Ecological and geological processes impacting speciation modes drive the formation of wide-range disjunctions within tribe Putorieae (Rubiaceae)

Wide-range geographically discontinuous distributions have long intrigued scientists. We explore the role of ecology, geology, and dispersal in the formation of these large-scale disjunctions, using the angiosperm tribe Putorieae (Rubiaceae) as a case study. From DNA sequences of nuclear ITS and six plastid markers, we inferred a phylogeny with 65% of all known Putorieae species. Divergence times, ancestral ranges, and diversification rate shifts were then estimated using Bayesian inference. We further explored species climatic tolerances and performed ancestral niche reconstruction to discriminate among alternative speciation modes, including geographical and ecological vicariance, and ecogeographical, ecological, and dispersal-mediated speciation. As a result, we identified seven major clades in Putorieae, some of which exhibit striking geographical disjunctions, matching the Rand Flora pattern, with sister species in the Canary Islands andeastern and southern Africa. Initial diversification within the tribe occurred in the early Miocene, coincident with a period of climate warming; however, most clades diverged within the last 10 Myr. Aridification and high extinction rates, coupled with ecological vicariance, explain the oldest disjunctions. Adaptation to new environmental conditions, after allopatry, is observed in several clades. Dispersal, either long-distance or via corridors made available by mountain uplift, is behind the most recent disjunctions. Some of these events were followed by ecological speciation and rapid diversification, with species becoming adapted to xeric or increasingly colder continental climates. We show that an integrative approach may help discriminate among speciation modes invoked to explain disjunctions at macroevolutionary time scales, even when extinction has erased the signature of past events.     

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.     

Psoralea corylifolia extracts stimulate cholinergic-like psoralen receptors of tadpole-tail melanophores,leading to skin darkening

The present work was carried out to determine the effects of lyophilized seed extracts of Psoralea corylifolia along with pure psoralen, its active ingredient on the isolated tail-piece melanophores of Bufo melanostictus, a type of disguised smooth muscle cells, which offer excellent in vitro opportunities for studying the effects of pharmacological and pharmaceutical agents. In the present study, it was found that lyophilized extract of P. corylifolia and its active ingredient psoralen induced powerful, dose-dependent, physiologically significant melanin dispersal effects in the isolated tail melanophores of B. melanostictus, which were completely blocked by atropine as well as hyoscine. The per se melanin dispersal effects of lyophilized extracts of P. corylifolia and its active ingredient psoralen were highly potentiated by neostigmine. It appears that the melanin dispersal effects of the extracts of P. corylifolia and psoralen are mediated by cholino-muscarinic or cholino-psoralen like receptors having similar properties that need to be studied further.     

Contrasting effects of climate change in continental vs. oceanic environments on population persistence and microevolution of Atlantic salmon

Facing climate change (CC), species are prone to multiple modifications in their environment that can lead to extinction, migration or adaptation. Identifying the role and interplay of different potential stressors becomes a key question. Anadromous fishes will be exposed to both river and oceanic habitat changes. For Atlantic salmon, the river water temperature, river flow and oceanic growth conditions appear as three main stressing factors. They could act on population dynamics or as selective forces on life‐history pathways. Using an individual‐based demo‐genetic model, we assessed the effects of these factors (1) to compare risks of extinction resulting from CC in river and ocean, and (2) to assess CC effects on life‐history pathways including the evolution of underlying genetic control of phenotypic plasticity. We focused on Atlantic salmon populations from Southern Europe for a time horizon of three decades. We showed that CC in river alone should not lead to extinction of Southern European salmon populations. In contrast, the reduced oceanic growth appeared as a significant threat for population persistence. An increase in river flow amplitude increased the risk of local extinction in synergy with the oceanic effects, but river temperature rise reduced this risk. In terms of life‐history modifications, the reduced oceanic growth increased the age of return of individuals through plastic and genetic responses. The river temperature rise increased the proportion of sexually mature parr, but the genetic evolution of the maturation threshold lowered the maturation rate of male parr. This was identified as a case of environmentally driven plastic response that masked an underlying evolutionary response of plasticity going in the opposite direction. We concluded that to counteract oceanic effects, river flow management represented the sole potential force to reduce the extinction probability of Atlantic salmon populations in Southern Europe, although this might not impede changes in migration life history.     

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade‐offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.     

Heavy metal pollution negatively correlates with anuran species richness and distribution in south‐eastern Australia

Heavy metal pollution has likely played an important role in global biodiversity decline, but there remains a paucity of information concerning the effects of metals on amphibian diversity. This study assessed anuran species richness and distribution in relation to sediment metal content and water chemistry in wetlands located along the Merri Creek corridor in Victoria, south‐eastern Australia. Anurans were present in 60% (21/35) of study sites, with a total of six species detected: the eastern common froglet (Crinia signifera), the eastern sign‐bearing froglet (Crinia parinsignifera), the southern brown tree frog (Litoria ewingii), the growling grass frog (Litoria raniformis), the eastern banjo frog (Limnodynastes dumerilii) and the spotted marsh frog (Limnodynastes tasmaniensis). Mean species richness was 1.77 ± 0.32 per site, and species richness ranged from zero to six species per site. Across sites, species richness correlated negatively with sediment concentrations of six heavy metals: copper, nickel, lead, zinc, cadmium and mercury. Species richness also correlated negatively with wetland water electrical conductivity (a proxy for salinity) and concentrations of orthophosphate. Distributions of the three most commonly observed frog species (C. signifera, L. tasmaniensis and L. ewingii) were significantly negatively associated with the total level of metal contamination at individual sites. The study is the first to provide evidence for an association between metal contamination and anuran species richness and distribution in the southern hemisphere, adding to a small but growing body of evidence that heavy metal pollution has contributed to global amphibian decline.     

Individual dispersal,landscape connectivity and ecological networks

Connectivity is classically considered an emergent property of landscapes encapsulating individuals' flows across space. However, its operational use requires a precise understanding of why and how organisms disperse. Such movements, and hence landscape connectivity, will obviously vary according to both organism properties and landscape features. We review whether landscape connectivity estimates could gain in both precision and generality by incorporating three fundamental outcomes of dispersal theory. Firstly, dispersal is a multi‐causal process; its restriction to an ‘escape reaction’ to environmental unsuitability is an oversimplification, as dispersing individuals can leave excellent quality habitat patches or stay in poor‐quality habitats according to the relative costs and benefits of dispersal and philopatry. Secondly, species, populations and individuals do not always react similarly to those cues that trigger dispersal, which sometimes results in contrasting dispersal strategies. Finally, dispersal is a major component of fitness and is thus under strong selective pressures, which could generate rapid adaptations of dispersal strategies. Such evolutionary responses will entail spatiotemporal variation in landscape connectivity. We thus strongly recommend the use of genetic tools to: (i) assess gene flow intensity and direction among populations in a given landscape; and (ii) accurately estimate landscape features impacting gene flow, and hence landscape connectivity. Such approaches will provide the basic data for planning corridors or stepping stones aiming at (re)connecting local populations of a given species in a given landscape. This strategy is clearly species‐ and landscape‐specific. But we suggest that the ecological network in a given landscape could be designed by stacking up such linkages designed for several species living in different ecosystems. This procedure relies on the use of umbrella species that are representative of other species living in the same ecosystem.     

Brachiopod shell thickness links environment and evolution

While it is well established that the shapes and sizes of shells are strongly phylogenetically controlled, little is known about the phylogenetic constraints on shell thickness. Yet, shell thickness is likely to be sensitive to environmental fluctuations and has the potential to illuminate environmental perturbations through deep time. Here we systematically quantify the thickness of the anterior brachiopod shell which protects the filtration chamber and is thus considered functionally homologous across higher taxa of brachiopods. Our data come from 66 genera and 10 different orders and shows well-defined upper and lower boundaries of anterior shell thickness. For Ordovician and Silurian brachiopods we find significant order-level differences and a trend of increasing shell thickness with water depth. Modern (Cenozoic) brachiopods, by comparison, fall into the lower half of observed shell thicknesses. Among Ordovician–Silurian brachiopods, older stocks commonly have thicker shells, and thick-shelled taxa contributed more prominently to the Great Ordovician Biodiversification but suffered more severely during the Late Ordovician Mass Extinction. Our data highlight a significant reduction in maximum and minimum shell thickness following the Late Ordovician mass extinction. This points towards stronger selection pressure for energy-efficient shell secretion during times of crisis.     

Changhsingian brachiopod communities along a marine depth gradient in South China and their ecological significance in the end-Permian mass extinction

Diversity indices (dominance and evenness) and ecological spatial structure (lifestyles and relative abundances) are important features of Changhsingian brachiopod communities prior to the end-Permian mass extinction (EPME) and could predict temporal and spatial extinction patterns during the EPME. In South China, Changhsingian brachiopod communities show higher diversity than other contemporaneous brachiopod communities in the world and have been reported from a variety of sedimentary environments. In this paper, brachiopods from 18 sections in South China were selected to divide communities and compare their ecological structure. Based on the results of network analysis, cluster analysis and quantitative data from the selected sections, we show that Changhsingian brachiopod communities in South China can be categorized into three assemblages along a marine depth gradient: the Neochonetes–Fusichonetes–Paryphella Assemblage from the shallow-water clastic-rock facies, Spinomarginifera–Peltichia–Oldhamina Assemblage from the shallow-water carbonate platform facies and Fusichonetes–Crurithyris Assemblage from the deep-water siliciclastic intracontinental basin facies. Compared with communities from carbonate platform facies, the communities from siliciclastic facies were characterized by high dominance, low evenness and low lifestyle diversity, which might be important biotic factors leading to earlier extinctions. After the extinction began in all environments, the whole earliest Triassic brachiopod community was first dominated by Fusichonetes and then by Crurithyris. These patterns of domination and replacement could be explained by morphological and ecological advantages. The domination of these two genera, which were already adapted to the oxygen and food-limited deep-water habitat, indicates that the cooler deep-water environment might have been a relatively less stressed habitat after the beginning of the EPME. This suggests that global warming might be the main trigger among the previously proposed synergistic environmental stresses, while anoxia might not, at least for the beginning of EPME.