Predicted Effect of Landscape Position on Wildlife Habitat Value of Conservation Reserve Enhancement Program Wetlands in a Tile‐drained Agricultural Region

Justification for investment in restored or constructed wetland projects are often based on presumed net increases in ecosystem services. However, quantitative assessment of performance metrics is often difficult and restricted to a single objective. More comprehensive performance assessments could help inform decision‐makers about trade‐offs in services provided by alternative restoration program design attributes. The primary goal of the Iowa Conservation Reserve Enhancement Program is to establish wetlands that efficiently remove nitrates from tile‐drained agricultural landscapes. A secondary objective is provision of wildlife habitat. We used existing wildlife habitat models to compare relative net change in potential wildlife habitat value for four alternative landscape positions of wetlands within the watershed. Predicted species richness and habitat value for birds, mammals, amphibians, and reptiles generally increased as the wetland position moved lower in the watershed. However, predicted average net increase between pre‐ and post‐project value was dependent on taxonomic group. The increased average wetland area and changes in surrounding upland habitat composition among landscape positions were responsible for these differences. Net change in predicted densities of several grassland bird species at the four landscape positions was variable and species‐dependent. Predicted waterfowl breeding activity was greater for lower drainage position wetlands. Although our models are simplistic and provide only a predictive index of potential habitat value, we believe such assessment exercises can provide a tool for coarse‐level comparisons of alternative proposed project attributes and a basis for constructing informed hypotheses in auxiliary empirical field studies.     

Lincoln estimates of mallard (Anas platyrhynchos) abundance in North America

Estimates of range‐wide abundance, harvest, and harvest rate are fundamental for sound inferences about the role of exploitation in the dynamics of free‐ranging wildlife populations, but reliability of existing survey methods for abundance estimation is rarely assessed using alternative approaches. North American mallard populations have been surveyed each spring since 1955 using internationally coordinated aerial surveys, but population size can also be estimated with Lincoln's method using banding and harvest data. We estimated late summer population size of adult and juvenile male and female mallards in western, midcontinent, and eastern North America using Lincoln's method of dividing (i) total estimated harvest, , by estimated harvest rate, , calculated as (ii) direct band recovery rate, , divided by the (iii) band reporting rate, . Our goal was to compare estimates based on Lincoln's method with traditional estimates based on aerial surveys. Lincoln estimates of adult males and females alive in the period June–September were 4.0 (range: 2.5–5.9), 1.8 (range: 0.6–3.0), and 1.8 (range: 1.3–2.7) times larger than respective aerial survey estimates for the western, midcontinent, and eastern mallard populations, and the two population estimates were only modestly correlated with each other (western: r = 0.70, 1993–2011; midcontinent: r = 0.54, 1961–2011; eastern: r = 0.50, 1993–2011). Higher Lincoln estimates are predictable given that the geographic scope of inference from Lincoln estimates is the entire population range, whereas sampling frames for aerial surveys are incomplete. Although each estimation method has a number of important potential biases, our review suggests that underestimation of total population size by aerial surveys is the most likely explanation. In addition to providing measures of total abundance, Lincoln's method provides estimates of fecundity and population sex ratio and could be used in integrated population models to provide greater insights about population dynamics and management of North American mallards and most other harvested species.     

Genome evolution of a tertiary dinoflagellate plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata.     

Mourning dove reporting probabilities for web-address versus toll-free bands

Federal migratory bird bands have been inscribed with a postal address and toll-free telephone number (toll-free bands) since 1995 for their reporting, but in 2007 the postal mail address was replaced with an internet address (web-address bands). The reporting rate of web-address bands is unknown, and knowledge of band reporting probabilities is an integral part of bird band-recovery studies designed to obtain unbiased estimates of harvest rates and recovery rates if use of band types differs across space and time. We estimated web-address band reporting probabilities for mourning doves (Zenaida macroura) in the United States by comparing the relative recovery rate (ratio) of web-address to toll-free bands and applying this as an adjustment factor to the known reporting probabilities of toll-free bands. Cooperators banded 132,386 doves representing 57,982 (44%) web-address and 74,404 (56%) toll-free bands in July and August during 2008–2010 across 34 states, 12 regions, and 3 management units. Of the birds banded, 4,642 (3.5%) were direct recoveries, as a result of being shot, and all but 3 were reported via telephone or internet. Nationally, internet reporting accounted for 16.3% of toll-free bands and 42.9% of web-address bands recovered. Web-address bands had a greater recovery rate than toll-free bands (ratio = 1.081, SE = 0.027). We found some evidence of spatial variation in ratio estimates at management unit and regional scales, but the variation was primarily at the regional level where it was not great (range = 1.015–1.213) and statistical support for this variation was not particularly strong (SE = 0.129). Nationally, the web-address band reporting probability was 0.535 (SE = 0.021), an absolute increase of 0.040 compared to the reporting probability of toll-free bands. The additional reporting probability of web-address bands relative to toll-free bands must be accounted for in band-recovery studies used to obtain estimates of harvest rates and recovery rates if use of band types differs across space and time for mourning doves and possibly other species. © 2011 The Wildlife Society.     

DEEP DIVISION IN THE CHLOROPHYCEAE (CHLOROPHYTA) REVEALED BY CHLOROPLAST PHYLOGENOMIC ANALYSES1

The Chlorophyceae (sensu Mattox and Stewart) is a morphologically diverse class of the Chlorophyta displaying biflagellate and quadriflagellate motile cells with varying configurations of the flagellar apparatus. Phylogenetic analyses of 18S rDNA data and combined 18S and 26S rDNA data from a broad range of chlorophycean taxa uncovered five major monophyletic groups (Chlamydomonadales, Sphaeropleales, Oedogoniales, Chaetophorales, and Chaetopeltidales) but could not resolve their branching order. To gain insight into the interrelationships of these groups, we analyzed multiple genes encoded by the chloroplast genomes of Chlamydomonas reinhardtii P. A. Dang. and Chlamydomonas moewusii Gerloff (Chlamydomonadales), Scenedesmus obliquus (Turpin) Kütz. (Sphaeropleales), Oedogonium cardiacum Wittr. (Oedogoniales), Stigeoclonium helveticum Vischer (Chaetophorales), and Floydiella terrestris (Groover et Hofstetter) Friedl et O’Kelly (Chaetopeltidales). The C. moewusii, Oedogonium, and Floydiella chloroplast DNAs were partly sequenced using a random strategy. Trees were reconstructed from nucleotide and amino acid data sets derived from 44 protein‐coding genes of 11 chlorophytes and nine streptophytes as well as from 57 protein‐coding genes of the six chlorophycean taxa. All best trees identified two robustly supported major lineages within the Chlorophyceae: a clade uniting the Chlamydomonadales and Sphaeropleales, and a clade uniting the Oedogoniales, Chaetophorales, and Chaetopeltidales (OCC clade). This dichotomy is independently supported by molecular signatures in chloroplast genes, such as insertions/deletions and the distribution of trans‐spliced group II introns. Within the OCC clade, the sister relationship observed for the Chaetophorales and Chaetopeltidales is also strengthened by independent data. Character state reconstruction of basal body orientation allowed us to refine hypotheses regarding the evolution of the flagellar apparatus.     

The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants.

To gain insights into the nature of the mitochondrial genome in the common ancestor of all green plants, we have completely sequenced the mitochondrial DNA (mtDNA) of Mesostigma viride. This green alga belongs to a morphologically heterogeneous class (Prasinophyceae) that includes descendants of the earliest diverging green plants. Recent phylogenetic analyses of ribosomal RNAs (rRNAs) and concatenated proteins encoded by the chloroplast genome identified Mesostigma as a basal branch relative to the Streptophyta and the Chlorophyta, the two phyla that were previously thought to contain all extant green plants. The circular mitochondrial genome of Mesostigma resembles the mtDNAs of green algae occupying a basal position within the Chlorophyta in displaying a small size (42,424 bp) and a high gene density (86.6% coding sequences). It contains 65 genes that are conserved in other mtDNAs. Although none of these genes represents a novel coding sequence among green plant mtDNAs, four of them (rps1, sdh3, sdh4, and trnL[caa]) have not been reported previously in chlorophyte mtDNAs, and two others (rpl14 and trnI[gau]) have not been identified in the streptophyte mtDNAs examined so far (land-plant mtDNAs). Phylogenetic analyses of 19 concatenated mtDNA-encoded proteins favor the hypothesis that Mesostigma represents the earliest branch of green plant evolution. Four group I introns (two in rnl and two in cox1) and three group II introns (two in nad3 and one in cox2), two of which are trans-spliced at the RNA level, reside in Mesostigma mtDNA. The insertion sites of the three group II introns are unique to this mtDNA, suggesting that trans-splicing arose independently in the Mesostigma lineage and in the Streptophyta. The few structural features that can be regarded as ancestral in Mesostigma mtDNA predict that the common ancestor of all green plants had a compact mtDNA containing a minimum of 75 genes and perhaps two group I introns. Considering that the mitochondrial genome is much larger in size in land plants than in Mesostigma, we infer that mtDNA size began to increase dramatically in the Streptophyta either during the evolution of charophyte green algae or during the transition from charophytes to land plants.     

A closed-loop cadaveric foot and ankle loading model

Investigations of human foot and ankle biomechanics rely chiefly on cadaver experiments. The application of proper force magnitudes to the cadaver foot and ankle is essential to obtain valid biomechanical data. Data for external ground reaction forces are readily available from human motion analysis. However, determining appropriate forces for extrinsic foot and ankle muscles is more problematic. A common approach is the estimation of forces from muscle physiological cross-sectional areas and electromyographic data. We have developed a novel approach for loading the Achilles and posterior tibialis tendons that does not prescribe predetermined muscle forces. For our loading model, these muscle forces are determined experimentally using independent plantarflexion and inversion angle feedback control. The independent (input) parameters -- calcaneus plantarflexion, calcaneus inversion, ground reaction forces, and peroneus forces -- are specified. The dependent (output) parameters -- Achilles force, posterior tibialis force, joint motion, and spring ligament strain -- are functions of the independent parameters and the kinematics of the foot and ankle. We have investigated the performance of our model for a single, clinically relevant event during the gait cycle. The instantaneous external forces and foot orientation determined from human subjects in a motion analysis laboratory were simulated in vitro using closed-loop feedback control. Compared to muscle force estimates based on physiological cross-sectional area data and EMG activity at 40% of the gait cycle, the posterior tibialis force and Achilles force required when using position feedback control were greater.     

Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases

Sequence analysis of chloroplast and mitochondrial large subunit rRNA genes from over 75 green algae disclosed 28 new group I intron-encoded proteins carrying a single LAGLIDADG motif. These putative homing endonucleases form four subfamilies of homologous enzymes, with the members of each subfamily being encoded by introns sharing the same insertion site. We showed that four divergent endonucleases from the I-CreI subfamily cleave the same DNA substrates. Mapping of the 66 amino acids that are conserved among the members of this subfamily on the 3-dimensional structure of I-CreI bound to its recognition sequence revealed that these residues participate in protein folding, homodimerization, DNA recognition and catalysis. Surprisingly, only seven of the 21 I-CreI amino acids interacting with DNA are conserved, suggesting that I-CreI and its homologs use different subsets of residues to recognize the same DNA sequence. Our sequence comparison of all 45 single-LAGLIDADG proteins identified so far suggests that these proteins share related structures and that there is a weak pressure in each subfamily to maintain identical protein–DNA contacts. The high sequence variability we observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into how these proteins evolve new DNA specificity.     

Porcine model of diabetic dyslipidemia: insulin and feed algorithms for mimicking diabetes mellitus in humans

A weakness of many animal models of diabetes mellitus is the failure to use insulin therapy, which typically results in severe body wasting. Data collected from such studies must be interpreted cautiously to separate the effects of hyperglycemia from those of starvation. We provide several algorithms that were used by us in two long-term (20-week) experiments in which hyperglycemia (300 to 400 mg/dl), dyslipidemia (cholesterol [280 to 405 mg/dl] and triglycerides [55 to 106 mg/dl] concentrations), and positive energy balance were maintained in swine. Yucatan miniature swine groups included control, alloxan-induced diabetes mellitus, diabetes mellitus plus diet-induced dyslipidemia, and exercise-trained diabetic dyslipidemic pigs. The algorithms were developed for the porcine model because of several similarities to humans, including: cardiac anatomy and physiology, propensity for sedentary behavior, and metabolism of dietary carbohydrates and lipids. Acute toxic effects of alloxan (hypoglycemia, hyperglycemia, nephrotoxicosis) were minimized by preventive fluid loading and by use of algorithms in which insulin, food, and fluid therapy were administered. Long-term insulin and food maintenance algorithms elicited normal body weight gain in all three diabetic groups (lean experiment) and threefold greater body weight gain in pigs of an obesity experiment. Exercise-trained pigs of both experiments manifested significantly increased work performance and did not experience medical complications. We conclude that these algorithms can be used in swine, or similar algorithms can be developed for other animal species to maintain hyperglycemia and/or dyslipidemia, while avoiding diabetes-induced wasting. Importantly, animal models of diabetes mellitus that maintain positive energy balance and poor glycemic control provide a marked improvement over other models by more closely mimicking the human presentation of diabetes mellitus.