Development of EST‐SSRs from the Alpine Lady‐fern,Athyrium distentifolium

The utility of EST‐simple sequence repeats (EST‐SSRs) was evaluated in the fern Athyrium distentifolium. From 1152 frond cDNA clones, 165 microsatellites, including di‐, tri‐, tetra and penta‐nucleotide repeat motifs, were identified. Primer design was possible for 74 of the SSRs; subsequent screening of 10 loci on 186 individuals from six natural populations revealed between two and seven alleles per locus and expected heterozygosity (H_E) estimates ranging from 0.027 to 0.809. Eight of these loci were further examined for cross‐species and cross‐generic amplification in other Woodsiaceae species, and polymorphic products were detected. EST‐derived SSRs provide robust, informative and potentially transferable polymorphic markers suitable for biodiversity research.     

Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions

To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs). Genomic SSRs showed significantly higher levels of allelic diversity than EST-SSRs, but there was a significant correlation in the rank order of population diversities revealed by both marker types. When AFLPs, genomic SSRs, and EST-SSRs are considered, comparisons of different population diversity metrics/markers revealed a mixture of significant and nonsignificant rank-order correlations. However, no hard incongruence was detected (in no pairwise comparison of populations did different marker systems or metrics detect opposingly significant different amounts of variation). Comparable population pairwise estimates of F(ST) were obtained for all marker types, but whilst absolute values for genomic and EST-SSRs were very similar (F(ST) = 0.355 and 0.342, respectively), differentiation was consistently higher for AFLPs in pairwise and global comparisons (global AFLP F(ST) = 0.496). The two AFLP primer combinations outperformed 18 SSR loci in assignment tests and discriminatory power in phenetic cluster analyses. The results from marker comparisons on A. distentifolium are discussed in the context of the few other studies on natural plant populations comparing microsatellite and AFLP variability.     

The potential contribution of conifer plantations to the UK Biodiversity Action Plan

Summary

The detrimental effects of conifer plantations on open ground habitats have been well catalogued and discussed, but the potential contribution of planted forests to the conservation of woodland biodiversity has not been quantified to the same extent. This quantification is needed urgently to help forest managers fulfil commitments to biodiversity enhancement as outlined in the UK Biodiversity Action Plan, the UK Forestry Standard and the UK Woodland Assurance Scheme (UKWAS). Results are presented from a five-year programme of research aimed at obtaining baseline information on biodiversity in planted forests and evaluating the contribution of planted forests to the conservation of native flora and fauna. Fifty-two plots were surveyed in total, covering a range of different tree crops (Scots pine Pinus sylvestris L., Sitka spruce Picea sitchensis (Bong.) Carr., Norway spruce Picea abies L. and Corsican pine Pinus nigra var maritima (Aitón) Melville) and stand ages (pre-thicket, mid-rotation, mature and over-mature) in three contrasting bioclimatic zones (upland, foothills and lowlands) throughout Britain. Additional plots were established in semi-natural woodland to allow comparisons between the biodiversity of plantations and native stands. Over 2000 species were recorded in total, including 45 Red Data Book species. Planted stands had similar or richer fungal and invertebrate communities to those of the native stands but poorer lichen and vascular plant communities. The latter were strongly affected by shading, dense, mid-rotation Sitka spruce stands having the lowest species counts. In contrast, these stands had a high diversity of mycorrhizal fungi, including a number of rare and threatened species normally associated with native pine wood. Bryophyte species-richness was related more to climate than woodland type, with the wetter upland spruce and native oak stands having the most diverse communities. Compared to the younger planted stands, over-mature planted stands had a higher proportion of species characteristic of semi-natural woodland stands. This related to greater structural diversity and higher deadwood volumes in the over-mature stands. It is concluded that conifer plantations make a positive contribution to biodiversity conservation in the UK and hence to the UK Biodiversity Action Plan. No single stand or crop type provides ‘optimal’ conditions for biodiversity, but the habitat value of plantations could be enhanced by increasing the area managed under alternative systems to clear-felling, such as ‘continuous cover’ and/or non-intervention natural reserves.     

A review of progress towards the conservation of the Killarney Fern (Trichomanes speciosum Willd.) in the British Isles

Summary

The Killarney Fern (Trichomanes speciosum) was considered amongst the rarest and most vulnerable of Europe's plants. Research which fed into the Biodiversity Action Plan and developed alongside it, has forced us to reconsider the level of threat to this species. A hitherto overlooked stage of the life-cycle, the gametophyte, has been shown to be comparatively abundant, genetically diverse, largely threat-free and with the potential over time to regenerate the familiar sporophyte stage. This research also promoted wider public interest which itself generated additional records, such that even the sporophyte is now known at more British sites than at any time previously and the species is accordingly considered ‘recovered’. However, continued legal protection and the need for further research are still recommended.     

Maintenance and recovery of rare clonal plants: the Case of the twinflower (Linnaea borealis L.)

Summary

Populations of rare clonally spreading species are increasingly being shown to be composed of one or a few genotypes. Clones have potentially unlimited life but two factors, genetic erosion due to random events and increasing accumulation of genetic load in older genotypes, combine to expose them to sexual failure and loss of fertility. Non-breeding clonal populations are at risk of extinction because they lack the ability to adapt or escape from changing environments.

Twinflower (Linnaea borealis L.) has been lost from nearly 50 % of its pre-1970 sites. It is a clonal self-incompatible plant and sexual failure has been reported from Canada, Britain and Scandinavia. Sexual failure is due to high levels of within-clone pollination by flies. Seed set occurs naturally in Scottish populations which have some genetic diversity. A non-breeding population in Scotland has been restored to viability by experimental cross-pollination with pollen from a distant source. Conservation action for this species should therefore be directed to the prevention of loss of habitat and restoration of population viability by translocation of compatible mates.

Translocating plants into extant, but non-breeding, populations are still a matter of debate and are frequently opposed. However, experimental translocations must now be performed to establish whether intervention can secure the long-term survival of rare clonal plants without the constant need for re-introduction.     

A multivariate morphometric investigation of Atherina boyeri Risso, 1810 and A. presbyter Cuvier, 1829 (Teleostei: Atherinidae): morphometric evidence in support of the two species

Two recently developed morphometric methodologies, multiple group principal components analysis (MGPCA) and the box truss method of body form transformation are used to re-address whether Atherina boyeri Risso, 1810 and A. presbyter Cuvier, 1829 are morphometrically distinct. The results revealed that morphometric differences are present between A. boyeri and A. presbyter , consistent with expectations of the existence of two species.
Females of the two species were clearly discriminated into two separate groups because the within-group covariances of several characters within populations of each species were different between species i.e., the covariances were heteroscedastic. The occurrence of heteroscedasticity within the data, although statistically invalidating the results of canonical variates anslysis, indicated there to be a large amount of morphological variation between females of the two species. Males were differentiated as a result of differences in body 'shape', particularly the relationship between head 'shape' and body 'shape'.
Several probable reasons are given for the failure of a previous study to differentiate the two species. The data rejects the synonymy of the two species in support of the continued use of the taxa A. boyeri Risso, 1810 and A. presbyter Cuvier, 1829.     

Bioanthropological analysis of human occipital condyles using geometric morphometric method

Sex differences are present in all parts of the body, including the skeletal system. Several methods are used to analyze the sex differences of skeleton, while more recently, a new method called geometric morphometry has been used. The aim of this study was to examine the sexual dimorphism of occipital condyles on human skulls originating from the population of Bosnia and Herzegovina using the geometric morphometric method.Material and methodsThe study was conducted on 214 human skulls of known gender from Bosnian population. For analysis of sexual dimorphism of occipital condyles, we used geometric morphometry, where all the skulls were scanned to obtain three-dimensional skull models. On the obtained models, we marked anthropometric points on occipital condyles in a Landmark Editor program from which we exported data in the form NTSYS file and analyzed it in MorphoJ program.ResultsFirst principal component PC1 describes 26.917% of total variability, the second principal component PC2 describes 20.992% of total variability, while the first eight principal components together describe 100% of total variability. The greatest variability between the male skulls and female skulls was present in the anterior-posterior diameter (length of occipital condyles). Discriminant functional analysis of the shape and size of the occipital condyles was possible with 69.50% accuracy for male skulls and with 60.27% accuracy for female skulls. The size of the occipital condyles showed a statistically significant effect on sexual determination. Discriminant functional analysis of the shape of the occipital condyles without affecting size enabled the determination of gender with with 65.96% accuracy for male skulls and with 63.01% accuracy for female skulls.ConclusionAnalysis of sexual dimorphism of occipital condyles using geometric morphometry showed statistically significant differences in the shape and size of occipital condyles between the sexes. The accuracy of sex determination based on occipital condyles was higher for male gender.     

基于几何形态分析的栎属白栎组叶片形态特征

以壳斗科栎属白栎组的5个种作为研究对象进行叶片几何形态学分析(GMMs).选取了20个天然种群,共采集182个个体,887张叶片,对每张叶片采用几何形态学的标点法,数字化叶形态特征,使5个种的叶形态差异可视化.结果表明:广义普氏分析可以有效地排除叶片位置和大小对叶片形状的影响.基于个体水平的主成分分析表明,槲树分别与槲...     

Allozymic and morphometric analysis of populations in the Zygaena purpuralis complex (Lepidoptera, Zygaenidae)

In Central Europe and Asia Minor Zygaena purpuralis and Z. minos are two sibling species exhibiting a considerable geographic variation in several features. In this study we examine some populations from the Central and Southern Apennines (Italy) by comparing multivariate analyses of individual allozymic multilocus profiles and of individual morphometric profiles of male genitalia in order to assess their genetic and phenetic relationships.
Results indicate that populations of Z. purpuralis in the Apennines behave in rather different ways with respect to the occurrence of gene exchange with other gene pools. No gene flow appears to occur between two geographically close southern populations; however, extensive introgression, revealable at both the allozymic and morphometric level, seems to occur between some purpuralis and minos -like sympatric populations from Abruzzi. Evolutionary relationships among these peninsular Italy populations are discussed with reference to historical factors, that is, the occurrence of multiple Pleistocene refugia, which could have determined different degrees of isolation among gene pools. This situation is rather different from that previously outlined for Central Europe and present results suggest that the Z. purpuralis complex might include more than two biological species.     

Grey Partridge Perdix perdix in the UK: recovery status,set‐aside and shooting

The Grey Partridge Perdix perdix is a European Species of Conservation Concern and a priority species under the UK Biodiversity Action Plan. The Game & Wildlife Conservation Trust (GWCT) launched a major programme to help partridge recovery in the UK, built on the GWCT’s Partridge Count Scheme (PCS) and including a demonstration site from 2002. We contrast the national picture of no population change since 1999 from BTO monitoring with a doubling of spring pair density on PCS sites. At the demonstration site, where set‐aside was used for habitat creation, Grey Partridge breeding density increased six‐fold, to 18 pairs/km², then fell back. The drop coincided with bad weather but also with the disappearance of rotational set‐aside when the set‐aside rate fell to zero, which halved the amount of brood‐rearing habitat. Non‐rotational set‐aside remained unchanged, as did the amount of nesting habitat that it provided. Grey Partridge density was significantly linked to rotational set‐aside, especially wild bird cover, but not to non‐rotational set‐aside. The demonstration project also showed that, with appropriate precautions, it was possible to shoot over 60% of Red‐legged Partridges Alectoris rufa while maintaining Grey Partridge losses below 5%. On PCS sites, the annual change in spring density in recent years differed in relation to neither shooting pressure nor intensity of Red‐legged Partridge releasing. Provision of brood‐rearing habitats and game cover increased with the latter, and probably counteracts the shooting losses of Grey Partridges on Red‐legged Partridge shoots when, as on PCS sites, active measures keep those losses below 20%. Targeted personal advice channelled through the PCS has been fundamental to these successes and must be expanded.     

Process‐Based Species Action Plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups

Many endemic plant species belong to taxonomically complex groups. These endemics have often arisen as a consequence of recent and rapid evolutionary divergence facilitated by processes such as hybridization, polyploidy and/or breeding system transitions. The rapid and dynamic nature of divergence in taxonomically complex groups leads to problems in the implementation of traditional species‐based approaches for the conservation of the biodiversity that they contain. Firstly, the taxa of interest can be difficult to define and identify, leading to practical difficulties in implementing conservation measures. Secondly, a species‐based approach often fails to capture the complexity of diversity present in the taxonomically complex group. To accommodate these challenges, we have developed a Process‐Based Species Action Plan approach. This is designed to conserve the processes leading to the generation of biodiversity, rather than focusing on the preservation of individual named taxa. We illustrate the approach using a group of endemic tree species (Sorbus) on the Scottish island of Arran that have originated via a combination of multiple recent hybridization events and apomixis. The plan focuses on the optimization of habitat management to ensure the reproduction and regeneration of Sorbus in the zone in which these evolutionary processes operate, and to facilitate hybridization that will ensure the continued generation of diversity in this group. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 194–203.     

Population morphometric analysis of the tropicopolitan bug Triatoma rubrofasciata and relationships with Old World species of Triatoma: evidence of New World ancestry

Quantitative analysis of morphological characters of the head was used to reconstruct the evolutionary history of the tropicopolitan bug Triatoma rubrofasciata (De Geer) (Hemiptera: Reduviidae) and seven species of Old World Triatoma. Multivariate analysis demonstrates that T. rubrofasciata and the Old World species have a high degree of similarity with Nearctic Triatoma species, particularly T. rubida (Uhler). We interpret this to imply a common ancestry for these groups. Dissemination of T. rubrofasciata and subsequent derivation of the Old World species of Triatoma is deduced to have occurred over a period of not more than 350 years.     

The contribution of the swimbladder to buoyancy in the adult zebrafish (Danio rerio): a morphometric analysis

Many teleost fishes use a swimbladder, a gas-filled organ in the coelomic cavity, to reduce body density toward neutral buoyancy, thus minimizing the locomotory cost of maintaining a constant depth in the water column. However, for most swimbladder-bearing teleosts, the contribution of this organ to the attainment of neutral buoyancy has not been quantified. Here, we examined the quantitative contribution of the swimbladder to buoyancy and three-dimensional stability in a small cyprinid, the zebrafish (Danio rerio). In aquaria during daylight hours, adult animals were observed at mean depths from 10.1 +/- 6.0 to 14.2 +/- 5.6 cm below the surface. Fish mass and whole-body volume were linearly correlated (r(2) = 0.96) over a wide range of body size (0.16-0.73 g); mean whole-body density was 1.01 +/- 0.09 g cm(-3). Stereological estimations of swimbladder volume from linear dimensions of lateral X-ray images and direct measurements of gas volumes recovered by puncture from the same swimbladders showed that results from these two methods were highly correlated (r(2) = 0.85). The geometric regularity of the swimbladder thus permitted its volume to be accurately estimated from a single lateral image. Mean body density in the absence of the swimbladder was 1.05 +/- 0.04 g cm(-3). The swimbladder occupied 5.1 +/- 1.4% of total body volume, thus reducing whole-body density significantly. The location of the centers of mass and buoyancy along rostro-caudal and dorso-ventral axes overlapped near the ductus communicans, a constriction between the anterior and posterior swimbladder chambers. Our work demonstrates that the swimbladder of the adult zebrafish contributes significantly to buoyancy and attitude stability. Furthermore, we describe and verify a stereological method for estimating swimbladder volume that will aid future studies of the functions of this organ.     

Use of morphometric analysis for characterization of tobacco root growth in relation to infection byPhytophthora parasitica var.nicotianae

Development of tobacco root systems was characterized under controlled environmental conditions by use of morphometric root analysis. According to the classification scheme of this system, roots terminating in apical meristems are defined as first-order roots. Elements of second-order roots begin where two first-order roots merge, and so forth. Growth of root systems was similar for susceptible and resistant tobacco cultivars in nonautoclaved and autoclaved soils. During 15 days of growth subsequent to transplanting of 2-week-old plants, relative multiplication and extension rates of first-order and second-order roots were constant. Apparent unit extension rates of first-order and second-order root elements increased through 15 days of root system growth. Classification of tobacco root systems by the morphometric scheme provided a useful means of partitioning susceptibility of tissues to infection byPhytophthora parasitica var.nicotianae. Zoospores applied at the tips of first-order roots were most successful in causing infections; 73.3% of the roots inoculated with 16 zoospores per root tip became infected. Percentages of infections after inoculation of first-order root tissues 2 cm behind root tips or after inoculation of second-order roots were 10 and 4.3%, respectively.Florida Agricultural Experiment Station, Journal Series Paper 8106.     

Morphological analysis of male mating organ in the Drosophila virilis species group: a multivariate approach

The shape of the male mating organ differs among 11 closely related species of the Drosophila virilis species group. Multivariate analyses of variation of a suite of 35 morphological traits (indices) describing the phallus shape were carried out in order to characterize interspecies variability of the traits. An overwhelming majority of the traits displayed species‐specific variability. The main result of the investigation was the revelation of the differences involved in the traits studied in the evolution of the D. virilis species group. The structure of species‐specific variability of some traits was discovered to be in accordance with the generally accepted taxonomy of the species group, while that of other traits required isolation of D. virilisper se from lummei phylad (former virilis phylad), and confirmed separation of montana phylad into three subphylads: montana proper, littoralis and kanekoi. Several subsets of traits having separate variability were determined in different parts of the male mating organ which correspond to spots of evolutionarily significant variability.     

Designing ecological corridors in a fragmented landscape: A fuzzy approach to circuit connectivity analysis

Landscape connectivity analysis is a major tool in supporting biodiversity conservation. Several methodologies have been developed to tackle it by following two main paths. The first path exploits graph approaches and models focal nodes’ connections on a resistance/conductance matrix depending on focal species’ movement potential. The second path considers geometrical pattern analyses based on the calculation of structural landscape metrics. These approaches separately investigate functional and structural features of the landscape, and may come short of a total definition if used separately. Here we propose a new scalable, modular, participative and open-source procedure based on Fuzzy logic to combine the functional and structural aspects of connectivity. We applied this method on the highly fragmented landscape of the Po Plain, focusing on its rare and endangered plain springs named fontanili. We identified an expert panel and involved it in the assignation of permeability values of land use classes with respect to the capacity of movement of animal species typical of fontanili. We concurrently performed a quantitative evaluation of the landscape fragmentation with a moving window. We found that the functional and structural evaluations were poorly correlated in the area under study (Pearson's r = −0.35, p < 0.001). We thus integrated these two non-overlapping analyses of the landscape by Fuzzy logic using thresholds and combination weights obtained from questionnaires proposed to the expert panel. The resulting index, termed Fuzzy Functionality Index (FFI), improved the level of information associated with landscape classification. By merging functional and structural aspects of the landscape, the FFI allowed us to discriminate different functional values of equally permeable parcels and vice versa. We demonstrate that FFI may act as a conductance measure in a circuit theory approach, highlighting ecological corridors between focal points of species’ distribution. We present FFI as an effective predictive index to inspect complex and non-linear landscape dynamics.     

Shape and size variations in the cranium of elephant-shrews: a morphometric contribution to a phylogenetic debate

A geometric morphometric analysis was carried out on the crania of 13 species of elephant-shrews (Macroscelidea), a group of African mammals whose phylogeny is still debated. The material examined consisted of 313 crania and included all the genera of Macroscelididae, the unique family recognized by taxonomists. The results obtained from the analysis of the cranium shape and size, either from dorsal or lateral view, were very similar. The first one appeared more reliable because of the higher number of intersection points fixed between the cranial sutures. All the cranial features that distinguished the genus Rhynchocyon were a consequence of the extreme enlargement of frontal bones. Instead, within the subfamily Macroscelidinae, the differences between genera were based on modification involving other bones, mainly mastoids and nasals, as shown by the deformation grids. A cluster analysis confirmed the traditional subdivision in two subfamilies (Rhynchocyoninae and Macroscelidinae) but suggested a different relationship among the recognized genera belonging to Macroscelidinae. Our results are congruent with data obtained from previous biochemical research and support the traditional subdivision in two subfamilies, the monophily of the genus Elephantulus and its closeness with Petrodromus, relating to their similar cranium shapes. The latter presumably is a case of gigantism as adaptation to forest habitats. Further studies on all the species of Elephantulus could provide new evidence for assessing the relationships within this clade, including Macroscelides that by the present analysis appeared as a well-distinguished taxonomic entity.