Browsing by Subject "Evolutionary Biology"

Now showing 1 - 4 of 4
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    Open Access
    Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora
    (BioMed Central Ltd, 2011) Warren, Ben; Bakker, Freek; Bellstedt, Dirk; Bytebier, Benny; ClaSZen-Bockhoff, Regine; Dreyer, Leanne; Edwards, Dawn; Forest, Felix; Galley, Chloe; Hardy, Christopher; Linder, H Peter; Muasya, A Muthama; Mummenhoff, Klaus; Oberlander, Kenneth; Quint
    BACKGROUND: The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. RESULTS: Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. CONCLUSIONS: Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.
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    Open Access
    Taxonomy, phylogeny and biogeography of cisticolas (Cisticola spp.)
    (2015) Davies, Owen R; Crowe, Timothy M; Bowie, Rauri Charles Kerr
    A review of the genus Cisticola was published in 1930 by Rear-admiral Lynes. While subsequent authors have modified Lynes' original groupings, his work remains the basis for modern syntheses of cisticolas. This study tests Lynes' hypotheses by analysing data that he presented in his review and with measurement and plumage data collected from museum specimens. Lynes' groupings were well recovered (98%) when data captured from his review were analysed phenetically, suggesting that he grouped species mostly by similarity. In contrast, when morpho-behavioural data were analysed using cladistic methods, many of his groupings were not monophyletic and the resultant cladogram had very little nodal support due to their highly conservative morphology. To resolve the structure of the genus and the relationships within it, two mitochondrial and four nuclear regions were sequenced from toe-pad samples taken from museum specimens. The molecular analyses included 44 of the 49 currently recognised species and represents the most taxon-dense molecular phylogeny of the genus. The resultant phylogeny separates species into five main clades, but many of Lynes' groupings were not monophyletic and there was also very little support for more recent groupings. Vocalisation analyses indicated that frequency components of songs were correlated with habitat type and body size. These correlations, though, disappeared when phylogeny was controlled for indicating that phylogenetic history rather than habitat preference influenced song character distribution. Some song types are mismatched to their environment, and some sympatric sister species appear to give similar calls. Cisticolas may overcome these attenuation and identification difficulties with behavioural adaptations and aerial displays. The biogeographic distribution of closely related species does not agree with many of the previously proposed hypotheses and a dated phylogeny estimates that most of the diversification in the genus has occurred within the last five million years. Most of the mean divergence date estimates correlated with periods of climate variability and episodes during which there is evidence for high lake levels in Africa, rather than correlating with Plio-Pleistocene glaciation, offering evidence that open habitats may have become fragmented during extremes of both arid and humid climates.
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    The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
    (2017) Trauner, Andrej; Liu, Qingyun; Via, Laura E; Liu, Xin; Ruan, Xianglin; Liang, Lili; Shi, Huimin; Chen, Ying; Wang, Ziling; Liang, Ruixia; Zhang, Wei; Wei, Wang; Gao, Jingcai; Sun, Gang; Brites, Daniela; England, Kathleen; Zhang, Guolong; Gagneux, Sébastien; Barry, Clifton E; Gao, Qian
    BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. RESULTS: By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. CONCLUSIONS: Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.
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    Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna
    (BioMed Central Ltd, 2008) Fuchs, Jerome; Pons, Jean-Marc; Goodman, Steven; Bretagnolle, Vincent; Melo, Martim; Bowie, Rauri; Currie, David; Safford, Roger; Virani, Munir; Thomsett, Simon; Hija, Alawi; Cruaud, Corinne; Pasquet, Eric
    BACKGROUND:The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (Otus: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa. RESULTS: Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles Otus insularis is genetically closer to the South-East Asian endemic O. sunia than to species from the Comoros and Madagascar. The Pemba Scops-owls O. pembaensis, often considered closely related to, if not conspecific with O. rutilus of Madagascar, is instead closely related to the African mainland O. senegalensis. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (O. sunia). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, O. pembaensis diverged from O. senegalensis about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages. CONCLUSION: Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.