Anne Ropiquet
Middlesex University, Science and Technology, Faculty Member
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Research Interests: Zoology, Geography, Biology, Biodiversity, Mitochondrial DNA, and 3 moreDomestication, Holotype, and Sexing
**Note: this is corrected version of the character matrix file.** Character matrix used in the present study. Autapomorphies are in red, hemiplasies in pink, homoplasies in green, synapomorphies in blue, and ambiguous characters in grey
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Mapping of the homoplasic characters on the dated consensus tree. O = absence of character 145
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The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic... more
The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic are taxonomically problematic, as they are referred to as either peralta ,o rantiquorum ,o rcongoensis. In this study, a mitochondrial fragment of 1765 nucleotide sites, covering the complete cytochrome b gene, three transfer RNAs and a large part of the control region, was sequenced to assess the relationships between several populations of giraffe. The phylogenetic analyses performed on the 12 identified haplotypes indicate that northern giraffes constitute a natural group, distinct from that of southern giraffes. Surprisingly, the giraffes of Niger are found to be more closely related to the giraffes of East Africa (subspecies rothschildi and reticulata )t han to those of central Africa. We conclude therefore that the subspecies peralta contains o...
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Despite Diplostomum baeri (Dubois, 1937) being one of the most widely distributed parasites of freshwater fish, there is no complete mitochondrial (mt) genome currently available. The complicated systematics presented by D. baeri has... more
Despite Diplostomum baeri (Dubois, 1937) being one of the most widely distributed parasites of freshwater fish, there is no complete mitochondrial (mt) genome currently available. The complicated systematics presented by D. baeri has hampered investigations into the species distributions and infective dynamics of the species. Within this study we obtained complete mt genome sequences of D. baeri and assessed its phylogenetic relationship with other species of Digenea. The complete mitochondrial genome of D. baeri is 14,480 bp in length, containing 36 genes in total. The phylogenetic tree resulting from Bayesian inference of concatenated 12 protein coding gene sequences placed D. baeri alongside published mt genomes of Diplostomidae, with the overall taxonomic placement of the genus being a sister lineage of the order Plagiochiida The characterization of further mitochondrial genomes within the family Diplostomidae will help progress phylogenetic and epidemiological investigations as well as providing a framework for the analysis of diagnostic markers to be used in further monitoring of the parasite worldwide.
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The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial... more
The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major gr...
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Microsatellite analyses suggest that spatial genetic structure among six leopard-sampling sites in southern Africa is the result of isolation by distance.
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Research Interests: Evolutionary Biology, Genetics, Systematic Biology, Biology, Medicine, and 14 moreRuminants, Coalescent Theory, DNA, Phylogeny, Mitochondrial DNA, Bovidae, Animals, Molecular Phylogenetics and Evolution, Introgression, Monophyly, Genetic Polymorphism, Phylogenetic Tree, Species Specificity, and Taxon
Research Interests: Engineering, Evolutionary Biology, Chemistry, Molecular Biology, Phylogenetics, and 15 moreBiology, Cytogenetic, Evolution, Medicine, Multidisciplinary, Genetic Algorithm, Cytogenetics, Genetics and cytogenetics, Fluorescence in situ hybridization, Animals, Karyotyping, Karyotype, Monophyly, Genetic variation, and Chromosome Banding
Research Interests: Evolutionary Biology, Genetics, Phylogenetics, Biology, Medicine, and 15 morePhylogeny, Bison, Mitochondrial DNA, Bovidae, Animals, Y chromosome, Biological evolution, Cattle, Phylogenetic Tree, Base Sequence, Bayes Theorem, Likelihood Functions, Genetic Markers, Buffaloes, and Molecular Sequence Data
The genetic structure of a large population of the white-clawed crayfish Austropotamobius pallipes was assessed with five microsatellite markers by sampling six sites along its extent. The level of genetic polymorphism was relatively high... more
The genetic structure of a large population of the white-clawed crayfish Austropotamobius pallipes was assessed with five microsatellite markers by sampling six sites along its extent. The level of genetic polymorphism was relatively high with a mean heterozygosity value of 0.394 for the whole population. No genetic differentiation was observed between the different sampled sites, indicating that this population was panmictic. The possibility of extensive gene flow along this brook, downstream as well as upstream, is discussed.
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Abstract In a recent paper, Galbreath, Mordacq & Weiler (2006) concluded that the kouprey Bos sauveli was not a natural species, but rather a feral animal derived from hybridization between banteng... more
Abstract In a recent paper, Galbreath, Mordacq & Weiler (2006) concluded that the kouprey Bos sauveli was not a natural species, but rather a feral animal derived from hybridization between banteng Bos javanicus and zebu Bos taurus indicus. Here, we analyze two mitochondrial genes (cytochrome b and subunit II of the cytochrome c oxidase) for all the seven species of the subtribe Bovina, including new sequences for several specimens of banteng, zebu and gaur of Cambodia. Our analyses indicate that mitochondrial ...
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Caprines include all bovids related to sheep and goat. The composition of the group is controversial and inter-generic relationships have been widely debated. Here, we analysed 2469 characters draw from three distinct molecular markers,... more
Caprines include all bovids related to sheep and goat. The composition of the group is controversial and inter-generic relationships have been widely debated. Here, we analysed 2469 characters draw from three distinct molecular markers, ie two mitochondrial genes (cytochrome b ...
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Research Interests: Evolutionary Biology, Molecular Systematics, Molecular Evolution, Biology, Hybridization, and 15 moreMitochondria, Medicine, Mammals, Biological Sciences, Mitochondrial DNA, Molecular clock, Fossils, Animals, Classification, Camels, Genome, Biological evolution, Cetacea, Phylogenetic Tree, and Buffaloes
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Please help us populate SUNScholar with the post print version of this article. It can be e-mailed to: scholar@sun.ac.zaNatuurwetenskappePlant- en Dierkund
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Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf... more
Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly, and made comparison to published buffalo genomes.The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 kbp and 19.83 kbp, respectively, mean coverage was 44x and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (i) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo, and (ii) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic featu...
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Viruses closely related to SARS-CoV-2, the virus responsible for the Covid-19 pandemic, have previously been identified in several Sunda pangolins (Manis javanica) seized in Guangdong and Guangxi provinces of China [1-4]. The virus... more
Viruses closely related to SARS-CoV-2, the virus responsible for the Covid-19 pandemic, have previously been identified in several Sunda pangolins (Manis javanica) seized in Guangdong and Guangxi provinces of China [1-4]. The virus extracted from Guangdong pangolins is particularly intriguing as the amino-acid sequence of the receptor binding domain of the spike protein is nearly identical to that of the human SARS-CoV-2 virus [2,3]. This characteristic suggests it is capable of binding to the human ACE2 receptor and may therefore be able to mediate infection of human cells. Here, we assembled SARS-CoV-2-like genomes from the Sequence Read Archive (SRA) data available in May 2020 for ten Guangdong pangolins. As previously described [5] the genome assemblies were of poor quality, having high levels of missing data and with possible DNA contamination from human, mouse and tiger. We found 10 circular RNAs (circRNAs) of 278-776 nucleotides (nt) containing SARS-CoV-2-like sequences in th...
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The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic... more
The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and
Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic are taxonomically
problematic, as they are referred to as either peralta, or antiquorum, or congoensis. In this study, a mitochondrial fragment of
1765 nucleotide sites, covering the complete cytochrome b gene, three transfer RNAs and a large part of the control region, was
sequenced to assess the relationships between several populations of giraffe. The phylogenetic analyses performed on the 12 identified
haplotypes indicate that northern giraffes constitute a natural group, distinct from that of southern giraffes. Surprisingly, the
giraffes of Niger are found to be more closely related to the giraffes of East Africa (subspecies rothschildi and reticulata) than to
those of central Africa. We conclude therefore that the subspecies peralta contains only the Niger giraffes, whereas the subspecies
antiquorum includes all populations living in Cameroon, Chad, the Central African Republic, and southwestern Sudan.We suggest
that the ancestor of the Nigerian giraffe dispersed from East to North Africa during the Quaternary period and thereafter migrated
to its current Sahelian distribution in West Africa, in response to the development of the Sahara desert. This hypothesis implies
that Lake Mega-Chad acted as a strong geographical barrier during the Holocene, preventing any contact between the subspecies
peralta and antiquorum. Our study has direct implications for conservation management, as we show that no subspecies peralta
is represented in any European zoos, only in Niger, with a small population of less than 200 individuals.
Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic are taxonomically
problematic, as they are referred to as either peralta, or antiquorum, or congoensis. In this study, a mitochondrial fragment of
1765 nucleotide sites, covering the complete cytochrome b gene, three transfer RNAs and a large part of the control region, was
sequenced to assess the relationships between several populations of giraffe. The phylogenetic analyses performed on the 12 identified
haplotypes indicate that northern giraffes constitute a natural group, distinct from that of southern giraffes. Surprisingly, the
giraffes of Niger are found to be more closely related to the giraffes of East Africa (subspecies rothschildi and reticulata) than to
those of central Africa. We conclude therefore that the subspecies peralta contains only the Niger giraffes, whereas the subspecies
antiquorum includes all populations living in Cameroon, Chad, the Central African Republic, and southwestern Sudan.We suggest
that the ancestor of the Nigerian giraffe dispersed from East to North Africa during the Quaternary period and thereafter migrated
to its current Sahelian distribution in West Africa, in response to the development of the Sahara desert. This hypothesis implies
that Lake Mega-Chad acted as a strong geographical barrier during the Holocene, preventing any contact between the subspecies
peralta and antiquorum. Our study has direct implications for conservation management, as we show that no subspecies peralta
is represented in any European zoos, only in Niger, with a small population of less than 200 individuals.