Biology subjects

Couvreur, T. L. P.

Publications and source records attributed to Couvreur, T. L. P..

9 recordsLinked to original sources

bioRxiv2025

Discrimination of Annonaceae using herbarium leaf reflectance spectra under limited sample size conditions

PremiseHerbarium collections offer an unparalleled archive of plant biodiversity, but their use for species identification through spectral data remains constrained by uncertain effects of preservation histories. This study assesses whether barium specimens can reliably predict species based on its leaf reflectance spectrum, despite variations in age, geographic origin, or conservation method under limited sample size conditions. MethodsWe scanned herbarium specimens of different ages and geographic distribution of 14 species of the pantropical Annonaceae. In addition, we used a second dataset of 9 species where some specimens were conserved in alcohol prior to drying and some not. We used five supervised classification models frequently used for high-dimensional data such as spectroscopy. ResultsAll models achieved high accuracy (>80%) when trained on multiple specimens per species. However, when using only one specimen per species, accuracy varied substantially depending on the taxon. DiscussionOur findings demonstrate that herbarium specimens often retain a strong taxonomic signal in their spectra, however, inter-individual variability affects accuracy in some taxa. These findings confirm the usefulness of herbarium spectroscopy as a non-destructive tool for species identification and offer a promising avenue for digitizing historical biodiversity data into high-dimensional trait space.

plant biology↗

bioRxiv2025

Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes

PremisePlastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. MethodsWe compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. ResultsPlastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. ConclusionsWe accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.

plant biology↗

bioRxiv2024

Towards a phylogenomic classification of Magnoliidae

PremiseMagnoliidae are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses of a limited number of mostly plastid markers have led to the current classification of magnoliids into four orders and 18 families. However, uncertainty remains regarding the placement of several families. MethodsHere we present the first comprehensive phylogenomic analysis of Magnoliidae as a whole, sampling 235 species from 199 (74%) genera and representing all families and most previously accepted subfamilies and tribes. We analyze newly generated data from the Angiosperms353 probe set using both coalescent and concatenation analyses and testing the impact of multiple filtering and alignment strategies. ResultsWhile our results generally provide further support for previously established phylogenetic relationships in both magnoliids as a whole and large families including Annonaceae and Lauraceae, they also provide new evidence for previously ambiguous relationships. In particular, we find support for the position of Hydnoraceae as sister to the remainder of Piperales and, for the first time, resolve the backbone of relationships among most genera of Myristicaceae. ConclusionsAlthough some of our results are limited by low gene recovery for a number of taxa and significant gene tree conflict for some relationships, this study represents a significant step towards reconstructing the evolutionary history of a major lineage of angiosperms. Based on these results, we present an updated phylogenetic classification for Magnoliidae, recognizing 21 families, summarizing previously established subfamilies and tribes, and describing new tribes for Myristicaceae.

evolutionary biology↗

bioRxiv2023

Truly the best of both worlds: merging lineage-specific and universal baiting kits to maximize phylogenomic inference

PREMISEThe development of RNA baiting kits for reduced representation approaches of genomic sequencing is popularized, with universal and clade-specific kits for flowering plants available. Here, we provided an updated version of the Annonaceae bait kit targeting 799 low copy genes, known as Annonaceae799. METHODSThis new version of the kit combines the original 469 genes from the previous version of the Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compared the results obtained using the Original Angiosperms353 kit with our custom approach. Parsimony informative sites (pis) were evaluated for all genes and combined matrices. RESULTSThe new version of the kit has extremely high rates of gene recovery. On average, 796 genes were recovered per sample, and 777.5 genes recovered with at least 50% of their size. Off-target reads were also obtained. Evaluating size, the proportion of on- and off-target regions, and the number of pis, the genes from the Angiosperms353 usually outperform the genes from the original Annonaceae bait kit. DISCUSSIONThe results obtained show that the new sequences from the Angiosperms353 aggregate variable and putative relevant bases for future studies on species-level phylogenomics, and within species studies. The merging of kits also creates a link between projects and makes available new genes for phylogenetic and populational studies.

evolutionary biology↗

bioRxiv2020

Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae)

The vegetable ivory palms (Phytelepheae) form a small group of Neotropical palms whose phylogenetic relationships are not fully understood. Three genera and eight species are currently recognized; however, it has been suggested that Phytelephas macrocarpa could include the species Phytelephas seemannii and Phytelephas schottii because of supposed phylogenetic relatedness and similar morphology. We inferred their phylogenetic relationships and divergence time estimates using the 32 most clock-like loci of a custom palm bait-kit formed by 176 genes and four fossils for time calibration. We additionally explored the historical biogeography of the tribe under the recovered phylogenetic relationships. Our fossil-dated tree showed the eight species previously recognized, and that P. macrocarpa is not closely related to P. seemanii and P. schottii, which, as a consequence, should not be included in P. macrocarpa. The ancestor of the vegetable ivory palms was widely-distributed in the Choco, the inter-Andean valley of the Magdalena River, and the Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma can be attributed to trans-Andean vicariance between the Choco/Magdalena and the Amazonia. Our results support the role of Andean uplift in the early diversification of Phytelephas under new phylogenetic relationships inferred from genomic data.

evolutionary biology↗

bioRxiv2020

Unravelling the phylogenomic relationships of the most diverse African palm genus Raphia (Calamoideae, Arecaceae)

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution and other eco-evolutionary aspects of this charismatic, socially and economically important palm genus.

plant biology↗

bioRxiv2019

Phylogenomic data reveal how a climatic inversion and glacial refugia shape patterns of diversity in an African rain forest tree species

AO_SCPLOWBSTRACTC_SCPLOWThe worlds second largest expanse of tropical rain forest is in Central Africa and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across central African rain forest plants, in particular a North-South genetic discontinuity close to the equator at the level of a climatic inversion. Here, we take a phylogeographic approach using 351 nuclear markers in 112 individuals across the distribution of the African rain forest tree species Annickia affinis (Annonaceae). We show for the first time that the North-South divide is the result of a single major colonisation event across the climatic inversion from an ancestral population located in Gabon. We suggest that differences in ecological niche of populations distributed either side of this inversion may have contributed to this phylogenetic discontinuity. We find evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly-developed genomic tools can provide invaluable insights into our understanding of tropical rain forest evolutionary dynamics.

evolutionary biology↗

bioRxiv2019

A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species based on two plastid barcoding genes, matK and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful to investigate different broad scale research questions in ecological and evolutionary biology.

evolutionary biology↗

bioRxiv2018

Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

evolutionary biology↗