Systematics of the genus Capra inferred from mitochondrial DNA sequence data

Traditional classification in the genus Capra is based mainly on horn morphology. However, previous investigations based on allozyme data are not consistent with this classification. We thus reexamined the evolutionary history of the genus by analyzing mitochondrial DNA (mtDNA) sequence variation. We collected bone samples from museums or dead animals found in the field. Thirty-four individuals were successfully sequenced for a portion of the mtDNA cytochrome b gene and control region (500 bp in total). We obtained a star-like phylogeny supporting a rapid radiation of the genus. In accordance with traditional classification, mtDNA data support the presence of two clades in the Caucasus and the hypothesis of a domestication event in the Fertile Crescent. However, in conflict with morphology, we found that C. aegagrus and C. ibex are polyphyletic species, and we propose a new scenario for Capra immigration into Europe.     

European rabbits as ecosystem engineers: warrens increase lizard density and diversity

Mammals that build extensive open burrow systems are often classified as ecosystem engineers, since they have the potential to modulate the availability of resources for themselves and other organisms. Lizards may benefit from the heterogeneity created by these structures, especially if coupled with an increased offer of sites for refuge and thermoregulation. However, information about these engineering effects by burrowing animals is scarce. We investigated the influence of European rabbit burrows on several parameters of a Mediterranean lizard community (abundance, density, diversity and body condition) in three different habitats (open pastures, holm oak and scrub patches). We found that lizards were positively associated with burrows, and that burrows determined lizard presence at otherwise unfavourable habitats. Moreover, community parameters such as density and species richness were higher in sites with burrows. Burrows influenced lizard species in different ways, and were also relevant for other Mediterranean vertebrates, as revealed by questionnaires to experts. We also explored the possible resources provided by burrows for lizards. Warrens offer relatively abundant prey and appropriate retreat sites for refuge and thermoregulation. Warrens may have further implications within the ecosystem, acting as stepping stones, allowing lizards to reach otherwise inaccessible habitat patches. This study shows that European rabbit warrens have a positive influence on lizard density and diversity, and confirms the role of rabbits as ecosystem engineers. This reinforces the need for appropriate conservation measures for rabbits, especially given their threatened status in the Iberian Peninsula. Furthermore, our study highlights that taking into account the influence of engineering activities increases our awareness of species interactions, and may translate into more adequate conservation measures for the preservation of biodiversity.     

Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences

Wild common carp from two lakes and two rivers in Greece were genetically characterized with sequencing analysis of two mitochondrial DNA segments: cytochrome b (1119 bp) and D-loop (646 bp). A total of 9 variable singleton sites and 7 unique haplotypes were detected. A common haplotype was found in three out of the four populations examined, which seems to be the ancestral one and represents the European origin of common carp from Greece. This haplotype could be also justified by the introductions reported with individuals belonging to the Central European race, into many natural habitats in Greece. Limited genetic variation — in Evros and Aliakmonas populations — could be due to bottleneck effects and small effective population sizes, whereas the different haplotypes found in Lake Volvi could represent different common carp stocks. Values of sequence divergence among Greek haplotypes ranged from 0.0006 to 0.0023. The Neighbour-Joining (NJ) phylogenetic tree constructed based on the combined sequences, reveals that the populations of common carp from Greece belong to the European group of populations — which is highly divergent from the South East-Asia cluster — and to the subspecies Cyprinus carpio carpio.     

A spatial aspect on mitochondrial DNA genealogy in Apodemus peninsulae from East Asia

Apodemus peninsulae is a field mouse that inhabits the broad-leafed forests of temperate Eurasia. We examined the mitochondrial cytochrome b gene in 57 individuals of A. peninsulae from northeastern Asia, including Siberia, Primorye, Magadan region, Sakhalin, Hokkaido, and the Korean Peninsula. The genealogy of the mitochondrial DNA (mtDNA) in A. peninsulae was shown to have substantial geographic affinity, suggesting geographic architecture of northeastern Asia, including the islands of Sakhalin and Hokkaido, played important roles on the cladogenesis. Taking into account the presence of region-specific anciently divergent mtDNA types, three parts of the regions of Primorye, Siberia, and the Korean Peninsula can be denoted as refugia for A. peninsulae during the substantial period of the Quaternary glacial ages. Among the geographic regions examined, Primorye is likely to be the most influential one, from which the mtDNA is thought to have migrated to the neighboring regions of Sakhalin, Hokkaido, the Magadan region, and Siberia during the evolution of this species.     

Intraspecific diversity of sugar beet (Beta vulgaris) mitochondrial DNA

Summary Mitochondrial (mt) DNA, isolated from different sugar beet populations, was analyzed using BamHI and EcoRI restriction enzymes. It was shown that plants possessing the new mtDNA types are revealed among O-type fertilizers quite frequently. Among cytoplasmic male sterile (cms) plants, which evolved during cultivation of O-type fertilizers, plants with altered mt genome were found.     

Stocking may increase mitochondrial DNA diversity but fails to halt the decline of endangered Atlantic salmon populations

Over the last 50 years, Spanish Atlantic salmon (Salmo salar) populations have been in decline. In order to bolster these populations, rivers were stocked with fish of northern European origin during the period 1974–1996, probably also introducing the furunculosis-inducing pathogen, Aeromonas salmonicida. Here we assess the relative importance of processes influencing mitochondrial (mt)DNA variability in these populations from 1948 to 2002. Genetic material collected over this period from four rivers in northern Spain (Cantabria) was used to detect variability at the mtDNA ND1 gene. Before stocking, a single haplotype was found at high frequency (0.980). Following stocking, haplotype diversity (h) increased in all rivers (mean h before stocking was 0.041, and 0.245 afterwards). These increases were due principally to the dramatic increase in frequency of a previously very low frequency haplotype, reported at higher frequencies in northern European populations proximate to those used to stock Cantabrian rivers. Genetic structuring increased after stocking: among-river differentiation was low before stocking (1950s/1960s Φ _ST = –0.00296–0.00284), increasing considerably at the height of stocking (1980s Φ _ST = 0.18932) and decreasing post-stocking (1990s/2002 Φ _ST = 0.04934–0.03852). Gene flow from stocked fish therefore seems to have had a substantial role in increasing mtDNA variability. Additionally, we found significant differentiation between individuals that had probably died from infectious disease and apparently healthy, angled fish, suggesting a possible role for pathogen-driven selection of mtDNA variation. Our results suggest that stocking with non-native fish may increase genetic diversity in the short term, but may not reverse population declines.     

Winter feeding behaviour of European rabbits in a temperate zone habitat

Herbivores living in seasonal environments commonly have to deal with reduced food availability and quality during the winter season. The present study investigated how European rabbits Oryctolagus cuniculus living in a grassland habitat adapt their feeding behaviour to cope with this situation. Both adult and subadult animals markedly increased their feeding rates throughout the course of the winter, with the rates in subadults being generally higher. Nevertheless, both age classes showed a significant decline in body mass throughout the winter averaging 22.3% of the autumn mass in subadult and 9.7% in adult animals. In late winter, an increase in the faecal sand content was found, indicating that the animals were feeding on ground-level plant parts. Measurements of nitrogen content of (1) grass leaves and stems and (2) ground-level sprouts and roots demonstrated a decrease in the food quality of grass leaves and stems from early to late winter. In contrast, the nitrogen content of roots and ground-level sprouts remained stable. It can be speculated that the animals increasingly switched to ground-level plant parts as alternative food in the course of the winter in order to satisfy their needs for a sufficient source of nitrogen.     

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences

Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.     

Do whiskers contribute to nipple-search and suckling behavior in newborn rabbits (Oryctolagus cuniculus)?

Rabbit pups are only nursed for about 3 min once a day. They depend on a pheromone on the mother's ventrum to locate nipples and on tactile stimulation of the muzzle to grasp them. In a continuing study of the sensory input guiding suckling behavior we investigated the whisker array in newborn pups and the possible contribution of the whiskers to suckling. Rabbits are born with approximately 76 whiskers arranged in seven to nine rows and increasing in length from rostral to caudal. No significant difference was found between pups with whiskers cut and intact controls in latency to perform the stereotyped nipple-search behavior, latency to attach to nipples, time spent on nipples, milk ingested, or in the strength of conditioning to a novel odor paired with suckling. Thus, the whiskers do not seem important for suckling in newborn rabbits.

Zusammenfassung

Tragen die Schnurrhaare bei neugeborenen Kaninchen (Oryctolgus cuniculus) zum Zitzensuch- und Saugverhalten bei?Jungkaninchen werden nur einmal am Tag für etwa drei Minuten gesäugt. Für das Auffinden der Zitzen sind sie auf ein Pheromon auf der Bauchhaut der Mutter angewiesen, und für deren Ergreifen auf periorale taktile Reize. In Fortsetzung unserer Untersuchungen zur sensorischen Kontrolle dieses Verhaltens beschreiben wir die Anordnung der Schnurrhaare bei neugeborenen Kaninchen und untersuchen ihren möglichen Beitrag zum Säugeverhalten. Bei der Geburt besitzen Jungkaninchen etwa 76, in 7–9 Reihen angeordnete Schnurrhaare, deren Länge von rostral nach caudal zunimmt. Nach Abschneiden der Schnurrhaare wurden keine signifikanten Unterschiede zwischen Jungen mit und ohne Schnurrhaare beobachtet, sowohl in der Latenz des Zitzensuchens, des Zitzenfassens, wie in der Besaugungsdauer, der erhaltenen Milchmenge oder dem Grad der Konditionierung auf einen neuen Geruchsstoff. Demnach spielen bei neugeborenen Kaninchen die Schnurrhaare keine wesentliche Rolle für das Auffinden und Besaugen von Zitzen.     

Genetic diversity and the biogeographical process of Acheilognathus macropterus revealed by sequence variations of mitochondrial cytochrome b gene

In this study, thirty-six individuals of Acheilognathus macropterus were collected from the Heilongjiang River, the Yangtze River, and the Nandujiang River. Partial mitochondrial cytochrome b gene region (636 base pair) was sequenced to these samples and 22 haplotypes were found. With A. chankaensis and A. tokinensis as outgroups, their relationships were analyzed. The p-distances were calculated with Mega software and a molecular phylogenetic tree was constructed using the neighbor-joining (NJ) method. The proportions of main morphological characters were compared as well. P-distances showed that the genetic differences in A. macropterus samples were far smaller than those between these samples and the outgroups. The molecular phylogenetic tree shows that samples with barbels and those without barbels were intermingled. There was no distinctive difference in proportions of morphological characteristics among them. These results suggested that samples with barbels and those without barbels (formally identified as A. taenianalis) are the same species; A. taenianalis is synonymous with A. macropterus. The thirtysix individuals were grouped into five clades and the positions of the samples in the clades were correspondingly grouped within their geographical distributions. Among the five clades, clades 1 and 5 included samples from the Heilongjiang River and Nandujiang River respectively. The samples from the Yangtze River scattered into clades 2, 3, and 4. There were distinctive genetic differences (>5%) among them. Interestingly, the distributions of the 21 samples in these three clades were not correlated to their geographical distributions. It is postulated that these genetic differences were due to the bitterlings’ mating choice mechanism, the prozygotic isolation. The genetic differences between the fish from Nandujiang River and those from the mainland indicated that they were separated early. However, the small genetic differences among the samples and the positions of the fish from the Heilonjiang River in the molecular phylogenetic tree indicate that fish in Heilongjiang River might have dispersed from the Yangtze River to that area much later. __________ Translated from Acta Hydrobiologica Sinica, 2006, 39(2): 134–140 [译自: 水生生物学报]     

Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs

Cryptic species diversity is thought to be common within the class Insecta, posing problems for basic ecological and population genetic studies and conservation management. Within the temperate bumble bee (Bombus spp.) fauna, members of the subgenus Bombus sensu stricto are amongst the most abundant and widespread. However, their species diversity is controversial due to the extreme difficulty or inability morphologically to identify the majority of individuals to species. Our character-based phylogenetic analyses of partial CO1 (700 bp) from 39 individuals spread across their sympatric European ranges provided unequivocal support for five taxa (3–22 diagnostic DNA base pair sites per species). Inclusion of 20 Irish specimens to the dataset revealed ≥2.3% sequence divergence between taxa and ≤1.3% within taxa. We developed a PCR-RFLP based method for unequivocally distinguishing amongst the four cryptic European taxa of this subgenus, B. cryptarum, B. lucorum, B. magnus and B. terrestris, and used it to analyse 391 females of the former three species collected across Ireland, all of which could be unambiguously assigned to species. Bombus lucorum was the most widely distributed and abundant of the cryptarum–lucorum–magnus species complex, comprising 56% of individuals, though it was significantly less abundant at higher altitudes (>200 m) whilst B. cryptarum was relatively more abundant at higher altitudes. Bombus magnus was rarely encountered at urban sites. Both B. lucorum and B. terrestris are nowadays reared commercially for pollination and transported globally. Our RFLP approach to identify native fauna can underpin ecological studies of these important cryptic species as well as the impact of commercial bumble bees on them.     

Molecular Phylogenetics of Gadidae and Related Gadiformes Based on Mitochondrial DNA Sequences

Mitochondrial DNA sequences of selected regions of the small subunit and large subunit ribosomal RNAs and cytochrome b genes were analyzed for 10 gadid species, representing 8 genera within Gadidae, and 10 species representing 5 other gadiform families. Phylogenetic analyses revealed that Gadiculus is the most basal gadid genus, and that Trisopterus and Micromesistius constitute a relatively basal clade. Lotidae was identified as the family most closely related to Gadidae. Estimation of divergence times indicated that the most ancient Gadidae split between Gadiculus and the remaining gadid genera occurred about 20 million years ago. The clade including the most recent species (Gadus, Boreogadus, Merlangius, Melanogrammus, and Pollachius) diverged from the Trisopterus/Micromesistius clade approximately 12 million years ago.     

Genetic structure of Schrenck newt <Emphasis Type="Italic">Salamandrella schrenckii</Emphasis> populations by mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> variation

The nucleotide sequence variation of the mitochondrial cytochrome b gene was studied in Schrenck newt Salamandrella schrenckii (Strauch, 1870) from populations of Primorye and the Khabarovsk region. Phylogenetic analysis revealed two haplotype clusters, southern cluster 1 and northern cluster 2, with a divergence of 3%. Analysis of the mtDNA and cytochrome b amino acid sequence variations made it possible to assume that the modern range of Schrenck newt was colonized from south Primorye northwards. In contrast to the southern cluster, the northern one demonstrated all the signs of demographic expansion (a unimodal distribution of pairwise nucleotide differences, specific results of tests for selective neutrality of mtDNA variation, and a good correspondence of genetic parameters to those expected from demographic expansion models).     

Phylogenetic relationships and biogeography of the genus Chondrostoma inferred from mitochondrial DNA sequences

A phylogeny of the species of the nase genus Chondrostoma was constructed from a complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise the current systematics of this group, and to infer a biogeographical model of the Mediterranean area during the Cenozoic period. We confirmed the monophyly of the genus Chondrostoma, and defined seven different lineages within it: Polylepis, Arcasii, Lemmingii, Toxostoma, Nasus, C. genei, and C. soetta. The separation of main lineages within Chondrostoma occurred in the Middle-Upper Miocene, approximately 11 million years ago, while the greatest species radiation took place in the Pliocene close to the time the current drainages system were created. It is unlikely that this genus experienced an extensive dispersal during the Messinian, in the Lago-Mare Phase. Given the level of current knowledge, a biogeographical model constructed on the basis of vicariant events seems more realistic than does a dispersalist model.     

PCR-RFLP analysis of mitochondrial DNA cytochrome b gene among Haruan (Channa striatus) in Malaysia

Haruan (Channa striatus) is in great demand in the Malaysian domestic fish market. In the present study, mtDNA cyt b was used to investigate genetic variation of C. striatus among populations in Peninsular Malaysia. The overall population of C. striatus demonstrated a high level of haplotype diversity (h) and a low-to-moderate level of nucleotide diversity (π). Analysis of molecular variance (AMOVA) results showed a significantly different genetic differentiation among 6 populations (F_ST = 0.37566, P = 0.01). Gene flow (Nm) was high and ranged from 0.32469 to infinity (∞). No significant relationship between genetic distance and geographic distance was detected. A UPGMA tree based on the distance matrix of net interpopulation nucleotide divergence (d_A) and haplotype network of mtDNA cyt b revealed that C. striatus is divided into 2 major clades. The neutrality and mismatch distribution tests for all populations suggested that C. striatus in the study areas had undergone population expansion. The estimated time of population expansion in the mtDNA cyt b of C. striatus populations occurred 0.72-6.19 million years ago. Genetic diversity of mtDNA cyt b and population structure among Haruan populations in Peninsular Malaysia will be useful in fisheries management for standardization for Good Agriculture Practices (GAP) in fish-farming technology, as well as providing the basis for Good Manufacturing Practices (GMP).     

Postnatal remains of the foetal membranes affect growth and survival of wild European rabbit pups

During a long-term study on reproduction of the European rabbit (Oryctolagus cuniculus L.) that was carried out on a population living under semi-natural conditions, occasionally single pups per litter were discovered being stuck in remnants of the foetal membranes. Here we describe this so far unknown phenomenon, quantify the occurrence, and investigate the consequences for the individual growth rate and for survival. Furthermore, we tested if maternal social rank and age were correlated with the occurrence of this phenomenon. Pups comprising the described adherence of the foetal membranes had lower growth rates than their unaffected litter siblings, and usually died during the nestling period or short after emergence above ground. Our findings point out that there was an individual predisposition of the mother for having affected litters. However, an impact of maternal social rank or age on the occurrence of this feature in their offspring was not supported by our data. Nevertheless, a pathological background also has to be considered as a possible cause.     

Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes

E. coli ribosomal DNA has been used to probe maize mitochondrial DNA. It hybridizes primarily with chloroplast ribosomal DNA sequences and with fungal and bacterial sequences which may contaminate the mtDNA preparations. It also hybridizes to the chloroplast 16S ribosomal RNA gene sequence present in the mitochondrial genome (1) as well as to the mitochondrial 18S ribosomal RNA gene sequence. Weak sequence homology was detected between E. coli rDNA and the mitochondrial 26S ribosomal RNA gene.