Papers by Olaf Bininda-Emonds
Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the nort... more Isopods of the species Ligia oceanica are typical inhabitants of the rocky intertidal of the northern European coastline. The aim of this study was to assess the genetic structure of this species using mitochondrial and nuclear sequence data. We analysed partial mitochondrial cytochrome c oxidase subunit I (CO1) and 16S rRNA gene sequence data of 161 specimens collected from ten sites ranging from Spain to Norway. For selected specimens, we also sequenced the hypervariable V7 expansion segment of the nuclear 18S rRNA gene as a supplementary marker. Furthermore, we studied the infection rate of all analysed specimens by the alphaproteobacterium Wolbachia. Our analyses revealed two deeply divergent mitochondrial lineages for Ligia oceanica that probably diverged in the late Pliocene to mid Pleistocene. One lineage comprised specimens from northern populations (‘lineage N’) and one primarily those from France and Spain (‘lineage S’). Distribution patterns of the haplotypes and the genetic distances between both lineages revealed two populations that diverged before the Last Glacial Maximum. Given that we found no homogenization of mitochondrial haplotypes, our present results also reject any influence of Wolbachia on the observed mtDNA variabilit
Analytical Biochemistry, 2019
The American Naturalist, 2007
Marine Mammal Science, 2000
Abstract.—Sequence heterochrony (changes in the order in which events occur) is a potentially imp... more Abstract.—Sequence heterochrony (changes in the order in which events occur) is a potentially important, but relatively poorly explored, mechanism for the evolution of development. In part, this is because of the inherent difficulties in inferring sequence heterochrony across species. The event-pairing method, developed independently by several workers in the mid-1990s, encodes sequences in a way that allows them to be examined in a phylogenetic framework, but the results can be difficult to interpret in terms of actual heterochronic changes. Here, we describe a new, parsimony-based method to interpret such results. For each branch of the tree, it identifies the least number of event movements (heterochronies) that will explain all the observed event-pair changes. It has the potential to find all alternative, equally parsimonious explanations, and generate a consensus, containing the movements that form part of every equally most parsimonious explanation. This new technique, which w...
Abstract: Although interest in the rate of molecular evolution and the molecular clock remains hi... more Abstract: Although interest in the rate of molecular evolution and the molecular clock remains high, our knowledge for most groups in these areas is derived largely from a patchwork of studies limited in both their taxon coverage and the number of genes examined. Using a comprehensive molecular data set of 44 genes (18 nDNA, 11 tRNA and 15 additional mtDNA genes) together with a virtually complete and dated phylogeny of extant mammals, I 1) describe differences in the rate of molecular evolution (i.e. substitution rate) within this group in an explicit phylogenetic and quantitative framework and 2) present the first attempt to localize the phylogenetic positions of any rate shifts. Significant rate differences were few and confirmed several long-held trends, including a progressive rate slowdown within hominids and a reduced substitution rate within Cetacea. However, many new patterns were also uncovered, including the mammalian orders being characterized generally by basal rate slo...
Bioconsensus, 2003
Page 245. DIM ACS Series in Discrete Mathematics and Theoretical Computer Science Volume 61. 2003... more Page 245. DIM ACS Series in Discrete Mathematics and Theoretical Computer Science Volume 61. 2003 MRP Supertree Construction in the Consensus Setting Olaf RP Bininda-Emonds ABSTRACT. MRP supertree construction ...
BMC Ecology and Evolution, 2021
Background 18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an i... more Background 18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core structure across eukaryotes exists for this molecule that can help to inform about its evolution in different groups. Using an alignment of 18S rDNA for Rotifera as traditionally recognized (=Bdelloidea, Monogononta, and Seisonacea, but not Acanthocephala), I fitted sequences for three exemplar species (Adineta vaga, Brachionus plicatilis, and Seison nebaliae, respectively) to the core structure and used these maps to reveal patterns of evolution for the remainder of this diverse group of microscopic animals. Results The obtained variability maps of the 18S rRNA molecule revealed a pattern of high diversity among the three major rotifer clades coupled with strong conservation within each of bdelloids and monogononts. A majority of individual sites (ca. 60%) were constant e...
Journal of Zoological Systematics and Evolutionary Research, 2020
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology, 2014
Science (New York, N.Y.), 2005
Many large animal species have a high risk of extinction. This is usually thought to result simpl... more Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.
BMC evolutionary biology, 2006
The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with d... more The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals.
Nature, 2007
Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the ... more Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct...
Proceedings of the National Academy of Sciences of the United States of America, Jan 12, 2008
Phylogenies describe the origins and history of species. However, they can also help to predict s... more Phylogenies describe the origins and history of species. However, they can also help to predict species' fates and so can be useful tools for managing the future of biodiversity. This article starts by sketching how phylogenetic, geographic, and trait information can be combined to elucidate present mammalian diversity patterns and how they arose. Recent diversification rates and standing diversity show different geographic patterns, indicating that cradles of diversity have moved over time. Patterns in extinction risk reflect both biological differences among mammalian lineages and differences in threat intensity among regions. Phylogenetic comparative analyses indicate that for small-bodied mammals, extinction risk is governed mostly by where the species live and the intensity of the threats, whereas for large-bodied mammals, ecological differences also play an important role. This modeling approach identifies species whose intrinsic biology renders them particularly vulnerab...
Journal of Mammalogy, 2003
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Papers by Olaf Bininda-Emonds