Protein Sequence Modules

Abstract

Conserved protein sequence segments are commonly believed to correspond to functional sites in the protein sequence. A novel approach is proposed to profile the changing degree of conservation along the protein sequence, by evaluating the occurrence frequencies of all short oligopeptides of the given sequence in a large proteome database. Thus, a protein sequence conservation profile can be plotted for every protein. The profile indicates where along the sequences the potential functional (conserved) sites are located. The corresponding oligopeptides belonging to the sites are very frequent across many prokaryotic species. Analysis of a representative set of such profiles reveals a common feature of all examined proteins: they consist of sequence modules represented by the peaks of conservation. Typical size of the modules (peak-to-peak distance) is 25–30 amino acid residues.     

Genetic variability characterization of the moroccan houbara bustard (Chlamydotis undulata undulata) inferred from pedigree analysis

A Moroccan Houbara Bustard pedigree was analyzed to evaluate the genetic variability in captive breeding population using genealogical approaches. The whole Houbara breeding flock (WP) for the period 1993–2004 was made up of 531 birds comprising 346 females and 185 males. The reference population (RP) comprised 198 individuals ready for reproduction from 2000 to 2004 cohorts. The corresponding percentage of known ancestors was estimated as 98.23% for the parent generation, 41.19% for the grandparent generation and 7.00% for the great grandparents generation. The average generation interval for Houbara was computed as 4.64 years. Genetic variability loss per generation was ascertained using the effective population size (), the founder genome equivalent (fge), the effective number of ancestors and founders (fa) and (fe), respectively, for the RP and across each cohort. The results showed no bottleneck events in the breed but some loss of genetic variability just after the initiation of the conservation program. However, the annual effective population size based on the realized increase in inbreeding () was estimated to be 207 for the RP and 1,000 for the WP. With regard to conservation breeding schemes, the genealogical evidence presented here is very useful as it revealed the positive effect of migration on Houbara breeding. The mating strategies will assist in the future control and management of the genetic variability of this population. Zoo Biol. 32:366‐373, 2013. © 2012 Wiley Periodicals, Inc.     

Aspects of reproduction and their implications for the conservation of the endangered limpet,Patella ferruginea

Summary

The protandric limpet, Patella ferruginea G., is the most endangered marine species in the Western Mediterranean and is at serious risk of extinction. Nevertheless, its biology and ecology are little known. In the present work, several reproductive aspects are studied. Recruitment take place in June and the largest individuals are the most scarce. The sex ratio is slanted towards the largest sizes, and the species seems to show sex change at sizes from 60 mm upwards, although males can be observed up to 80 mm. There is no correlation between size of oocytes and shell length; however, the larger females contribute greatly to the reproductive event, with high fecundity and GSI values. The mean diameter of oocytes was observed to be 149.78 μm, whereas the heads of spermatozoa were 3.78 μm long. The results of the present study increase the maximum length for males by double that cited in previous literature and highlight the importance of strictly protecting females (i.e., most of the largest individuals, >60 mm), since their population percentage is very low, in order to develop adequate strategies to preserve the species.     

Distribution of duck broods relative to habitat characteristics in the Prairie Pothole Region

Conservation programs for breeding ducks in the Prairie Pothole Region (PPR) of the United States and Canada require effective means of evaluating and characterizing breeding habitat across large landscapes. Extensive surveys of the distribution of duck broods in late-summer could help identify wetland basins with greater probabilities of occupancy. Broods are difficult to detect, however, rendering presence–absence data from single-visit surveys difficult to interpret, particularly when probability of detection is related to habitat features. Multiple-visit occupancy surveys offer a potential solution. From 20 July to 5 August 2007–2009, we conducted a 3-visit survey of wetland basins located on 167 10.4-km² study plots in the PPR. Our survey focused on broods of the 5 most common breeding duck species (Anas spp.). Our main objectives were to investigate ecological relationships between occupancy of wetland basins by broods and habitat characteristics and to examine if habitat-specific detection was of enough concern to warrant multi-survey approaches in the future. We surveyed 3,226 wetland basins during the study. Probability of occupancy of a wetland basin by a brood was positively related to the log of wet area for all 5 study species and was greater on wetlands located on plots with a greater proportion of herbaceous perennial cover for 4 of 5 species. For example, the median probability of occupancy for gadwall (Anas strepera) increased from 0.08 (90% Credible Interval [CrI]: 0.07, 0.10) to 0.28 (90% CrI: 0.23, 0.33) as wet area increased from 0.19 ha to 2.12 ha, and increased from 0.12 (90% CrI: 0.09, 0.16) to 0.20 (90% CrI: 0.16, 0.25) as proportion of perennial grass cover on the study plot increased from 0.03 to 0.99. Because occupancy and detection were both related to attributes of wetland basins, we concluded that the multiple-visit survey was a useful approach for identifying habitat relationships of duck broods. Our results indicated that most broods of the study species were found in 10.4-km² landscapes with greater densities of small- to mid-sized wetland basins and a greater proportion of herbaceous perennial vegetation. Our study provided new empirical support that could be used to help target conservation actions to the most productive landscapes for breeding ducks. © 2012 The Wildlife Society.     

Diversity and diversification of Eumolpinae (Coleoptera: Chrysomelidae) in New Caledonia

Contemporary taxonomic work on New Caledonian Eumolpinae (Chrysomelidae) has revealed their high species richness in this Western Pacific biodiversity hotspot. To estimate total species richness in this community, we used rapid DNA‐based biodiversity assessment tools, exploring mtDNA diversity and phylogenetic structure in a sample of 840 specimens across the main island. Concordance of morphospecies delimitation with units delimited by phenetic and phylogenetic algorithms revealed some 98–110 species in our sample, twice as many as currently described. Sample‐based rarefaction curves and species estimators using these species counts doubled this figure (up to 210 species), a realistic estimate considering taxonomic coverage, local endemism, and characteristics of sampling design, amongst others. New Caledonia, compared with larger tropical islands, stands out as a hotspot for Eumolpinae biodiversity. Molecular dating using either chrysomelid specific rates or tree calibration using palaeogeographical data dated the root of the ingroup tree (not necessarily a monophyletic radiation) at 38.5 Mya, implying colonizations after the Cretaceous breakage of Gondwana. Our data are compatible with the slowdown in diversification rates through time and are also consistent with recent faunal origins, possibly reflecting niche occupancy after an initial rapid diversification. Environmental factors (e.g. soil characteristics) seemingly played a role in this diversification process. © 2013 The Linnean Society of London     

Distribution,habitat disturbance and pollination of the endangered orchid Broughtonia cubensis (Epidendrae: Laeliinae)

The geographical distribution, population structure and pollination ecology are key aspects in the conservation and management of rare orchids. Here, we address these aspects and the main threats affecting the endangered Cuban orchid Broughtonia cubensis. This rewardless orchid is self‐compatible, but pollinator dependent. However, seed production can be negatively affected by insect‐mediated selfing. Three species of small bee (genera Ceratina and Lasioglossum) act as pollinators. As in the case of other nectarless orchids, we detected two species of plant producing large amounts of nectar in the area, the floral morphology of which closely resembles that of B. cubensis. The simultaneous flowering of these species could positively affect the reproductive success of B. cubensis. Nonetheless, the fitness of this orchid in natural conditions is low, possibly related to strong pollen limitation. To the problems arising from reduced fitness is added the fact that its historical distribution range has been greatly reduced in recent years. Throughout this study, we have detected dramatic reductions in the population sizes, in some cases as a result of human plundering, but also as a consequence of hurricanes. Based on the results of this study, we propose some guidelines to manage and conserve this orchid. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 345–357.     

Dispersal,fragmentation, and isolation shape the phylogeography of the European lineages of Polyommatus (Agrodiaetus) ripartii (Lepidoptera: Lycaenidae)

Polyommatus ripartii is a biogeographically and taxonomically poorly understood species of butterfly with a scattered distribution in Europe. Recently, it has been shown that this species includes several European endemic and localized taxa (galloi, exuberans, agenjoi) that were previously considered species and even protected, a result that poses further questions about the processes that led to its current distribution. We analysed mitochondrial DNA and the morphology of P. ripartii specimens to study the phylogeography of European populations. Three genetically differentiated but apparently synmorphic lineages occur in Europe that could be considered evolutionarily significant units for conservation. Their strongly fragmented and counterintuitive distribution seems to be the result of multiple range expansions and contractions along Pleistocene climatic oscillations. Remarkably, based on the 79 specimens studied, these genetic lineages do not seem to extensively coexist in the distributional mosaic, a phenomenon most evident in the Iberian Peninsula. One of the important gaps in the European distribution of P. ripartii is reduced by the discovery of new Croatian populations, which also facilitate a better understanding of the biogeography of the species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 817‐829.     

Local genetic structure in the critically endangered,cave‐associated perennial herb Primulina tabacum (Gesneriaceae)

The local spatial genetic structures of cave‐associated plants are seldom studied. Given that these plants are mainly confined to small areas in and around the entrances of caves, we hypothesized that they might lack genetic structures at local scales. To test this hypothesis, we sampled two large populations (named D and T) of a critically endangered perennial herb, Primulina tabacum, which is endemic to karst caves in southern China. We analysed nine microsatellite loci and sequenced four chloroplast DNA (cpDNA) intergenic spacer regions to study the genetic diversity and structure within and between both populations. Both populations have distinct genetic characteristics. Samples from two subpopulations in population D showed considerable genetic divergence. This is not consistent with the hypothesis that P. tabacum has a weak genetic structure at a local scale. However, 94% of the individuals in population T shared the same multilocus genotype, which indicates little genetic structure within this population. The contributions of seed flow, pollen flow and (sub)population history to the genetic diversity and structure in each and both populations are discussed. Our study is the first to investigate local genetic diversity and structure in a cave‐associated plant, and provides valuable information for the sustainable conservation of such species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 747–756.     

The impact of habitat fragmentation on fitness‐related traits in a native prairie plant,Chamaecrista fasciculata (Fabaceae)

Loss and fragmentation of the native prairies in the Midwestern United States have resulted in isolated and smaller habitats and populations. The populations remaining in these prairies are expected to show a decline in the extent of genetic variation and an increase in genetic drift load (accumulation of deleterious recessive alleles due to genetic drift) in fitness‐related traits. Using complementary greenhouse experiments, we tested whether these expected changes have occurred in the native annual prairie plant Chamaecrista fasciculata. In the first experiment, open pollinated C. fasciculata seeds from 12 prairie fragments representing a range in area of habitat were grown in competition with Schizachyrium scoparium to determine if there are changes in plant vigour with changes in fragment size and corresponding changes in population size. Plants from smaller prairie fragments exhibited a slight but significant decline in biomass, suggesting an increase in genetic drift load. In the second experiment, a formal genetic crossing design of four prairie fragment populations was used to estimate quantitative genetic diversity and genetic drift load. We did not find extensive quantitative genetic variation, but we did find a strong effect of genetic drift load on five traits in this experiment. Our overall conclusion is that a decline in relative‐fitness traits in smaller prairie fragments is probably associated with fixation of deleterious alleles due to more isolated and smaller populations, i.e. genetic drift load. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.