Universal primer cocktails for fish DNA barcoding

Reliable recovery of the 5′ region of the cytochrome c oxidase 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all fish species. In this study, we develop and test primer cocktails with a view towards increasing the efficiency of barcode recovery. Specifically, we evaluate the success of polymerase chain reaction amplification and the quality of resultant sequences using three primer cocktails on DNA extracts from representatives of 94 fish families. Our results show that M13‐tailed primer cocktails are more effective than conventional degenerate primers, allowing barcode work on taxonomically diverse samples to be carried out in a high‐throughput fashion.     

Fat frogs,mobile genes: unexpected phylogeographic patterns for the ornate chorus frog (Pseudacris ornata)

The southeastern coastal plain of the United States is a region marked by extraordinary phylogeographic congruence that is frequently attributed to the changing sea levels that occurred during the glacial‐interglacial cycles of the Pleistocene epoch. A phylogeographic break corresponding to the Apalachicola River has been suggested for many species studied to date that are endemic to this region. Here, we used this pattern of phylogeographic congruence to develop and test explicit hypotheses about the genetic structure in the ornate chorus frog (Pseudacris ornata). Using 1299 bp of mtDNA sequence and seven nuclear microsatellite markers in 13 natural populations of P. ornata, we found three clades corresponding to geographically distinct regions; one spans the Apalachicola River (Southern Clade), one encompasses Georgia and South Carolina (Central Clade) and a third comprises more northerly individuals (Northern Clade). However, it does not appear that typical phylogeographic barriers demarcate these clades. Instead, isolation by distance across the range of the entire species explained the pattern of genetic variation that we observed. We propose that P. ornata was historically widespread in the southeastern United States, and that a balance between genetic drift and migration was the root of the genetic divergence among populations. Additionally, we investigated fine‐scale patterns of genetic structure and found the spatial scale at which there was significant genetic structure varied among the regions studied. Furthermore, we discuss our results in light of other phylogeographic studies of southeastern coastal plain organisms and in relation to amphibian conservation and management.     

Behaviour, home-range size and habitat use by male Great Bittern Botaurus stellaris in Britain

This paper describes the first use of radiotracking to follow closely the secretive Great Bittern Botaurus stellaris , and to quantify its reedbed habitat preferences at a fine scale. Eight males were tracked at two sites in Britain, at which they were mainly resident through the winter. Their median home-range sizes were 14.6, 19.3 and 33.1 ha during the booming, moult and winter periods, respectively, and home-ranges were, on average, composed of 30% open pools and 48% reedbed edge (of 30 m width). Great Bitterns were most often active in reed with 20 cm water depth within the 30-m reed edge next to water, whereas areas of reedbed near scrub or further from the water's edge were avoided. Reed edge adjacent to open pools was preferred over that adjacent to channels and ditches. These results provide a basis for conservation recommendations on the quantity and composition of reedbed habitat and provide the scientific basis for a national programme of reedbed rehabilitation and restoration.     

Demography of Ferruginous Hawks Breeding in Western Canada

Abstract: We assessed age-dependent survival, site-fidelity, and, together with data on prey and reproduction, trends in the population of ferruginous hawks (Buteo regalis) breeding in western Canada. Our analysis included 7,129 ferruginous hawks banded near Hanna, Alberta, and Kindersley-Alsask, Saskatchewan, from 1972 to 2003. We estimated annual adult survival rate to be 0.708 (SE = 0.024) and first year survival for nestlings was 0.545 (SE = 0.147). Resighting probability was modeled as a constant for nestlings (0.009, SE = 0.010), but it varied among years for adults consistent with our sampling efforts. Band reporting rate was at 0.022 (SE = 0.007) for both nestlings and adults. Fidelity to the study site was 1.00 (SE = 0.000) for adults and 0.035 (SE = 0.014) for nestlings. Nesting density ranged from 3.1 to 14.0 pairs/100 km² and averaged 9.8 pairs/100 km². We observed an average clutch size of 3.2 (SE=0.06) and brood sizes of 2.71 (SE=0.07) near Hanna and 2.79 (SE = 0.99) at Kindersley-Alsask. Richardson's ground squirrels (Spermophilus richardsonii) made up 95% of ferruginous hawk prey. Prey availability was positively correlated with number of offspring near Hanna and Kindersley-Alsask. We believe the lower than expected adult survival did not result in population decrease; rather, declines in reproduction resulting from declines in the abundance of ground squirrels better explain an observed 4.5-fold decline in nesting densities during the study. The results suggest that ferruginous hawk management should address prey in addition to habitat management, and that management needs are regional in scope with particular emphasis on the breeding range within the northern Great Plains.     

A phylogeny of the families of fossil and extant tetraodontiform fishes (Acanthomorpha, Tetraodontiformes), Upper Cretaceous to Recent

A data matrix is presented of 210 morphological characters (mostly osteological, some external) for 20 extant taxa of the ten Recent families of tetraodontiform fishes and 36 fossil tetraodontiforms. The oldest of these are from the Upper Cretaceous (95 Mya); most are from the Lower to Middle Eocene (50–58 Mya). There are two outgroup taxa (a zeiform and a caproid). A cladistic analysis of this matrix for only the extant taxa produced two equally parsimonious trees that call into question the monophyly of some of the previously accepted major higher-level tetraodontiform clades. Inclusion in the analysis of the large number of available fossil taxa helps to resolve relationships between family level clades. The new phylogenetic hypothesis, together with stratigraphic and biogeographical data, is used to discuss scenarios of the origin and evolution of the major clades of the order.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 565−617.     

Influence of Soil Moisture on Soil Solution Chemistry and Concentrations of Minerals in the Calcicoles Phleum phleoides and Veronica spicata Grown on a Limestone Soil

Veronica spicata and Phleum phleoides are calcicole plants,mainly occurring on neutral or alkaline soil. An experimentof 16 weeks duration was performed in a glasshouse with theobjective of elucidating the influence of soil moisture levelon soil solution chemistry, and biomass concentrations and uptakeof mineral nutrients by the plants. Seven levels of moisture,corresponding to 35–85% of the water holding capacity(WHC) of the soil, were tested. Soil solution HCO₃, P and Mnconcentrations, and pH, increased, whereas Ca, Mg and Zn concentrationsdecreased, with increasing soil moisture. Concentrations ofK were highest at 50–70% WHC. Concentrations and amountsof P, Zn and Mn in the two species were usually related to soilsolution concentrations; these are elements with low solubilityand availability in calcareous soils. Concentrations of nutrientsin biomass were more influenced by soil moisture in V. spicatathan inP. phleoides . This indicates that P. phleoides is morecapable of controlling its uptake of mineral nutrients, whereasV. spicata is sensitive to variations in soil moisture. It isconcluded that variation in soil moisture regime may greatlyinfluence concentrations of mineral nutrients in calcareoussoil solutions and their uptake by plants. Species able to utilizethese solubility fluctuations may have an advantage in competitionfor nutrients. Variation in soil moisture content might evenbe a prerequisite for adequate acquisition of mineral nutrientsand growth of plants on limestone soils, thereby influencingthe field distribution of native plants among habitats. Copyright1999 Annals of Botany Company Calcareous, calcicole, concentration, mineral, moisture, nutrient, Phleum phleoides, soil, soil solution, uptake, Veronica spicata, water.     

Reproduction in marine invertebrates in “stable” environments: the deep sea model

Summary

Studies over the last 15 years have revealed that deep-sea benthic megainvertebrates show a variety of reproductive patterns that are adapted to the deep-sea, an environment in which the fauna occurs at low densities and resources are sparse. In the NE Atlantic the majority of species reproduce year round whilst a limited number of species reproduce on a seasonal basis believed to be entrained by the deposition of surface derived organic material on the deep-sea bed. A third pattern of rapid growth and early reproduction is found in a limited number of species that utilize unpredictable and ephemeral resources in the deep sea. Examination of the fertilization and behavioural biology of species from the bathyal depths suggest some species enhance fertilization success by forming pairs during their breeding season. However, the same concentration of sperm, as seen in shallow water invertebrates, is required for successful fertilization. At least one deep-sea species of echinoid requires high pressure for successful embryogenesis suggesting a depth-related segregation of deep-sea fauna. The origin of megafaunal populations of deep-sea invertebrates in the N. Atlantic is discussed in the light of these new data in relation to varying reproductive patterns and the environmental changes that have occurred during the last deglaciation.     

The distribution of breeding dippers (Cinclus cinclus (L.); Aves) in relation to stream acidity in upland Wales

SUMMARY. 1. The distribution of breeding dippers was assessed in 1984 over seventy-four sites on soft-water streams throughout mid and north Wales.
2. Sites without breeding dippers had significantly higher mean concentrations of filterable aluminium, lower mean pH, fewer trichopteran larvae and ephemeropteran nymphs, and were on rivers with more conifer afforestation on their catchments, than sites where dippers were present.
3. We speculate that influences which increase the acidity of soft-water streams could be detrimental to their populations of dippers, although further data are required on causative mechanisms.