multimark: an R package for analysis of capture–recapture data consisting of multiple “noninvasive” marks

I describe an open‐source R package, multimark , for estimation of survival and abundance from capture–mark–recapture data consisting of multiple “noninvasive” marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left‐ and right‐sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack–Jolly–Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture–recapture data consisting of a single‐mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left‐ and right‐sided encounter histories for bobcats (Lynx rufus) collected from remote single‐camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap “happy” response) that is otherwise indiscernible using conventional single‐sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark–recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user‐friendly interface for performing Bayesian multimodel inference using capture–recapture data consisting of a single conventional mark or multiple noninvasive marks.     

Proximate Composition and Nutrient Elements in the “Unusual” Algal “Jellies” of Lake Oguta in Southern Nigeria

The proximate composition, nutrient and trace elements of the planktonic algal “jellies” of Lake Oguta in Southern Nigeria, are provided as guides to their utilization and control, using flood (rainy) and dry season samples. These “jellies” are an unusual, macroscopic planktonic algal community in the lake, made up mostly of blue-green algae (Microcystis, Anabaena, Chroococcus) with some green algae (e. g. Spirogyra) and pennate diatoms (e.g. Navicula) rather epiphytic on the mucous jellies of the blue-green algae. Water content was high (98.2% mean, range 97.5-99.5%). Ash, protein and fat had values of 41.7 (39.0-46.2%), 16.9 (15.6-19.4%), and 2.0 (1.7-2.1%) respectively. Crude fibre and carbohydrates were high (25.8% and 12.4%). The levels of phosphorus and nitrogen were rather high, so were the major cations whose order of dominance (Ca > K > Mg > Na) differed from that of the lake water. Macronutrients increased in their concentrations during the rainy flood season while the reverse was the case with the micronutrients. Diagenesis of the endogenic minerals rather than anthropogenic factors are thought to be the reason for the seasonal changes in the ionic concentrations. Possible uses of the algal jellies are discussed as well as their control options.     

Sex‐specific selection on plant architecture through “budget” and “direct” effects in experimental populations of the wind‐pollinated herb,Mercurialis annua

Sexual selection may contribute to the evolution of plant sexual dimorphism by favoring architectural traits in males that improve pollen dispersal to mates. In both sexes, larger individuals may be favored by allowing the allocation of more resources to gamete production (a “budget” effect of size). In wind‐pollinated plants, large size may also benefit males by allowing the liberation of pollen from a greater height, fostering its dispersal (a “direct” effect of size). To assess these effects and their implications for trait selection, we measured selection on plant morphology in both males and females of the wind‐pollinated dioecious herb Mercurialis annua in two separate experimental common gardens at contrasting density. In both gardens, selection strongly favored males that disperse their pollen further. Selection for pollen production was observed in the high‐density garden only, and was weak. In addition, male morphologies associated with increased mean pollen dispersal differed between the two gardens, as elongated branches were favored in the high‐density garden, whereas shorter plants with longer inflorescence stalks were favored in the low‐density garden. Larger females were selected in both gardens. Our results point to the importance of both a direct effect of selection on male traits that affect pollen dispersal, and, to a lesser extent, a budget effect of selection on pollen production.     

Curious structure in “canonical” alanine-based peptides

We have performed all atom simulations of blocked peptides of the form (AAXAA)₃, where X = Gln, Asn, Glu, Asp, Arg, and Lys with explicit water molecules to examine the interactions between side chains spaced i,i–5 in the sequence. Although side chains in this i,i–5 arrangement are commonly believed to be noninteracting, we have observed the formation of unusual i,i–5 main chain hydrogen bonding in such sequences with positively charged residues (Lys) as well as polar uncharged groups (Gln). Our results are consistent with the unusual percentage of hydrogen bonding curves produced by amide exchange measurements on the well-studied sequence acetyl-(AAQAA)₃-amide in water (Shalongo, W., Dugad, L., Stellwagen, E. J. Am. Chem. Soc. 116:8288–8293, 1994). Analysis of our simulations indicated that the glutamine side chain showed the greatest propensity to support π helix formation and that the i,i–5 intramolecular hydrogen bonds were stabilized by water-bridging side chain interactions. This intermittent formation of the unusual π helix structure was observed for up to 23% of the total simulation time in some residues in (AAQAA)₃. Control studies on peptides with glutamine side chains spaced i,i–3, i,i–4, and i,i–6 did not reveal similar unique structures, providing stronger evidence for the unique role side chain interactions with i,i–5 spacing. © 1997 Wiley-Liss Inc.     

Geographical variation in reproductive traits and trade‐offs between size and number of eggs in the king ratsnake,Elaphe carinata

We collected gravid king ratsnakes (Elaphe carinata) from three geographically separated populations in Chenzhou (CZ), Lishui (LS) and Dinghai (DH) of China to study the geographical variation in female reproductive traits and trade‐offs between the size and number of eggs. Not all reproductive traits varied among the three populations. Of the traits examined, five (egg‐laying date, post‐oviposition body mass, clutch size, egg mass and egg width) differed among the three populations. The egg‐laying date, ranging from late June to early August, varied among populations in a geographically continuous trend, with females at the most northern latitude (DH) laying eggs latest, and females at the most southern latitude (CZ) laying eggs earliest. Such a trend was less evident or even absent in the other traits that differed among the three populations. CZ and DH females, although separated by a distance of approximately 1100 km as the crow flies, were similar to each other in most traits examined. LS females were distinguished from CZ and DH females by the fact that they laid a greater number of eggs, but these were smaller. The egg size–number trade‐off was evident in each of the three populations and, at a given level of relative fecundity, egg mass was significantly greater in the DH population than in the LS population. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 701–709.     

Alpha male chimpanzee grooming patterns: implications for dominance “style”

In social primates, individuals use various tactics to compete for dominance rank. Grooming, displays and contact aggression are common components of a male chimpanzee's dominance repertoire. The optimal combination of these behaviors is likely to differ among males with individuals exhibiting a dominance “style” that reflects their tendency to use cooperative and/or agonistic dominance tactics. Here, we examine the grooming behavior of three alpha male chimpanzees at Gombe National Park, Tanzania. We found that (1) these males differed significantly in their tendency to groom with other males; (2) each male's grooming patterns remained consistent before, during and after his tenure as alpha, and (3) the three males tended to groom with high‐ middle‐ and low‐ranking partners equally. We suggest that body mass may be one possible determinant of differences in grooming behavior. The largest male exhibited the lowest overall grooming rates, whereas the smallest male spent the most time grooming others. This is probably because large males are more effective at physically intimidating subordinates. To achieve alpha status, a small male may need to compensate for reduced size by investing more time and energy in grooming, thereby ensuring coalitionary support from others. Rates of contact aggression and charging displays conformed to this prediction, suggesting that each male exhibited a different dominance “style.” Am. J. Primatol. 71:136–144, 2009. © 2008 Wiley‐Liss, Inc.     

When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes

Animals exist as biodiverse composite organisms that include microbial residents, eukaryotic cells, and organs that collectively form a human being. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body or the holobiont secures growth, health, and reproduction. As such, the survival of a holobiont is dependent on the maintenance of biological order including metabolic homeostasis by tight regulation of the communication between its eukaryotic and prokaryotic residents. In this review an overview and perspective are provided on the bidirectional communication between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships between the components of the holobiont. An emphasis is placed on exemplifying microbiome‐mediated effects on host functions—aiming to integrate microbiome functionality to host physiology, be it health or disease. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex transkingdom interactions are provided.     

Sexual dimorphism of heads and abdomens: Different approaches to ‘being large’ in female and male lizards

Sexual‐size dimorphism (SSD) is widespread in animals. Body length is the most common trait used in the study of SSD in reptiles. However, body length combines lengths of different body parts, notably heads and abdomens. Focusing on body length ignores possible differential selection pressures on such body parts. We collected the head and abdomen lengths of 610 lizard species (Reptilia: Squamata: Sauria). Across species, males have relatively larger heads, whereas females have relatively larger abdomens. This consistent difference points to body length being an imperfect measure of lizard SSD because it comprises both abdomen and head lengths, which often differ between the sexes. We infer that female lizards of many species are under fecundity selection to increase abdomen size, consequently enhancing their reproductive output (enlarging either clutch or offspring size). In support of this, abdomens of lizards laying large clutches are longer than those of lizards with small clutches. In some analyses, viviparous lizards have longer abdomens than oviparous lizards with similar head lengths. Our data also suggest that male lizards are under sexual selection to increase head size, which is positively related to winning male–male combats and to faster grasping of females. Thus, larger heads could translate into higher probability to mate. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 665–673.     

Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps

The Ramachandran map clearly delineates the regions of accessible conformational (φ–ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high‐resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely “arid”, fully allowed region in the top left quadrant establishes that side‐chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ–ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12 ) and the i + 1 position of Type II′ β turns (Bin 13) . Of the 516 non‐Gly residues in Bin 13 , 384 occupied the i + 1 position of Type II′ β turns. Further examination of these turn segments revealed a high propensity to occur at the N‐terminus of helices and as a tight turn in β hairpins. The β strand–helix motif with the Type II′ β turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101–1112. © 2013 Wiley Periodicals, Inc.     

“Infant Mortality in Armenia 1992–2003”: A comment

The purpose of this comment is to counsel caution in some of the conclusions drawn in an otherwise fine article recently published in Economics and Human Biology on infant mortality in Armenia by Hakobyan, Mkrtchyan and Yepiskoposyan. These relate first, to the reliability of estimates and trends in infant mortality estimated from DHS data; second, to the interpretation of what the authors consider to be a ‘low’ infant mortality rate in former communist countries given their level of economic development; and third, to the role of the health care infrastructure in countries of the former Soviet Union in producing these ‘low’ infant mortality levels. This comment argues that trends in infant mortality in Armenia and other CIS countries, although probably declining, are perhaps less certain than the authors allow, that existing evidence does not suggest that they are uniformly low by global standards, or that the health care systems in CIS countries are uniformly effective in reducing infant deaths.     

Preliminary Observations on the Nature,Taxonomic Composition,Distribution, Behaviour and Nutrient Requirements of the “Unusual” Algal “Jellies” of Oguta Lake in Southeastern Nigeria

Preliminary observations were made between October 1982 and May 1983 on the nature, taxonomic composition, spatial distribution, buoyancy behaviour and nutrient requirements of some unusual planktonic algal “jellies” in Oguta Lake in Southeastern Nigeria. These “jellies” are macroscopic, blue-green algal masses whose excessive mucilage of high consistency acts as substrata for other epiphytic components viz. diatoms and green algae. They are more abundant in the lentic areas of the lake, undergo diurnal vertical movements and have their growth enhanced by spikes of nitrogen and phosphorus salts into their aquatic medium. The effects of these “jellies” on the ecology and general water use of the lake are discussed. Speculations on the reasons for their occurrence are given and possible control measures outlined.     

The significance of Aleš Hrdlička's “Neanderthal phase of man”: A historical and current assessment

Ale? Hrdli?ka's hypothesis on a Neandertal phase of human evolution is examined in light of current data and interpretations on Neandertals. Hrdli?ka's interpretations are related to his ideas regarding the peopling of the New World. A major early statement of Hrdli?ka's views on Neandertal was his Huxley Memorial Lecture of 1927. We assess this formulation and subsequent development of his hypothesis. Hrdli?ka's position is compared with the “presapiens” and “pre-neandertal” hypotheses on the basis of current theory and data.     

Vocal production in nonhuman primates: Acoustics,physiology, and functional constraints on “honest” advertisement

The physiological mechanisms and acoustic principles underlying sound production in primates are important for analyzing and synthesizing primate vocalizations, for determining the range of calls that are physically producible, and for understanding primate communication in the broader comparative context of what is known about communication in other vertebrates. In this paper we discuss what is known about vocal production in nonhuman primates, relying heavily on models from speech and musical acoustics. We first describe the role of the lungs and larynx in generating the sound source, and then discuss the effects of the supralaryngeal vocal tract in modifying this source. We conclude that more research is needed to resolve several important questions about the acoustics of primate calls, including the nature of the vocal tract's contribution to call production. Nonetheless, enough is known to explore the implications of call acoustics for the evolution of primate communication. In particular, we discuss how anatomy and physiology may provide constraints resulting in “honest” acoustic indicators of body size. © 1995 Wiley-Liss, Inc.     

REPORT OF A NEW INVASIVE ALGA IN THE ATLANTIC UNITED STATES: “HETEROSIPHONIA” JAPONICA IN RHODE ISLAND1

Recent collections of tetrasporangiate “Heterosiphonia” japonica Yendo from Watch Hill to Point Judith, Rhode Island, represent the first report of this nonnative alga in the western Atlantic. Native to the Pacific Ocean, this species was unintentionally introduced into European waters by 1984 and has subsequently invaded the eastern Atlantic Ocean widely from France to Norway and south into the Mediterranean Sea. Thus far, all western Atlantic collections of this species are confined to the outer coast of Rhode Island, and at present are not found in Narragansett Bay or in Long Island Sound along the Connecticut coast. Molecular and morphological studies confirm the identity of this newly introduced invasive species.