The Molecular Phylogenetic Signature of Clades in Decline

Molecular phylogenies have been used to study the diversification of many clades. However, current methods for inferring diversification dynamics from molecular phylogenies ignore the possibility that clades may be decreasing in diversity, despite the fact that the fossil record shows this to be the case for many groups. Here we investigate the molecular phylogenetic signature of decreasing diversity using the most widely used statistic for inferring diversity dynamics from molecular phylogenies, the γ statistic. We show that if a clade is in decline its molecular phylogeny may show evidence of the decrease in the diversification rate that occurred between its diversification and decline phases. The ability to detect the change in diversification rate depends largely on the ratio of the speciation rates of the diversification and decline phases, the higher the ratio the stronger the signal of the change in diversification rate. Consequently, molecular phylogenies of clades in relative rapid decline do not carry a signature of their decreasing diversification. Further, the signal of the change in diversification rate, if present, declines as the diversity drop. Unfortunately, the molecular signature of clades in decline is the same as the signature produced by diversity dependent diversification. Given this similarity, and the inability of current methods to detect declining diversity, it is likely that some of the extant clades that show a decrease in diversification rate, currently interpreted as evidence for diversity dependent diversification, are in fact in decline. Unless methods can be developed that can discriminate between the different modes of diversification, specifically diversity dependent diversification and declining diversity, we will need the fossil record, or data from some other source, to distinguish between these very different diversity trajectories

A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms

The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself

Diversity dynamics in New Caledonia: towards the end of the museum model?

<p>Abstract</p> <p>Background</p> <p>The high diversity of New Caledonia has traditionally been seen as a result of its Gondwanan origin, old age and long isolation under stable climatic conditions (the museum model). Under this scenario, we would expect species diversification to follow a constant rate model. Alternatively, if New Caledonia was completely submerged after its breakup from Gondwana, as geological evidence indicates, we would expect species diversification to show a characteristic slowdown over time according to a diversity-dependent model where species accumulation decreases as space is filled.</p> <p>Results</p> <p>We reanalyze available datasets for New Caledonia and reconstruct the phylogenies using standardized methodologies; we use two ultrametrization alternatives; and we take into account phylogenetic uncertainty as well as incomplete taxon sampling when conducting diversification rate constancy tests. Our results indicate that for 8 of the 9 available phylogenies, there is significant evidence for a diversification slowdown. For the youngest group under investigation, the apparent lack of evidence of a significant slowdown could be because we are still observing the early phase of a logistic growth (i.e. the clade may be too young to exhibit a change in diversification rates).</p> <p>Conclusions</p> <p>Our results are consistent with a diversity-dependent model of diversification in New Caledonia. In opposition to the museum model, our results provide additional evidence that original New Caledonian biodiversity was wiped out during the episode of submersion, providing an open and empty space facilitating evolutionary radiations.</p

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-

Host-plant flowering status and the concentration of sugar in phloem sap: Effects on an ant-treehopper interaction

Host-plant mediation in ant-hemipteran mutualisms requires three conditions. First, hemipteran attractiveness to ants should vary with plant quality. Second, ants should preferentially tend those Hemiptera that produce the most nutritious attractant. Third, increased ant attendance based on a richer food reward should have a significant effect on some measure of hemipteran fitness. A field experiment is used to test these conditions. This is the first study to simultaneously test these three conditions, and the first to test the effect of plant flowering status on the ant-derived benefits for a honeydew-producing hemipteran. It is hypothesized that membracids (Guayaquila xiphias) feeding on plants (Didimopunax vinosum) with flowers ingest phloem sap of higher quality (higher sugar concentration), produce a higher-quality honeydew and, as a result, are attended by more ants and are better protected compared to those on plants without flowers. Total nitrogen content of the phloem sap of plants with or without flowers did not differ significantly, whereas the sugar concentration vas higher in the sap of plants with flowers. Honeydew sugar concentration, honeydew production, and ant tending levels did not Nary significantly with flowering status. Membracid survival increased, and natural enemy abundance decreased when ants were present. Plant flowering status did not affect the ant-derived protection afforded to treehoppers, but plants with flowers accumulated more natural enemies through time than plants without flowers. The results suggest that a trade-off between feeding on a higher-quality food and running increased risk of predation on flowering plants could underlie this ant-hemipteran interaction. Based on the parameters measured in this study it is concluded that host-plant mediation does not occur in the ant-Guayaquila system. The results suggest, however, that the way in which the host-plant could affect ant-Guayaquila interactions is complex and likely to involve other species.102220120

Population dynamics of the marsupial Micoureus demerarae in small fragments of Atlantic Coastal Forest in Brazil

Patterns of population fluctuation, reproductive activity and age structure were studied in populations of the marsupial, Micoureus demerarae occupying two small (7.0 and 8.8 ha) fragments of Atlantic Coastal Forest in southteastern Brazil, from 1995 to 1998. Males, but not females, were observed to move between populations. Estimated sizes of the populatious in each fragment were very small, usually below 20 individuals. Breeding usually occurred from September to April. Population peaks came mostly by the end of this season, the delay reflecting the time required for the young to become trappable. In August 1997, the area was hit by a fire severely affecting the smaller fragment. Populations were synchronous before the fire, although they became asynchronous after it, possibly in the short tcr m only. Small population sizes, synchrony and presumable male-biased mig ration are all likely to make the set of populations more vulnerable to extinction than expected for a metapopulation.o TEXTO COMPLETO DESTE ARTIGO, ESTARÁ DISPONÍVEL À PARTIR DE AGOSTO DE 2015.17333935