Diego F. Morales-Briones

Ludwig-Maximilians-University of Munich | LMU · Systematics, Biodiversity and Evolution of Plants

Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla , while distinguish...

Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies, and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evid...

Three new species of Lachemilla (Rosaceae), two from Colombia and one from Peru, are described and illustrated. Lachemilla rothmaleriana is characterized by its stout stems, sericeous-villous indumentum, and wide ascending sheaths with trilobate lateral lobes. Lachemilla argentea presents a unique combination of tripartite basal leaves with an adax...

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a co...

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common...

Maleae is one of the most widespread tribes of Rosaceae and includes several important fruit crops and ornamental plants. We used nuclear genes from 62 transcriptomes/genomes, including 26 newly generated transcriptomes, to reconstruct a well‐supported phylogeny and study the evolution of fruit and leaf morphology and the possible effect of whole g...

Flaveria (Asteraceae) is the prime model for the study of C4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C3-C4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of trai...

The genetic bases of halophytes for salinity tolerance are crucial for genetically breeding salt-tolerant crops. All natural Nitrariaceae species that exclusively occur in arid environments are highly tolerant to salt stress, but the underlying genomic bases to this adaptation remain unknown. Here we present a high-quality, chromosome-level genome...

The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of...

The genus Lonicera L. is widely distributed and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly known. In this study, we sampled 37 accessions of Lonicera, covering four sectio...

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analy...

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny as a basis for a stable taxonomy and for macroevolutionary comparisons....

C 2 photosynthesis is characterised using recapturing photorespiratory CO 2 by RuBisCo in Kranz‐like cells and is therefore physiologically intermediate between C 3 and C 4 photosynthesis. C 2 can be interpreted as an evolutionary precursor of C 4 and/or as the result of hybridisation between a C 3 and C 4 lineage. We compared the expression of pho...

Flaveria (Asteraceae) is the prime model for the study of C 4 photosynthesis evolution and seems to support a stepwise acquisition of the pathway through C 3 -C 4 intermediate phenotypes, still existing in Flaveria today. Molecular phylogenies of Flaveria based on concatenated data matrices are currently used to reconstruct the complex sequence of...

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times beyond. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by including 95...

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We s...

Background and Aims Abelia (Caprifoliaceae) is a small genus with five species, including one artificial hybrid and several natural hybrids. The genus has a discontinuous distribution in Mainland China, Taiwan Island and the Ryukyu Islands, providing a model system to explore the mechanisms of species dispersal in the East Asian flora. However, the...

Understanding biological diversity and the mechanisms of the Sino-Japanese disjunctions are major challenges in eastern Asia biogeography. The Sino-Japanese flora has been broadly studied as an ideal model for plant phylogeography. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese region. How...

C2 photosynthesis is characterized by recapturing photorespiratory CO2 by RuBisCO in Kranz-like cells and is therefore physiologically intermediate between C3 and C4 photosynthesis. C2 is either interpreted as an evolutionary precursor of C4 or as the result of hybridization between a C3 and C4 lineage. We compared the expression of photosynthetic...

Disjunctive distribution patterns and drivers of the Sino-Japanese flora in East Asia have attracted much attention in the past decades, which is also served as an important glacial sanctuary during the quaternary glacial period. However, few studies have focused on the phylogeography, diversification and evolution of morphological character at the...

Background and Aims Abelia (Caprifoliaceae) is a small genus with five species (including one artificial hybrid). The genus has a disjunct distribution across mainland China, Taiwan and the Ryukyu Islands, providing a model system to explore species dispersal mechanisms of the East Asian flora. However, the current phylogenetic relationships within...

The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment dat...

The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment dat...

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include...

Gene tree discordance in large genomic datasets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a co...

Premise: Chloroplast primers were developed for phylogenetic and comparative studies in Thalictrum (Ranunculaceae). Methods and results: We assembled and annotated the complete plastome sequence of T. thalictroides by combining multiple whole genome sequencing libraries. Using transcriptome-sequencing libraries, we also assembled a partial plast...

Motivation: Quality of gene expression analyses using de novo assembled transcripts in species that experienced recent polyploidization remains unexplored. Results: Differential gene expression (DGE) analyses using putative genes inferred by Trinity, Corset and Grouper performed slightly differently across five plant species that experienced var...

Premise of the study: Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discor...

Motivation Quality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored. Results Five plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or bett...

Premise of the Study Targeted enrichment strategies for phylogenomic inference are a time‐ and cost‐efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results We...

Premise of the study Targeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results We...

• Premise of the study: Chloroplast primers were developed from genomic data for the taxonomically challenging genus Castilleja. We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade. • Methods and Results: Using a combination of three low-coverage Cas...

A new species of Lachemilla (Rosaceae), Lachemilla mexiquense D.F. Morales-B., from Mexico is described and illustrated. This species is similar to Lachemilla aphanoides by its tripartite leaves and glomerulate inflorescence with entirely glabrous flowers, but it differs by its stonoliferous habit, persistent basal leaves and basal stipules, and sm...

Two new species of Lachemilla (Rosaceae) are described and illustrated. Lachemilla jaramilloi Romoleroux &Morales-Briones from Ecuador is characterized by its decumbent habit, villous-hirsute pubescence, long basal petiole, and deeply tri-parted leaf blades. The flowers are sessile to subsessile and subtended by episepals, and the hypanthia elongat...

Relaciones filogenéticas de Lachemilla (Focke) Rydb. (Rosaceae) inferidas a partir de secuencias de ADN nuclear y cloroplástico, con énfasis en las especies del norte de Sudamérica. Disertación previa a la obtención del título de Licenciado en Ciencias Biológicas