Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

Detarieae sensu lato (Fabaceae) from the Late Oligocene (27.23 Ma) Guang River flora of north‐western Ethiopia

New species of caesalpinioid legumes, Cynometra sensu lato and Afzelia, are described from the Late Oligocene (27.23 Ma) Guang River flora in north‐western Ethiopia. Both taxa show leaf characteristics that are shared with extant species in the Guineo‐Congolian, Sudanian and/or Zambezian regions of Africa today. The presence of these two species in Ethiopia during the Palaeogene provides further evidence of the importance of the legume tribe Detarieae in northern and north‐eastern Africa throughout much of the Cenozoic, even although the clade is poorly represented in these regions today. The fossil record documents a significant palaeogeographical and evolutionary history of Detarieae in Africa, especially compared with that of Europe and Anatolia. Based on this evidence, it is unlikely that significant diversification of extant African Detarieae took place on the Eurasian landmass. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 44–54.     

Inter‐regional comparison of land‐use effects on stream metabolism

1. Rates of whole‐system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first‐order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions. 2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban‐influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input. 3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams. 4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike’s information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land‐use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land‐use categories in the catchment as regulators of ER. 5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land‐use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER. 6. Overall, consideration of the data separated by land‐use categories showed reduced inter‐regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism.     

Estimation and Correction of Visibility Bias in Aerial Surveys of Wintering Ducks

Abstract: Incomplete detection of all individuals leading to negative bias in abundance estimates is a pervasive source of error in aerial surveys of wildlife, and correcting that bias is a critical step in improving surveys. We conducted experiments using duck decoys as surrogates for live ducks to estimate bias associated with surveys of wintering ducks in Mississippi, USA. We found detection of decoy groups was related to wetland cover type (open vs. forested), group size (1–100 decoys), and interaction of these variables. Observers who detected decoy groups reported counts that averaged 78% of the decoys actually present, and this counting bias was not influenced by either covariate cited above. We integrated this sightability model into estimation procedures for our sample surveys with weight adjustments derived from probabilities of group detection (estimated by logistic regression) and count bias. To estimate variances of abundance estimates, we used bootstrap resampling of transects included in aerial surveys and data from the bias-correction experiment. When we implemented bias correction procedures on data from a field survey conducted in January 2004, we found bias-corrected estimates of abundance increased 36–42%, and associated standard errors increased 38–55%, depending on species or group estimated. We deemed our method successful for integrating correction of visibility bias in an existing sample survey design for wintering ducks in Mississippi, and we believe this procedure could be implemented in a variety of sampling problems for other locations and species. (JOURNAL OF WILDLIFE MANAGEMENT 72(3):808–813; 2008)     

Linked Genes for Calmodulin and E2 Ubiquitin-Conjugating Enzyme in Trichomonas vaginalis

ABSTRACT In searching the genomes of early-diverging protists to study whether the possession of calmodulin is ancestral to all eukaryotes, the gene for calmodulin was identified in Trichomonas vaginalis. This flagellate is a member of the Parabasalia, one of the earliest lineages of recognized eukaryotes to have diverged. This sequence was used to isolate a homologous 1.250-kb fragment from the T. vaginalis genome by inverse polymerase chain reaction. This fragment was also completely sequenced and shown to contain the 3' end of the single-copy calmodulin gene and the 3' end of a gene encoding a protein with high similarity to E2 ubiquitin-conjugating enzymes, a family which has previously only been identified in animals, plants, and fungi. Phylogenetic analysis of 50 members of the E2 family distinguishes at least nine separate subfamilies one of which includes the T. vaginalis E2-homologue and an uncharacterized gene from yeast chromosome XII.     

Caterpillars escape predation in habitat and thermal refuges

1. Climate and, therefore, abiotic conditions, are changing rapidly, and many ecological interactions depend on them. In this study, how abiotic conditions mediate a predator–prey interaction were examined. 2. Caterpillars of Platyprepia virginalis (Boisduval) (Arctiidae) were found previously to be more abundant in wet habitats and thick litter cover compared with drier habitats and little or no litter. We hypothesised that wet litter provided caterpillars with refuges from an important ant predator, Formica lasioides. It was further hypothesised that caterpillars would be able to move at lower temperatures than ants, thus providing them with a thermal refuge. 3. In the lab, caterpillars were more likely to escape ant predation and survive on wet litter and at lower temperatures. At all temperatures, ant recruitment was lower in wet litter than dry litter although ants were more active on litter than bare soil. Thus, wet litter may serve as a habitat refuge for caterpillars from ants. 4. Caterpillars were able to maintain activity at temperatures 8–14 °C lower than F. lasioides. Thus colder temperatures may serve as a thermal refuge for caterpillars from ants. 5. It was hypothesised that caterpillars can escape ant predation when precipitation causes wet litter and at temperatures that they experience commonly in the field. This mismatch between caterpillars and their predators in ability to tolerate wet litter and low temperatures may affect their field distribution and abundance. Expected future warmer and drier conditions may not provide these refuges.     

Adult survival and numbers in a coastal breeding population of Redshank Tringa totanus in northwest England

The results of a long-term capture-mark-recapture ringing programme carried out on a coastal population of breeding Redshanks Tringa totanus between 1974 and 1988 are presented.
Both sexes were equally likely to be recaptured in subsequent years, as were birds captured for the first time compared with those that had been captured previously. Older birds were more frequently recaptured than were young birds. There was no significant difference in male and female adult survival rates, with a mean of 72% of females and 75% of males surviving each year.
The breeding population fluctuated annually with estimated breeding densities of 122–285 pairs per km². Variation in breeding numbers (males), but not survival, was partially attributable to winter air temperature.     

Metal cation binding by the hyperthermophilic microorganism,Archaea Methanocaldococcus Jannaschii,and its effects on silicification

Abstract: A series of experiments was conducted to determine the capacity of an archaeal strain, Methanocaldococcus jannaschii, to bind metals and to study the effects of metal binding on the subsequent silicification of the microorganisms. The results showed that M. jannaschii can rapidly bind several metal cations (Fe³⁺, Ca²⁺, Pb²⁺, Zn²⁺, Cu²⁺). Considering the lack of silicification of this strain without metal binding, these experiments demonstrate that Fe(III) ion binding to the cell wall components was of fundamental importance for successful silicification and, especially, for the excellent preservation of the cell wall. This study brings new elements to the understanding of fossilization processes, showing that the positive effect of Fe(III) on silicification, already known for Bacteria, can also apply to Archaea and that this preliminary binding can be decisive for the subsequent fossilization of these organisms. Knowledge of these mechanisms can be helpful for the search and the identification of microfossils in both terrestrial and extraterrestrials rocks, and in particular on Mars.     

Recovery of plant DNA using a reciprocating saw and silica‐based columns

The time needed for hand grinding and the cost of commercially available extraction kits remain to be the major limitations in plant DNA extraction for many researchers. We present inexpensive techniques for (i) simultaneously machine grinding large numbers of plant samples for DNA extraction using a commercially available reciprocating saw; and (ii) DNA recovery using silica column‐based extractions similar to that used in some commercially available kits. Used together, these allow for the rapid recovery of plant DNA at relatively low cost. Furthermore, these methods appear to be widely applicable within plants with good yields recovered in test extractions across major plant groups (ferns, gymnosperms, monocots and eudicots).     

Mistletoe macroecology: spatial patterns in species diversity and host use across Australia

Mistletoes are parasitic plants, the spatial distributions of which are poorly understood on macroecological scales. Because of their highly unusual life history, investigating mistletoe macroecology may provide new insight into broad‐scale patterns in species distributions. We collated data on the spatial distribution and host use of 65 species of Loranthaceous mistletoes across the continent of Australia, and tested two predictions. First, we predicted mistletoe diversity would be unrelated to productivity (i.e. evapotranspiration and precipitation), as the parasitic lifestyle might relax environmental constraints on their distributions. Second, we predicted that mistletoe host ranges (number of infected host species) would increase in areas with more potential host species. The basis of this prediction is that greater host generality is likely to evolve in regions with greater host diversity because of greater unpredictability in encounter rates with particular host species. Conversely, in regions with fewer potential hosts, randomly dispersing mistletoe propagules are likely to repeatedly encounter particular host species, thus favouring the evolution of host specialization. The results were generally consistent with these predictions. Mistletoe diversity across Australia was weakly associated with environmental conditions, whereas mistletoe host ranges increased significantly with total plant diversity. Macroecological patterns in mistletoes are unusual. In contrast to non‐parasitic plants, mistletoe diversity is poorly correlated with productivity. Host ranges varied predictably across Australia, providing the first quantitative support for the hypothesis that mistletoes in diverse regions tend to be host generalists, whereas mistletoes in depauperate regions tend to be host specialists. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 459–468.