The geographic ranges of Martes species (Carnivora,Mustelidae) in the Middle Urals in the Late Pleistocene and Holocene

Martes mandibles from Late Pleistocene and Holocene sites in the Middle Urals were identified to the species level using discriminant analysis. As has been shown, sable lived there in the Late Pleistocene, with its geographic range covering all this area until the end of the 18th century; however, its range started to reduce towards the north and northeast in the early 19th century. Over 150 years, the southwestern boundary of the sable range shifted by 3° to reach the current position by the mid-20th century. The pine marten appeared in the Middle Urals in the Holocene no later than 8000 years ago and inhabits this territory at present.     

Genetic analysis of Turkish martens: Do two species of the genus Martes occur in Anatolia?

Stone marten (Martes foina) and European pine marten (M. martes) occur in western Eurasia. Current distributions of martens within Turkey and phylogenetic relationships among the Turkish and other populations of the two species within Eurasia remain relatively unknown. In this study, we aimed to determine genetic diversity within Martes populations inhabiting Turkey and to reveal the phylogenetic relationships among the Turkish and conspecific populations of the two marten species, using mitochondrial cytochrome b (CytB) sequences. Twenty‐four (24) haplotypes were identified among 86 marten samples collected across Turkey, including 23 novel haplotypes. Genetic distances among the Turkish haplotypes ranged from 0.1% to 0.8%, with an average of 0.3%. The 24 Turkish haplotypes were analysed together with those of conspecific populations deposited in GenBank. Phylogenetic (Bayesian Inference, maximum likelihood, neighbor‐joining) and network analyses revealed that all of the Turkish samples belonged to M. foina and that samples of M. martes were not encountered. Haplotypes of M. foina were divided into five haplogroups. The haplogroup including the two Chinese samples differed markedly from other the haplogroups. The remaining haplogroups contained samples from both the Turkish and European populations. We found that there was a genetically close relationship between the Turkish and the European stone marten populations. As a result of this study, M. martes may not be distributed in the Anatolian part of Turkey, possibly due to a barrier effect of two straits (Dardanelles and Bosporus) and the Caucasus Mountains. On the other hand, M. foina is distributed in both the Anatolian and Thracian parts of Turkey. Our results suggest that Turkey was likely one of the refuges for M. foina during Pleistocene glacial periods and is one of the centres of distribution of stone marten for Europe and the surrounding regions.     

New methods for species and sex determination in three sympatric Mustelids, Mustela itatsi, Mustela sibirica and Martes melampus

We developed novel species and sex determination methods for three Japanese mustelid species. We used DDX3Y to determine sex and generated a primer set to amplify both DDX3X and DDX3Y DNA in Mustela itatsi, M. sibirica and Martes melampus. To determine species and sex simultaneously, we generated fluorescence-labelled primers that give different fragment lengths at D-loop, DDX3X and DDX3Y of these three species using a DNA sequencer.     

Range expansion of the pine marten (Martes martes) in an agricultural landscape matrix (NW Italy)

Habitat segregation is considered to favour the coexistence of sympatric pine martens Martes martes and stone martens M. foina, the latter being displaced to agricultural and urbanised areas. Subsequent to the report of pine martens in cultivated areas of the western River Po plain (NW Italy), we reviewed all available information on the presence of this species in plain areas of northern Italy and, for two study areas, applied a non-invasive PCR-RFLP method for the identification of Martes species from faecal mtDNA.A total of 24 pine marten records were collected, grouped in the western part of the River Po plain. The number of records showed an exponential increase from 1988 to 2007, the percentage of woods in a 10 km² wide circular plot surrounding the location of records being inversely correlated to its distance from the 300 m a.s.l. contour line. In the two study areas, 36 out of 119 “marten-like” faeces were assigned to the pine marten, whilst none belonged to the stone marten. In the best monitored area, the pine marten was present almost constantly.Our results suggest that the pine marten is expanding its range to include cultivated areas which were previously considered a prerogative of the more synanthropic stone marten.     

A non-invasive genetic method to identify the sympatric mustelids pine marten (<Emphasis Type="Italic">Martes martes</Emphasis>) and stone marten (<Emphasis Type="Italic">Martes foina</Emphasis>): preliminary distribution survey on the northern Iberian Peninsula

The closely related mustelids European pine marten (Martes martes) and stone marten (Martes foina) sympatrically inhabit a large area of Europe. However, given our limited knowledge of their bioecological relationships, their extremely elusive behaviour and the fact that their faeces cannot be distinguished on the basis of morphology alone, it is very difficult to monitor their populations. In this study, we describe a reliable non-invasive polymerase chain reaction (PCR)–restriction fragment length polymorphism (PCR-RFLP) method for distinguishing between M. martes and M. foina based on the analysis of deoxyribonucleic acid extracted from faeces samples. The method was specifically designed to avoid possible interference from potential prey mammals and other sympatric carnivores. The procedure consists of PCR amplifying a mitochondrial D-loop region followed by digesting the resulting 276-bp-long amplicons with the restriction enzymes HaeIII and RsaI. To assess the efficiency of this technique, we conducted a preliminary field study across the potential sympatric distribution areas of both marten species in the northern Iberian Peninsula. Out of 359 faeces samples collected, we identified 80 as specimens from the stone marten and 235 from the pine marten. Unequivocal species identification was thus possible in 88% of the faeces samples collected. These findings reveal the combined use of non-invasive genetic sampling and GIS technology to be a reliable and cost-effective procedure for improving our knowledge of the spatial distributions of sympatric marten species. This protocol could also be used to identify and improve information gaps, to develop effective research and management programmes and in population and landscape genetics studies of marten species. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Non-invasive genetic sampling of sympatric marten species (Martes martes and Martes foina): assessing species and individual identification success rates on faecal DNA genotyping

The use of non-invasive genetic sampling (NGS) has become increasingly popular in wildlife research but needs well-planned sampling strategies and reliable laboratory protocols. In this study, we planned to assess the reliability and success of species and individual identifications of sympatric martens (European pine marten Martes martes and stone marten Martes foina) by genotyping non-invasively collected faecal samples. First, we developed a novel and accurate multiplex panel of 15 microsatellite loci, selected by cross species amplification of 41 loci. The application of this panel facilitated species distinction, discarding the presence of putative hybrids. Then, we assessed the impact of sample collector skills on the lab protocol performances. The faecal DNA quality was evaluated by (a) the success of polymerase chain reaction–restriction fragment length polymorphism identification of the two Martes species and (b) the genotyping success and error rates of individual pine marten identifications. The survey was conducted over all the sympatric range of the two species in the Iberian Peninsula by three groups of sample collectors with different experience: expert wildlife biologist, trained volunteers and technical staff from natural parks. Results show that the different expertise between sample collectors significantly influences the success rate of pine marten individual genotyping, but not the species identification success rate. Based on our results, we recommend conducting sampling by experienced field biologist to maximise the quality of NGS and ensure accurate genotyping success. Application of our methods to field collected scats can be used in a cost-effective way to investigate distribution, patterns of genetic diversity and structure as well as to estimate population abundance for sympatric martens.     

The genetic status of naturally occurring black-nosed impala from northern South Africa

The impala (Aepyceros melampus ssp.) is a widespread antelope species occurring in sub-Saharan Africa. The two recognized subspecies have non-overlapping distribution ranges, with no known natural mixture of these subspecies until human interference. A number of common impala individuals (A. m. melampus) displaying phenotypic characteristics commonly observed in the black-faced impala (A. m. petersi), namely black facial markings, were seen on a farm in the Limpopo Province, South Africa. This farm falls outside the natural distribution range of A. m. petersi. We therefore aimed to identify the taxonomic placement of these individuals (i.e. A. m. melampus or A. m. petersi) through phylogenetic and molecular clock analyses using D-loop and cytochrome subunit b sequence data. Our results showed that these black-nosed impala from Limpopo are in fact A. m. melampus individuals. The existence of the black-nose phenotype in common impala could be more widespread than previously estimated. The occurrence of introgression between the two subspecies in this region could, however, not be fully excluded, and can only be fully assessed through the use of nuclear DNA analysis.     

Revision of genus Melamphaes (Melamphaidae): Part 4. Multi-raker species: M. ebelingi, M. occlusus sp. nova, and M. nikolayi sp. nova

In the fourth part of the revision of the genus Melamphaes (Melamphaidae) multi-raker species (20 and more rakers at the first gill arch, rarely 19??in M. ebelingi) with eight soft rays in the ventral fin are considered. In this species, temporal spine is absent, there are 15 rays in the pectoral fin, and there are 11 to 12 abdominal vertebrae. M. ebelingi inhabits tropical and subtropical waters of the Atlantic Ocean. A new catch of this rare species in the northeastern part of the ocean is reported. The new species M. occlusus is described from one specimen from the subtropical part of the southwestern part of the Indian Ocean. Still another new species, M. nikolayi, is described from one specimen from the northwestern part of the Pacific Ocean (subtropical waters). A table for identification of 15 multi-raker species of the genus Melamphaes is provided.     

Freshwater Pearl mussels of the genus Margaritifera (Mollusca: Bivalvia) described as M. elongata (Lamarck, 1819) and M. borealis (Westerlund, 1871) should be classified with M. margaritifera (Linnaeus, 1758)

The shells of Pearl mussels from the basins of the Solza, Keret’, and Umba rivers flowing into the White Sea have been measured to determine the ratio of shell convexity to its maximum height. This ratio is the main character that, according to Bogatov et al. (2003), allows one to distinguish between three species of the genus Margaritifera: M. margaritifera, M. elongata, and M. borealis. It has been found that the above ratio gradually increases as the shell grows. Therefore, this character is unsuitable for species diagnosis, the more so that no hiatus in it between the three forms of pearl mussels has been revealed in any of the samples studied. On this basis, it may be concluded that Northern Europe, including Russia, is inhabited by only one species of pearl mussels, M. margaritifera.     

A PCR-RFLP method on faecal samples to distinguish <Emphasis Type="Italic">Martes martes</Emphasis>, <Emphasis Type="Italic">Martes foina</Emphasis>, <Emphasis Type="Italic">Mustela putorius</Emphasis> and <Emphasis Type="Italic">Vulpes vulpes</Emphasis>

A non-invasive genetic approach has been recently employed in the population genetics of wild species, using faeces that could be easily collected, particularly of elusive or endangered species. However, faeces of pine (Martes martes) and beech marten (M. foina) can be morphologically similar and could be confused with those of polecat (Mustela putorius) and red fox (Vulpes vulpes). On this basis, a rapid, simple and inexpensive RFLP protocol using a cytochrome b (Cyt b) gene fragment of mtDNA, isolated from faecal samples, was performed to distinguish the above-mentioned species.     

An analysis of two Myosorex species (Soricidae) from the Early Pliocene site of Langebaanweg (West coast, South Africa) using geometric morphometrics, linear measurements, and non-metric characters

This represents the first study of the soricid community from the Early Pliocene site of Langebaanweg (LBW) which is represented by four species, two of which belong to the soricid genus Myosorex (Forest shrew). Using geometric morphometrics the two Myosorex fossil species are compared with each other, and the extant western and eastern Cape species: Myosorex varius, M. cafer and M. longicaudatus. In addition, the results from an analysis of a number of non-metric characters and linear measurements on the fossil species are presented. The mandibles of the fossil species are characterized by extremely broad teeth, ascending rami which are relatively gracile and differ in shape and size from modern species, and the existence of a number of primitive features of the mandibles and teeth. This evidence is interpreted as indicating that the two LBW Myosorex species represent an archaic lineage now extinct in southern Africa.     

Interspecific differences in prey items in relation to morphological characteristics among four lutjanid species (Lutjanus decussatus, L. fulviflamma, L. fulvus and L. gibbus)

Clarifying interspecific differences in prey items in relation to morphological characteristics is a fundamental aspect to understand the mechanism enabling the diversity of feeding ecology of fishes. The aim of the present study was to clarify the relationship between prey items and body shape variation, teeth and mandible characteristics for four lutjanid species: Lutjanus decussatus, L. fulviflamma, L. fulvus and L. gibbus. Stomach contents analysis revealed that the main prey items of L. decussatus were fishes, L. fulviflamma were crabs and fishes, and L. fulvus and L. gibbus was crabs. Body shape analysis revealed that L. decussatus and L. fulviflamma had a shallower body depth whereas L. fulvus and L. gibbus had a deeper body depth. The two species with a shallower body had long teeth whereas the other two species with a deeper body depth had shorter teeth. The jaw-lever mechanics were compared and L. decussatus and L. fulviflamma have a faster mouth opening–closing mechanism. Canonical correspondence analysis revealed that fishes was the major prey item for the species having a shallower body depth, higher teeth length and lower ratios of in-lever to out-lever of mandibles, whereas crabs was the major prey item for the species having a deeper body depth, lower teeth length and higher ratios of in-lever to out-lever of mandibles. It is suggested that the interspecific differences in main prey items among the four species are directly related to behavioral differences based on body shape, teeth characteristics and jaw-lever mechanics.     

Remotely plucked hair genotyping: a reliable and non-invasive method for censusing pine marten (Martes martes,L. 1758) populations

We investigated the feasibility of using genetic techniques to census pine marten (Martes martes) populations by genotyping non-invasively collected samples (plucked hair and scats), with particular reference to the genetically depauperate Irish population. Novel real-time polymerase chain reaction methods were developed for species and sex identification, targeting short DNA sequences. Background genetic variation at 17 microsatellite loci was very low in the Irish population, with an average of 2.29 alleles per locus and expected heterozygosity of 0.35. Despite such low polymorphism, a panel of eight loci with a sibling probability of identity of 0.011 reliably identified individual pine marten and their gender, as determined by reference to genotypes of live trapped individuals. With high nuclear DNA amplification success rates (93.8%) and low genotyping error rates (1.8%), plucked hairs may represent a more reliable and cost-effective DNA source than scats for monitoring populations of this elusive carnivore, and similar taxa such as the sympatric stone marten Martes foina.

     

Susceptibility of Several Common Subtropical Weeds to Meloidogyne arenaria,M. incognita,and M. javanica

Experiments were conducted in the greenhouse to assess root galling and egg production of three root-knot nematode species, Meloidogyne arenaria, M. incognita, and M. javanica, on several weeds common to Florida agricultural land. Weeds evaluated were Amaranthus retroflexus (redroot pigweed), Cyperus esculentus (yellow nutsedge), Eleusine indica (goosegrass), Portulaca oleracea (common purslane), and Solanum americanum (American black nightshade). Additionally, although it is recommended as a cover crop in southern regions of the U.S., Aeschynomene americana (American jointvetch) was evaluated as a weed following the detection of root galling in a heavy volunteer infestation of an experimental field in southeastern Florida. Weeds were propagated from seed and inoculated with 1000 nematode eggs when plants reached the two true-leaf stage. Tomato (Solanum lycopersicum ‘Rutgers’) was included as a positive control. Aeschynomene americana and P. oleracea roots supported the highest number of juveniles (J₂) and had the highest number of eggs/g of root for all three species of Meloidogyne tested. However, though P. oleracea supported very high root levels of the three nematode species tested, its fleshy roots did not exhibit severe gall symptoms. Low levels of apparent galling, combined with high egg production, increase the potential for P. oleracea to support populations of these three species of root-knot nematodes to a degree that may not be appropriately recognized. This research quantifies the impact of P. oleracea as a host for M. arenaria, M. incognita, and M. javanica compared to several other important weeds commonly found in Florida agricultural production, and the potential for A. americana to serve as an important weed host of the three species of root-knot nematode tested in southern regions of Florida.     

Revision of the genus <Emphasis Type="Italic">Melamphaes</Emphasis> (Melamphaidae): 6. oligo-raker species: <Emphasis Type="Italic">M. papavereus,M. simus,M. hubbsi</Emphasis>

Three oligo-raker species (≤19 rakers on the first gill arch) of the genus Melamphaes have been considered. A new species, M. papavereus, out of the group “M. typhlops” has been described from the Bay of Bengal of the Indian Ocean. M. simus and M. hubbsi out of the group “M. simus” have been revised. M. simus inhabits all oceans between 40° N and 40° S. M. hubbsi has been known from single specimens caught in the central part of the South Atlantic between 11° and 19° S.     

An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII,VIII, IX,X and XI

Species and subspecies within the Salmonella genus have been defined for public health purposes by biochemical properties; however, reference laboratories have increasingly adopted sequence-based, and especially whole genome sequence (WGS), methods for surveillance and routine identification. This leads to potential disparities in subspecies definitions, routine typing, and the ability to detect novel subspecies. A large-scale analysis of WGS data from the routine sequencing of clinical isolates was employed to define and characterise Salmonella subspecies population structure, demonstrating that the Salmonella species and subspecies were genetically distinct, including those previously identified through phylogenetic approaches, namely: S. enterica subspecies londinensis (VII), subspecies brasiliensis (VIII), subspecies hibernicus (IX) and subspecies essexiensis (X). The analysis also identified an additional novel subspecies, reptilium (XI). Further, these analyses indicated that S. enterica subspecies arizonae (IIIa) isolates were divergent from the other S. enterica subspecies, which clustered together and, on the basis of ANI analysis, subspecies IIIa was sufficiently distinct to be classified as a separate species, S. arizonae. Multiple phylogenetic and statistical approaches generated congruent results, suggesting that the proposed species and subspecies structure was sufficiently biologically robust for routine application. Biochemical analyses demonstrated that not all subspecies were distinguishable by these means and that biochemical approaches did not capture the genomic diversity of the genus. We recommend the adoption of standardised genomic definitions of species and subspecies and a genome sequence-based approach to routine typing for the identification and definition of novel subspecies.