Brian I. Crother

Elevational Patterns of Species Richness, Evenness, and Abundance of the Costa Rican Leaf-Litter Herpetofauna

The abundance, species richness, and evenness of the Costa Rican leaf-litter herpetofauna was estimated during the late wet season of 1985 by quantitative sampling of replicate plots at ten sites encompassing an elevation range of 3 to 1670 m. Species richness was positively correlated with leaf-litter depth, and negatively correlated with elevation. Herpetofaunal density also tended to increase with litter depth and decline with elevation. A strong positive correlation existed between species richness and herpetofaunal density. Evenness was highly variable and independent of both leaf-litter depth and elevation. Analysis of a subset of the data, representing an elevational transect from Tortuguero to the Braulio Carrillo National Park Extension, yielded similar results. Tropical leaf-litter reptiles and amphibians appear to be both more diverse and more abundant at lower elevations. Sites with deep leaf litter generally sustain dense and diverse reptile and amphibian populations. Local herpetofaunas typically consist of a few very common species along with a large number of comparatively rare species. REPTILES AND AMPHIBIANS are a major constituent of the fauna inhabiting tropical forest litter. Studies of tropical leaf-litter herpetofaunas have emphasized patterns of abundance and distribution among geographic regions (Lloyd et al. 1968; Heyer & Berven 1973; Scott 1976, 1982; Inger 1980a, b; Heatwole 1982), vegetational zones (Brown & Alcala 1961, Heatwole & Sexton 1966, Heyer 1967), and elevational gradients (Brown & Alcala 1961, Scott 1976) as well as seasonal changes (Lieberman 1982, 1986). It has become generally accepted that leaf-litter reptiles and amphibians are more abundant in the New World Tropics than in Southeast Asia (Scott 1976, Inger 1980b, Duellman & Trueb 1986) although the exact reason remains a subject of debate (May 1980). Similarly, the general consensus is that the abundance of tropical leaf-litter herpetofaunas increases with increasing elevation, while species richness and equitability both decline (Brown & Alcala 1961, Scott 1976, Heatwole 1982, Duellman & Trueb 1986). Scott (1976) attributed this pattern to greater overall forest productivity at intermediate elevations, coupled with increased densities of the most common species at higher elevations. Before attempting to determine the mechanisms responsible for observed patterns of tropical leaf-litter herpetofaunal abundance and diversity, we must document the phenomenon conclusively. Previous quantitative studies have sampled few sites, have been unable to provide replicated samples (Brown & Alcala 1961), or may have confounded site and year effects by sampling different sites in different years (Scott 1976). We surveyed the Costa Rican leaf-litter herpetofauna by quantitatively sampling replicate plots at ten sites, ranging from 3 to 1670 m in elevation, during the late wet season of July-September 1985. Our sampling strategy permitted statistical analyses to determine the relationship between litter depth and elevation, and leaf-litter herpetofaunal richness, evenness and abundance. The results of our study contradict several of the generally accepted patterns of tropical leaf-litter herpetofaunal abundance and diversity.

Evolution of predetermined germ cells in vertebrate embryos: implications for macroevolution

Summary The germ line is established in animal embryos with the formation of primordial germ cells (PGCs), which give rise to gametes. Therefore, the need to form PGCs can act as a developmental constraint by inhibiting the evolution of embryonic patterning mechanisms that compromise their development. Conversely, events that stabilize the PGCs may liberate these constraints. Two modes of germ cell determination exist in animal embryos: (a) either PGCs are predetermined by the inheritance of germ cell determinants (germ plasm) or (b) PGCs are formed by inducing signals secreted by embryonic tissues (i.e., regulative determination). Surprisingly, among the major extant amphibian lineages, one mechanism is found in urodeles and the other in anurans. In anuran amphibians PGCs are predetermined by germ plasm; in urodele amphibians PGCs are formed by inducing signals. To determine which mechanism is ancestral to the tetrapod lineage and to understand the pattern of inheritance in higher vertebrates, we used a phylogenetic approach to analyze basic morphological processes in both groups and correlated these with mechanisms of germ cell determination. Our results indicate that regulative germ cell determination is a property of embryos retaining ancestral embryological processes, whereas predetermined germ cells are found in embryos with derived morphological traits. These correlations suggest that regulative germ cell formation is an important developmental constraint in vertebrate embryos, acting before the highly conserved pharyngula stage. Moreover, our analysis suggests that germ plasm has evolved independently in several lineages of vertebrate embryos.

Evolution of the germ line-soma relationship in vertebrate embryos

The germ line and soma together maintain genetic lineages from generation to generation: the germ line passes genetic information between generations; the soma is the vehicle for germ line transmission, and is shaped by natural selection. The germ line and somatic lineages arise simultaneously in early embryos, but how their development is related depends on how primordial germ cells (PGC) are specified. PGCs are specified by one of two means. Epigenesis describes the induction of PGCs from pluripotent cells by signals from surrounding somatic tissues. In contrast, PGCs in many species are specified cell-autonomously by maternally derived molecules, known as germ plasm, and this is called preformation. Germ plasm inhibits signaling to PGCs; thus, they are specified cell-autonomously. Germ plasm evolved independently in many animal lineages, suggesting convergent evolution, and therefore it would be expected to convey a selective advantage. But, what this is remains unknown. We propose that the selective advantage that drives the emergence of germ plasm in vertebrates is the disengagement of germ line specification from somatic influences. This liberates the evolution of gene regulatory networks (GRNs) that govern somatic development, and thereby enhances species evolvability, a well-recognized selective advantage. We cite recent evidence showing that frog embryos, which contain germ plasm, have modified GRNs that are not conserved in axolotls, which represent more basal amphibians and employ epigenesis. We also present the correlation of preformation with enhanced species radiations, and we discuss the mutually exclusive trajectories influenced by germ plasm or pluripotency, which shaped chordate evolution.

IS “SOME BETTER THAN NONE” OR DO ALLELE FREQUENCIES CONTAIN PHYLOGENETICALLY USEFUL INFORMATION?

Cladists do not employ continuous characters in cladogram construction because continuous characters do not yield synapomorphic information, the central problem being delineation ofcharacter states along a continuum. This is not to say that data like those derived from morphometric studies do not possess synapomorphic information, on the contrary they surely must, but extraction of synapomorphies from continuous data remains problematic. One type of continuous data that is commonly employed for phylogenetic reconstruction is allele frequencies as derived from protein electrophoresis studies. The continuum ranges from the expression of the allele as fixed within a taxon to the complete absence of expression of the allele. Numerous arguments (e.g. Farris, 1981, 1985) have been presented against the use of allele frequencies in phylogenetic reconstruction, but these have focused mainly on the flaws ofthe particular analytical methods employed for frequency data. The absence of synapomorphy, non-metricity and a clock assumption are some ofthese flaws. Farris (1981 ) also suggested that frequencies were unnecessary in phylogenetic analyses (based on his survey of empirical data, where he noted frequency arrays were either similar between a pair of taxa or were essentially fixed for different alleles) because alleles appeared not to possess information that would alter a set of relationships based only on fixed differences. Farris further contended that allele frequency information was inappropriate for defining relationships, but the inappropriateness was due to the methods of analysis and not to the nature of the data. I suggest in this essay that i t is the nature of allele frequencies that renders the data inappropriate for phylogenetic analysis. Recently, Swofford and Berlocher (1987) presented a parsimony method for employing allele frequency data that addressed the flaws elucidated by Farris (1981). Swofford and Berlocher (1987) defend the inclusion of allele frequency data in phylogenetic analysis because of a large sampling error inherent to presence/absence coding. They demonstrate the error quite clearly and also demonstrate that the inclusion of frequency data sharply reduces the error and thus reduces the probability of erroneously identifying distinct populations (taxa?) when they actually share the allele. Swofford and Berlocher ( 1987) essentially argue that based on the reduction ofsampling error by the inclusion of allele frequencies “some is better than none”. The method is an important advance over distance analyses and as such should be commended. However, the implicit assumption that allele frequencies contribute to, therefore are able to depict, macroevolutionary patterns (phylogenies) needs to be questioned. For this reason I suggest that the continuing focus on methodology (e.g. Rogers, 1986; Swofford and Berlocher, 1987; Krimbas and Sourdis, 1987; Rohlf and Wooten, 1988) for extracting

Expression of Dazl and Vasa in turtle embryos and ovaries: evidence for inductive specification of germ cells.

SUMMARY In bilaterian animals, germ cells are specified by the inductive/regulative mode or the predetermined (germ plasm) mode. Among tetrapods, mammals and urodeles use the inductive mode, whereas birds and anurans use the predetermined mode. From histological data it has been predicted that some reptiles including turtles use the inductive mode. Examining turtle oocytes, we find that Dazl RNA, Vasa RNA, and Vasa protein are not localized, suggesting that germ plasm is not present. In turtle embryos at somite stages, primordial germ cells (PGCs) expressing Dazl lie on a path from the lateral posterior extraembryonic endoderm through the gut to the gonad as previously described. In gastrulating embryos, cells expressing Dazl are found in the blastoporal plate and subsequently below the blastoporal plate, indicating that PGCs are generated at the equivalent of the early posterior primitive streak of mammals. Vasa RNA is expressed in somatic cells of gastrula to early somite stages, and Vasa RNA and protein are expressed in PGCs of later embryos. Taken together the evidence strongly suggests that turtles, and other reptiles (lacertoid lizards) with the same location of PGCs in embryos, use the inductive mode of germ cell specification. Phylogenetic analysis of the available evidence supports the following hypotheses: (1) the inductive mode is basal among reptiles, indicating that this mode was maintained as basal tetrapods evolved to amniotes, (2) the predetermined mode arose twice within reptiles, and (3) the induced mode may be used in several lepidosaurs whose PGCs are located in an unusual pattern distributed around the embryo.

Genetic consequences of population reduction and geographic isolation in the critically endangered frog, Rana sevosa.

Abstract Anthropogenic habitat fragmentation and reduction are major causes of population declines and extinction. As these processes intensify, our ability to rescue imperiled taxa is critically dependent on an understanding of historical, demographic, and genetic parameters of diminishing populations. We assessed the effects of recent geographic isolation and population reduction on genetic variability for endangered Dusky Gopher Frogs, Rana sevosa. Only two populations of R. sevosa exist, each is geographically isolated and restricted to a single breeding pond, and one of them may have gone locally extinct. Therefore, we studied the largest and perhaps only population of R. sevosa. The only option for comparison to non-isolated populations was of its ecologically similar sister species (other Gopher Frogs, R. capito) and of the sister species to R. sevosa and R. capito (Crawfish Frogs, R. areolata). Variation in seven microsatellite DNA loci was assessed for each population to determine the effects of isolation and population bottleneck on R. sevosa. In comparison to the average non-isolated population, R. sevosa had significantly lower genetic variation and a strong signature of population bottleneck. In fact, R. sevosa had HO that was 72%, HE that was 81%, and A that was 61% of the average non-isolated population. Results indicated a severe, negative genetic consequence of recent population reduction and geographic isolation via lack of gene flow, enhanced effects of drift, and inbreeding. Extensive demographic data have been collected for R. sevosa beginning when the species was rediscovered in 1987 and continuing through our study. These previously collected demographic data aid in interpretation of our genetic data and discussion of implications for conservation and management.

Evolution of germ cell development in tetrapods: comparison of urodeles and amniotes

SUMMARY. The embryonic development of germ cells in tetrapods is described, focusing on groups with the inductive mode of germ cell specification. In mammals PGCs are induced early in the gastrulation process, they are internalized with future extraembryonic mesoderm in the early posterior primitive streak, and specified soon thereafter. Strong evidence indicates that a similar process occurs in turtles and some other reptiles. In amniotes, the PGCs appear well before formation of the gonad in the posterior trunk, resulting in a period in which they are located outside the embryo before their migration to the gonad. In contrast, in urodeles the PGCs appear relatively late, and throughout development maintain a position close to precursors of the somatic cells of the gonad so that migration is not required. In lampreys early development of germ cells is strikingly similar to that in urodeles, suggesting this is the primitive process. As amniotes evolved large yolky eggs and better access to nutrition, development of the posterior half of the trunk became more dependent on cell proliferation; this was followed or accompanied by a shift of early germ cell development to the equivalent of the early primitive streak. A similar process may have occurred as some basal vertebrates developed large yolky eggs.

Cloning, nucleotide sequencing and characterization of a polyurethanase gene (pueB) from Pseudomonas chlororaphis

Abstract A second gene (pueB, polyurethane esterase B) encoding an extracellular polyurethanase (PueB) was cloned from Pseudomonas chlororaphis into Escherichia coli. The recombinant polyurethanase showed esterase activity when assayed with various p-nitrophenyl substrates and lipase activity when assayed with triolein. Nucleotide sequencing of pueB showed an open reading frame of 1695 bp encoding a 60-kDa protein of 565 amino acid residues, with the serine hydrolase consensus sequence GXSXG and a C-terminal secretion signal (G-G-X-G-X-D-X-X-X). Unlike the PueA polyurethanase, PueB contains a putative N-terminal signal peptide. Comparison between the amino acid and nucleotide sequences of these two genes revealed that they share 42% and 59% identity respectfully. Parsimony analysis of the predicted amino acid sequences for the PueB, PueA, and other polyurethanase enzymes and similar lipase enzymes was performed. Interestingly the polyurethanase enzymes do not form a single cluster, but appear to be distributed among multiple lineages. These analyses suggest that the polyurethanase enzymes thus far studied have evolved from lipases, and are not derived from a single source.

Effects of hurricanes Ivan, Katrina, and Rita on a southeastern Louisiana herpetofauna

Tropical weather disturbances are a major influence on coastal wetlands in North America. However, studies of their impact on biotic communities are rare. The abundance and species composition of amphibians and reptiles were investigated within levee, herbaceous marsh, and forested swamp habitats in southeastern Louisiana from 2002 to 2004 and again in 2005 to 2006. During the course of this study, three major hurricanes (Ivan, Katrina, and Rita) affected our study sites. This allowed us to opportunistically document the effect of major storm disturbances by comparing species richness, diversity, community assemblage, and abundance of amphibians and reptiles before and after hurricane events. We also used a previous study conducted in the same area during the late 1980’s to assess longterm community composition changes. We documented the highest species richness in the forested swamp habitat (23 species), but the most diverse assemblage was found in marsh habitat (H′ = 2.082). Overall, herpetofaunal diversity decreased and evenness increased in each habitat following hurricanes Ivan and Katrina/Rita. Drastic decreases in overall abundance of amphibians occurred, while the effect on reptile abundance varied with habitat. Reduced abundance of reptiles in marsh was recorded over the course of the study, while abundances in adjacent levee habitat increased, suggesting displacement of certain reptiles from the marsh to the levee. Significant saltwater intrusion was recorded in marsh and levee habitats, but not in the forested swamp. The hurricanes altered community composition and increased species evenness within each habitat, potentially affecting long-term community dynamics and species interactions.

Is the PTP Test Useful

We show empirically that the PTP test has very little discriminatory power, with highly significant PTP test probabilities often being associated with parsimony data that produce trees with low confidence (as measured by bootstrapping) and resolution. Because of this, we argue that the PTP test is useful only in the following, very limited way: if a data set fails the PTP test, it should not be used in a phylogenetic analysis. More conservative methods of measuring confidence such as the bootstrap or decay index are preferable.