interaction terms), but the relationships disappear after accounting for continental and local richness of families. Families that are species‐rich within occupied localities have small numbers of polyploidy and monoploid chromosome numbers or both, independent of their own regional richness and the local richness of all other locally co‐occurring species in the plots. Relationships between WGCs and family species‐richness persisted after accounting for niche characteristics and life histories.Conclusions: Families that have few chromosomes, either monoploid or holoploid, succeed in maintaining many species in local communities and across a continent and, as indirect consequence of both, across a region. We suggest evolutionary mechanisms to explain how small chromosome numbers and ploidy levels might decrease rates of local extinction and increase rates of colonization. The genome of a macroevolutionary lineage may ultimately control whether its species can ecologically coexist.

Gibberellic acid (GA) is a major plant hormone involved in several biological processes from the flowering to the symbiosis with microorganisms. Thus, the GA regulation is crucial for plant biology. This regulation occurs via the DELLA proteins that belong to the GRAS transcription factor family. DELLA proteins are characterised by a DELLA N-terminal and a GRAS C-terminal domains. It is well known that DELLA activity appears after the bryophytes divergence and then evolved in the vascular plant lineages. Here we present the phylogeny of DELLA across 75 species belonging to various lineages from algae, liverworts and angiosperms. Our study confirmed two main duplication events, the first occurring before the angiosperms divergence and the other specific to the eudicots lineage. Comparative analysis of DELLA subclades in angiosperms revealed the loss in Poaceae and strong alteration in other species of the DELLA functional domain in the DELLA2 clade. In addition, molecular evolution analysis suggests that each of the clades (named DELLA1.1, DELLA1.2 and DELLA2) evolved differently but copies of each subclade are under strong purifying selection. This also suggests that, although the DELLA functional domain is altered in DELLA2, DELLA2 orthologs are still functional and operate in a different way compared to DELLA1 copies. In angiosperms, additional duplication events occurred and led to duplicate copies in species, genus or family such as in the Fabaceae subfamily Papilionoideae. This duplication led to the formation of additional paralogs in the DELLA1.2 subclade (DELLA1.2.1 and DELLA1.2.2). Interestingly, both copies appeared to be under relaxing selection revealing different evolutionary fate of the DELLA duplicated copies.

We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.

The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.