A first-generation microsatellite-based integrated genetic and cytogenetic map for the European rabbit (Oryctolagus cuniculus) and localization of angora and albino

Although the European rabbit (Oryctolagus cuniculus) is used both in agronomics and in research, genomic resources for this species are still limited and no microsatellite-based genetic map has been reported. Our aim was to construct a rabbit genetic map with cytogenetically mapped microsatellites so as to build an integrated genetic and cytogenetic map. A reference population of 187 rabbits comprising eight three-generation families with 10-25 offspring per family was produced. One hundred and ninety-four of 305 previously identified microsatellites were included in this study. Of these, 158 were polymorphic with two to seven alleles. The map reported here comprises 111 markers, including 104 INRA microsatellites, five microsatellites from another source and two phenotypic markers (angora and albino). Ninety markers were integrated into 20 linkage groups. The remaining 21 microsatellites mapped to separate linkage groups, 19 with a precise cytogenetic position and two with only a chromosomal assignment. The genetic map spans 2766.6 cM and covers 20 rabbit chromosomes, excluding chromosomes 20, 21 and X. The density of this map is limited, but we used it to verify the location of angora and albino on chromosomes 15q and 1q, respectively, in agreement with previously published data. This first generation genetic/cytogenetic map will help gene identification and quantitative trait loci mapping projects in rabbit.     

Colonization history of Mallorca Island by the European rabbit,Oryctolagus cuniculus,and the Iberian hare,Lepus granatensis (Lagomorpha: Leporidae)

The Mediterranean islands have a long history of human‐mediated introductions resulting in frequent replacements of their fauna and flora. Although these histories are sometimes well documented or may be inferred from paleontological studies, the use of phylogenetic and population genetic reconstruction methods provides a complementary perspective for answering questions related to the history of insular species. In the present study, we infer the colonization history of Mallorca (Balearic Islands) by the European rabbit (Oryctolagus cuniculus) and the Iberian hare (Lepus granatensis) using sequence variation of the mitochondrial DNA control region from continental and insular specimens (total of 489 sequences). Additionally, the taxonomic identity of Mallorcan L. granatensis was confirmed using a diagnostic nuclear marker. For both Mallorcan rabbits and hares, genetic diversity was comparable to the continental populations, suggesting the introduction of multiple lineages. Two Mallorcan haplogroups were found in hares, which likely correspond to two introduction events. Rabbits from Mallorca were identified as belonging to the subspecies Oryctolagus cuniculus cuniculus, and may have been originated both from Iberian and French populations. The molecular estimates of the timing of the colonization events of the Mallorcan lagomorphs are consistent with human‐mediated introductions by early settlers on the islands. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 748–760.     

The phylogeny of lower Hymenoptera (Insecta), with a summary of the early evolutionary history of the order

A cladistic analysis of the lower Hymenoptera, including all the ‘symphytan’ families and the apocritan families Stephanidae, Megalyridae, Trigonalyidae, Ibaliidae, Vespidae and Gasteruptiidae, has been undertaken. A total of 98 characters were scored for 21 taxa. Twenty equally parsimonious minimum-length trees were obtained. The phylogenetic status of the Xyelidae is uncertain: they might be monophyletic. or the Xyelinae might be the sistergroup of the rest of the Hymenoptera. The non-xyelid Hymenoptera are probably monophyletic; the phylogeny Tenthredinoidea + (Megalodontoidea + (Cephidae + (Anaxyelidea + (Siricidae + (Xiphydriidae + (Orussidae + Apocrita)))))) is proposed for this clade. The Blasticotomidae are probably the sistergroup of all othe Tenthredinoidea, but tenthredinoid phylogeny is otherwise uncertain. Substantial homoplasy occurs within the ‘siricoid’ families, making the relative positions of the Anaxyelidae and Siricidae uncertain. The Stephanidae might be the sistergroup of the rest of the Apocrita; the phylogeny of the remaining apocritan taxa included is insufficiently elucidated. The phylogeny proposed here supports the hypothesis that the appearance of parasitism in the Hymenoptera took place in the common ancestor of Orussidae + Apocrita, the host of which was probably wood boring insect larvae. The exact larval mode of feeding of the ancestral hymenopteran cannot be determined due ot the diversity of lifestyles in the basal lineages of the order.     

Status and relationships of the extinct giant Canary Island lizard Gallotia goliath (Reptilia: Lacertidae), assessed using ancient mtDNA from its mummified remains

Ancient mitochondrial DNA sequences (378 base pairs of cytochrome b and 368 of 12S rRNA) extracted from a mummified extinct giant lizard, Gallotia goliath , from eastern Tenerife, Canary Islands, were used to assess the species status and relationship of this form within the genus. G. goliath is clearly a member of the G. simonyi group of the western Canary islands (Tenerife, La Gomera, El Hierro and La Palma) and is not closely related to the giant G. stehlini of Gran Canaria. Contrary to recent opinion, it is phylogenetically distinct, within the G. simonyi group, from the extant G. simonyi of El Hierro and also from the recently discovered live G. gomerana on La Gomera and from G. intermedia in north-western Tenerife. It may be the sister taxon of either all the other members of the G. simonyi group or of G. intermedia . The phylogenetic distinctness of G. goliath makes Tenerife unique among oceanic islands in having had one giant and two medium-sized lizard species that were probably substantially herbivorous, the others being G. intermedia and G. galloti . Gallotia shows great community differences on other islands in the Canaries, two having a single small species, one a single giant, and three a giant and a medium-sized form. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 659–670.     

Phylogenetic placement of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum,and the anamorphic yeastSympodiomycopsis paphiopedili by means of 18S rRNA gene sequence analysis

The 18S ribosomal RNA gene sequences of the basidiomycetous yeastsKondoa malvinella andRhodosporidium dacryoidum, and an anamorphic yeastSympodiomycopsis paphiopedili were determined. The 18S rRNA gene ofR. dacryodium IAM 13522 (ex type) revealed the presence of an intron-like region with a length of 404 nucleotides, which is presumably assigned to a group I intron. The phylogenetic tree, including 34 published reference sequences, was inferred from 1493 sites which could be unambiguously aligned. The molecular phylogeny, using the ascomycetes as an outgroup, divided the basidiomycetes into three major lineages. The first lineage was composed of the smut fungi (Ustilaginales), represented byUstilago maydis, U. hordei, andTilletia caries, includingS. paphiopedili. The second lineage included the type species of teliospore-forming yeast generaLeucosporidium, Rhodosporidium, andSporidiobolus, and the generaErythrobasidium andKondoa, both previously included in the Filobasidiaceae.Rhodosporidium dacryodium showed a close relationship withE. hasegawianum, which was backed by a high bootstrap support. The rust fungiCronartium ribicola andPeridermium harknessii were also included in this lineage. The last lineage was formed by the filobasidiaceous yeasts,Cystofilobasidium capitatum, Mrakia frigida, Filobasidium floriforme, andFilobasidiella neoformans, and the anamorphic yeastsBullera alba (the anamorph ofBulleromyces albus) andTrichosporon cutaneum. Members ofTremella and selected hymenomycetous genera were also included in this lineage.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with the following accession numbers D13459 (Rhodosporidium dacryodium), D13776 (Kondoa malvinella), and D14006 (Sympodiomycopsis paphiopedili).     

A conservation paradox for the 21st century: the European wild rabbit Oryctolagus cuniculus,an invasive alien and an endangered native species

• 1 This review highlights the status of the European wild rabbit Oryctolagus cuniculus, which is threatened within its native range and yet is a highly successful colonizer across its worldwide, introduced range.
• 2 The European wild rabbit is a keystone species in Iberia, and the survival of a range of threatened predator species, including the Iberian lynx Lynx pardinus and Spanish imperial eagle Aquila aldabertii, is dependent upon the restoration of rabbit populations. Although not native to the UK, the rabbit also performs significant ecosystem services for nationally rare UK species, by maintaining short sward heights in heathland and grassland ecosystems, and serving as a prey item for populations of predators.
• 3 We identify the European wild rabbit as an excellent model to demonstrate the wide range of complex effects that an introduced mammalian species may exert on ecosystems to which it has been introduced. These effects include habitat degradation following overgrazing, competition with native mammals and facilitating meso‐predator release and hyperpredation.
• 4 We also show that rabbit eradication from some sites may generate more problems than are solved because of the impacts of trophic cascades stemming from dependence on rabbits by native predator assemblages.

     

Morphology and phylogeny of three trachelocercids (Protozoa,Ciliophora, Karyorelictea), with description of two new species and insight into the evolution of the family Trachelocercidae

Although trachelocercid ciliates are common in marine sandy intertidal zones, methodological difficulties mean that their biodiversity and evolutionary relationships have not been well documented. This paper investigates the morphology and infraciliature of two novel Trachelolophos and one rarely known form, Tracheloraphis similis Raikov and Kovaleva, 1968, collected from the coastal waters of southern and eastern China. The small subunit (SSU) rRNA gene sequences of two of the species are presented, allowing the phylogenetic position of the genus Trachelolophos to be revealed for the first time. Phylogenetic analyses based on SSU rRNA gene sequences indicate that Trachelolophos branches with Kovalevaia and forms a sister clade with the group including Prototrachelocerca, Trachelocerca and Tracheloraphis. The monophyly of Trachelocerca is not rejected by the approximately unbiased (AU) test (P = 0.209, > 0.05) but that of Tracheloraphis is rejected (P = 3e‐033, < 0.05). The newly sequenced genus Trachelolophos, and recent studies on the morphology and phylogeny of the family Trachelocercidae, suggest two new hypotheses about the evolution of the seven genera within Trachelocercidae, based on either infraciliature or molecular evidence. Both hypotheses suppose the compound circumoral kineties in the oral apparatus is a plesiomorphic feature while the single circumoral kinety is synapomorphic. More evidence is still needed, however, as to whether the closed circumoral kinety with no brosse feature in Trachelocerca is ancestral or secondarily reduced. © 2015 The Linnean Society of London     

The hemopexin locus: Its assignment to Linkage Group I in the laboratory rabbit (Oryctolagus cuniculus) and evidence for a fourth allele*

The hemopexin locus phenotypes were determined for 450 animals with polyacrylamide gel electrophoresis, and the presence of a fourth allele at this locus was revealed. Of the 19 mating types segregating at this locus, 17 demonstrated segregation ratios consistent with the hypothesis of a four allele, codominant, autosomal system. Studies of three of our largest inbreeding lines indicated that fixation at this locus has occurred in two of them. Linkage studies showed that the Hx locus is located between the color locus, c , and the Hq blood group locus; therefore it is assigned to Linkage Group I of the rabbit.     

The life cycle and parasitism of the European grasshopper mite Eutrombidium trigonum (Hermann 1804) (Prostigmata: Parasitengonae: Microthrombidiidae), a potential agent for biological control of grasshoppers (Saltatoria)

The European grasshopper mite Eutrombidium trigonum (Hermann) lives concealed in the soil in relatively warm and xeric biotopes. The eggs and spermatophores display a moderate drought resistence. The adults, during mating and larvae leave the soil and are to be found on the soil surface. The host range of the parasitic larva is restricted to Saltatoria. The larval growth is much greater than that of other instars of E. trigonum; however, no damage or other effects on the hosts were obvious and usually the hosts survived parasitism. The active post-larval instars of E. trigonum are predatory and feed exclusively on the eggs of Acrididae. The life cycle of E. trigonum is uni- to semi-voltine and is synchronized by an obligatory diapause of the adult instar before reproduction.Deceased.     

Morphological and molecular taxonomy of a new Daptonema (Nematoda,Xyalidae) with comments on the systematics of some related taxa

A new species of Daptonema is described based upon morphological characters and 18S rRNA sequence. Daptonema matrona sp. nov. was collected in Pina Basin (north‐eastern Brazil). It differs from all other species of the genus by the presence of reduced cephalic setae and straight spicules. These features require an adaptation of the generic diagnosis. Moreover, the females are characterized by intra‐uterine development of the offspring, considered herein as their major autapomorphic feature. Molecular systematic analyses supported Daptonema matrona sp. nov. as a distinct genetic and evolutionary lineage. The data also indicate hypotheses of taxonomic synonymies amongst some related taxa from Xyalidae as well as the paraphyly of Daptonema. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 1–15.     

Postglacial dispersal of the European rabbit (Oryctolagus cuniculus) on the Iberian peninsula reconstructed from nested clade and mismatch analyses of mitochondrial DNA genetic variation

Nested clade analysis was applied to cytochrome b restriction site data previously obtained on 20 natural populations of the European rabbit across the Iberian Peninsula to test the hypothesis of postglacial dispersal from two main refugia, one in the northeast and the other in the southwest. Apart from historical fragmentation that resulted in geographic discontinuity of two distinct mitochondrial DNA (mtDNA) clades A and B, patterns of haplotype genetic variability have been shaped mostly by restricted gene flow via isolation by distance. The distribution of tip versus interior haplotypes suggests that dispersal occurred from both the southwestern and northeastern groups. Dispersal from the southwest had a north and northwest direction, whereas from the northeast it had mostly a western and southern orientation, with subsequent overlap in a southeastern-northwestern axis across the Iberian Peninsula. The analysis of the pairwise mismatch distribution of a 179-181-bp fragment of the mtDNA control region, for seven of those populations, further supports the idea that major patterns of dispersal were in the direction of central Iberia. Additionally, rabbit populations do not show signs of any significant loss of genetic diversity in the recent past, implying that they maintained large population sizes and structure throughout the ice ages. This is congruent with the fact that the Iberian Peninsula was itself a glacial refugium during Quaternary ice ages. Nonetheless, climatic oscillations of this period, although certainly milder than in northern Europe, were sufficient to affect the range distributions of Iberian organisms.     

The morphology and systematics of Mammalodon colliveri (Cetacea: Mysticeti), a toothed mysticete from the Oligocene of Australia

Mammalodon colliveri is an unusual toothed archaic mysticete (Cetacea) from the Upper Oligocene Jan Juc Formation of south‐east Australia. The morphology of the holotype skull and postcrania are described in detail. Superimposed on the generally plesiomorphic archaeocete‐like morphology of Mammalodon are subtle mysticete synapomorphies. Derived features of Mammalodon include a short and bluntly rounded rostrum, reduced premaxillae, and anterodorsally directed orbits. Within Mysticeti, this suite of features is unique. The aberrant rostral morphology of Mammalodon suggests specialization for suction feeding. Janjucetus hunderi is placed in an expanded family Mammalodontidae. Phylogenetic analysis corroborates the monophyly of Basilosauridae, Neoceti, Odontoceti, and Mysticeti, and yields a novel hypothesis of toothed mysticete relationships: a basal clade of undescribed toothed mysticetes from South Carolina, a Llanocetidae + Mammalodontidae clade, and monophyletic Aetiocetidae are posited as successive sister taxa to edentulous baleen whales (Chaeomysticeti). Toothed archaic mysticetes clearly employed diverse prey capture strategies, with exaptations for filter feeding evolving sequentially in stem group Mysticeti. A stratigraphically calibrated phylogeny implies that the initial diversification of Mysticeti occurred during the Late Eocene. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 367–476.     

New contributions to the taxonomy of urostylid ciliates (Ciliophora,Hypotrichia), with establishment of a new genus and new species

Hypotrichia, one of the most complex and highly differentiated groups in Ciliophora, has been the object of extensive studies, especially in recent years. Nevertheless, methodological difficulties and insufficient faunistic studies have limited our understanding of their biodiversity and phylogeny. In this study, one novel urostylid ciliate, Pseudoholosticha zhaoi nov. gen., nov. spec. and two populations of Anteholosticha monilata (Kahl, 1928) Berger, 2003, type species of the latter genus, are studied using an integrative approach (live observation, protargol impregnation, scanning electron microscopy, and phylogenetic analysis) to provide further insights into the diversity, classification, and phylogeny of this group of ciliates. Pseudoholosticha nov. gen. can be separated from other morphologically similar genera mainly by the absence of buccal and caudal cirri. A key to 12 morphologically similar genera and illustrations of their cirral patterns are provided. The validation of the new genus and new species is supported by both morphological and phylogenetic analyses. The first 18S rRNA gene sequence of A. monilata, with detailed morphological data, provided a reliable clarification of A. monilata populations and corroborated the phylogenetic position of the type species of the polyphyletic genus Anteholosticha.     

Taxonomic revision of oil‐producing green algae,Chlorococcum oleofaciens (Volvocales,Chlorophyceae), and its relatives

Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re‐examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil‐producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov.     

Morphology,Morphogenesis and Small Subunit rRNA Gene Sequence of a Soil Hypotrichous Ciliate,Perisincirra paucicirrata (Ciliophora,Kahliellidae), from the Shoreline of the Yellow River,North China

The morphology, morphogenesis, and 18S rRNA gene sequence of a soil hypotrichous ciliate Perisincirra paucicirrata, isolated from north China, were investigated. Perisincirra paucicirrata differs from its congeners in: (1) having a body length to width ratio in vivo of 4:1, (2) its adoral zone occupying between 15% and 25% of the total body length, and (3) the presence of two parabuccal cirri, three left (with 10–16 cirri each) and two right marginal rows (with 14–24 cirri each), and three dorsal kineties. Our study offers a first attempt to begin to map the morphogenetic processes of the genus, which are mainly characterised by the following: the formation of four frontal ventral transverse anlagens for each daughter cell, with the proter's anlage I originating from the reorganised anterior part of the parental paroral; the paroral and endoral anlage developed from the reorganised old endoral and do not contribute the first frontal cirrus; the frontoventral transverse anlage I contributing the left frontal cirrus; anlage II generating the middle frontal and the buccal cirri; anlage III developing the right frontal cirrus and the anterior parabuccal cirrus; and anlage IV contributing the posterior parabuccal cirrus. As an additional contribution, we judge that the inner one or the two right rows of P. kahli and P. longicirrata are marginal rows. Phylogenetic analysis based on SSU rDNA sequences suggests that Perisincirra is related to sporadotrichids, but provides no credible evidence for its taxonomic position.     

The evolution of the diatoms (Bacillariophyta). I. Origin of the group and assessment of the monophyly of its major divisions

The diatoms are one of the best characterised algal groups. Despite this, little is known of the evolution of the group from the earliest cell to the myriad of taxa known today. Relationships among taxa at the family or generic level have been recognised in some diatoms. However, relationships at higher taxonomic levels are poorly understood and have often been strongly influenced by the first appearances of key taxa in the fossil record. An independent assessment of relationships among the diatoms at these higher taxonomic levels has been made using rRNA sequence data to infer phylogenetic relationships. In this paper we present an analysis of 18S rRNA data from several chosen centric, araphid and raphid pennate taxa. The phylogenetic inferences from these 18S rRNA sequences are supported by evidence from the fossil record and evidence from ontogenetic data. Ribosomal RNA data indicate that both the centric and araphid pennate lineages may not be monophyletic.     

Two New Endozoic Ciliates,Clevelandella lynni sp. n. and Nyctotherus galerus sp. n., Isolated from the Hindgut of the Wood‐feeding Cockroach Panesthia angustipennis (Illiger, 1801)

Two new ciliate species, Clevelandella lynni sp. n. and Nyctotherus galerus sp. n., were discovered in the hindgut of wood‐feeding panesthiine cockroaches. Their morphology was studied using standard methods, and their phylogenetic positions within the order Clevelandellida were determined using the 18S rRNA gene sequences. Clevelandella lynni is characterized by a prominent peristomial projection, a notched left body margin, a tear‐shaped to broadly ovoidal macronucleus, a karyophore attached to the right body margin, and by an adoral zone composed of on average 48 membranelles and extending about 51% of body length. The diagnostic features of N. galerus include a short posterior body projection, a spherical to broadly ellipsoidal macronucleus, a karyophore attached to the right and left body margins, refractile bodies densely packed anterior to the macronucleus, and an adoral zone composed of on average 57 membranelles and extending about 70% body length. The order Clevelandellida was consistently depicted as monophyletic in 18S rRNA gene phylogenies. Nyctotherus galerus was placed in the paraphyletic family Nyctotheridae, as sister taxon to all other Nyctotherus and Clevelandella species isolated from cockroaches. Clevelandella lynni fell in the monophyletic family Clevelandellidae, as sister taxon to C. panesthiae KC139718 but with very poor statistical support.