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Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established.
Background: The West African country of Burkina Faso (BFA) is an example for the enduring importance of traditional plant use today. A large proportion of its 17 million inhabitants lives in rural communities and strongly depends on local plant products for their livelihood. However, literature on traditional plant use is still scarce and a comprehensive analysis for the country is still missing.
Methods: In this study we combine the information of a recently published plant checklist with information from ethnobotanical literature for a comprehensive, national scale analysis of plant use in Burkina Faso. We quantify the application of plant species in 10 different use categories, evaluate plant use on a plant family level and use the relative importance index to rank all species in the country according to their usefulness. We focus on traditional medicine and quantify the use of plants as remedy against 22 classes of health disorders, evaluate plant use in traditional medicine on the level of plant families and rank all species used in traditional medicine according to their respective usefulness.
Results: A total of 1033 species (50%) in Burkina Faso had a documented use. Traditional medicine, human nutrition and animal fodder were the most important use categories. The 12 most common plant families in BFA differed considerably in their usefulness and application. Fabaceae, Poaceae and Malvaceae were the plant families with the most used species. In this study Khaya senegalensis, Adansonia digitata and Diospyros mespiliformis were ranked the top useful plants in BFA. Infections/Infestations, digestive system disorders and genitourinary disorders are the health problems most commonly addressed with medicinal plants. Fabaceae, Poaceae, Asteraceae, Apocynaceae, Malvaceae and Rubiaceae were the most important plant families in traditional medicine. Tamarindus indica, Vitellaria paradoxa and Adansonia digitata were ranked the most important medicinal plants.
Conclusions: The national-scale analysis revealed systematic patterns of traditional plant use throughout BFA. These results are of interest for applied research, as a detailed knowledge of traditional plant use can a) help to communicate conservation needs and b) facilitate future research on drug screening.
Aim: To provide distribution information and preliminary conservation assessments for all species of the pineapple family (Bromeliaceae), one of the most diverse and ecologically important plant groups of the American tropics—a global biodiversity hotspot. Furthermore, we aim to analyse patterns of diversity, endemism and the conservation status of the Bromeliaceae on the continental level in the light of their evolutionary history.
Location: The Americas.
Methods: We compiled a dataset of occurrence records for 3,272 bromeliad species (93.4% of the family) and modelled their geographic distribution using either climate‐based species distribution models, convex hulls or geographic buffers dependent on the number of occurrences available. We then combined this data with information on taxonomy and used the ConR software for a preliminary assessment of the conservation status of all species following Criterion B of the International Union for the Conservation of Nature (IUCN).
Results: Our results stress the Atlantic Forest in eastern Brazil, the Andean slopes, Central America and the Guiana Highlands as centres of bromeliad diversity and endemism. Phylogenetically ancient subfamilies of bromeliads are centred in the Guiana highlands whereas the large radiations of the group spread across different habitats and large geographic area. A total of 81% of the evaluated bromeliad species are Possibly Threatened with extinction. We provide range polygons for 3,272 species, as well as newly georeferenced point localities for 911 species in the novel “bromeliad” r package, together with functions to generate diversity maps for individual taxonomic or functional groups.
Main conclusions: Diversity centres of the Bromeliaceae agreed with macroecological patterns of other plant and animal groups, but show some particular patterns related to the evolutionary origin of the family, especially ancient dispersal corridors. A staggering 2/3rds of Bromeliaceae species might be threatened with extinction, especially so in tropical rain forests, raising concerns about the conservation of the family and bromeliad‐dependent animal species.
Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate choice component of prezygotic RI. Mate choice tests across drainages (with stimulus males from another drainage) suggest that specific features of the males coupled with a general female preference for yellow color patterns explain the observed variation. Analyses of male body coloration identified the intensity of yellow fin coloration as a strong candidate to explain this pattern, and common-garden rearing suggested heritable population differences. Male sexual ornamentation apparently evolved differently across sulfide-adapted populations, for example because of differences in natural counterselection via predation. The ubiquitous preference for yellow color ornaments in poeciliid females likely undermines the emergence of strong RI, as female discrimination in favor of own males becomes weaker when yellow fin coloration in the respective sulfide ecotype increases. Our study illustrates the complexity of the (partly non-parallel) pathways to divergence among replicated ecological gradients. We suggest that future work should identify the genomic loci involved in the pattern reported here, making use of the increasing genomic and transcriptomic datasets available for our study system.
Background: We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis.
Result: The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, fˆGf^G and fˆhomf^hom, to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background.
Conclusions: The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations.
One of the major problems in evolutionary biology is to elucidate the relationships between historical events and the tempo and mode of lineage divergence. The development of relaxed molecular clock models and the increasing availability of DNA sequences resulted in more accurate estimations of taxa divergence times. However, finding the link between competing historical events and divergence is still challenging. Here we investigate assigning constrained-age priors to nodes of interest in a time-calibrated phylogeny as a means of hypothesis comparison. These priors are equivalent to historic scenarios for lineage origin. The hypothesis that best explains the data can be selected by comparing the likelihood values of the competing hypotheses, modelled with different priors. A simulation approach was taken to evaluate the performance of the prior-based method and to compare it with an unconstrained approach. We explored the effect of DNA sequence length and the temporal placement and span of competing hypotheses (i.e. historic scenarios) on selection of the correct hypothesis and the strength of the inference. Competing hypotheses were compared applying a posterior simulation analogue of the Akaike Information Criterion and Bayes factors (obtained after calculation of the marginal likelihood with three estimators: Harmonic Mean, Stepping Stone and Path Sampling). We illustrate the potential application of the prior-based method on an empirical data set to compare competing geological hypotheses explaining the biogeographic patterns in Pleurodeles newts. The correct hypothesis was selected on average 89% times. The best performance was observed with DNA sequence length of 3500-10000 bp. The prior-based method is most reliable when the hypotheses compared are not temporally too close. The strongest inferences were obtained when using the Stepping Stone and Path Sampling estimators. The prior-based approach proved effective in discriminating between competing hypotheses when used on empirical data. The unconstrained analyses performed well but it probably requires additional computational effort. Researchers applying this approach should rely only on inferences with moderate to strong support. The prior-based approach could be applied on biogeographical and phylogeographical studies where robust methods for historical inferences are still lacking.
Fossil dental remains are an archive of unique information for paleobiological studies. Computed microtomography based on X-ray microfocus sources (X-μCT) and Synchrotron Radiation (SR-μCT) allow subtle quantification at the micron and sub-micron scale of the meso- and microstructural signature imprinted in the mineralized tissues, such as enamel and dentine, through high-resolution “virtual histology”. Nonetheless, depending on the degree of alterations undergone during fossilization, X-ray analyses of tooth tissues do not always provide distinct imaging contrasts, thus preventing the extraction of essential morphological and anatomical details. We illustrate here by three examples the successful application of neutron microtomography (n-μCT) in cases where X-rays have previously failed to deliver contrasts between dental tissues of fossilized specimen.
Significance
Identifying the earliest members of the genus Homo is crucial for understanding when and where selective pressures resulted in its emergence from a Plio-Pleistocene hominin taxon. Our revision of a large part of the dental fossil record from southern Africa provides evidence suggesting a paucity of Homo remains and indicates increased levels of dental variation in australopith taxa. Results of the Ba/Ca, Sr/Ca, and elemental mapping of enamel and dentine also indicate that some of the purported Homo specimens show a paleoecological signal similar to that of the australopiths.
Abstract
The origins of Homo, as well as the diversity and biogeographic distribution of early Homo species, remain critical outstanding issues in paleoanthropology. Debates about the recognition of early Homo, first appearance dates, and taxonomic diversity within Homo are particularly important for determining the role that southern African taxa may have played in the origins of the genus. The correct identification of Homo remains also has implications for reconstructing phylogenetic relationships between species of Australopithecus and Paranthropus, and the links between early Homo species and Homo erectus. We use microcomputed tomography and landmark-free deformation-based three-dimensional geometric morphometrics to extract taxonomically informative data from the internal structure of postcanine teeth attributed to Early Pleistocene Homo in the southern African hominin-bearing sites of Sterkfontein, Swartkrans, Drimolen, and Kromdraai B. Our results indicate that, from our sample of 23 specimens, only 4 are unambiguously attributed to Homo, 3 of them coming from Swartkrans member 1 (SK 27, SK 847, and SKX 21204) and 1 from Sterkfontein (Sts 9). Three other specimens from Sterkfontein (StW 80 and 81, SE 1508, and StW 669) approximate the Homo condition in terms of overall enamel–dentine junction shape, but retain Australopithecus-like dental traits, and their generic status remains unclear. The other specimens, including SK 15, present a dominant australopith dental signature. In light of these results, previous dietary and ecological interpretations can be reevaluated, showing that the geochemical signal of one tooth from Kromdraai (KB 5223) and two from Swartkrans (SK 96 and SKX 268) is consistent with that of australopiths.