Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

<p>Abstract</p> <p>Background</p> <p>Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within <it>Lepus</it>, therefore it is possible that introgressive hybridization events also occur among Chinese <it>Lepus </it>species and contribute to the current taxonomic confusion.</p> <p>Results</p> <p>Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese <it>Lepus </it>species. Remarkably, the mtDNA of <it>L. mandshuricus </it>was completely replaced by mtDNA from <it>L. timidus </it>and <it>L. sinensis</it>. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species.</p> <p>Conclusion</p> <p>This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.</p

Glaciation Effects on the Phylogeographic Structure of Oligoryzomys longicaudatus (Rodentia: Sigmodontinae) in the Southern Andes

The long-tailed pygmy rice rat Oligoryzomys longicaudatus (Sigmodontinae), the major reservoir of Hantavirus in Chile and Patagonian Argentina, is widely distributed in the Mediterranean, Temperate and Patagonian Forests of Chile, as well as in adjacent areas in southern Argentina. We used molecular data to evaluate the effects of the last glacial event on the phylogeographic structure of this species. We examined if historical Pleistocene events had affected genetic variation and spatial distribution of this species along its distributional range. We sampled 223 individuals representing 47 localities along the species range, and sequenced the hypervariable domain I of the mtDNA control region. Aligned sequences were analyzed using haplotype network, Bayesian population structure and demographic analyses. Analysis of population structure and the haplotype network inferred three genetic clusters along the distribution of O. longicaudatus that mostly agreed with the three major ecogeographic regions in Chile: Mediterranean, Temperate Forests and Patagonian Forests. Bayesian Skyline Plots showed constant population sizes through time in all three clusters followed by an increase after and during the Last Glacial Maximum (LGM; between 26,000–13,000 years ago). Neutrality tests and the “g” parameter also suggest that populations of O. longicaudatus experienced demographic expansion across the species entire range. Past climate shifts have influenced population structure and lineage variation of O. longicaudatus. This species remained in refugia areas during Pleistocene times in southern Temperate Forests (and adjacent areas in Patagonia). From these refugia, O. longicaudatus experienced demographic expansions into Patagonian Forests and central Mediterranean Chile using glacial retreats

Functional Genomic Insights into Regulatory Mechanisms of High-Altitude Adaptation

Recent studies of indigenous human populations at high altitude have provided proof-of-principle that genome scans of DNA polymorphism can be used to identify candidate loci for hypoxia adaptation. When integrated with experimental analyses of physiological phenotypes, genome-wide surveys of DNA polymorphism and tissue-specific transcriptional profiles can provide insights into actual mechanisms of adaptation. It has been suggested that adaptive phenotypic evolution is largely mediated by cis-regulatory changes in genes that are located at integrative control points in regulatory networks. This hypothesis can be tested by conducting transcriptomic analyses of hypoxic signaling pathways in conjunction with experimental measures of vascular oxygen supply and metabolic pathway flux. Such studies may reveal whether the architecture of gene regulatory networks can be used to predict which loci (and which types of loci) are likely to be “hot spots” for adaptive physiological evolution. Functional genomic studies of deer mice (Peromyscus maniculatus) demonstrate how the integrated analysis of variation in tissue-specific transcriptomes, whole-animal physiological performance, and various subordinate traits can yield insights into the mechanistic underpinnings of high-altitude adaptation

Data from: Copy number polymorphism in the α-globin gene cluster of European rabbit (Oryctolagus cuniculus).

Comparative genomic studies have revealed that mammals typically possess two or more tandemly duplicated copies of the α-globin (HBA) gene. The domestic rabbit represents an exception to this general rule, as this species was found to possess a single HBA gene. Previous electrophoretic surveys of HBA polymorphism in natural populations of the European rabbit (Oryctolagus cuniculus) revealed extensive geographic variation in the frequencies of three main electromorphs. The variation in frequency of two electromorphs is mainly partitioned between two distinct subspecies of European rabbit, and a third is restricted to the hybrid zone between the two rabbit subspecies in Iberia. Here we report the results of a survey of nucleotide polymorphism which revealed HBA copy number polymorphism in Iberian populations of the European rabbit. By characterizing patterns of HBA polymorphism in populations from the native range of the European rabbit we were able to identify the specific amino acid substitutions that distinguish the previously characterized electromorphs. Within the hybrid zone, we observed the existence of a second HBA gene duplicate, named HBA2, that mostly represents a novel sequence haplotype which occurs in higher frequency within the hybrid zone and thus appears to have arisen in hybrids of the two distinct subspecies. While this novel gene is also present in other wild Iberian populations, it is almost absent from French populations which suggest a recent ancestry, associated with the establishment of the post-Pleistocene contact zone between the two European rabbit subspecies

Trophic Transfer of Arsenic from an Aquatic Insect to Terrestrial Insect Predators

The movement of energy and nutrients from aquatic to terrestrial ecosystems can be substantial, and emergent aquatic insects can serve as biovectors not only for nutrients, but also for contaminants present in the aquatic environment. The terrestrial predators Tenodera aridifolia sinensis (Mantodea: Mantidae) and Tidarren haemorrhoidale (Araneae: Theridiidae) and the aquatic predator Buenoa scimitra (Hemiptera: Notonectidae) were chosen to evaluate the efficacy of arsenic transfer between aquatic and terrestrial environments. Culex tarsalis larvae were reared in either control water or water containing 1000 µg l(−1) arsenic. Adults that emerged from the control and arsenic treatments were fed to the terrestrial predators, and fourth instar larvae were fed to the aquatic predator reared in control or arsenic contaminated water. Tenodera a. sinensis fed arsenic-treated Cx. tarsalis accumulated 658±130 ng g(−1) of arsenic. There was no significant difference between control and arsenic-fed T. haemorrhoidale (range 142–290 ng g(−1)). Buenoa scimitra accumulated 5120±406 ng g(−1) of arsenic when exposed to arsenic-fed Cx. tarsalis and reared in water containing 1000 µg l(−1) arsenic. There was no significant difference between controls or arsenic-fed B. scimitra that were not exposed to water-borne arsenic, indicating that for this species environmental exposure was more important in accumulation than strictly dietary arsenic. These results indicate that transfer to terrestrial predators may play an important role in arsenic cycling, which would be particularly true during periods of mass emergence of potential insect biovectors. Trophic transfer within the aquatic environment may still occur with secondary predation, or in predators with different feeding strategies

No alternatives to fast-food outlets - one explanation for high diabetes rates in Western Metropolitan Melbourne

Objectives: To quantify and categorise food outlets at the suburb level across western metropolitan Melbourne; to identify the relationship between food outlet types and the rats of diabetes across this region; to translate findings to recommendations for food outlet planning at local government planning level