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Understanding the diversity of a species and its history, in order to better exploit it, is a challenge that breeders often face when creating new varieties adapted to the current environment. Many questions still remain about the first phases of cocoa domestication in Central and Latin America. Using a multidisciplinary approach, associating archaeologists with genomics and biochemistry scientists, we tried to retrace the history of the past domestication of cocoa trees, and their migrations in South America and Central America. Plant paleogenomics is a new field of research, that traces the evolution of cultivated plants in response to human domestication and natural selection since very ancient times. It is based on the analysis of ancient DNA (aDNA) from archaeological remains and can provide direct access to plant varieties consumed several thousand years ago. The oldest traces of cocoa consumption date back 5,500 years and have been identified in the southern Ecuadorian Amazon. New studies, reported in this paper, have been carried out from more than 300 archaeological samples collected mainly all along the Pacific coast of Ecuador and Colombia as well as in Central America and from diverse civilizations, the oldest of which dates back to more than 5000 years before our era. Analyzes have revealed traces of ancient cocoa DNA and methylxanthines (theobromine, theophylline and caffeine) in the ceramic residues of many pre-Columbian cultures. They show a wide use of cocoa throughout the Latin America continent and at very varied times which can go back more than 5000 years. The genetic origin of varieties consumed several thousand years ago could have sometimes been identified by comparison with a large collection of modern genetic resources representing the diversity of the T. cacao species. These results provide new keys to unraveling the past domestication of T. cacao in Latin and Central America.

Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.

In shelled molluscs, assigning valid species names to independent evolutionary lineages can be a difficult task. Most original descriptions are based on empty shells and the high levels of variation in shape, color and pattern in some groups can make the shell a poor proxy for species-level identification. The deep-sea gastropod turbinid genus Bolma is one such example, where species-level identification based on shell characters alone is challenging. Here, we show that in Bolma both traditional and molecular taxonomic treatments are associated with a number of pitfalls that can lead to biased inferences about species diversity. Challenges derive from the few phylogenetically informative characters of shells, insufficient information provided in original descriptions and sampling artefacts, which at the molecular level in spatially fragmented organisms can blur distinctions between genetically divergent populations and separate species. Based on a comprehensive dataset combining molecular, morphological and distributional data, this study identified several cases of shell-morphological plasticity and convergence. Results also suggest that what was thought to be a set of distinct, range-restricted species corresponds instead to a smaller number of more widespread species. Overall, using an appropriate sampling design, including type localities, allowed us to assign available names to evolutionarily significant units.

Morphological (shell) and molecular examination of a large suite of specimens of pleurotomariids from around New Caledonia and the Coral Sea reveals the existence of four species in the complex of Perotrochus caledonicus: Perotrochus deforgesi Métivier, 1990 and P. pseudogranulosus sp. nov. live allopatrically on the plateaus and guyots of the Coral Sea; Perotrochus caledonicus Bouchet & Métivier, 1982 and Perotrochus wareni sp. nov. live sympatrically - but essentially not syntopically - on the slopes of New Caledonia, Norfolk Ridge and the Loyalty Ridge. All species live in the 300–500 m interval, and together form a significant component of the mollusc fauna living on hard bottoms in the SW Pacific, with individual dredge hauls containing up to 25 specimens of Perotrochus.