Causal inference and large-scale expert validation shed light on the drivers of SDM accuracy and variance

Aim

To develop a causal understanding of the drivers of Species distribution model (SDM) performance.

Location

United Kingdom (UK).

Methods

We measured the accuracy and variance of SDMs fitted for 518 species of invertebrate and plant in the UK. Our measure of variance reflects variation among replicate model fits, and taxon experts assessed model accuracy. Using directed acyclic graphs, we developed a causal model depicting plausible effects of explanatory variables (e.g. species' prevalence, sample size) on SDM accuracy and variance and quantified those effects using a multilevel piecewise path model.

Results

According to our model, sample size and niche completeness (proportion of a species' niche covered by sampling) directly affect SDM accuracy and variance. Prevalence and range completeness have indirect effects mediated by sample size. Challenging conventional wisdom, we found that the effect of prevalence on SDM accuracy is positive. This reflects the facts that sample size has a positive effect on accuracy and larger sample sizes are possible for widespread species. It is possible, however, that the omission of an unobserved confounder biased this effect. Previous studies, which reported negative correlations between prevalence and SDM accuracy, conditioned on sample size.

Main conclusions

Our model explicates the causal basis of previously reported correlations between SDM performance and species/data characteristics. It also suggests that niche completeness has similarly large effects on SDM accuracy and variance as sample size. Analysts should consider niche completeness, or proxies thereof, in addition to sample size when deciding whether modelling is worthwhile.     

The efficacy of CGS 20267 in suppressing estrogen biosynthesis in patients with advanced stage breast cancer

The pharmacologic inhibition of aromatase activity has been the focus of clinical trials in patients with advanced stage breast cancer. Recent developments with imidazole compounds that inhibit aromatase activity suggest their clinical use as potent inhibitors of estrogen biosynthesis in postmenopausal breast cancer patients. In this Phase I, open-label, dose-range finding study, we examined the inhibitory potency of CGS 20267 on blood and urine levels of estradiol, estrone and estrone sulfate in 8 patients with metastatic breast cancer. Studies included evaluation of adrenal and thyroid function to look for evidence of general hydroxylase inhibition at dose levels effective for aromatase blockade. Patients were administered CGS 20267 at doses of 0.1 and 0.25 mg, once a day in ascending doses over a 12-week period. Preliminary data reveal that CGS 20267 elicits a striking suppression in plasma estradiol, estrone and estrone sulphate which was observed in some patients as quickly as within 24 h of the first dose. Estrogen suppression of over 90% was achieved within 2 weeks of therapy. No alterations in either baseline or ACTH (cortrosyn) stimulated cortisol and aldosterone levels were observed through the 12 weeks of therapy. In addition, 24 h urine sodium and potassium values were not appreciably altered during therapy. We conclude that CGS 20267 is a potent, specific inhibitor of estrogen biosynthesis in postmenopausal patients with metastatic breast cancer and effectively reduces blood and urine estrogens to undetectable levels.     

Neo-tropical felid activity patterns in relation to potential prey and intraguild competitors in the Calakmul Biosphere Reserve,Mexico

Predator behaviors influence, and are influenced by, prey and competitor behaviors. Jaguars (Panthera onca), pumas (Puma concolor), and ocelots (Leopardus pardalis) coexist throughout their geographic range as the three largest predators in a multi-predator community across diverse environments. This study tested for non-random segregation and overlap in the activity patterns of these felids and their shared prey in the southern buffer zone of the Calakmul Biosphere Reserve, in southern Mexico, using camera traps during February to August 2019. We detected little temporal segregation between the nocturnal activities of jaguars, pumas, and ocelots, although pumas were more active closer to dawn. Jaguars had low activity overlap with species likely to be common prey, whereas ocelots had high overlap with their potential prey. Pumas displayed finer-scale similarities in activity with species likely to be common prey. In an understudied area of conservation importance, this study shows that temporal segregation is an unlikely mechanism of coexistence. Further research should incorporate spatio-temporal avoidance and dietary differences to improve our understanding of the mechanisms that drive coexistence between generalist species in a diverse assemblage of threatened felids. Abstract in Spanish is available with online material.     

A MOLECULAR AND MORPHOLOGICAL ANALYSIS OF THE GYMNOGONGRUS DEVONIENSIS (RHODOPHYTA) COMPLEX IN THE NORTH ATLANTIC1

The Gymnogongrus devoniensis (Greville) Schotter complex in the North Atlantic Ocean was elucidated by comparative molecular, morphological, and culture studies. Restriction fragment length patterns and hybridization data on organellar DNA revealed two distinct taxa in samples from Europe and eastern Canada. Nucleotide sequences for the intergenic spacer between the large and small subunit genes of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), and the adjoining regions of both genes, differed by 12.5–13.4% between the two taxa. One of the taxa, which included material from the type locality of G. devoniensis at Torbay, Devon, England, was taken to represent authentic G. devoniensis. Within this taxon, samples from Ireland, England, northern France, northern Spain, and southern Portugal showed great morphological variation, particularly in habit, but their Rubisco spacer sequences were identical or differed by only a single nucleotide. Constant morphological features included the development, from a single auxiliary cell, of the spherical cystocarp with a thick mucilage sheath that appears to be typical of Gymnogongrus species with internal cystocarps. Two life-history types were found. Northern isolates underwent a direct-type life history, recycling apomictic females by carpospores, whereas the Portuguese isolate followed a heteromorphic life history in which carpospores gave rise to a crustose tetrasporophyte. The second group of samples, from Nova Scotia and Northern Ireland, provisionally referred to as Gymnogongrus sp., showed little morphological variation. The life history in both areas consists of apomictically reproducing diploid female gametophytes and diploid crustose bisporophytes and tetrasporophytes. Rubisco spacer sequences of the samples were identical, and the plasmid previously described in the Nova Scotian samples was also present in the Northern Ireland population. This species is widely distributed in the western Atlantic, from Newfoundland to Massachusetts. In Europe, gametophytes are known only at one site, but crusts are distributed from Denmark, Scotland (and probably Norway) to France. It is very likely that this species was introduced from one side of the North Atlantic to the other by shipping during the early nineteenth century. Several morphological features are unusual within the genus but are shared with G. leptophyllus J. Agardh from the eastern Pacific Ocean, and further work is necessary to determine whether Gymnogongrus sp. and G. leptophyllus are conspecific.     

Song Learning in Zebra Finches Exposed to a Series of Tutors during the Sensitive Phase

Young male zebra finches exposed to a series of adult males during their sensitive phase for song learning tended to learn from several of them, in contrast to those exposed to two or more tutors simultaneously. There is a tendency to learn more from later tutors, either because the memory of their elements over-writes that of earlier ones or because sensitivity is greater at this stage. No clear relation could be found between features of the song or behaviour of tutors and whether or not they were copied. In common with earlier studies, tutor song output, beyond a certain minimum was found to be unimportant.     

CYTOCHROME P450 1A1 EXPRESSION IN CETACEAN INTEGUMENT: IMPLICATIONS FOR DETECTING CONTAMINANT EXPOSURE AND EFFECTS

Contaminant related health risks to marine mammals are typically inferred from the levels of contaminants measured in blubber. Such measurements alone are insufficient to indicate the likelihood of biological effects from contaminant exposure, especially for contaminants that do not bioaccumulate. Cytochrome P450 1A1 (CYP1A1) in mammals is induced by, and involved in, the metabolism of planar halogenated aromatic hydrocarbons and polycyclic aromatic hydrocarbons, chemicals of concern in aquatic systems. CYP1A induction is a molecular response to exposure to these inducers in many vertebrates. Using immunohistochemistry, we semiquantitatively measured CYP1A1 expression in integument (epidermis and blubber) collected by biopsy or at necropsy from 17 species of cetaceans. CYP1A1 expression was detected in all species and, in some cases, varied both within and between species. CYP1A1 expression in mysticetes was comparable to that in odontocetes. Assessing how the differences in contaminant burdens, life history parameters, and physiological condition between individuals, populations, or species affect CYP1A1 expression in cetacean integument is essential to the interpretation of this induction as a biomarker of exposure to and effects of contaminants. Detection of CYP1A1 expression in integument samples offers a relatively simple, non-lethal technique to study biological changes associated with contaminant exposure in cetaceans.     

Chirality differences in amino acid retention and release from the acid-extractable pool of cultured mammalian cells

In previous work, no chiral differences were found between D and L enantiomers of Leu in their ability to displace one another from the acid-extractable pool in mammalian cells. Recent evidence suggested otherwise. Our aim is to examine whether, in physiological range, D-amino acids have an equivalent ability to displace L-amino acids from the acid-extractable pool of HeLa cells, and vice versa. In the millimolar range, D-Leu and L-Leu have similar uptake and displacement properties with regard to the acid-extractable pool in HeLa cells, despite only the latter isomer being incorporated into protein. Below millimolar concentrations however, a distinct difference was found in the displacement of tritium-labelled L-Leu from the pool by unlabelled D-Leu compared with unlabelled L-Leu. Thus, unlabelled L-Leu in the external medium at 10⁻⁴ or 10⁻⁵ M displaced an equivalent amount of label from the pool as D-Leu introduced at a concentration approx. one order of magnitude higher, respectively. Reciprocal experiments, in which the acid-extractable pool was preloaded with ³H-D-Leu, confirmed this finding. The chirality difference was noted whether pool prelabelling was carried out at 37 or 0°C; but in order to avoid the complications of active transport mechanisms, the competition work reported here was done at 0°C. Similar chirality differences were observed with other hydrophobic amino acids, including His, Ile and Phe, such as, preferential displacement by the L-Leu racemer compared with the D-Leu racemer below mM levels. This was also true for the D and L forms of the non-utilisable isomer of Leu, norleucine (nLeu). We conclude that D-forms of hydrophobic amino acids have lower affinity for similar or the same intracellular binding sites involved in the acid-extractable pool than their L-forms. The significance of these chirality findings to amino acid pools in cells, and to the predominance of L-forms of amino acids in the biosphere is considered.     

Binding-protein expression is subject to temporal,developmental and stress-induced regulation in terminally differentiated soybean organs

Binding protein (BiP) is a widely distributed and highly conserved endoplasmic-reticulum luminal protein that has been implicated in cotranslational folding of nascent polypeptides, and in the recognition and disposal of misfolded polypeptides. Analysis of cDNA sequences and genomic blots indicates that soybeans (Glycine max L. Merr.) possess a small gene family encoding BiP. The deduced sequence of BiP is very similar to that of other plant BiPs. We have examined the expression of BiP in several different terminally differentiated soybean organs including leaves, pods and seed cotyledons. Expression of BiP mRNA increases during leaf expansion while levels of BiP protein decrease. Leaf BiP mRNA is subject to temporal control, exhibiting a large difference in expression in a few hours between dusk and night. The expression of BiP mRNA varies in direct correlation with accumulation of seed storage proteins. The hybridization suggests that maturing-seed BiP is likely to be a different isoform from vegetative BiPs. Levels of BiP protein in maturing seeds vary with BiP mRNA. High levels of BiP mRNA are detected after 3 d of seedling growth. Little change in either BiP mRNA or protein levels was detected in maturing soybean pods, although BiP-protein levels decrease in fully mature pods. Persistent wounding of leaves by whiteflies induces massive overexpression of BiP mRNA while only slightly increasing BiP-protein levels. In contrast single-event puncture wounding only slightly induces additional BiP expression above the temporal variations. These observations indicate that BiP is not constitutively expressed in terminally differentiated plant organs. Expression of BiP is highest during the developmental stages of leaves, pods and seeds when their constituent cells are producing seed or vegetative storage proteins, and appears to be subject to complex regulation, including developmental, temporal and wounding.The mention of vendor or product does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over vendors of similar products not mentioned.Abbreviations BiP binding protein The sequences reported in this paper have been submitted to Gen-Bank and are identified with the accession numbers BiP-A (U08384), BiP-B (U08383), BiP-C (U08382) and -1,3 glucanase (U08405).     

Effects of temperature and food level on growth and development of a planktonic water mite

We analysed the relative effects of food availability and temperature on rates of growth and development of a predatory planktonic water mite, Piona exigua. Growth in length of mites fed Daphnia, Ceriodaphnia and Chydorus was analysed by Gompertz or von Bertalanffy curves; these curves were compared by parallel curve analysis. Growth rates of nymphs and adult female mites increased with temperature; the duration of the imagochrysalis stage decreased. Females grown at 10 °C were smaller at final size than females grown at 15 °C, 18 °C or 22 °C. Females reared at food levels of 15 or 30 prey l⁻¹ grew more slowly and were smaller than those provided with 60 or 120 prey l⁻¹. Nymphs grew more slowly when Daphnia were the only prey, than when smaller prey were available. Food level did not affect nymph growth at 10 °C or 15 °C, but growth at 18 °C or 22 °C may have been slowed at the lowest food levels. Synergistic effects of temperature and food level on nymph growth were apparent only from analysis of growth curves and not from stage duration data.     

Glycans of the early human yolk sac

Summary The pattern of glycan distribution in the early human yolk sac has been investigated using a panel of lectins. Two 6-week and one 8-week human yolk sacs, and one 8-week fetal liver from live, ectopic pregnancies were fixed and embedded in epoxy resin. Lectin histochemistry was carried out on sections of these tissues using 23 biotinylated lectins and an avidin-biotin peroxidase revealing system. Mesothelial surfaces expressed most subsets of N-glycans (other than high mannose types),N-acetyl-lactosamine, sialic acid, andα1,6-N-acetylgalactosamine. Endodermal surface and lateral membranes resembled those of mesothelium, but showed a preponderance ofα2,6-sialyl residues. Most intracellular granules contained N-glycan. There was a marked heterogeneity of granules in the endodermal cells, with different subsets varying in both staining and positional characteristics. The mesenchymal matrix bound most of the lectins used in the study, and expressed fucosyl residues which were also detected in the endothelium. Fetal liver parenchyma showed very similar staining patterns to those seen in the endoderm except for the distribution ofN-acetylglucosamine, which was sparse. Despite some common features, each germ cell layer had a distinct ‘glycotype’, with some saccharides showing extreme topographical restriction.