Genome size diversity in the family Drosophilidae

Flies in the genus Drosophila have been the dominant model organisms in genetics for over a century and, with a dozen complete sequences now available, continue as such in modern comparative genomics. Surprisingly, estimates of genome size for this genus have been relatively sparse, covering less than 2% of species. Here, best practice flow cytometric genome size estimates are reported for both male and female flies from 67 species from six genera in the family Drosophilidae, including 55 species from the genus Drosophila. Direct and phylogenetically corrected correlation analyses indicate that genome size is positively correlated with temperature-controlled duration of development in Drosophila, and there is indication that genome size may be positively related to body size and sperm length in this genus. These findings may provide some explanation for the streamlined genomes found in these insects, and complement recent work demonstrating possible selective constraints on further deletion of noncoding DNA.     

Genome size and chromosome number in velvet worms (Onychophora)

The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5–19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results.     

Transposable elements and the evolution of genome size in eukaryotes

It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.     

The food and feeding ecology of Adélie penguins (Pygoscelis adeliae) and Chinstrap penguins (P. antarctica) at Signy Island, South Orkney Islands

Adélie Pygoscelis adeliae and Chinstrap P. antarctica penguins are important consumers of Southern Ocean marine resources. The stomach contents of adult penguins at Signy Island, South Orkney Islands, were analysed quantitatively throughout the chick-rearing period. They consisted almost exclusively of Antarctic krill Euphausia superba , Adélies eating 35–63% by number and 23–28% by weight of juvenile krill and Chinstraps 72–87% by number and 90–95% by weight of mature krill, as well as small amounts offish and amphipods. Interspecific dietary differences may partly be attributable to Adélies starting breeding one month before Chinstraps but, as they persist when both are simultaneously rearing chicks, the two species may also forage in somewhat different areas.
Krill data from net hauls indicate a substantial overlap in the size of krill taken by scientific, and probably also commercial, operations and by Adélie and Chinstrap penguins.
Chicks were fed c. 300 g of food 0–5-0-8 times per day, Chinstrap chicks without a sibling being fed most frequently. Chicks of both species were most often fed in the late afternoon, and from estimates of swimming speed and feeding frequency adults may feed quite extensively at night.     

南极磷虾行为与生理生态学研究进展

行为生态学和生理生态学是生态学领域的两个重要研究范畴,开展相关研究可以更好地理解海洋生物的生活习性及其对环境的适应能力.南极磷虾是南大洋生态系统中的关键物种,探究其行为和生理生态学可以了解磷虾类等海洋生物应对极端环境的能力.本文从行为生态和生理生态两方面总结了南极磷虾的典型生态学特征.行为生态学包括其集群(规模、行为)及游泳(游泳角度、附肢摆动)等;生理生态学包括呼吸、排泄与代谢以及蜕皮与生长等.目前关于南极磷虾的生理生态学和行为生态学的研究仍较为有限,且多数研究结果基于陆基实验室的暂养.鉴于陆基实验室暂养与自然的南极磷虾栖息环境差异较大,开展南极磷虾的现场实验生态学研究迫在眉睫.     

Dietary segregation of krill-eating South Georgia seabirds

The diets of six of the main seabird species (two petrels, two albatrosses, two penguins) breeding at Bird Island, South Georgia were studied simultaneously during the chick-rearing period in 1986. For five species, Antarctic krill Euphausia superba was the main food (39–98% by mass); grey-headed albatrosses took mainly the ommastrephid squid Martialia hyadesi (71%) and only 16% krill. The size of the krill taken was similar between seabird species, although there were small but significant differences between penguins and the other species. Sex and reproductive status of krill, however, was different between all seabird species, reflecting some combination of differences in foraging ranges, selectivity by predators, or differences in escape responses of krill. For the krill-eating species, the rest of the diet varied substantially between species, comprising Martialia and nototheniid fish (blackbrowed albatross and, along with lanternfish, white-chinned petrel), lanternfish and amphipods (Antarctic prion and macaroni penguin), and icefish (gentoo penguin). Long-term data on breeding success and information on diet in 5–10 other years suggest that in 1986 seabird diet and reproductive performance was indicative of a year of good availability of krill around South Georgia. In such circumstances, ecological segregation between krill-eating species appears to be maintained chiefly by differences in foraging range and feeding methods, which are reviewed. This situation is rather different from the few studies of seabird communities elsewhere, where prey type and size are believed to be the main mechanisms of dietary segregation.     

Horizontal niche partitioning of humpback and fin whales around the West Antarctic Peninsula: evidence from a concurrent whale and krill survey

A dedicated aerial cetacean survey was conducted concurrently to a standardised net trawl survey for krill in order to investigate distribution patterns of large whales and different krill species and to investigate relationships of these. Distance sampling data were used to produce density surface models for humpback (Megaptera novaeangliae) and fin whales (Balaenoptera physalus) around the West Antarctic Peninsula (WAP). Abundance for both species was estimated over two strata in the Bransfield Strait and Drake Passage. Distinct distribution patterns suggest horizontal niche partitioning of the two whale species around the WAP, with fin whales aggregating at the shelf edge of the South Shetland Islands in the Drake Passage and humpback whales in the Bransfield Strait. Krill biomass estimated from the concurrent krill survey was used along with CTD data from the same expedition, bathymetric parameters and satellite data on chlorophyll-a and ice concentration to model krill distribution. Comparisons of the predicted distributions of both whale species with the predicted distributions of Euphausia superba, Euphausia crystallorophias and Thysanoessa macrura suggest a complex relationship rather than a straightforward correlation between krill and whales. However, results indicate that fin whales were feeding in an area dominated by T. macrura, while humpback whales were found in areas of higher E. superba biomass. Our results provide abundance estimates for humpback whales and, for the first time, fin whales in the WAP and contribute important information on feeding ecology and habitat use of these two species in the Southern Ocean.     

Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa

The Gesneriaceae (Lamiales) is a family of flowering plants comprising >3000 species of mainly tropical origin, the most familiar of which is the cultivated African violet (Saintpaulia spp.). Species of Gesneriaceae are poorly represented in the lists of taxa sampled for genome size estimation; measurements are available for three species of Ramonda and one each of Haberlea, Saintpaulia, and Streptocarpus, all species of Old World origin. We report here nuclear genome size estimates for 10 species of Sinningia, a neotropical genus largely restricted to Brazil. Flow cytometry of leaf cell nuclei showed that holoploid genome size in Sinningia is very small (approximately two times the size of the Arabidopsis genome), and is small compared to the other six species of Gesneriaceae with genome size estimates. We also documented intraspecific genome size variation of 21%-26% within a group of wild Sinningia speciosa (Lodd.) Hiern collections. In addition, we analyzed 1210 genome survey sequences from S. speciosa to characterize basic features of the nuclear genome such as guanine-cytosine content, types of repetitive elements, numbers of protein-coding sequences, and sequences unique to S. speciosa. We included several other angiosperm species as genome size standards, one of which was the snapdragon (Antirrhinum majus L.; Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10? base pairs, which is approximately 40% of the previously published estimate.     

Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species

The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although "whole"-genome sequences, such as those now available for 12 Drosophila species, provide information about euchromatic DNA content, they cannot give an accurate estimate of genome sizes that include heterochromatin or repetitive DNA content. Moreover, genome sequences typically represent only one strain or isolate of a single species that does not reflect intraspecies variation. To more accurately estimate whole-genome DNA content and compare these estimates to newly assembled genomes, we used flow cytometry to measure the 2C genome values, relative to Drosophila melanogaster. We estimated genome sizes for the 12 sequenced Drosophila species as well as 91 different strains of 38 species of Drosophilidae. Significant differences in intra- and interspecific 2C genome values exist within the Drosophilidae. Furthermore, by measuring polyploid 16C ovarian follicle cell underreplication we estimated the amount of satellite DNA in each of these species. We found a strong correlation between genome size and amount of satellite underreplication. Addition and loss of heterochromatin satellite repeat elements appear to have made major contributions to the large differences in genome size observed in the Drosophilidae.     

Long-term changes in Krill biomass and distribution in the Barents Sea: are the changes mainly related to capelin stock size and temperature conditions?

Krill plays a significant role in the Barents Sea ecosystem, providing energy transport between different trophic levels. The current paper presents the results of a long-term study (1980–2009) based on pelagic trawl catches from August to September. Our investigations show that the krill species were distributed widely in the Barents Sea and that the largest krill concentrations were restricted to the west-central and eastern parts of the Barents Sea. The current paper presents the relative biomass indices, and the estimates must be interpreted as minimum biomass. The mean annual krill biomass was estimated to be 22 million tonnes in wet weight, with the highest values being as much as 48 million tonnes. Capelin is the largest pelagic stock, and in some years, their biomass can amount to 4–7 million tonnes, which can impose high predation pressure on krill. When their biomass is high, capelin may consume close to 26 million tonnes annually. The predation from pelagic (herring and blue whiting) and bottom (cod and haddock) fish species was much lower, being 9 and 1 million tonnes, respectively. A negative relationship between krill biomass and capelin stock size above 74°N was observed during the study period. However, during the last decade, the krill biomass has increased despite heavy predation from capelin in some years. A positive significant linear relationship between the mean annual Kola temperature and the krill biomass seems to indicate that the recent warming conditions have favourable impacts on the krill populations in the Barents Sea.     

Multilocus analyses reveal little evidence for lineage‐wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus)

Estimates from molecular data for the fraction of new nonsynonymous mutations that are adaptive vary strongly across plant species. Much of this variation is due to differences in life history strategies as they influence the effective population size (N_e). Ample variation for these estimates, however, remains even when comparisons are made across species with similar values of N_e. An open question thus remains as to why the large disparity for estimates of adaptive evolution exists among plant species. Here, we have estimated the distribution of deleterious fitness effects (DFE) and the fraction of adaptive nonsynonymous substitutions (α) for 11 species of soft pines (subgenus Strobus) using DNA sequence data from 167 orthologous nuclear gene fragments. Most newly arising nonsynonymous mutations were inferred to be so strongly deleterious that they would rarely become fixed. Little evidence for long‐term adaptive evolution was detected, as all 11 estimates for α were not significantly different from zero. Nucleotide diversity at synonymous sites, moreover, was strongly correlated with attributes of the DFE across species, thus illustrating a strong consistency with the expectations from the Nearly Neutral Theory of molecular evolution. Application of these patterns to genome‐wide expectations for these species, however, was difficult as the loci chosen for the analysis were a biased set of conserved loci, which greatly influenced the estimates of the DFE and α. This implies that genome‐wide parameter estimates will need truly genome‐wide data, so that many of the existing patterns documented previously for forest trees (e.g. little evidence for signature of selection) may need revision.     

Length–weight relationships of five fish species associated with krill fishery in the Atlantic sector of the Southern Ocean

Length–weight relationships (LWRs) of five fish species commonly associated with Antarctic krill fishery, were determined. Samples were collected with Chinese krill trawler (codend mesh size 2 cm) in the Atlantic sector of the Southern Ocean from January to August 2016. Data on LWRs and the relationships between weight and standard length as well as weight and total length of those species were updated for the database of FishBase. Those data on fish species derived from Antarctic krill fishery will be very helpful in understanding the interaction between krill fishery and the associated fish community.     

Nuclear DNA content in species ofEleusine (Gramineae): A critical re-evaluation using laser flow cytometry

Interest in dinitroaniline herbicide resistant biotypes ofEleusine indica, and an as yet undetermined taxon ofEleusine, necessitated a revaluation of reported nuclear genome size estimates for available species in the genus. Laser flow cytometry showed that the nuclear DNA content of six of the seven species examined had 15 to 50% less DNA than reported previously. It was also determined that roots, as contrasted to leaves, possessed a large fraction of nuclei at the 4C or 8C DNA content level, in diploid or tetraploid species, respectively (i.e. the G2/M peak). Two major reasons for the previously reported overestimation may include sampling only of root tissues where endopolyploid and normal diploid nuclei both occur and the inappropriate choice of onion nuclei as an internal standard.     

The mitochondrial genome is large and variable in a family of plants (cucurbitaceae)

The genome sizes of mitochondrial DNA from darkgrown (etiolated) shoots of several higher plants were determined by reassociation kinetics and restriction analysis. Kinetic complexities obtained from reassociation kinetics measured spectrophotometrically indicate a mitochondrial genome size of 1600 Md for muskmelon, 1000 Md for cucumber, 560 Md for zucchini squash and 220 Md for watermelon (four species in the cucurbit family), as well as 240 Md for pea and 320 Md for corn. The kinetic curves also reveal the presence (except in corn) of sequences of a few magadaltons of complexity, reiterated about 10-50 times and representing 5%- 10% of the DNA in each mitochondrial genome. Molecular weight summation of fragments resulting from digestion with restriction endonucleases Sal I and Kpn I give genome size estimates similar to those obtained from reassociation kinetics, except for muskmelon and cucumber, for which the large number of fragments of similar size limits our estimate to at least 500 Md. The number of mitochondrial genomes per diploid cell is estimated to be about 110 to 140 for muskmelon, zucchini and watermelon. We consider the possible evolutionary mechanisms by which the mitochondrial genome has grown within the cucurbit family and the possible reasons for the existance of a seven to eight-fold range in mitochondrial genome size among such closely related species.     

Genome Size and Species Diversification

Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone.     

Living krill, zooplankton and experimental investigations: a discourse on the role of krill and their experimental study in marine ecology

Krill occupy critical positions in a many marine ecosystems and have been the subject of a number of concerted studies yet there are large areas of their biology that still remain a mystery. Most species of krill are open ocean animals, which makes direct observation and sampling difficult. Krill also exhibit a number of physiological and behavioural attributes which frustrate attempts to understand their life history. Krill are conceptually difficult to come to terms with; they are obviously different from larger marine organisms such as squid, fish, whales and fish yet they are also quite distinct from those animals classed as zooplankton such as copepods. Despite these differences they have most often been grouped with zooplankton and have been studied using techniques developed for animals which are orders of magnitude smaller than they. This mismatch has affected our view of their interactions with the physical world and also affects their perceived trophic interactions. Their size and mobility also interferes with our ability to sample them effectively and thus to develop our appreciation of their true role in the marine ecosystem. Understanding how intermediate-sized animals, such as krill, function in aquatic ecosystem is critical to better management of the marine environment.     

Living krill,zooplankton and experimental investigations: a discourse on the role of krill and their experimental study in marine ecology

Krill occupy critical positions in a many marine ecosystems and have been the subject of a number of concerted studies yet there are large areas of their biology that still remain a mystery. Most species of krill are open ocean animals, which makes direct observation and sampling difficult. Krill also exhibit a number of physiological and behavioural attributes which frustrate attempts to understand their life history. Krill are conceptually difficult to come to terms with; they are obviously different from larger marine organisms such as squid, fish, whales and fish yet they are also quite distinct from those animals classed as zooplankton such as copepods. Despite these differences they have most often been grouped with zooplankton and have been studied using techniques developed for animals which are orders of magnitude smaller than they. This mismatch has affected our view of their interactions with the physical world and also affects their perceived trophic interactions. Their size and mobility also interferes with our ability to sample them effectively and thus to develop our appreciation of their true role in the marine ecosystem. Understanding how intermediate-sized animals, such as krill, function in aquatic ecosystem is critical to better management of the marine environment.     

Using flow cytometry to estimate pollen DNA content: improved methodology and applications

Background and Aims

Flow cytometry has been used to measure nuclear DNA content in pollen, mostly to understand pollen development and detect unreduced gametes. Published data have not always met the high-quality standards required for some applications, in part due to difficulties inherent in the extraction of nuclei. Here we describe a simple and relatively novel method for extracting pollen nuclei, involving the bursting of pollen through a nylon mesh, compare it with other methods and demonstrate its broad applicability and utility.

Methods

The method was tested across 80 species, 64 genera and 33 families, and the data were evaluated using established criteria for estimating genome size and analysing cell cycle. Filter bursting was directly compared with chopping in five species, yields were compared with published values for sonicated samples, and the method was applied by comparing genome size estimates for leaf and pollen nuclei in six species.

Key Results

Data quality met generally applied standards for estimating genome size in 81 % of species and the higher best practice standards for cell cycle analysis in 51 %. In 41 % of species we met the most stringent criterion of screening 10 000 pollen grains per sample. In direct comparison with two chopping techniques, our method produced better quality histograms with consistently higher nuclei yields, and yields were higher than previously published results for sonication. In three binucleate and three trinucleate species we found that pollen-based genome size estimates differed from leaf tissue estimates by 1·5 % or less when 1C pollen nuclei were used, while estimates from 2C generative nuclei differed from leaf estimates by up to 2·5 %.

Conclusions

The high success rate, ease of use and wide applicability of the filter bursting method show that this method can facilitate the use of pollen for estimating genome size and dramatically improve unreduced pollen production estimation with flow cytometry.     

Analysis of the sources of variance in the mean size of krill consumed by Chinstrap and Adélie penguins at South Orkney Islands

The CCAMLR Ecosystem Monitoring Program aims at detecting possible impacts of the krill fishery on predator populations. Population parameters of Chinstrap and Adélie penguins are monitored at Point Martin, Laurie Island, South Orkneys Islands as part of the Program. Diet information is collected to aid in the interpretation of population data. In the present study, the diet of both species is compared in order to detect differences between them as well as to ascertain whether the krill consumed by both species might be pooled in single estimates of prey parameters. A nested ANOVA model was fitted to the dataset obtained in the seasons from 1997/1998 to 2005/2006. The overall variance was decomposed into variance components: within penguins (krill in stomachs), between penguins (means within each date), between dates (date means in each season), and between years (annual means). The within penguins component was similar in both species (18?% difference), while the between penguins was 64?% larger in Adelies. The within and between penguins variance components of both species showed consistent interannual changes. The annual means of both species differed significantly in three seasons, but not consistently. The sources of variance are tentatively attributed to biological characteristics: the within penguins component would reflect searching and feeding at the individual level; the between penguins might be associated with their foraging ranges, an assumption to be tested tracking individuals. Given their differences, the information from both species should be viewed as complementary and not be pooled.