Christopher M. Murray

Parsimony analysis of endemism under the “areas of endemism as individuals” thesis

Cladistic biogeography relies on two operational processes: one that diagnoses fundamental units and another that utilizes them. Discussion of the latter methodology has resulted in numerous protocols (e.g. Nelson and Platnick, 1981; Wiley, 1988; Page, 1990; Nelson and Ladiges, 1991; Brooks et al., 2001; Wojcicki and Brooks, 2005; Eckstut et al., 2011) that hypothesize area relationships based on areas of endemism, which are considered the fundamental units of historical biogeography (Crisci et al., 2003; Crother and Murray, 2011). Methods to diagnose areas of endemism have also been privy to meticulous examination and contested protocol formation (M€ uller, 1973; Rosen, 1988; Axelius, 1991; Crisci et al., 1991; Henderson, 1991; Platnick, 1991; Morrone, 1994). The most notable protocol for diagnosing areas of endemism that emerged from these discussions was parsimony analysis of endemism (PAE). PAE was originally designed by Rosen (1988) and Rosen and Smith (1988) as a method to generate a historical hypothesis of the relationships between the biotas of sampled localities, producing area cladograms (Rosen, 1988). Rosen (1988) also pointed out that PAE results in patterns of endemicity specific to a set study scale comprised of taxonomically incomplete biotas. Morrone (1994) adopted this method for diagnosing areas of endemism using a scale-appropriate, grid-based locality designation. These two functions represent the dynamic (area relationships) versus static (identification of areas of endemism) approaches of the method (Rosen, 1988; Nihei, 2006). Consistent with the method throughout its initial interpretations is the use of areas as operational taxonomic units (OTUs), presence/absence of taxa as characters, and shared biota as synapomorphies between OTUs. Morrone explained the PAE protocol using the distrubution of the beetle genus Sciobius in South Africa. A summary \of this protocol is as follows. 1 Twenty-one quadrats were assigned to the southeastern portion of South Africa in which at least one locality of the focus clade exists (Fig. 1). 2 A data matrix was constructed with species as characters, presence/absence as character states, and quadrats as OTUs with a hypothetical root OTU with all absent taxa. 3 A parsimony analysis of the data matrix was performed (Fig. 2a). Morrone (1994) interpreted his parsimony analysis by recognizing groups of quadrats that are defined by at least two species as areas of endemism. The Sciobius distribution analysis in South Africa recovered three areas of endemism according to Morrone’s (1994) interpretation (Fig. 2a). The distributions of the taxa delimited in the cladogram were then superimposed on a map to delineate the boundaries of the areas of endemism.

Can Reproductive Allometry Assess Population Marginality in Crocodilians? A Comparative Analysis of Gulf Coast American Alligator (Alligator mississippiensis) Populations

This study uses the American Alligator (Alligator mississippiensis) to assess the use of reproductive allometry as a tool to infer crocodilian population marginality based on conformation to advantageous life-history strategies. It is hypothesized that reproductive allometry, a morphometric relationship between mothers size and her reproductive output, varies intraspecifically between populations and that this variation reflects population marginality based on size, stress, temporal exploitation, habitat fragmentation, and/or the presence of social hierarchy. This hypothesis is tested using relative comparisons of allometric correlation between a marginal population inundated with saline storm surge from Hurricane Ike in southeastern Texas and a hypothesized unstressed core population in southeastern Louisiana. Heterophil to lymphocyte ratios fail to falsify the hypothesis of a saline stressor. The number of significant morphometric correlations between various parameters, degree of correlation (R2), and slope of correlation between mother and her respective nest and clutch varied greatly between study sites. Reproductive allometry, as a measure of relative population marginality, may provide a cost effective way to prioritize management with local support for crocodilian taxa.

Sexual Kidneys in the Red-spotted Newt (Notophthalmus viridescens)

Abstract Functional nephrons of the kidney with secondary sexual function are rare in vertebrates and descriptions of these structures do not unequivocally conclude that they aid in reproduction. This statement holds true for the collecting ducts of the pelvic kidneys in male salamanders, which appear to synthesize abundant secretory material during times of reproductive activity. To indirectly test the hypothesis that collecting ducts of the pelvic kidneys in salamanders are indeed secondary sexual structures, we investigated the correlation of collecting duct secretory activity with that of the seasonal secretory and growth cycles of three known secondary sexual structures: genial glands, dorsal glands of the cloaca, and tail. Male Red-spotted Newts (Notophthalmus viridescens) were captured every month and their urogenital organs were processed for general histological examination. To quantify the seasonal activity of the pelvic kidney collecting ducts, we measured the epithelial height of the collecting ducts, by month, and compared these data with the epithelial heights of the genial glands and dorsal glands and tail depth. The data indicate that there is a significant correlation between the seasonal secretory activity of the collecting duct epithelium and the seasonal activity of previously identified secondary sexual structures. Previously identified secondary sexual structures increase in epithelial height and tail height during the fall, winter, and spring and the collecting duct epithelium mirrors these increases directly. The strength of this correlation provides novel evidence that the salamander kidney collecting ducts may function as secondary sexual structures. However, the actual function of the secretions remains unknown.

Cohort-Dependent Sex Ratio Biases in the American Crocodiles (Crocodylus acutus) of the Tempisque Basin

A male-biased sex ratio of 3:1 has been reported for a population of American crocodiles (Crocodylus acutus) in the Tempisque River Basin, Guanacaste, Costa Rica. If confirmed, this would constitute one of the largest male-biased sex ratios reported for any population of a member of the genus Crocodylus. Here, we examine the aforementioned population of C. acutus and report on sex ratios of hatchling, juvenile, and adult age classes within a sample of 474 crocodiles captured in the Tempisque Basin between May 2012 and June 2014. Hatchling sex ratio is exceptionally male biased (3.5:1), an imbalance that is maintained in juveniles but is reduced in adults (1.5:1). Mark–recapture data document that juvenile males disperse from the study site, potentially to avoid competition, a process that reduces male bias in the adult age class. An increased role of males in human–crocodile conflict may be a result of juvenile males dispersing to human-inhabited areas.

The sexual segment of Hemidactylus turcicus and the evolution of sexual segment location in squamata.

The kidneys of the Mediterranean Gecko, Hemidactylus turcicus (Gekkonidae), were investigated using light and electron microscopy with the primary focus placed on morphology of the sexual segment of the kidney. The nephrons of male H. turcicus are composed of five distinct regions: 1) a renal corpuscle and glomerulus, 2) a proximal convoluted tubule, 3) an intermediate segment, 4) a distal convoluted tubule, and 5) the sexual segment of the kidney/collecting duct. Female H. turcicus is similar but lack a sexual segment of the kidney. The sexual segment of the kidney is hypertrophied during the months of March through August, which corroborates previous reports of reproductive activity. During inactive months, the sexual segment of the kidney is nondiscernable from the collecting ducts. The sexual segment consists of tall columnar epithelial cells with basally positioned nuclei. Perinuclear Golgi complexes and rough endoplasmic reticulum are present. Secretory granules, which fill the apices of the epithelial cells, are electron dense and released into the lumen by a merocrine secretory process. Narrow intercellular canaliculi separate each epithelial cell and are sealed by tight junctions at the luminal aspect. Basally, leukoctyes are observed within the intercellular canaliculi and outside the basal lamina. Mast cells can be found just outside the basal lamina in close association with renal capillaries. The sexual segment of the kidney of H. turcicus is similar to that of three unrelated lizards for which ultrastructure was investigated with secretion mode being the major difference Also, H. turcicus is similar to most other lizards in that complete regression occurs during reproductive inactivity, but differs in this trait from the skink, Scincella lateralis, and most snakes which display a hypertrophied sexual segment of the kidney throughout the entire year. Although some unique similarities appear during the optimization, no direct patterns or directions are observed, and only the molecular based phylogeny resolves the ancestral condition of the Squamata as the sexual segment of the kidney being observed in the distal convoluted tubule, collecting duct, and ureter. J. Morphol., 2011.

Testable but not falsifiable

We are puzzled by a recent comment that suggested that historical hypotheses can be tested but are unfalsifiable. We argue that phylogenetic hypotheses are falsifiable without the aid of a time machine and that they are like any other hypothesis: they are tentative knowledge propositions capable of falsification with character evidence.

Salinity and Egg Shape Variation: A Geometric Morphometric Analysis

Abstract The harvest and incubation of American Alligator (Alligator mississippiensis) eggs is an important component to the commercial alligator harvest industry in the southeastern United States. As a result, various methodologies have been used to monitor alligator populations including abundance counts, stress quantification, and nesting surveys. Past studies have dismissed the importance of egg shape in crocodilians, Squamates, and turtles and deemed egg shape in birds and other amniotes as similar, in relation to functionality. The complexity of crocodilian eggs has been examined, and both turtle and Squamate eggs have been regarded recently as physiologically more intricate than bird eggs. This study introduces a physiological approach to monitor alligator populations in freshwater and low salinity environments by quantifying egg shape in correlation with varying salinity. We introduce a fractional semilandmark-shape template method to quantify egg shape within a geometric morphometric framework. This approach is beneficial because it allows for the quantification of shape for curved structures, such as eggs, which lack homologous landmarks. The results from this study suggest that alligator egg shape is correlated with varying salinity levels, such that variation in alligator egg shape at low salinities changes in gradient-like fashion, whereas salinities high enough to be deemed stressful result in reversion back to a low salinity egg shape or desiccation. This study elucidates a correlation that can be implemented in management and breeding techniques and opens the door to in-depth physiological examination of the system.

Regional warming and the thermal regimes of American crocodile nests in the Tempisque Basin, Costa Rica

Spatial variation in global climate change makes population-specific responses to this enigmatic threat pertinent on a regional scale. Organisms with temperature-dependent sex determination (TSD) potentially possess a unique physiological susceptibility that threatens population viability if rapid environmental effects on sex ratios render populations non-viable. A heavily male-biased sex ratio for hatchling American crocodiles of the Tempisque Basin, Costa Rica requires assessment of how nest temperature affects sex determination at this site, how females might compensate for these effects when creating nests, and how current patterns of climate change might alter future sex ratios and survival in hatchling cohorts. We demonstrate high within-nest variation in temperature but predict a female bias at hatching based on nest temperatures quantified here. Further, our data suggest that egg size and metabolic heating associated with this factor outweighs microhabitat parameters and depth in influencing nest thermal regimes. Finally, we document regional warming in the Tempisque Basin over the last 15 years and project that further heating over the next 15 years will not yield hatchling sex ratios as male biased as those currently found at this site. Thus, we find no support for nest temperature or climate change as likely explanations for male-biased American crocodile (Crocodylus acutus) sex ratios in the Tempisque Basin.

Methyltestosterone alters sex determination in the American alligator (Alligator mississippiensis).

Effects of xenobiotics can be organizational, permanently affecting anatomy during embryonic development, and/or activational, influencing transitory actions during adulthood. The organizational influence of endocrine-disrupting contaminants (EDCs) produces a wide variety of reproductive abnormalities among vertebrates that exhibit temperature-dependent sex determination (TSD). Typically, such influences result in subsequent activational malfunction, some of which are beneficial in aquaculture. For example, 17-αmethyltestosterone (MT), a synthetic androgen, is utilized in tilapia farming to bias sex ratio towards males because they are more profitable. A heavily male-biased hatchling sex ratio is reported from a crocodile population near one such tilapia operation in Guanacaste, Costa Rica. In this study we test the effects of MT on sexual differentiation in American alligators, which we used as a surrogate for all crocodilians. Experimentally, alligators were exposed to MT in ovo at standard ecotoxicological concentrations. Sexual differentiation was determined by examination of primary and secondary sex organs post hatching. We find that MT is capable of producing male embryos at temperatures known to produce females and demonstrate a dose-dependent gradient of masculinization. Embryonic exposure to MT results in hermaphroditic primary sex organs, delayed renal development and masculinization of the clitero-penis (CTP).

Entities on a Temporal Scale

Ontological understanding of biological units (i.e. what kinds of things are they) is crucial to their use in experimental design, analysis, and interpretation. Conceptualizing fundamental units in biology as individuals or classes is important for subsequent development of discovery operations. While the criteria for diagnosing individuals are acknowledged, temporal boundedness is often misinterpreted and temporal minima are applied to units in question. This results in misdiagnosis or abandonment of ontological interpretation altogether. Biological units such as areas of endemism in biogeography and species in evolutionary biology fall victim to such problems. Our goal here is to address the misconception that biological individuals such as species and areas of endemism have a temporal minimum. Areas of endemism can persist within small temporal boundaries in the context of metapopulation dynamics, island biogeography, and range expansion and contraction. Similarly, lineage reticulation illustrates examples of short-lived species. Here, examples of known entities are provided to illustrate their persistence on short time scales in attempt to rescue future interpretation of biological units from ontological misdiagnosis, elucidate the philosophical individuality of areas of endemism and species with short lifespans, and provide justification for the “snapshot in time” diagnostic approach.