Brood sex ratio in expansive and non-expansive tern species in east-central Poland

Capsule Evidence from two tern species does not support the theory that species in expansion should bias their brood sex ratios towards the more dispersing sex.

Aims Sex ratio theory predicts that when a species is in expansion, the sex ratio should be biased towards the more dispersing sex. We compared the sex ratio of nestlings in two closely related species of terns, characterized by different expansion rates: the White-winged Tern Chlidonias leucopterus (an expansive species) and the Black Tern Chlidonias niger (a non-expansive species).

Methods The fieldwork was carried out in the valleys of the Rivers Bug and Narew in east-central Poland, from 2008 to 2014, during which time eight White-winged Tern colonies and ten Black Tern colonies were monitored. Nest inspections began around 15–20 May, when the first eggs were laid, and continued until mid-July, when the last nestlings were 7–20 days old.

Results The nestling sex ratios were similar in both species, and the differences between number of females and males were not significant (White-winged Tern: 56.6% females vs. 43.4% males; Black Tern: 57.4% females vs. 42.6% males).

Conclusions The lack of differences in nestling sex ratio in these species may be due to the cessation of the White-winged Tern's expansion in this area or because the sex ratio is characteristic of Sternidae species, as similar results have been reported for other tern species.     

Mitochondrial DNA polymorphism in the natural populations of the Drosophila virilis species group

Restriction fragment length polymorphism (RFLP) analysis has been used to evaluate mitochondrial DNA (mtDNA) variation in 12 sibling species forming the Drosophila virilis species group. The variation thresholds corresponding to the interspecific and interstrain levels have been determined. The results indicate that interspecific hybridization has significantly contributed to the evolutionary history of the virilis species group.     

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high‐copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost‐effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under‐studied groups.     

Migration-selection polymorphism in dioecious populations

Summary Conditions are derived for a protected polymorphism in a dioecious population subdivided into an arbitrary number of demes which exchange migrants. Generations are discrete and nonoverlapping; mutation and random drift are neglected. The analysis is restricted to a diallelic autosomal locus. In contrast to the monoecious case, the protection criteria depend on the order of migration and selection; they become identical for adult and juvenile migration if both the male and female backward migration matrices are symmetric, or the migration or selection patterns in the two sexes are the same. The protection conditions are presented explicitly for the Levene model. A recessive allele is protected in a panmictic dioecious population if the unweighted average of the recessive-to-dominant fitness ratios in the two sexes exceeds unity.Supported by the National Science Foundation (Grant No. DEB77-21494)     

Genome organization and species formation in vertebrates

Some years ago Wilson and co-workers proposed that the higher rates of karyotypic change and species formation of mammals compared to cold-blooded vertebrates are due to the formation of small demes, as favored by the social structuring and brain development of the former. Here, evidence is reviewed which indicates that mammals are more prone to karyotypic change and species formation than cold-blooded vertebrates because of their different genome organization. Similar evidence has also recently become available for birds. While this different organization appears to be a necessary and, in all likelihood, a sufficient condition for the increased rates of karyotypic change and species formation found in mammals, it is still possible that social structuring and brain development may have played an additional accelerating role.This paper was presented at the International Conference on Genome Plasticity held in Cancun, Mexico (December 8–12, 1991)     

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2–3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3–4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.     

Genome size in wild Pisum species

Genome size was measured in 75 samples of the wild pea species Pisum abyssinicum, P. elatius, P. fulvum and P. humile by ethidium-bromide (EB) flow cytometry (internal standard: Triticum monococcum) and Feulgen densitometry (internal standard: Pisum sativum Kleine Rheinländerin). Total variation of EB-DNA between samples covered 97.7% to 114.9% of the P. sativum value, and Feulgen DNA values were strongly correlated with EB-DNA values (r=0.9317, P < 0.001). Only P. fulvum was homogeneous in genome size (108.9% of P. sativum). Wide variation was observed between samples in P. abyssinicum (100.9–109.7%), P. elatius (97.7–114.9%) and P. humile (98.3–111.1% of P. sativum). In view of the world-wide genome size constancy in P. sativum, the present data are interpreted to show that the pea taxa with variable genome size are genetically inhomogeneous and that the current classification is not sufficient to describe the biological species groups adequately.     

Genome ecosystem and transposable elements species

Transposable elements are known to be “selfish DNA” sequences able to spread and be maintained in all genomes analyzed so far. Their evolution depends on the interaction they have with the other components of the genome, including genes and other transposable elements. These relationships are complex and have often been compared to those of species living and competing in an ecosystem. The aim of this current work is a proposition to fill the conceptual gap existing between genome biology and ecology, assuming that genomic components, such as transposable elements families, can be compared to species interacting in an ecosystem. Using this framework, some of the main models defined in the population genetics of transposable elements can then been reformulated, and some new kinds of realistic relationships, such as symbiosis between different genomic components, can then be modelled and explored.     

Insertion polymorphism of retrotransposable elements in populations of the insular, endemic species Drosophila madeirensis

The insertion site numbers of the retrotransposable elements (TE) 412, gypsy and bilbo were determined in individuals of five distinct natural populations of the endemic species Drosophila madeirensis from the island of Madeira. The TE distributions were compared to those of the paleartic, widespread and phylogenetically closely related species, D. subobscura. In situ hybridization and Southern blots showed that in D. madeirensis the number of insertion sites ranged between 10 and 15, three and six, and 35 and 42 for elements 412, gypsy and bilbo, respectively. The corresponding values for D. subobscura were similar. Two of these elements, 412 and gypsy, had very few insertions in the heterochromatin, unlike bilbo, which displayed a high heterochromatic insertion number. The Southern band polymorphism was very high, leading to within-population variation of 97.2%, whatever the population and the TE concerned. Using the polymorphic TE insertion sites as markers to analyse population structure by AMOVA, adapted for RAPD (Randomly Amplified Polymorphic DNA) data, we found small but significant genetic differences between the populations on Madeira. This slight differentiation, coupled with similar copy numbers for each TE between populations, suggests that the D. madeirensis species consists of a single, only slightly subdivided population. These data also show that insular populations and endemic species of Drosophila can have as many copies of TEs as more widespread species.     

Genome size variation and species diversity in salamanders

Salamanders (Urodela) have among the largest vertebrate genomes, ranging in size from 10 to 120 pg. Although changes in genome size often occur randomly and in the absence of selection pressure, nonrandom patterns of genome size variation are evident among specific vertebrate lineages. Several reports suggest a relationship between species richness and genome size, but the exact nature of that relationship remains unclear both within and across different taxonomic groups. Here, we report (a) a negative relationship between haploid genome size (C‐value) and species richness at the family taxonomic level in salamander clades; (b) a correlation of C‐value and species richness with clade crown age but not with diversification rates; (c) strong associations between C‐value and both geographic area and climatic‐niche rate. Finally, we report a relationship between C‐value diversity and species diversity at both the family‐ and genus‐level clades in urodeles.     

Evidence for genetic differentiation among Caspian tern (Hydroprogne caspia) populations in North America

The Caspian tern (Hydroprogne caspia) is a globally distributed seabird that breeds throughout North America, generally in low numbers. Many colonies are threatened by habitat loss and pollution. Additionally, adult terns compete directly with salmonid stocking programs on the west coast, where a large proportion of the fish they feed their young are stocked salmon smolts. North America colonies have been classified into five ‘breeding groups’ based on banding data and geography. To help delineate effective management units, we characterized variation in mitochondrial DNA (488 base pair fragment of cytochrome b) and five microsatellite loci among 111 terns from six sites representing three of the North American breeding areas. We found significant range-wide population differentiation (cytochrome b: global Φ_ST = 0.12, P < 0.01; microsatellites: global F_ST = 0.094, P < 0.001). Pacific Coast sites differed genetically from sites east of the Rocky Mountains, and sites in Central Canada differed from those in the Great Lakes region. Gene flow among these three regions appears to be restricted. Thus, our results indicate that at least three of the breeding regions delineated using banding data and geography should be treated as separate management units.     

34种秋海棠基因组大小比较与分析

以34种野生秋海棠(包括4个变种)为试材,水稻(Oryza sativa L.subsp.japonica Kato)为外标,采用流式细胞法测定其基因组大小,比较不同种、组之间基因组大小的差异,并分析与染色体数的相关性。结果表明:34种秋海棠基因组大小在0.292~2.554 pg之间,最大值约为最小值的9倍,平均基因组大小为0.863 pg,最小的为盾叶秋海棠(Begonia peltatifolia H.L.Li),最大的为水鸭脚秋海棠(B.formosana(Hayata)Masam.)。中国原产的30种秋海棠平均基因组大小(1C=0.925 pg)较南美洲原产的4种的(1C=0.398 pg)大,中国台湾原产的3种秋海棠基因组均比大陆原产的27种的大。中国原产秋海棠不同组间基因组的大小存在差异,同一组内基因组大小亦不相同,本研究所测材料以四室组的基因组最大,为1.285 pg,组内变化近3.2倍;秋海棠组和二室组次之,分别为0.895 pg和0.888 pg,组内变化近6.4、6.8倍;侧膜胎座组基因组最小,为0.721 pg,组内变化约1.2倍。相关性分析表明秋海棠基因组大小与染色体数无显著相关性。本结果可为秋海棠遗传多样性分析及基因组学研究提供一定的基础数据。     

The role of chromosomal polymorphism in divergence of populations and species of the genus Chironomus (Diptera)

The data on the structure and level of chromosomal polymorphism in natural populations of species of the genus Chironomus are summarized. A very high level of chromosomal polymorphism was noted for most species. Paracentric inversions prevailed among the chromosomal rearrangements found in natural populations. Changes in the set and frequency of inversion sequences are the most important factor of cytogenetic divergence of populations. Several cytogenetic types of populations were distinguished. The Palaearctic and Nearctic populations of Holarctic species diverged to a greater extent due to the formation of endemic Palearctic and Nearctic inversion sequences. The sequences common for both regions indicated a common ancestry of the populations. The cytogenetic distances between the Palearctic and Nearctic populations are greater by an order of magnitude than those between populations within each zoogeographic region. Divergence of species karyotypes was found to result from fixation of different inversion sequences in the course of evolution. The karyotypes of Palearctic and Nearctic species mainly differ by the presence of endemic Palearctic and Nearctic banding sequences. Several basic sequences common for some species allow the cytogenetic history of their origin to be revealed. A NJ phylogenetic tree was built for the genus Chironomus, demonstrating chromosomal evolution of its species.     

Genome organization and polymorphism of the murine beta-glucuronidase region

Thirty-eight kilobases of mouse genomic DNA which surround and include the coding sequences for beta-glucuronidase has been mapped. Intron-exon arrangements were determined by hybridization of genomic sequences with cDNA clones, and minimum estimates of gene length (11-17 kb) and intron number were obtained. Only a single gene was observed when genomic DNA was probed with subclones containing beta-glucuronidase coding sequence; there was no evidence of duplicated or pseudogenes. However, sequences distal to the 3' end of the gene are present elsewhere in the genome in a limited number of copies. Eight haplotypes of the beta-glucuronidase region with differing regulatory genotypes were compared for restriction fragment polymorphisms. Surprisingly little was found, considering the diverse origin of the haplotypes. Two of the polymorphisms that were found may be correlated with regulatory phenotypes. A BamHI site is missing from the CS and CL haplotypes that share regulatory properties, and a 0.2-kb insertion is consistently present in haplotypes showing increased response to induction by androgens in kidney.