The Balkan chamois,an archipelago or a peninsula? Insights from nuclear and mitochondrial DNA

The Balkan chamois (Rupicapra rupicapra balcanica) is widespread on the Balkan Peninsula, along mountain massifs from Croatia in the north to Greece in the south and Bulgaria in the east. Knowledge on the genetic structure of Balkan chamois populations is limited and restricted to local studies. Therefore, the main objective of this study was to use nuclear (16 microsatellites) and mitochondrial (partial 376 base pairs control region) markers to investigate the genetic structure of this chamois subspecies throughout its distribution range and to obtain information on the degree of connectivity of the different (sub)populations. We extracted DNA from bone, dried skin and muscle tissue and successfully genotyped 92 individuals of Balkan chamois and sequenced the partial control region in 44 individuals. The Bayesian analysis suggested 3 genetic clusters and assigned individuals from Serbia and Bulgaria to two separate clusters, while individuals from the other countries belonged to the same cluster. Thirty new haplotypes were obtained from partial mitochondrial DNA sequences, with private haplotypes in all analyzed populations and only two haplotypes shared among populations, indicating the possibility of past translocations. The subspecies genetic composition presented here provides the necessary starting point to assess the conservation status of the Balkan chamois and allows the development of conservation strategies necessary for its sustainable management and conservation.

     

Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?

Glass sponges (Hexactinellida) are a group of deep-water benthicanimals that have a unique syncytial organization and possessa characteristic siliceous skeleton. Although hexactinellidsare traditionally grouped with calcareous and demosponges inthe phylum Porifera, the monophyly of sponges and the phylogeneticposition of the Hexactinellida remain contentious. We determinedand analyzed the nearly complete mitochondrial genome sequencesof the hexactinellid sponges Iphiteon panicea and Sympagellanux. Unexpectedly, our analysis revealed several mitochondrialgenomic features shared between glass sponges and bilateriananimals, including an Arg Ser change in the genetic code, acharacteristic secondary structure of one of the serine tRNAs,highly derived tRNA and rRNA genes, and the presence of a singlelarge noncoding region. At the same time, glass sponge mtDNAcontains atp9, a gene previously found only in the mtDNA ofdemosponges (among animals), and encodes a with an atypical A11–U24 pair that is alsofound in demosponges and placozoans. Most of our sequence-basedphylogenetic analyses place Hexactinellida as the sister groupto the Bilateria; however, these results are suspect given acceleratedrates of mitochondrial sequence evolution in these groups. Thus,it remains an open question whether shared mitochondrial genomicfeatures in glass sponges and bilaterian animals reflect theirclose phylogenetic affinity or provide a remarkable exampleof parallel evolution.     

Endemic or introduced? Phylogeography of Asparagopsis (Florideophyceae) in Australia reveals multiple introductions and a new mitochondrial lineage

The red seaweed Asparagopsis taxiformis embodies five cryptic mitochondrial lineages (lineage 1–5) introduced worldwide as a consequence of human mediated transport and climate change. We compared globally collected mitochondrial cox2‐3 intergenic spacer sequences with sequences produced from multiple Australian locations and South Korea to identify Asparagopsis lineages and to reveal cryptic introductions. We report A. taxiformis lineage 4 from Cocos (Keeling) Islands, Australia, and the highly invasive Indo‐Pacific Mediterranean lineage 2 from South Korea and Lord Howe Island, Australia. Phylogeographic analysis showed a clear haplotype and geographic separation between western Australian and Great Barrier Reef (GBR) isolates belonging to the recently described lineage 5. The same lineage, however, was characterized by a substantial genetic and geographic break between the majority of Australian specimens and Asparagopsis collections from South Solitary Island, Southern GBR, Lord Howe Island, Kermadec Islands, Norfolk Island, New Caledonia and French Polynesia. The disjunct geographic distribution and sequence divergence between these two groups supports the recognition of a sixth cryptic A. taxiformis mitochondrial lineage. As climatic changes accelerate the relocation of biota and offer novel niches for colonization, periodic surveys for early detection of cryptic invasive seaweeds will be critical in determining whether eradication or effective containment of the aliens are feasible.     

New evidence from observations of progressions of mandrills (Mandrillus sphinx): a multilevel or non-nested society?

African papionins are well known for the diversity of their social systems, ranging from multilevel societies based on one-male-multifemale units (OMUs) to non-nested societies. However, the characteristics of Mandrillus societies are still unclear due to difficult observational conditions in the dense forests of central Africa. To elucidate the characteristics of mandrill societies and their social systems, I analysed the age–sex compositions, behaviours, and progression patterns of their horde/subgroups using videos of them crossing open places. The progressions were very cohesive, and the very large aggregations (169–442 individuals) had only 3–6 adult males (1.4–1.8 % of all individuals) and 11–32 subadult males (6.5–7.2 %). No herding behaviours were observed in the males, and most of the small clusters within the progressions were not analogous to the OMUs of a multilevel society but instead consisted of only adult females and immatures. The progressions of alert mandrills showed patterns similar to those observed in a non-nested social system: females with dependent infants were concentrated toward the rear and adult and subadult males toward the front. These results suggest that cohesive aggregations and a female-biased sex ratio are common characteristics of mandrill species. Mandrills may form female-bonded and non-nested societies, although their fission–fusion dynamics may be different from those typical of savannah baboons.     

Narrow species concepts in the Frullania dilatata–appalachiana–eboracensis complex (Porellales, Jungermanniopsida): evidence from nuclear and chloroplast DNA markers

We investigated the phylogeny of a Holarctic-Asian group of Frullania species, the Frullania dilatata–F. appalachiana–F. eboracensis complex, using multiple accessions of morphologically circumscribed taxa and three molecular markers (nrITS region, cp DNA trnL-F and atpB-rbcL regions). Maximum parsimony and likelihood analyses indicated monophyly of morphologically defined taxa. Our phylogenies support a species rather than a subspecies concept within the complex, with four species in North America (F. appalachiana, F. eboracensis, F. parvistipula and F. virginica), and two species in Europe (F. dilatata and F. parvistipula). Accessions of F. dilatata from Southeast Europe and Asia are separated from other European accessions, indicating a former disjunct range of the species.     

Do pregnant lizards resorb or abort inviable eggs and embryos? Morphological evidence from an Australian skink,Pseudemoia pagenstecheri

Although pregnant viviparous squamates are sometimes claimed to be able to resorb inviable eggs and embryos from the uterus, definitive evidence for such resorption is not available. After placing pregnant female Pseudemoia pagenstecheri into conditions under which embryonic development is terminated, we periodically harvested the gravid oviducts and examined them histologically. Females contained abnormal and degenerating eggs and embryos that had died in various stages of development. Dead embryos had undergone extensive cytolysis, dissolution, and aseptic necrosis and vitelline masses showed signs of deterioration and passage down the oviduct. The uterine mucosa lay in direct contact with the vitelline material, with no intact shell membrane intervening between them. Yolk was sometimes displaced into the exocoelom and allantoic cavity due to rupture of the extraembryonic membranes. Histological examination revealed no evidence of the uptake of yolk by the uterine epithelium or its accumulation in the subepithelial connective tissue. In many specimens, the uterine epithelium showed minuscule, apical granules. The position, appearance, and staining properties of the granules suggests them to be secretory, a manifestation of placentotrophy. Our observations indicate that P. pagenstecheri females retain dead eggs and embryos for several weeks or longer, yet do not resorb them during that period. This lizard is the second placentotrophic skink species in which resorption has been suspected, but in which abortive eggs appear to be retained or extruded instead of being resorbed by the oviducts. Researchers should not assume that squamates can digest and resorb oviductal eggs without definitive morphological evidence.     

A preliminary study on genetic differentiation in Littorina saxatilis from Galway Bay,Ireland: Littorina tenebrosa Montagu – a valid species or ecotype?

Littorina tenebrosa is a small fragile-shelled periwinkle which lives on permanently submerged algae in coastal lagoons and non-tidal brackish pools. This periwinkle is a member of the rough periwinkle group which also comprises Littorina saxatilis, L. arcana, L. compressa and L. neglecta and is most closely related to L. saxatilis although its exact systematic status is in some doubt. Based on its unique ecology many believe L. tenebrosa to be a valid species. However, shell morphometric and allozyme analyses on Scottish and Swedish populations of L. tenebrosa and L. saxatilis have indicated that the two periwinkles are virtually identical. Preliminary results on five allozyme loci (AAT-1, GPI, PGM-1, PGM-2 and PNP) in samples of L. tenebrosa and L. saxatilis from Golam Head, Lettermullen, and other locations on the west coast of Ireland show L. tenebrosa to be genetically differentiated from L. saxatilis At Golam Head, where opportunities for gene flow occur between the two taxa, L. tenebrosa is as genetically differentiated from local L. saxatilis as it is from L. saxatilis from more geographically distant locations.     

Does enemy release matter for invasive plants? evidence from a comparison of insect herbivore damage among invasive,non-invasive and native congeners

One of the most popular single-factor hypotheses that have been proposed to explain the naturalization and spread of introduced species is the enemy release hypothesis (ERH). One ramification of the ERH is that invasive plants sustain less herbivore damage than their native counterparts in the invaded range. However, introduced plants, invasive or not, may experience less herbivore damage than the natives. Therefore, to test the role of natural enemies in the success of invasive plants, studies should include both invasive as well as non-invasive introduced species. In this study, we employed a novel three-way comparison, in which we compared herbivore damage among native, introduced invasive, and introduced non-invasive Eugenia (Myrtaceae) in South Florida. We found that introduced Eugenia, both invasive and non-invasive, sustained less herbivore damage, especially damage by oligophagous and endophagous insects, than native Eugenia. However, the difference in insect damage between introduced invasive and introduced non-invasive Eugenia was not significant. Escape from herbivores may not account for the spread of invasive Eugenia. We would not have been able to draw this conclusion without inclusion of the non-invasive Eugenia species in the study.     

Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2′-β-Hydroxylase, from Brevundimonas sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls

A carotenoid biosynthesis gene cluster mediating the production of 2-hydroxyastaxanthin was isolated from the marine bacterium Brevundimonas sp. strain SD212 by using a common crtI sequence as the probe DNA. A sequence analysis revealed this cluster to contain 12 open reading frames (ORFs), including the 7 known genes, crtW, crtY, crtI, crtB, crtE, idi, and crtZ. The individual ORFs were functionally analyzed by complementation studies using Escherichia coli that accumulated various carotenoid precursors due to the presence of other bacterial crt genes. In addition to functionally identifying the known crt genes, we found that one (ORF11, named crtG) coded for a novel enzyme, carotenoid 2,2′-β-hydroxylase, which showed intriguingly partial homology with animal sterol-C5-desaturase. When this crtG gene was introduced into E. coli accumulating zeaxanthin and canthaxanthin, the resulting transformants produced their 2-hydroxylated and 2,2′-dihydroxylated products which were structurally novel or rare xanthophylls, as determined by their nuclear magnetic resonance and high-performance liquid chromatography/photodiode array detector/atmospheric pressure chemical ionization mass spectrometry spectral data. The new carotenoid produced was suggested to have a strong inhibitory effect on lipid peroxidation.     

Does the Gonostomum-patterned oral apparatus in hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora,Spirotrichea)

The classification of hypotrichs based on the gonostomatid oral structure is widely accepted, but the phylogenetic signal of this character is unknown. Here, we infer the species phylogeny of those gonostomatids for which molecular data are available, plus26 new sequences of SSU-rDNA, ITS1-5.8 S-ITS2 and LSU-rDNA genes. The results indicate that:(i) the endoral is more phylogenetically informative than the paroral;(ii) the structure of the endoral and the Gonostomum-pattern adoral zone of membranelles are plesiomorphies for the hypotrichs sensu stricto;(iii) the group of species possessing these features is monophyletic in all our phylogenetic analyses, except that for the SSU-rDNA;(iv) Schmidingerotrichidae is monophyletic in all trees, suggesting that it is a well-defined family;(v) the Gonostomatidae is polyphyletic in the SSU-rDNA and ITS1-5.8 S-ITS2 trees, with Gonostomum, Cladotricha, Cotterillia, Metagonostomum, Paragonostomum and Wallackia distributed among separate clades, but monophyletic in the LSU-rDNA and concatenated trees;(vi) higher hypotrich taxa such as core urostyloids and core sporadotrichids/stichotrichids might have evolved from species that possessed a gonostomatid oral apparatus.     

Similarity of different β-strands flanked in loops by glycines and prolines from distinct (α/β)8-barrel enzymes: Chance or a homology?

Many (alpha/beta)8-barrel enzymes contain their conserved sequence regions at or around the beta-strand segments that are often preceded and succeeded by glycines and prolines, respectively. alpha-Amylase is one of these enzymes. Its sequences exhibit a very low degree of similarity, but strong conservation is seen around its beta-strands. These conserved regions were used in the search for similarities with beta-strands of other (alpha/beta)8-barrel enzymes. The analysis revealed an interesting similarity between the segment around the beta 2-strand of alpha-amylase and the one around the beta 4-strand of glycolate oxidase that are flanked in loops by glycines and prolines. The similarity can be further extended on other members of the alpha-amylase and glycolate oxidase subfamilies, i.e., cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, and flavocytochrome b2, respectively. Moreover, the alpha-subunit of tryptophan synthase, the (alpha/beta)8-barrel enzyme belonging to the other subfamily of (alpha/beta)8-barrels, has both investigated strands, beta 2 and beta 4, similar to beta 2 of alpha-amylase and beta 4 of glycolate oxidase. The possibilities of whether this similarity exists only by chance or is a consequence of some processes during the evolution of (alpha/beta)8-barrel proteins are briefly discussed.     

Winter hatching in New England populations of invasive pheretimoid earthworms <Emphasis Type="Italic">Amynthas agrestis</Emphasis> and <Emphasis Type="Italic">Amynthas tokioensis</Emphasis>: a limit on population growth,or aid in peripheral expansion?

Some Asian megascolecid earthworms, e.g. Amynthas agrestis and Amynthas tokioensis, are highly invasive and have only recently been reported from natural ecosystems in the northeastern USA. There, they are annual earthworms that survive the winter as cocoons (an egg in a tough covering). Hatching occurs in mid-April when temperatures rise consistently above 10 °C. In some years, winter temperatures also reach 10 °C during short warming episodes, but hatchlings then are likely to die when temperatures drop again. To test this hypothesis, soil was collected on 7 sampling dates during January–May 2016 at one site in the Champlain Valley, Vermont and extracted for the cocoons. Both hatched and unhatched cocoons were enumerated and identified to species by both size and sequencing of the mitochondrial cytochrome c oxidase I gene (COI). A regression model on the number of unhatched cocoons over time predicted that ~ a quarter (A. agrestis) and ~ a third (A. tokioensis) would hatch before mid-May; no hatchlings were observed. Thus, hatching during warming periods in winter seemingly resulted in high mortality. Such winter hatching, and loss, may increase with climate warming in the region because winter warming periods should become more common. Climate warming could therefore reduce ability of the invasive earthworms to persist in northern habitats. Conversely, rapid hatching when the soil warms in spring could have an ecological benefit by allowing opportunities to expand at the thermal edge of the range as the climate continues to warm.