Understanding the impact of correlation within pair‐bonds on Cormack–Jolly–Seber models

1. The Cormack–Jolly–Seber (CJS) model and its extensions have been widely applied to the study of animal survival rates in open populations. The model assumes that individuals within the population of interest have independent fates. It is, however, highly unlikely that a pair of animals which have formed a long‐term pairing have dissociated fates.
2. We examine a model extension which allows animals who have formed a pair‐bond to have correlated survival and recapture fates. Using the proposed extension to generate data, we conduct a simulation study exploring the impact that correlated fate data has on inference from the CJS model. We compute Monte Carlo estimates for the bias, range, and standard errors of the parameters of the CJS model for data with varying degrees of survival correlation between mates. Furthermore, we study the likelihood ratio test of sex effects within the CJS model by simulating densities of the deviance. Finally, we estimate the variance inflation factor c^ for CJS models that incorporate sex‐specific heterogeneity.
3. Our study shows that correlated fates between mated animals may result in underestimated standard errors for parsimonious models, significantly deflated likelihood ratio test statistics, and underestimated values of c^ for models taking sex‐specific effects into account.
4. Underestimated standard errors can result in lowered coverage of confidence intervals. Moreover, deflated test statistics will provide overly conservative test results. Finally, underestimated variance inflation factors can lead researchers to make incorrect conclusions about the level of extra‐binomial variation present in their data.

     

A hierarchical classification of freshwater mussel diversity in North America

Aim North America harbours the most diverse freshwater mussel fauna on Earth. This fauna has high endemism at the continental scale and within individual river systems. Previous faunal classifications for North America were based on intuitive, subjective assessments of species distributions, primarily the occurrence of endemic species, and do not portray continent‐wide patterns of faunal similarity. The aim of this study is to provide an analytical portrayal of patterns of mussel diversity in a hierarchical framework that informs the biogeographical history of the fauna. Location The study considered the mussel fauna of North America from the Rio Grande system northwards. Methods Patterns of mussel faunal similarity in 126 river systems or lake watersheds across North America were examined. The dataset was developed from the literature and consisted of recent species presence/absence (282 species) in each drainage unit; subspecies were not included. Patterns of mussel diversity were examined with hierarchical cluster analysis, based on a pairwise distance matrix between all drainage units. Results Cluster analysis revealed 17 faunal provinces within four major faunal regions: Mississippian, Atlantic, Eastern Gulf and Pacific. The Mississippian Region dominates the North American fauna with 11 provinces, including five not recognized by previous classifications: Mississippi Embayment, Upper Mississippi, Great Plains, Ohioan and Pontchartrain–Pearl–Pascagoula. Within the Eastern Gulf Region (containing three provinces), the Escambia–Choctawhatchee Province is distinctive from the Apalachicolan Province, under which it was previously subsumed. Patterns of diversity in the Atlantic Region (two provinces) and Pacific Region (one province) were similar to previous classifications. Main conclusions The classification proposed in this study largely corroborates earlier schemes based on the occurrence of endemic species but identifies additional heterogeneity that reflects unique assemblages of widely distributed species. The study proposes a hierarchical structure that illustrates relationships among these provinces. Although some provinces in the Mississippian Region have high endemism, all Mississippian provinces share a group of widely distributed species. The Atlantic and Eastern Gulf regions have distinctive, endemic faunas suggesting limited past connectivity with the Mississippian Region. The Pacific Region is the most distinct fauna in North America and bears close affinity to the Eurasian mussel fauna.     

Different functions of QTL for estrogen-dependent tumor growth of the rat pituitary

Estrogen treatment to rats of the Fischer 344 (F344) strain induces growth of pituitary tumors that exhibit accelerated cell proliferation, breakdown of basement membrane, and formation of hemorrhagic lakes. Estrogen-dependent pituitary growth is due to variation in a group of quantitative trait loci (QTL), called Edpm for estrogen-dependent pituitary mass, that we previously identified in an F₂ intercross of F344 and the tumor-resistant Brown Norway strain. We previously identified 5 QTL, and microsatellite markers developed since our earlier work have allowed us to scan new chromosomal regions, resulting in two new QTL for estrogen-dependent pituitary mass: Edpm9-2 and a possible QTL on the X Chromosome (Chr). Here we report evidence that these QTL differ from each other in how they affect growth. To examine the effect of the Edpm QTL on biochemical components of tumor growth, we tested their effects in 138 progeny of a backcross to the F344 strain which were given a 10-week chronic estrogen treatment. Hemoglobin/DNA ratio (a measure of blood volume relative to cell number) and total pituitary DNA (a measure of cell number) correlated only weakly, and very large pituitaries were observed which had a low hemoglobin/DNA ratio resembling a normal gland. Through QTL mapping, we found that Edpm2-1, Edpm3, Edpm5, and Edpm9-2 all had significant effects on pituitary mass, but Edpm2-1 and Edpm9-2 primarily affected DNA content, Edpm5 primarily affected hemoglobin/DNA ratio, and Edpm3 affected all traits equally. Received: 16 March 2000 / Accepted: 17 May 2000     

Preferential accumulation of d-pinitol in Acrostichum aureum gametophytes in response to salt stress

Growth and metabolic responses to salt stress were studied in gametophytes of Acrostichum aureum L. (a mangrove fern). Gametophytes were cultured in 0–170 m M NaCl solutions. The growth of gametophytes was best in low NaCl concentrations (35 and 85 m M ), and was retarded at higher NaCl concentrations. Photosynthetic rate of gametophytes was also significantly reduced when grown in high NaCl concentrations. Severe salt stress (>120 m M NaCl) led to a preferential accumulation of d -pinitol in gametophytes, whereas the sporophyte accumulated d -1- O -methyl- muco -inositol. The content of d -pinitol reached up to 50% of the soluble carbohydrate pool of gametophytes under 155 and 170 m M NaCl. The accumulation of d -pinitol and other cyclitols in gametophytes was correlated with the retention of photochemical efficiency of photosystem II and the survival of gametophytes after transfer to solutions containing 340 and 600 m M NaCl, respectively.     

Uptake and Distribution of Labeled Carbon from 14C-Asparagine by Mycobacterium tuberculosis

Asparagine supplies not only nitrogen but also carbon to growing cells of Myobacterium tuberculosis. The carbon of asparagine is rapidly taken up and extensively utilized.     

Effects of Liming on an Acid—Sensitive Southern Appalachian Stream

Laurel Branch (Tennessee, U.S.A.), an acid-sensitive stream in the southern Appalachian Mountains, was limed as a part of the Acid Precipitation Mitigation Program funded by the U.S. Fish and Wildlife Service. Objectives were (1) to evaluate the effectiveness of stream liming by means of a hydropowered doser design, and (2) to monitor stream response(s) to increased pH and alkalinity. Precipitation in the region was documented to be acidic, with a mean pH of 4.54 in 1987. Preliming evaluations conducted from 1986 through 1988 depicted Laurel Branch as soft (hardness less than 5 mg/L CaCO₃, pH 6.2–6.6), dilute (ionic strength less than 400 μeq/L), and lightly buffered (alkalinity less than 100 μeq/L). Because of the apparent relationship between flow and water chemistry, Laurel Branch was considered susceptible to episodic acidification caused by storms. In June 1989, a hydro–powered limestone doser was installed to treat the lower 3 km of the stream. Approximately 8.2 tonnes of crushed limestone were added during an 18–month treatment phase that concluded in December 1990. Technical and design problems with the doser reduced efficiency and limited the scale of liming through much of the first 6 months of operation. Design modifications and equipment upgrades in late 1989 corrected most of the problems and improved doser performance in 1990. No substantial chemical or biological changes were detected within the treated reach of Laurel Branch as a result of liming. Time–series statistical analyses showed small but significant changes in total alkalinity (10 μeq/L average increase) and dissolved calcium at all limed sites. pH (as hydrogen ion) increased 0.16 and 0.13 units at two limed sites that were 1 km and 2 km below the doser, respectively. At the lowermost limed site 3 km below the doser, a significant decrease in pH was detected which was probably flow-related. Mean length of age–0 (juvenile) and age-1 rainbow trout increased marginally during liming, suggesting improved fish growth, but increases were not significant. Densities of an acid-sensitive macrobenthic taxon (Baetis spp.) increased during liming, whereas densities of an acid-tolerant taxon (Leuctra spp.) remained unchanged. In general, observed biological changes were considered minimal; they were judged unrelated to liming but rather of seasonal and/or spatial origin. The regional drought of 1987 and 1988 was considered a confounding factor. With most of the baseline data collected during these years, vastly differing hydrology in 1989 and 1990 (“wet” years regionally) became problematic and may have distorted some responses and masked others. It is also possible that biological responses may have been delayed because of the small magnitude of chemical changes, particularly pH and alkalinity. A calcium mass budget estimated that up to 62% of the calcium added was accounted for in chemistry data from limed sites, with increases most visible in the spring and summer of 1990. Results indicated that, although the Laurel Branch watershed does receive acidic precipitation, current biological communities show high levels of integrity and little apparent degradation related to acidification. If watershed buffering capabilities are depleted from continued acidic deposition, however, stream biota may be at risk in the future.     

Angiotensin stimulates cortisol biosynthesis in human adrenal cells in vitro

Adrenal glands obtained from patients undergoing therapeutic adrenalectomy were used to study the effects of angiotensin on human adrenal steroidogenesis. It was observed that angiotensin stimulated cortisol biosynthesis. Although this has been demonstrated to occur in canine and bovine adrenals, angiotensin-induced cortisol biosynthesis has not been established in man. The possibility that angiotensin merely stimulated glomerulosa cells to secrete precursor steroids which accumulated in the medium and then diffused into fasciculata cells to provide substrate for cortisol biosynthesis was excluded by demonstrating that 3β-hydroxy-5-pregnen-20-one (pregnenolone) and progesterone (the only pertinent precursors) did not accumulate in angiotensinstimulated cell suspensions. In addition, angiotensin stimulated cortisol biosynthesis in a fasciculata cell suspension in which angiotensin did not stimulate aldosterone production. Therefore, in human adrenal cell suspensions angiotensin appeared to act directly to stimulate cortisol synthesis by fasciculata cells. In normal subjects pre-treated with dexamethasone, angiotensin infusions failed to stimulate an increase in plasma cortisol. The physiological importance of angiotensin as a regulator of cortisol secretion remains, therefore, to be established.