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September 2021 - present
April 2016 - September 2021
April 2007 - February 2014
Publications
Publications (76)
We obtained full (647 bp) or mini (291 bp) DNA barcodes of 140 mostly African and European specimens of 25 Accipiter (Aves: Accipitridae) species. Kimura two-parameter (K2P) distances were calculated between barcodes to determine the thresholds of intra- and interspecific species boundaries. Thresholds were comparable to or higher than those in pre...
The genetics underlying Cyto-Nuclear Incompatibility (CNI) was studied in Pelargonium interspecific hybrids. We created hybrids of 12 closely related crop wild relatives (CWR) with the ornamental P. × hortorum. Ten of the resulting 12 (F1) interspecific hybrids segregate for chlorosis suggesting biparental plastid inheritance. The segregation ratio...
The repetitive part of the genome (the 'repeatome') contains a wealth of often overlooked information that can be used to resolve phylogenetic relationships and test evolutionary hypotheses for clades of related plant species such as Pelargonium. We have generated genome skimming data for 18 accessions of Pelargonium section Ciconium and one outgro...
Lumpy Skin Disease virus is a poxvirus from the genus Capripox that mainly affects bovines and it causes severe economic losses to livestock holders. The Lumpy Skin Disease virus is currently dispersing in Asia, but little is known about detailed phylogenetic relations between the strains and genome evolution. We reconstructed a whole-genome-sequen...
We have studied the inheritance of mitochondria in Pelargonium section Ciconium using interspecific crosses. We generated 36 different interspecific crosses. We designed KAPS markers targeting four individual mitochondrial markers, belonging to the four main crossing parents, that discriminate between an individual species and the other section Cic...
Cyto-Nuclear Incompatibility (CNI), in which there is a mismatch in the interaction between organelles and nucleus, impacts plant species evolution as it has a direct effect on the fitness of plants. It can reduce fertility and/or result in bleached plants devoid of functional chloroplasts. Understanding the processes leading to CNI could help to i...
Jongkindia, a small tree species endemic to a local area in southeast Liberia, is described as a new monotypic genus of Passifloraceae sens. lat. Its only species Jong-kindia mulbahii combines floral characteristics of the Turneraceae and fruit characteristics of the Passifloraceae s.s. (or subfamily Passifloroideae in APG) and can therefore be reg...
Many nominal species of microscopic animals traditionally fitting the ‘everything is everywhere’ paradigm have been revealed to be complexes of cryptic species. Here, we explore species diversity within the micrometazoan flatworm Gyratrix hermaphroditus—unique among meiofauna because of its global occurrence in a wide variety of brackish, freshwate...
The Congolese and Lower Guinean ichthyological provinces are understudied hotspots of the global fish diversity. Here, we barcoded 741 specimens from the Lower and Middle Congo River and from three major drainage basins of the Lower Guinean ichthyological province, Kouilou‐Niari, Nyanga and Ogowe. We identified 194 morphospecies belonging to 82 gen...
We obtained 398 COI barcodes of 96 morphospecies of Lake Tanganyika (LT) cichlids from the littoral zone. The potential of DNA barcoding in these fishes was tested using both species identification and species delineation methods. The best match (BM) and best close match (BCM) methods were used to evaluate the overall identification success. For th...
The stunning diversity of cichlid fishes has greatly enhanced our understanding of speciation and radiation. Little is known about the evolution of cichlid parasites. Parasites are abundant components of biodiversity, whose diversity typically exceeds that of their hosts. In the first comprehensive phylogenetic parasitological analysis of a vertebr...
We used a 298 bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) to examine sequence variation in (mostly) museum specimens of the African Goshawk Accipiter tachiro. Our results showed two clades with high bootstrap support in a phylogenetic analysis and two groups in a nonmetric multidimensional scaling (NMDS) analysis. Eac...
Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for...
Identification by DNA barcoding is more likely to be erroneous when it is based on a large distance between the query (the barcode sequence of the specimen to identify) and its best match in a reference barcode library. The number of such false positive identifications can be decreased by setting a distance threshold above which identification has...
Intra-specific morphological variation in the cichlid Tropheus duboisi from 10 localities over its
entire known distribution area along the central eastern and northern shore of Lake Tanganyika was
investigated. This revealed significant differences between various populations that are geographically
isolated. These morphological observations only...
Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur mor...
We propose a general working strategy to deal with incomplete reference libraries in the DNA barcoding identification of species. Considering that (1) queries with a large genetic distance with their best DNA barcode match are more likely to be misidentified and (2) imposing a distance threshold profitably reduces identification errors, we modelled...
DNA barcoding identification of 188 intercepted tephritid specimens using a reference library of 622 tephritid DNA barcodes (see Data S1). For each specimen, best DNA barcode match, genetic distance, number of base pair (bp) differences, bp overlapping query-best match, outcome of best match identification (ID) and of best close match ID (with a di...
Diptera. Best Close Match (BCM) identification. Proportions of True Positives (TP), False Positives (FP), True Negatives (TN) and False Negatives (FN) at 30 distance thresholds. For each distance threshold percentages of a) queries discarded, b) accuracy ((TP+TN)/total n. of queries) and c) precision (TP/n. of not discarded queries) were calculated...
Hymenoptera. Best Close Match (BCM) identification. Proportions of True Positives (TP), False Positives (FP), True Negatives (TN) and False Negatives (FN) at 30 distance thresholds. For each distance threshold percentages of a) queries discarded, b) accuracy ((TP+TN)/total n. of queries) and c) precision (TP/n. of not discarded queries) were calcul...
Lepidotera. Best Close Match (BCM) identification. Proportions of True Positives (TP), False Positives (FP), True Negatives (TN) and False Negatives (FN) at 30 distance thresholds. For each distance threshold percentages of a) queries discarded, b) accuracy ((TP+TN)/total n. of queries) and c) precision (TP/n. of not discarded queries) were calcula...
Distributions of interspecific (grey squares) and intraspecific (white circles) pairwise K2P distances in a library of 602 tephritid DNA barcodes. In grey: overlap between the 95% percentiles of intra- and interspecific distributions (6.23%<K2P<7.98%)
(EPS)
Morphological identification, sampling locations and DNA barcode sequences of 602 reference tephritid specimens (tephritid reference library, sheet 1) and 188 intercepted tephritids (tephritid interceptions, sheet 2). The economic status of speces included in the two datasets is summarised in sheets 3 and 4.
(XLS)
Ad hoc distance thresholds for Best Close Match (BCM) identification.
(DOC)
DNA barcoding surveys of small insects usually extract DNA from either a complete insect or a leg. Little is known about how to optimize DNA quantity and quality from different insect parts while preserving a morphological voucher. Here, we quantify DNA yield from different body parts (antenna, hind leg, forewing, hind wing and abdomen) of the micr...
Large parts of the everwet tropics have been burned, leaving many unburned–burned forest edges. Here we studied a Bornean forest edge to determine: (1) how unburned and burned forest differ in vegetation structure, diversity, composition and plant functional traits 7 yr after fire, and (2) if these variables showed significant edge effects. Environ...
The ornithological collections of the Royal Museum for Central Africa in Tervuren and the Royal Belgian Institute of Natural Sciences in Brussels contain approximately 155 000 specimens collected in the Democratic Republic of the Congo (DRC). They include type specimens and other samples from historical populations that represent an exceptional sou...
For many years the status of Ploceus ruweti Louette and Benson 1982, described from the unique male type specimen obtained in 1960 at Lake Lufira (an artificial impoundment on the Lufira River), remained obscure. However, in 2009 MH revisited the type locality, photographed the birds breeding there (including females and young birds), and recorded...
The nominate subspecies of Frances's Sparrowhawk Accipiter francesiae lives on Madagascar, while three of the Comoro Islands have distinct subspecies. Morphological variation among these four populations is peculiar: Whereas on Madagascar a sexual difference in color pattern occurs, plumage differences are small in the Comoros populations, with mas...
Tree species rarely exposed to burning, like in everwet tropical forests, are unlikely to be fire adapted. Therefore, one could hypothesize that these species are affected equally by burning and that tree abundance changes are linked solely to fire behavior. Alternatively, if species do react differentially to burning, abundance changes should be l...
The family of Tephritid fruit flies (Tephritidae, Diptera) is composed of more than 4000 species and more than 350 are of economic importance (EI). The Tephritid Barcoding Initiative (TBI) aims at obtaining DNA barcodes for all EI species and the majority of their congeners. Dry pinned specimens from natural history collections are an important res...
Inventories of tree species are often conducted to guide conservation efforts in tropical forests. Such surveys are time consuming, demanding of expertise, and expensive to perform and interpret. Approaches to make survey efforts simpler or more effective would be valuable. In particular, it would be good to be able to easily identify areas of old-...
Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also
contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions.
In recent decades, however, tropical forest fires occur mor...
Previously, nucleotide substitution rates in mitochondrial DNA of Geraniaceae and Plantaginaceae have been shown to be exceptionally high compared with other angiosperm mtDNA lineages. It has also been shown that mtDNA introns were lost in Geraniaceae and Plantaginaceae. In this study we compile 127 DNA sequences from two partial exons of the mtDNA...
Questions
Question (1)
I have recently performed a General Mixed Yule Coefficient analysis to find which groups are supported in the context of a DNA barcoding study. After I finsihed the work and checked to see which clusters are supported and found that the colours generally match the supported clades, but in a few cases the colours do not alternate, but for instance the same colour is used twice. What does this mean? I have uploaded the output from R and one can see in the top of the picture two supported clades that are green (C66/C65 and in the bottom of the picture two that are pink (C46/C47). At first I thought the assignment of the colours was random, but these two examples lead me to think otherwise. In both cases it concerns groups that are closely related. Can anyone tell me if R assigns colours ad random or if it means for instance that the clade is supported one level higher as well and that there is simply also more refined support within the groups?
