Simultaneous cloning of multiple nuclear genes by pooling PCR products of variable size: a cost‐effective method of improving efficiency in large‐scale genetic analyses

I present a simple approach to overcome the high cost and low efficiency of cloning polymerase chain reaction (PCR) products for individuals in wide‐scale population genetic analyses. The methodology reduces the number of cloning reactions per individual by engineering a suite of genetic markers that differ in size and pooling these PCR products prior to cloning. Alleles from each gene are then recovered by screening transformed bacterial colonies and identifying the inserts corresponding to each gene based on size. I demonstrate the utility of this technique by presenting the results I obtained from cloning four nuclear genes in 118 individuals from three species of sea urchins (Strongylocentrotus purpuratus, S. droebachiensis and S. pallidus). Of the 472 different PCR products I cloned, I recovered at least one allele for 432 of them (91.5%) by screening between 16 and 32 bacterial colonies for each individual. There existed a bias with respect to recovery efficiency: the two largest fragments (1130–800 bp) were recovered 100% of the time, while the two smaller fragments (580–650 bp) were recovered in 85.6% and 81.4% of the experiments, respectively. I discuss the promise of this application for wide‐scale genetic analyses.     

Carbon allocation in boreal black spruce forests across regions varying in soil temperature and precipitation

A common hypothesis for northern ecosystems is that low soil temperatures inhibit plant productivity. To address this hypothesis, we reviewed how separate components of ecosystem carbon (C) cycling varied along a soil temperature gradient for nine well-drained, relatively productive boreal black spruce ( Picea mariana Mill. [B.S.P.]) forests in Alaska, USA, and Saskatchewan and Manitoba, Canada. Annual soil temperature [expressed as soil summed degree days (SDD)] was positively correlated with aboveground net primary productivity (ANPP), while negatively correlated with total belowground carbon flux (TBCF). The partitioning of C to ANPP at the expense of root processes represented a nearly 1 : 1 tradeoff across the soil temperature gradient, which implied that the amount of C cycling through these black spruce ecosystems was relatively insensitive to variation in SDD. Moreover, the rate at which C accumulated in the ecosystem since the last stand replacing fire was unrelated to SDD, but SDD was positively correlated to the ratio of spruce-biomass : forest-floor-mass. Thus, plant partitioning of C and the distribution of ecosystem C were apparently affected by soil temperature, although across regions, precipitation co-varied with soil temperature. These two factors likely correlated with one another because of precipitation's influence on soil heat balance, suggesting that a soil temperature–precipitation interaction could be responsible for the shifts in C allocation. Nonetheless, our results highlight that for this boreal ecosystem, ANPP and TBCF can be negatively correlated. In tropical and temperate forests, TBCF and ANPP have been reported as positively correlated, and our results may reflect the unique interactions between soil temperature, forest floor accumulation, rooting depth, and nutrient availability that characterize the black spruce forest type.     

The role of leaf wounding and an epigeal predator on caterpillar damage to tomato plants

The effects of leaf wounding and the presence of a New Zealand carabid predator, Megadromus antarcticus, on the mortality of, and leaf damage caused by, Spodoptera litura on tomatoes were examined in glass houses. The presence of the non-climbing carabid increased S. litura mortality with a subsequent decrease in leaf damage. Leaf wounding produced a possible decrease in herbivory but did not affect S. litura mortality. Neither leaf wounding or the presence of carabids affected the vertical distribution of leaf damage on the tomato plants. The role of M. antarcticus as a biocontrol agent for tomato pests in New Zealand is briefly discussed.     

Historical influences on genital morphology among sympatric species: gonopod evolution and reproductive isolation in the crayfish genus Orconectes (Cambaridae)

Freshwater crayfishes represent an incredibly diverse component of temperate aquatic ecosystems. The genus Orconectes (Cambaridae) comprises approximately 17% of total global crayfish diversity and is native to central and eastern North America. Using both Bayesian and parsimony-based phylogenetic hypotheses from complete cytochrome c oxidase subunit I (COI) mtDNA sequence data (1545 bp) along with information on male gonopod shape and species distribution patterns, we examined the evolution of male genital morphology and its potential influence on species co-occurrence. We found that sympatric species exhibited similar male genital morphology more often than expected based on the frequency of genital shapes within the genus. When evolutionary history was incorporated into this analysis, the result was no longer significant, suggesting that species co-occurrence and the associated genital shapes of sympatric congeners cannot be explained solely by interspecific ecological interactions. Our results also do not support the current subgeneric classifications within Orconectes or the monophyly of the genus, both of which have been based previously on male genital morphology.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 1–12.     

Modulation of syllable period‐selective phonotaxis by prothoracic neurones in crickets (Acheta domesticus): juvenile hormone,picrotoxin and photoinactivation of the ON1 neurones

Abstract In response to model calling songs (CSs), the phonotaxis of female Acheta domesticus ranges from being very selective to unselective. Within 15 min of nanoinjecting juvenile hormone III (JHIII) or picrotoxin (PTX) into the prothoracic ganglion, females become more selective for syllable period (SP) than in pre‐tests. Controls for JHIII experiments, including nanoinjection of acetone into the prothoracic ganglion or nanoinjection of JHIII into the metathoracic ganglion, do not influence selectivity. Similarly, nanoinjection of saline into the prothoracic ganglion and nanoinjection of PTX outside of the prothoracic ganglion does not change the overall selectivity of the female’s phonotaxis. These results indicate that circuits in the prothoracic ganglion modulate the SP‐selectivity of phonotaxis. Photoinactivating both of the ON1 prothoracic auditory interneurones in old females that were previously unselective for SP also results in greater SP‐selectivity during phonotaxis. Evidence suggesting that ON1 has this effect via its inhibitory input to L3 (another prothoracic auditory neurone) includes: photoinactivation of one ON1 neurone causes angular errors in the female’s orientation to CSs at 85 dB (above the threshold of the L3), stimulation with 60 dB CSs (above the threshold of ON1 but below the threshold of L3) does not induce errors in angular orientation, inactivation of ON1 in old crickets results in greater angular errors (85 dB stimulus) than it does when ON1 is inactivated in young females, and photoinactivation of ON1 increases the firing rate of the L3 neurone.     

A NEW SEA SPIDER (ARTHROPODA: PYCNOGONIDA) WITH A FLAGELLIFORM TELSON FROM THE LOWER DEVONIAN HUNSRÜCK SLATE, GERMANY

Abstract:  A new Lower Devonian sea spider (Arthropoda: Pycnogonida) from the Hunsrück Slate, Germany, is described as Flagellopantopus blocki gen. et sp. nov. This is only the sixth fossil pycnogonid species to be described. Its most remarkable and unique aspect is the long, flagelliform telson. Although our fossil apparently lacks chelifores (an apomorphy), the retained telson and the segmented trunk end behind the last pair of legs resolve F. blocki to a fairly basal position in the pycnogonid stem lineage. It probably lies between Palaeoisopus problematicus Broili, which has a lanceolate telson and the most trunk segments of any sea spider, and all other Silurian–Recent Pycnogonida. Our new material shows that at least two fossil pycnogonids retained a telson, albeit with very different morphologies, and further supports the idea that a greater diversity of body plans existed among the Palaeozoic pycnogonid taxa.     

Locus effects and sources of error in noninvasive genotyping

In spite of more than a decade of research on noninvasive genetic sampling, the low quality and quantity of DNA in noninvasive studies continue to plague researchers. Effects of locus size on error have been documented but are still poorly understood. Further, sources of error other than allelic dropout have been described but are often not well quantified. Here we analyse the effects of locus size on allelic dropout, amplification success and error rates in noninvasive genotyping studies of three species, and quantify error other than allelic dropout.     

STRATOCLADISTICS AND EVALUATION OF EVOLUTIONARY MODES IN THE FOSSIL RECORD: AN EXAMPLE FROM THE AMMONITE GENUS SEMIFORMICERAS

Abstract:  At least two predominating modes of evolution have been proposed for the Early Tithonian oppeliid ammonite genus Semiformiceras , including phyletic transformation of a single lineage ( S. darwini – S. semiforme – S. fallauxi ) and, most recently, a bifurcating or cladogenetic model of speciation. We discuss methodological obstacles in past studies that have focused on specific modes of evolution, and offer a reanalysis of the morphological data first presented by Cecca and Rouget [ Palaeontology , 49 , 1069–1080] using the stratocladistic software StrataPhy. The present analysis utilizes 11 ammonite taxa and 15 characters (14 morphological and one stratigraphic) and assesses all previous phylogenetic hypotheses, including those that recruit OTUs in ancestral or 'nodal' positions, without excluding evolutionary modes. The results cast doubt on the monophyly of S. darwini , S. semiforme and S. fallauxi , but do not follow completely the direct anagenetic progression proposed by stratophenetic hypotheses. We conclude that stratocladistics is a helpful tool for elucidating the extent of anagenesis and cladogenesis in extinct lineages owing to its capacity to reconstruct phylograms in their temporal framework, and to assess the distinctness and monophyly, not just of clades but of the OTUs themselves. Ultimately, this study addresses the novel utility of computer-assisted stratocladistic analysis in assessing evolutionary modes beyond the reach of traditional cladistic-based methodologies.     

Patterns of persistence and isolation indicate resilience to climate change in montane rainforest lizards

Globally, montane tropical diversity is characterized by extraordinary local endemism that is not readily explained by current environmental variables indicating a strong imprint of history. Montane species often exist as isolated populations under current climatic conditions and may have remained isolated throughout recent climatic cycles, leading to substantial genetic and phenotypic divergence. Alternatively, populations may have become contiguous during colder climates resulting in less divergence. Here we compare responses to historical climate fluctuation in a montane specialist skink, Lampropholis robertsi, and its more broadly distributed congener, L. coggeri, both endemic to rainforests of northeast Australia. To do so, we combine spatial modelling of potential distributions under representative palaeoclimates, multi‐locus phylogeography and analyses of phenotypic variation. Spatial modelling of L. robertsi predicts strong isolation among disjunct montane refugia during warm climates, but with potential for localized exchange during the most recent glacial period. In contrast, predicted stable areas are more widespread and connected in L. coggeri. Both species exhibit pronounced phylogeographic structuring for mitochondrial and nuclear genes, attesting to low dispersal and high persistence across multiple isolated regions. This is most prominent in L. robertsi, for which coalescent analyses indicate that most populations persisted in isolation throughout the climate cycles of the Pleistocene. Morphological divergence, principally in body size, is more evident among isolated populations of L. robertsi than L. coggeri. These results highlight the biodiversity value of isolated montane populations and support the general hypothesis that tropical montane regions harbour high levels of narrow‐range taxa because of their resilience to past climate change.