Evaluating the effects of urbanisation on salamander abundances using a before‐after control‐impact design

1. Urbanisation represents a significant threat to semi‐aquatic amphibian populations, especially stream‐dwelling salamanders. Although studies of urbanisation effects on amphibians have been conducted, there is an urgent need to follow populations over longer time periods, account for imperfect detection and determine the response time to urbanisation. Consequently, we used a before‐after control‐impact (BACI) study design to estimate changes in abundances of larval and adult salamanders in streams affected by urbanisation. 2. From 2005 to 2009, we used standard sampling techniques to obtain a count of salamanders in 13 first‐order streams that underwent urbanisation of their catchments after the first year of sampling. Simultaneously, we counted salamanders in 17 streams that experienced no disturbance within stream catchments. Additionally, we measured environmental variables at each stream. 3. We used Royle’s binomial mixture model to estimate annual mean abundances and individual detection probabilities, and Bayesian inference was used to estimate population parameters for each stage and species. 4. Although mean abundance estimates varied among years in control and urbanised streams, we found that urbanisation had a negative effect on larval and adult salamander abundances. Larval salamander abundances at sites 1 year after urbanisation were significantly lower than abundances from control sites. Abundances of adult two‐lined salamanders (Eurycea cirrigera) at urbanised sites were lower than abundances at control sites 2 years post‐urbanisation, and adult dusky salamander (Desmognathus fuscus) abundances at urbanised sites were lower than abundances at control sites 3 years post‐urbanisation. Maximum conductivity, sedimentation level and maximum stream channel width differed between urban and non‐urban streams. 5. Our results suggest that stream‐dwelling salamanders exhibit little resistance to urbanisation. Our study also highlights the use of the BACI design to study how urbanisation affects populations in semi‐aquatic habitats. We emphasise that inferences regarding urbanisation effects on population response may be compromised unless urban populations are compared to populations in control sites, especially for species in which populations fluctuate.     

Prey-Dependent Cell Size In A Protozoan Predator*

SYNOPSIS. the cell size of Didinium nasutum was found to be dependent on the size of the Paramecium species available as prey. Didinium feeding on P. tetraurelia averaged 5.6 × 10⁵μm³. the cell volume of Didinium increased with increasing prey size for the 5 prey species tested, to 9.1 × 10⁵μm³ for Didinium feeding on P. caudatum. Didinium nearing a cell division ranged in size from 8.6 × 10⁵μm³ on P. tetraurelia to 12.9 × 10⁵μm³ on P. caudatum. the range in cell volume is such that Didinium feeding on P. caudatum are larger than the size at which Didinium divide when feeding on P. tetraurelia. This morphologic plasticity in cell volume allows Didinium to exploit a wide size range of Paramecium species as prey. It is proposed that the size of a Didinium may have profound effects on its ability to encounter and capture prey of different sizes.     

Genetically and geographically isolated lineages of a tropical bat (Chiroptera: Molossidae) show demographic stability over the late Pleistocene

The newly described molossid bat, Chaerephon atsinanana Goodman et al., 2010, endemic to eastern Madagascar, shows notably high levels of phylogeographic and genetic structure compared with allopatric Chaerephon leucogaster Grandidier, 1869 from western Madagascar. Such highly significant structuring of haplotypes among altitudinally and latitudinally stratified population groups is contrary to the expected panmixia in strong flying bats. The null model of concordance in historical demographic patterns across these two Chaerephon species was not supported. Mismatch and Bayesian skyline analyses indicated ancient stable C. atsinanana populations of constant size during the last two major Pleistocene glacial periods, making retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure, in accordance with expectations for tropical bats. Analyses were consistent with post‐refugial population expansion in the less diverse and structured C. leucogaster during the end of the last Pleistocene glacial period. We hypothesise that the pronounced genetic structuring in C. atsinanana may result from female philopatry. Furthermore, differing demographic histories of the two species may have been shaped by differing climate or habitat preferences, consistent with evidence from MaxEnt ecological niche modelling, which shows differences in variables influencing the current predicted distributions. Fossil Quaternary pollen deposits further indicate greater stability in past climatic patterns in eastern versus western Madagascar. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 18–40.     

P-values for group sequential testing

Group sequential testing procedures are widely employed in long-termclinical trials. We discuss several methods for computing theP-value following a group sequential trial based on differentoutcome-space orderings. We use a criterion defined in thispaper to compare these methods and point out interesting differences.     

Isolation and characterization of 13 polymorphic microsatellite loci for the Florida pompano,Trachinotus carolinus

Here we describe 13 polymorphic, dinucleotide microsatellite loci for Trachinotus carolinus (Florida pompano), isolated by using PIMA, a polymerase chain reaction‐based technique. The number of alleles at each locus ranged from 3 to 29 (mean = 11.4) in 45 specimens collected from bay and nearshore waters around St Petersburg, Florida. Levels of expected and observed heterozygosities ranged from 0.15 to 0.94 (mean = 0.69) and from 0.16 to 0.98 (mean = 0.70), respectively. No significant departures from Hardy–Weinberg equilibrium expectations were observed. In exact tests for genotypic disequilibrium, there was no evidence of linkage for any pair of loci. The ability of these markers to cross‐amplify in two congeneric Trachinotus species —T. falcatus (permit) and T. goodei (palometa) — was also assessed. The loci were well‐resolved, highly polymorphic, and independently segregating in these taxa, also suggesting a general utility for intraspecific studies, species identification, and investigation of interspecific hybridization.     

Upwind Movement of Achenes of Centaurea eriophora L. on the Ground

The lightly compressed achenes of Centaurea eriophora L. beara pappus composed of stiff bristles at their apex and have anelaiosome appendage at their base. The pappus is ineffectivein keeping the achene wind-borne but does serve to regulatethe movement of the achene on the ground in response to wind.In wind the achene swivels like a weather vane with the baseof the achene pointing into the wind. In weak wind the pappusbristles prevent the achene from blowing away. In stronger windthe bristles move due to their flattened, flexible, hinge-likebases and act like ratchets against the substratum, thus enablingthe achene to move upwind. In either case achenes remain ingroups. Ants are attracted to the elaiosome and disperse theachenes. Wind-induced movement was explored by testing acheneson various substrata in a wind tunnel at free-stream speedsbetween 2 and 7 m s^-1. Wind dispersal; Centaurea eriophora ; seeds; achenes     

Overcoming the issue of small sample sizes in fragmentation genetics

Nazareno & Jump (2012) highlight potential issues with using small sample sizes in population genetic studies. By reanalysing allelic richness data from our recent publication on habitat fragmentation (Struebig et al. 2011), they assert that the observed relationship has been driven by three sites with the lowest number of individuals sampled. While sample size issues have been raised before in the genetic literature, Nazareno & Jump’s (2012) comment serves as a useful reminder to us all. Nevertheless, we disagree that our findings were significantly biased by sampling limitations. Here, we demonstrate by jackknifing that, contrary to the claims of Nazareno & Jump (2012), our correlations of allelic richness and fragment area are not driven solely by sites with low sample sizes. We maintain that small sample sizes can be accounted for in fragmentation studies and that sampling limitations should not detract from undertaking conservation genetic research.     

Population Indices Versus Correlated Density Estimates of Black-Footed Ferret Abundance

ABSTRACT Estimating abundance of carnivore populations is problematic because individuals typically are elusive, nocturnal, and dispersed across the landscape. Rare or endangered carnivore populations are even more difficult to estimate because of small sample sizes. Considering behavioral ecology of the target species can drastically improve survey efficiency and effectiveness. Previously, abundance of the black-footed ferret (Mustela nigripes) was monitored by spotlighting and generating indices of relative abundance because reintroduced populations were slow to establish. Indices, however, lack variance estimates and are costly to generate for the black-footed ferret. We therefore used spotlight surveys and live-trapping in conjunction with a robust mark-recapture estimator to improve abundance monitoring for the black-footed ferret, one of North America's most endangered carnivores. We estimated abundance of the black-footed ferret at Shirley Basin, Wyoming, USA, using correlated density estimates and Program MARK. We compared our results to 2 indices of relative abundance, minimum number alive and predicted number of ferrets from litter counts. The correlated density estimate for the black-footed ferret (N̂_R = 229; 95% CI = 161–298) was similar to minimum number alive (N̂_R = 192) and predicted number of ferrets from litter counts (N̂_R= 235). The efficiency and effectiveness of survey methods we used for the black-footed ferret were high by carnivoran standards. Our results suggest that the sampling approach we utilized can be implemented for a fraction of the cost and effort required to generate 2 indices of relative abundance for the black-footed ferret. Although we recommend managers implement a similar survey approach to monitor abundance of reintroduced populations of the black-footed ferret, analysis with sparse data sets will be problematic. Until the black-footed ferret becomes widespread and abundant at a reintroduction site, spotlighting will remain preferable as a means to generate indices of distribution and relative abundance for the black-footed ferret.     

New Zealand phylogeography: evolution on a small continent

New Zealand has long been a conundrum to biogeographers, possessing as it does geophysical and biotic features characteristic of both an island and a continent. This schism is reflected in provocative debate among dispersalist, vicariance biogeographic and panbiogeographic schools. A strong history in biogeography has spawned many hypotheses, which have begun to be addressed by a flood of molecular analyses. The time is now ripe to synthesize these findings on a background of geological and ecological knowledge. It has become increasingly apparent that most of the biota of New Zealand has links with other southern lands (particularly Australia) that are much more recent than the breakup of Gondwana. A compilation of molecular phylogenetic analyses of ca 100 plant and animal groups reveals that only 10% of these are even plausibly of archaic origin dating to the vicariant splitting of Zealandia from Gondwana. Effects of lineage extinction and lack of good calibrations in many cases strongly suggest that the actual proportion is even lower, in keeping with extensive Oligocene inundation of Zealandia. A wide compilation of papers covering phylogeographic structuring of terrestrial, freshwater and marine species shows some patterns emerging. These include: east–west splits across the Southern Alps, east–west splits across North Island, north–south splits across South Island, star phylogenies of southern mountain isolates, spread from northern, central and southern areas of high endemism, and recent recolonization (postvolcanic and anthropogenic). Excepting the last of these, most of these patterns seem to date to late Pliocene, coinciding with the rapid uplift of the Southern Alps. The diversity of New Zealand geological processes (sinking, uplift, tilting, sea level change, erosion, volcanism, glaciation) has produced numerous patterns, making generalizations difficult. Many species maintain pre‐Pleistocene lineages, with phylogeographic structuring more similar to the Mediterranean region than northern Europe. This structure reflects the fact that glaciation was far from ubiquitous, despite the topography. Intriguingly, then, origins of the flora and fauna are island‐like, whereas phylogeographic structure often reflects continental geological processes.