46 research outputs found
Dated Plant Phylogenies Resolve Neogene Climate and Landscape Evolution in the Cape Floristic Region
In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13-17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5-8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied
Cryptic Diversity of African Tigerfish (Genus Hydrocynus) Reveals Palaeogeographic Signatures of Linked Neogene Geotectonic Events
The geobiotic history of landscapes can exhibit controls by tectonics over biotic evolution. This causal relationship positions ecologically specialized species as biotic indicators to decipher details of landscape evolution. Phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, including fishes, can reveal key events of drainage evolution, notably where geochronological resolution is insufficient. Where geochronological resolution is insufficient, phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, notably fishes, can reveal key events of drainage evolution. This study evaluates paleo-environmental causes of mitochondrial DNA (mtDNA) based phylogeographic records of tigerfishes, genus Hydrocynus, in order to reconstruct their evolutionary history in relation to landscape evolution across Africa. Strong geographical structuring in a cytochrome b (cyt-b) gene phylogeny confirms the established morphological diversity of Hydrocynus and reveals the existence of five previously unknown lineages, with Hydrocynus tanzaniae sister to a clade comprising three previously unknown lineages (Groups B, C and D) and H. vittatus. The dated phylogeny constrains the principal cladogenic events that have structured Hydrocynus diversity from the late Miocene to the Plio-Pleistocene (ca. 0â16 Ma). Phylogeographic tests reveal that the diversity and distribution of Hydrocynus reflects a complex history of vicariance and dispersals, whereby range expansions in particular species testify to changes to drainage basins. Principal divergence events in Hydrocynus have interfaced closely with evolving drainage systems across tropical Africa. Tigerfish evolution is attributed to dominant control by pulses of geotectonism across the African plate. Phylogenetic relationships and divergence estimates among the ten mtDNA lineages illustrates where and when local tectonic events modified Africa's Neogene drainage. Haplotypes shared amongst extant Hydrocynus populations across northern Africa testify to recent dispersals that were facilitated by late Neogene connections across the Nilo-Sahelian drainage. These events in tigerfish evolution concur broadly with available geological evidence and reveal prominent control by the African Rift System, evident in the formative events archived in phylogeographic records of tigerfish
Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences
The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & NemĂ©sio 2007; Donegan 2008, 2009; NemĂ©sio 2009aâb; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported
by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on
18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based
researchers who signed it in the short time span from 20 September to 6 October 2016
Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial
Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; pâ=â0.40). There was no significant effect of DMF on any secondary outcome
Dimethyl fumarate in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial
Dimethyl fumarate (DMF) inhibits inflammasome-mediated inflammation and has been proposed as a treatment for patients hospitalised with COVID-19. This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing multiple treatments in patients hospitalised for COVID-19 (NCT04381936, ISRCTN50189673). In this assessment of DMF performed at 27 UK hospitals, adults were randomly allocated (1:1) to either usual standard of care alone or usual standard of care plus DMF. The primary outcome was clinical status on day 5 measured on a seven-point ordinal scale. Secondary outcomes were time to sustained improvement in clinical status, time to discharge, day 5 peripheral blood oxygenation, day 5 C-reactive protein, and improvement in day 10 clinical status. Between 2 March 2021 and 18 November 2021, 713 patients were enroled in the DMF evaluation, of whom 356 were randomly allocated to receive usual care plus DMF, and 357 to usual care alone. 95% of patients received corticosteroids as part of routine care. There was no evidence of a beneficial effect of DMF on clinical status at day 5 (common odds ratio of unfavourable outcome 1.12; 95% CI 0.86-1.47; pâ=â0.40). There was no significant effect of DMF on any secondary outcome
The evolutionary history and taxonomy of the Kobus leche species complex of South-Central Africa in the context of palaeo-drainage dynamics
Dissertation (PhD)--University of Stellenbosch, 2006.ENGLISH ABSTRACT: This multi-disciplinary study compiled taxonomic and biogeographical data to elucidate the
extant diversity of lechwe antelopes (Kobus leche complex), and reconstruct their evolutionary
history. Their diversification has been confined to wetlands across the south-central Africa
plateaux. Lechwes are specialist grazers in water meadow floodplains; these stenotopic habitat
requirements are invoked to explain why their evolution is atypical of terrestrial large mammals.
Combined analyses of morphological (171 adult males), genetic (208 genotyped individuals)
and palaeo-environmental datasets, revealed a recent (Middle Pleistocene) pulse of speciation in
the K. leche complex. Multivariate morphometric analyses revealed the presence of five distinct
groups that could be tied to the geography of the region. Furthermore, the genetic analyses
supported the existence of at least four of these lineages, which show significant population
separation at the level of the mtDNA control region. Most of the differences among populations
were confined to frequency differences among populations and Bayesian analyses strongly
suggest that the pattern obtained is the result of the retention of ancestral haplotypes with
limited female geneflow among the extant populations. Evolution of the five lineages identified
by the morphological and population genetic analyses were further investigated by making use
of additional genetic data (mtDNA cyt b, SPTNB, SRY, Protamine 1, and b-Fibrinogen) and a
subset of the samples. Topologies were largely unresolved due to the recent common ancestry
of the lineages. Following the Evolutionary Species Concept, which was motivated by a
philosophical review, five allopatric species could be recognized (anselli, kafuensis, leche,
robertsi and smithemani). A model of drainage evolution compiled disparate facets of biological
and geological evidence to detail interlinked histories of wetlands and their biota across the
south-central Africa plateaux. This wetland archipelago is recognized as a distinct
biogeographical unit in its own right - the Katanga-Chambeshi region. Evolutionary
diversification of lechwes represents a dominant biogeographical signal reflecting how the
aquatic biota have evolved in tandem with palaeo-drainage dynamics across this evolutionary
theatre. Delimitation of key events in lechwe and drainage evolution was refined by
archaeological dating of the Victoria Falls Formation, to decipher when the Zambezi river
eroded the Batoka gorge. Demographic expansion in K. leche s.s (early Middle Pleistocene)
corresponds to dessication of Palaeo-Lake Makakgadikgadi while more recent phylogeographic
signals correspond to the tenure of Palaeo-Lake Bulozi. These speciation events in the Middle
Pleistocene preceded peripatric speciation of K. kafuensis that accompanied the morphosis of
the Kafue Flats (from palaeo-lake to floodplain), when the Kafue River attained its modern
topology. The present study highlights that Lechwes represent a biota of evolutionary vibrant
clades, rich in endemic species. As ecologically-dominant species in wetlands, lechwes deserve priority conservation attention, which is challenged to perpetuate evolutionary and ecological
processes across an archipelago straddling five countries.AFRIKAANSE OPSOMMING: Die multidisiplinĂȘre studie bring saam taksonomiese en biogeografiese data om die evolusionĂȘre
geskiedenis en huidige diversitiet van basterwaterbokke (Kobus leche kompleks) te verklaar.
Hulle diversifikasie is beperk to vleilande regoor die suid-sentraal Afrika plato.
Basterwaterbokke is gespesialiseerde grasvreters in grasvloedvlaktes; hierdie stenotipiese
habitatsvereiste word voorgehou om te verduidelik hoekom die evolusie van hierdie diere atipies
is vir terrestriële groot soogdiere. Gekombineerde analise van morfologie (171 volwasse
manlike diere), geneties (208 genotipes) en plaeo-omgewings datstelle toon aan dat daar ân
onlangse (middel Pleistoseen) pols van spesiasie plaasgevind het in die K. lechwe kompleks.
Multivariate morfometriese analyses het aangetoon dat vyf verskillende groepe diere bestaan
wat ook sin gemaak het op grond van geografiese ligging. Verdermeer, die genetiese analise het
die bestaan van ten minste vier van hierdie lyne geondersteun wat betekenisvolle bevolkings
isolasie vertoon het op die vlak van die mtDNA kontrole gebied. Meeste van die verskille tussen
bevolkings was beperk to frekwensieverkille tussen die bevolkings en Bayesian analise het sterk
aanduidings getoon dat die patroon wat gekry is die gevolg was van die behoud van
voorvaderlike haplotiepes met beperkte vroulike geenvloei tussen die huidige bevolkings.
Evolusie van die vyf lyne wat deur die morfologie en bevolkingsgenetika studies geidentifiseer
is was verder ondersoek deur gebruik te maak van addisionele genetiese data (mtDNA cytb,
SPTBN, SRY, Protamien 1, en b-Fibrinogeen) en ân subset van die monsters. TopologieĂ« was
hoofsaaklik onopgelos as gevolg van die kort tyd tot die onlangse gemeenskaplike voorouer van
lyne. Deur die EvolusionĂȘre Spesies Konsep aan te hang, wat gemotiveer is deur ân filosofiese
oorsig, is vyf allopatriese spesies herken (anselli, kafuensis, leche, robertsi and smithemani). ân
Model wat dreinerings evolusie voorstel het verskeie fasette van biologiese en geologiese
bewyse saamgvat om die verbindingsgeskiedenis van vleilande en hulle biota oor die suidsentraal
Afrika plato te beskryf. Die vleiland argipelago word herken as ân onafhanklike
biogeografiese eenheid in sy eie reg â die Katanga-Chambeshi streek. EvolusionĂȘre
diversifikasie van basterwaterbokke verteenwoordig ân dominante biogeografiese sein wat
voortsel hoe die akwatiese biota ontwikkel het in tandem met die palaeo-dreinerings dinamika
in hierdie evolusionĂȘre konsert. Die afbakening van sleutelgebeure in basterwaterbok en
dreinerigsevolusie is beter toegelig deur argeologiese datering wat gebasseer was op die
vorming van die Victoria Valle om te bepaal waneer die Zambezi rivier die Batoka skeurgroef gevorm het. Demografiese uitbreiding binne K. leche s.s (gedurende die vroë Middel
Pleistoseen) stem ooreen met die uitdroging van Palaeo-Meer Makakgadikgadi terwyl meer
onlangse filogeografiese syne ooreenstem met die ontstaan van Palaeo-Meer Bulozi. Hierdie
spesiasie gebeure in die Middel Pleistoseen het die peripatriese spesiasie van K. kafuensis
voorafgegaan wat die morfose van die Kafue Vlaktes vergesel het (van palaeo-meer na
vloedvlakte), toe die Kafue Rivier sy huidige vorm aangeneem het. Die huidige studie het
uitgelig dat basterwaterbokke verteenwoordig ân biota van evolusionĂȘre energieke eenhede, ryk
aan endemiese spesies. As ân ekologiese dominante spesie in vleilande, moet basterwaterbokke
as ân prioriteit gesien word in bewaring, waar dit dan die geleentheid sal hĂȘ om voort te bou op
die evolusionĂȘre en ekologiese prossese van die archipelago wat oor vyf lande strek
Mammal taxonomy without taxonomists : a reply to Zachos and Lovari
CITATION: Gippoliti, S., Cotterill, F. P. D. & Groves, C. P. 2013. Mammal taxonomy without taxonomists : a reply to Zachos and Lovari. Hystrix, the Italian Journal of Mammalogy, 24(2):145â147, doi:10.4404/hystrix-24.1-8881.The original publication is available at http://www.italian-journal-of-mammalogy.itOntological and epistemological properties of the Phylogenetic Species Concept (PSC) as applied in recent mammalian taxonomic works are redefined and defended against criticisms raised by Zachos and Lovari (2013), which we find inapplicable to taxonomy because they relate more to the field of population biology. We summarize the negative impacts of the polytypic species concept for conservation and evolutionary biology, with emphasis on Rhinocerotidae. The priority need to embrace and strengthen museum-based taxonomic research is emphasized.http://www.italian-journal-of-mammalogy.it/article/view/8881Publisher's versio
Lake Tanganyika - a melting pot of ancient and young cichlid lineages (teleostei: cichlidae)?
CITATION: Weiss, J. D., Cotterill, F. P. D. & Schliewen, U. K. 2015. Lake Tanganyika - a melting pot of ancient and young cichlid lineages (teleostei: cichlidae)?. PLoS ONE, 10(4): 1-29 doi:10.1371/journal.pone.0125043.The original publication is available at http://journals.plos.org/plosoneA long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika (âancient mouthbroodersâ) was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor lineages which diversified in ancient rivers and precursor lakes and then amalgamated in the extant L. Tanganyika basin is put forward as an alternative: the 'melting pot Tanganyika' hypothesis.http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125043Publisher's versio
Data from: Dated plant phylogenies resolve Neogene climate and landscape evolution in the Cape Floristic Region
In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions show remarkable consistency across all 12 clades with regard to both the types of environments identified as ancestral, and the timing of shifts to alternative conditions. They reveal that Early Miocene land surfaces of the CFR were wetter than at present and were dominated by quartzitic substrata. These conditions continue to characterize the higher-elevation settings of the Cape Fold Belt, where they have fostered the persistence of ancient fynbos lineages. The Middle Miocene (13â17 Ma) saw the development of perennial to weakly-seasonal arid conditions, with the strongly seasonal rainfall regime of the west coast arising ~6.5â8 Ma. Although the Late Miocene may have seen some exposure of the underlying shale substrata, the present-day substrate diversity of the CFR lowlands was shaped by Pliocene-Pleistocene events. Particularly important was renewed erosion, following the post-African II uplift episode, and the reworking of sediments on the coastal platform as a consequence of marine transgressions and tectonic uplift. These changes facilitated adaptive radiations in some, but not all, lineages studied
Data from: Lake Tanganyika - a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae)?
A long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika (âancient mouthbroodersâ) was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor lineages which diversified in ancient rivers and precursor lakes and then amalgamated in the extant L. Tanganyika basin is put forward as an alternative: the 'melting pot Tanganyika' hypothesis