Published Substitution Rates Research Articles

Contributions of biogeographical functions to species accumulation may change over time in refugial regions

AbstractAimElevated biodiversity is the result of the cradle, museum or sink functions. The contributions of these three functions to species accumulation and their changes through time remain unknown for glacial refugia. Additionally, our understanding of the role these functions played during pre‐glacial periods is limited. We test for changes in contributions of functions through time leading to the current diversity patterns using a model refugium and taxon.LocationAnatolia, Western Palaearctic.TaxonFreshwater neritid snails (genusTheodoxus).MethodsAssessments were made to define molecular operational taxonomic units (MOTUs) forTheodoxusand reaffirm the genus as a suitable model taxon with elevated interspecific diversity in noted glacial refugia. Thereafter, we constructed a time‐calibrated multilocus Bayesian phylogeny of mtDNAandnDNAby using both fossil data and published substitution rates. Ancestral area estimation was performed on the phylogeny to define the contribution of the functions through time.ResultsAccumulation ofTheodoxusdiversity in Anatolia over the Miocene–Pliocene transition is attributed to the museum function, but its contribution was small as only few divergence events occurred. The cradle function dominated during the Pliocene and Early Pleistocene, when most interspecific diversity built up and extant lineages in Anatolia were established. The sink function acted from the Middle Pleistocene to present‐day, but with only a small contribution to the total extant Anatolian interspecific diversity.Main conclusionOur results do not entirely mitigate the role glacial cycles played in species accumulation, but highlight Ice Ages may have been less effective in forcing temperate aquatic interspecific diversity into more opportune areas. The elevated diversity in refugia may rather be the result of earlier in situ diversification. Elevated interspecific diversity attributed to the legacy of glacially forced retreats may need to be re‐evaluated in cases where refugia have long and complex geological histories such as Anatolia. These results highlight the importance of considering species accumulation through a temporal perspective to adequately explain present‐day biodiversity patterns.

Phylogenetic biogeography reveals the timing and source areas of the Adiantum species (Pteridaceae) in the West Indies, with a special focus on Cuba

AbstractAimThe processes that shaped the West Indian fern flora remain poorly understood. We attempt to investigate earlier biogeographical patterns described for the region using the genus Adiantum as model. These patterns propose that the West Indian fern flora has (1) an essentially continental rather than insular character, having a rich representation of species occurring in tropical America; (2) the Greater Antilles have a higher fern diversity and higher endemism than the Lesser Antilles, and (3) adaptive speciation has been an important process in shaping the fern diversity of the Greater Antilles.LocationWest Indies.MethodsAdiantum is a subcosmopolitan genus that comprises 200–225 species of which 33 occur in the West Indies. We compiled the most comprehensive molecular dataset of Adiantum available to date, including the chloroplast markers rbcL, atpA, atpB and trnL‐F of 407 accessions belonging to 101 species, 24 of which occur in the West Indies. Maximum likelihood and Bayesian inference approaches were applied to generate phylogenetic hypotheses. Divergence times were estimated using published substitution rates. Ancestral areas were estimated using BioGeoBEARS.ResultsThe extant West Indian Adiantum species originate from at least 17 predominantly Miocene immigration events, 11 from South America and six from Central America, in combination with two cladogenetic events. The Cuban endemics Adiantum alomae and A. sericeum, as well as the Greater Antillean A. deltoideum, A. cristatum and A. pyramidale first appeared during the Pleistocene. The emergence of A. alomae and A. deltoideum coincides with the formation of the karstic relief of the Cuban coasts.Main conclusionsImmigration, rather than cladogenesis, governed the evolution of the West Indian Adiantum species. Our results concur with theoretical models proposed for island communities, suggesting that geologically younger and smaller island assemblages mainly derive from immigration, whereas cladogenesis plays an important role in older and larger islands.

Reconstruction of the late Miocene biogeographical history of tits and chickadees (Aves: Passeriformes: Paridae): A comparison between discrete area analyses and probabilistic diffusion approach

AbstractAimTo infer the biogeographical history of the avian clade Paridae (tits and chickadees) using methods based on discrete, a priori defined, geographical areas and a method that uses actual species distributions and a relaxed random walk in a Bayesian context. We compared their relative performances and how different area codings influenced the outcome in the discrete analyses.LocationHolarctic, Indomalaya, Afrotropics.MethodsThe phylogeny was reconstructed using Bayesian inference and time‐calibrated using published substitution rates and a fossil calibration point. The discrete analyses were performed in BioGeoBEARS. For the probabilistic diffusion analysis, the extant distribution of each species was shaped as polygons in Google Earth and analysed together with the posterior distribution of time‐calibrated trees in beast. The diffusion process was modelled as a relaxed random walk.ResultsThe earliest divergences occurred between 10 and 15 Ma and the probabilistic diffusion analysis, and one of the discrete analyses indicated that the parids originated in the mountains of East Asia (Sino‐Himalayas). Due to a different categorization of the geographical areas, a partly overlapping but conceptually different region was indicated in the second discrete analysis. Between 8 and 5 Ma parids started to spread from the Sino‐Himalayas and became established in North America and Africa before 5 Ma. However, the inferred dispersal patterns differed between the analyses.Main conclusionOverall, the analyses were congruent and together with the divergence time analysis provided a solid biogeographical history for the parids. However, some discrepancies were evident and the diffusion analysis often indicated a more stationary pattern in the Sino‐Himalayas in contrast to the more widespread ancestors indicated by the discrete analyses. The discrete analyses were influenced both by the biogeographical model and delimitation of the a priori areas.

A review of molecular-clock calibrations and substitution rates in liverworts, mosses, and hornworts, and a timeframe for a taxonomically cleaned-up genus Nothoceros

Absolute times from calibrated DNA phylogenies can be used to infer lineage diversification, the origin of new ecological niches, or the role of long distance dispersal in shaping current distribution patterns. Molecular-clock dating of non-vascular plants, however, has lagged behind flowering plant and animal dating. Here, we review dating studies that have focused on bryophytes with several goals in mind, (i) to facilitate cross-validation by comparing rates and times obtained so far; (ii) to summarize rates that have yielded plausible results and that could be used in future studies; and (iii) to calibrate a species-level phylogeny for Nothoceros, a model for plastid genome evolution in hornworts. Including the present work, there have been 18 molecular clock studies of liverworts, mosses, or hornworts, the majority with fossil calibrations, a few with geological calibrations or dated with previously published plastid substitution rates. Over half the studies cross-validated inferred divergence times by using alternative calibration approaches. Plastid substitution rates inferred for “bryophytes” are in line with those found in angiosperm studies, implying that bryophyte clock models can be calibrated either with published substitution rates or with fossils, with the two approaches testing and cross-validating each other. Our phylogeny of Nothoceros is based on 44 accessions representing all suspected species and a matrix of six markers of nuclear, plastid, and mitochondrial DNA. The results show that Nothoceros comprises 10 species, nine in the Americas and one in New Zealand (N. giganteus), with the divergence between the New Zealand species and its Chilean sister species dated to the Miocene and therefore due to long-distance dispersal. Based on the new tree, we formally transfer two species of Megaceros into Nothoceros, resulting in the new combinations N. minarum (Nees) J.C. Villarreal and N. schizophyllus (Gottsche ex Steph.) J.C. Villarreal, and we also newly synonymize eight names described in Megaceros.

On the Biogeography of Centipeda: A Species-Tree Diffusion Approach

Reconstructing the biogeographic history of groups present in continuous arid landscapes is challenging due to the difficulties in defining discrete areas for analyses, and even more so when species largely overlap both in terms of geography and habitat preference. In this study, we use a novel approach to estimate ancestral areas for the small plant genus Centipeda. We apply continuous diffusion of geography by a relaxed random walk where each species is sampled from its extant distribution on an empirical distribution of time-calibrated species-trees. Using a distribution of previously published substitution rates of the internal transcribed spacer (ITS) for Asteraceae, we show how the evolution of Centipeda correlates with the temporal increase of aridity in the arid zone since the Pliocene. Geographic estimates of ancestral species show a consistent pattern of speciation of early lineages in the Lake Eyre region, with a division in more northerly and southerly groups since ∼840 ka. Summarizing the geographic slices of species-trees at the time of the latest speciation event (∼20 ka), indicates no presence of the genus in Australia west of the combined desert belt of the Nullabor Plain, the Great Victoria Desert, the Gibson Desert, and the Great Sandy Desert, or beyond the main continental shelf of Australia. The result indicates all western occurrences of the genus to be a result of recent dispersal rather than ancient vicariance. This study contributes to our understanding of the spatiotemporal processes shaping the flora of the arid zone, and offers a significant improvement in inference of ancestral areas for any organismal group distributed where it remains difficult to describe geography in terms of discrete areas.

Exploring phenotypic plasticity and biogeography in emerald moths: A phylogeny of the genus Nemoria (Lepidoptera: Geometridae)

The moth genus Nemoria (Lepidoptera: Geometridae) includes 134 described species whose larvae and adults display a considerable range of phenotypic plasticity in coloration and morphology. We reconstructed the phylogeny of 54 species of Nemoria and seven outgroups using characters from the mitochondrial genes, Cytochrome Oxidase I and II ( COI and COII), and the nuclear gene, Elongation Factor-α ( EF-1α). Maximum parsimony, maximum likelihood and Bayesian inference were used to infer the phylogeny. The 54 ingroup species represented 13 of the 15 recognized species groups of Nemoria [Ferguson, D.C., 1985. Fasc. 18.1, Geometroidea: Geometridae (in part). In: Dominick, R.B. (Ed.), The Moths of America North of Mexico, Fasc. 18.1. Wedge Entomological Research Foundation, Washington; Pitkin, L.M., 1993. Neotropical emerald moths of the genera Nemoria, Lissochlora and Chavarriella, with particular reference to the species of Costa Rica (Lepidoptera: Geometridae, Geometrinae). Bull. Br. Mus. Nat. Hist. 62, 39–159], and the seven outgroups came from four tribes of Geometrinae. These data support Nemoria as a monophyletic group and largely recover the species groupings proposed in previous taxonomic analyses using morphological characters. Phenotypic plasticity of larvae is not correlated with plasticity of adults among those species of Nemoria where life histories are known, and appears to be evolutionarily labile for both life history stages: Species exhibiting larval phenotypic plasticity, such as N. arizonaria and N. outina, are placed in several distinct clades, suggesting that this trait has evolved multiple times, and species displaying adult phenotypic plasticity are likewise distributed throughout the phylogeny. A comparative analysis of the biogeographic history of Nemoria supports a South American origin for the genus with multiple introductions into North America, and an application of published substitution rates to the phylogram provides an age estimate of 7.5 million years.

The molecular phylogeny and systematics of the actinomycetes.

Sequences of 16S ribosomal RNA have provided actinomycetologists with a phylogenetic tree that allows the investigation of the evolution of actinomycetes and also provides a basis for classification. The origin of actinomycetes and, except for bifidobacteria, the order by which the main sublines evolved, cannot yet be determined with certainty. However, calibration of rRNA sequence divergence with palaeochemical data, and previously published substitution rates of endosymbiotic bacteria, suggest that the main radiation occurred less than 1 billion years ago. Within this radiation, several phylogenetically homogeneous, but sometimes phenotypically heterogeneous, clades appear to have diverged over a short evolutionary period. The resolution of the 16S rRNA molecule appears to be insufficient to clearly determine the branching patterns between clades in this area of the phylogenetic tree. The distribution of some morphological and chemotaxonomic traits such as types of peptidoglycan, menaquinone, phospholipids, cell wall sugars, and fatty acids facilitate the phenotypic delineation of genera within each clade. At higher taxonomic levels, e.g. at the family level, phenotypic similarities are unpredictable and tend to be less conserved. With the exception of mycolic acids, most traits are polyphyletic--hence they are unreliable indicators per se of phylogenetic relationships. Nevertheless, combinations of phenotypic properties are invaluable for predicting whether a new organism is likely to be a member of an established or a novel taxon. Current knowledge about the phylogenetic structure of the actinomycetes provides not only a sound basis for future taxonomic work but also a framework for the rational exploration of their ecology and biotechnological potential.