Virus impact at the interface of an ancient ecosystem and a recent agroecosystem: studies on three legume-infecting potyviruses in the southwest Australian floristic region

The southwest Australian floristic region (SWAFR) is an internationally recognized 'hot spot' of global biodiversity and has an endangered flora. It represents a unique interface between an ancient ecosystem and a recent agroecosystem, providing the opportunity to investigate encounters where the recipient of the virus is an introduced crop and the donor a native plant and vice versa. Phylogenetic analysis of the virus coat-protein genes was used to study isolates of three potyviruses representing different 'new encounter' scenarios at this interface. The incidence, symptomatology, host range, non-persistent aphid transmission and considerable genetic diversity of the first indigenous virus described from the SWAFR, where it infects the native legume Hardenbergia comptoniana , and its potential to damage lupin, a locally important, newly introduced cultivated grain legume, was studied. The name Hardenbergia mosaic virus is proposed for this virus. Two other examples of 'new encounter' scenarios involving other legume-infecting potyviruses studied were: Passion fruit woodiness virus , which has been found only in Australasia, where it damages recently introduced species of Passiflora and legumes; and Bean yellow mosaic virus, which is not indigenous to Australia and was introduced recently to the SWAFR, where it infects a number of introduced legumes, but also damages the local native legume Kennedia prostrata . Isolates of the former had considerable genetic diversity consistent with the virus being indigenous, while isolates of the latter virus from K. prostrata had a low genetic diversity consistent with recent arrival. This research illustrates how introduced viruses can damage indigenous plants and indigenous viruses can damage introduced cultivated plants within this unique ecosystem, and how human activities can facilitate damaging 'new encounters' between plants and viruses.     

Alpine and Apennine barriers determining the differentiation of the rudd (Scardinius erythrophthalmus L.) in the Italian peninsula

Abstract –  A phylogeographic study of rudd Scardinius erythrophthalmus L. (Pisces: cyprinidae) was addressed to determine the differentiation of Italian populations in relation to the presence of mountain barriers, which identify two biogeographic districts (Padano-Venetian, Tuscano-Latium). At this scope, 409 bp long sequences of mtDNa cytochrome b gene were obtained from Italian and central European samples. Italian rudds phylogeny showed low level of divergence which although resulted from the central European haplotypes. The genetic structure of haplotypes in the studied districts revealed a significant recent fragmentation event. The Padano-Venetian populations showed patterns of past range expansion caused by the specie dispersion by river connections occurred during Pleistocene. This pattern provides evidence for (i) the role of Alps as a barrier for rudd dispersion; (ii) a significant genetic structure among the studied districts related to recent isolation events by the Apennine barrier; (iii) the role of Pleistocene sea level variations in determining phylogeography of the Padano-Venetian populations.     

A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds

As the fast pace of genomic research continues to identify mitochondrial lineages in animals, it has become apparent that many independent studies are needed to support a robust phylogenetic inference. The aim of this study was thus to further characterize the maternal lineage, proposed to originate in southwestern region of China, using a wider survey of diverse goat breeds in China. To this end, we sequenced the mitochondrial hypervariable region 1 (HVR1) of the mtDNA control region in 145 goats of 12 Chinese breeds. Phylogenetic analysis revealed that Chinese goats were classified into four distinct lineages (A, B, C and D) as previously reported. A Mantel test and the analysis of Analysis of Molecular Variance (ANOVA) indicated that there was not an obvious geographic structure among Chinese goat breeds. Population expansion analysis based on mismatch distribution and Fu's Fs statistic indicate that two expansion events in Chinese goats occurred respectively at about 11 and 29 mutational time units ago, revealing two star-like subclades in lineage B corresponding to two population expansion events. Moreover, lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China. Multiple lines of evidence from this study and previous studies indicate that for Chinese goats mtDNA lineage B originated from the southwestern region of China.     

Ancient and modern mitochondrial haplotypes of common bream (Abramis brama L.) in Poland

Abstract –  Genetic data on archaeological specimens provide complementary information for addressing questions on distribution and migration of fishes over long time scales. In this study DNA was extracted from common bream bones ( N  = 4), dated c. 6000–1000  bp , and a 172 bp fragment of mitochondrial cytochrome b gene has been sequenced. The obtained sequences differed from homologous sequences of breams living contemporarily ( N  = 4), inhabiting the same geographical areas as 'ancient' fish. None of ancient mitochondrial haplotype was found in fish living at present. Our results suggest that fish vicariance could be affected also by other than glacial retreat historical events, and the mechanisms that influenced present distribution of freshwater fishes are still unclear.     

Are hotspots of evolutionary potential adequately protected in southern California?

Reserves are often designed to protect rare habitats, or “typical” exemplars of ecoregions and geomorphic provinces. This approach focuses on current patterns of organismal and ecosystem-level biodiversity, but typically ignores the evolutionary processes that control the gain and loss of biodiversity at these and other levels (e.g., genetic, ecological). In order to include evolutionary processes in conservation planning efforts, their spatial components must first be identified and mapped. We describe a GIS-based approach for explicitly mapping patterns of genetic divergence and diversity for multiple species (a “multi-species genetic landscape”). Using this approach, we analyzed mitochondrial DNA datasets from 21 vertebrate and invertebrate species in southern California to identify areas with common phylogeographic breaks and high intrapopulation diversity. The result is an evolutionary framework for southern California within which patterns of genetic diversity can be analyzed in the context of historical processes, future evolutionary potential and current reserve design. Our multi-species genetic landscapes pinpoint six hotspots where interpopulation genetic divergence is consistently high, five evolutionary hotspots within which genetic connectivity is high, and three hotspots where intrapopulation genetic diversity is high. These 14 hotspots can be grouped into eight geographic areas, of which five largely are unprotected at this time. The multi-species genetic landscape approach may provide an avenue to readily incorporate measures of evolutionary process into GIS-based systematic conservation assessment and land-use planning.     

Admixture analyses and phylogeographic relationships reveal complete genetic distinctiveness of Polish farm and wild red foxes (Vulpes vulpes) and the North American origin of farm‐bred individuals

A number of studies showed that many mtDNA haplotypes were shared among contemporary farm red foxes bred on different continents and the historical wild red foxes of North American origin. Therefore, in this study, the population genetic structure and phylogeographic relationships of Polish red foxes kept on fur farms and their wild conspecifics were investigated to assess the ancestry of the farm red foxes in Poland. A total of 330 tissue samples (200 from farm foxes and 130 from wild foxes) were used for the genetic analyses. Thirty microsatellite loci and two regions of mtDNA were used to assess the level of admixture between farm‐ and wild red foxes, to construct haplotype networks and create a phylogenetic tree. The genetic structure analysis clearly indicated two genetic clusters as being the most probable number of genetically distinct populations. The fixation index revealed a significant genetic distance between the farm‐ and wild red fox populations (F_ST = 0.27, p < 0.05). Haplotype networks based on frequencies showing relationships between concatenated haplotypes of Polish farm‐ and wild red foxes and the constructed phylogenetic tree clearly indicated two genetically distinct groups. The results of this study provide strong evidence confirming the North American origin of red foxes bred on Polish farms and the genetic distinctiveness of both studied populations.     

Low genetic variability of the white‐clawed crayfish in the Iberian Peninsula: its origin and management implications

• 1. A study on the genetic variability of the white‐clawed crayfish was carried out based on mitochondrial cytochrome oxidase subunit I gene sequences. The sequences applied were more informative regarding white‐clawed crayfish genetic variability than others previously used.
• 2. Two haplotypes were found to exist in the Iberian Peninsula. The haplotypes exhibit a strong geographic subdivision (Φ_ST=0.83). One of the Iberian haplotype s was similar to north Italian haplotypes and the second differed in only one mutation. This pattern of genetic variability contrasts with those found in glacial refugial areas of France, Italy and the Balkan Peninsula.
• 3. Two hypotheses on the origin of the white‐clawed crayfish in the Iberian Peninsula are discussed: (i) one based on an anthropogenic origin, and (ii) a second based on a successive number of postglacial ancient and recent bottlenecks, i.e. the disjunction between Iberian and Italian populations of white‐clawed crayfish species is due to competition between A. italicus and A. pallipes, in addition to the impact of crayfish plague and human translocations.
• 4. New references for the white‐clawed crayfish in the Iberian Peninsula were found in medieval and Arabic texts. The results show that this species has been thriving in this peninsula since ancient periods and that its indigenous status should not be questioned.
• 5. Conservation action and plans should consider the low genetic diversity as a limitation for farm‐raising specimens more adapted and resistant to changing environments and diseases.

Copyright © 2007 John Wiley & Sons, Ltd.     

Molecular evolutionary analysis reveals Arctic-like rabies viruses evolved and dispersed independently in North and South Asia

BackgroundArctic-like (AL) lineages of rabies viruses (RABVs) remains endemic in some Arctic and Asia countries. However, their evolutionary dynamics are largely unappreciated.ObjectivesWe attempted to estimate the evolutionary history, geographic origin and spread of the Arctic-related RABVs.MethodsFull length or partial sequences of the N and G genes were used to infer the evolutionary aspects of AL RABVs by Bayesian evolutionary analysis.ResultsThe most recent common ancestor (tMRCA) of the current Arctic and AL RABVs emerged in the 1830s and evolved independently after diversification. Population demographic analysis indicated that the viruses experienced gradual growth followed by a sudden decrease in its population size from the mid-1980s to approximately 2000. Genetic flow patterns among the regions reveal a high geographic correlation in AL RABVs transmission. Discrete phylogeography suggests that the geographic origin of the AL RABVs was in east Russia in approximately the 1830s. The ancestral AL RABV then diversified and immigrated to the countries in Northeast Asia, while the viruses in South Asia were dispersed to the neighboring regions from India. The N and G genes of RABVs in both clades sustained high levels of purifying selection, and the positive selection sites were mainly found on the C-terminus of the G gene.ConclusionsThe current AL RABVs circulating in South and North Asia evolved and dispersed independently.     

Conservation genetic assessment of the paleback darter,Etheostoma pallididorsum,a narrowly distributed endemic in the Ouachita Highlands,Arkansas, USA

1. The paleback darter, Etheostoma pallididorsum, is considered imperilled and has recently been petitioned for listing under the Endangered Species Act. Previous allozyme-based studies found evidence of a small effective population size, warranting conservation concern. The objective of this study was to assess the population dynamics and the phylogeographical history of the paleback darter, using a multilocus microsatellite approach and mitochondrial DNA.
2. The predictions of this study were that: paleback darter populations will exhibit low genetic diversity and minimal gene flow; population structure will correspond to the river systems from which the samples are derived; reservoir dams impounding the reaches between the Caddo and Ouachita rivers would serve as effective barriers to gene flow; and the Caddo and Ouachita rivers are reciprocally monophyletic.
3. Microsatellite DNA loci revealed significant structure among sampled localities (global F_st = 0.17, P < 0.001), with evidence of two distinct populations representing the Caddo and Ouachita rivers. However, Bayesian phylogeographical analyses resulted in three distinct clades: Caddo River, Ouachita River, and Mazarn Creek. Divergence from the most recent ancestor shared among the river drainages was estimated at 60 Kya. Population genetic diversity was relatively low (H_e = 0.65; mean alleles per locus, A = 6.26), but was comparable with the population genetic diversity found in the close relatives slackwater darter, Etheostoma boschungi (H_e = 0.65; A = 6.74), and Tuscumbia darter, Etheostoma tuscumbia (H_e = 0.57; A = 5.53).
4. These results have conservation implications for paleback darter populations and can be informative for other headwater specialist species. Like other headwater species with population structuring and relatively low genetic diversity, the persistence of paleback darter populations is likely to be tied to the persistence and connectivity of local breeding and non-breeding habitat. These results do not raise conservation concern for a population decline; however, the restricted distribution and endemic status of the species still renders paleback darter populations vulnerable to extirpation or extinction.

     

Population structure,genetic diversity,and colonization history of the eastern pondmussel,Sagittunio nasutus,in the Great Lakes drainage

1. The eastern pondmussel, Sagittunio nasutus (Bivalvia: Unionida), has declined in abundance and distribution in eastern North America over the last few decades. The declines are predominantly the result of infestation by invasive dreissenid mussels and changes in habitat. The species is now considered imperilled across large portions of its distribution, especially in the Laurentian Great Lakes region.
2. The genetic diversity and structure of the remnant populations in the Great Lakes region were assessed using 10 newly developed microsatellite DNA loci for S. nasutus. Understanding the remaining populations can inform future management projects and determine whether the remnant populations have experienced a genetic bottleneck or a founder effect. We hope that this will inform the conservation of other species in regions founded by, and isolated from, a more genetically diverse source population or with disjointed geographical distributions.
3. Focusing on the Great Lakes region, samples (n = 428) from 62 collection sites in 28 water bodies were collected. Across the locations sampled for S. nasutus 11 genetic populations were identified, with significant genetic differentiation among them. The genetic structure of the species was assessed, with genetic similarities among populations compared and with geographical routes of colonization and gene flow evaluated.
4. Initial colonization from the Atlantic coast into Lake Erie and Lake Ontario is evident, followed by colonization events into nearby inland rivers and lakes. Analyses found evidence of inbreeding in all but one population and evidence of past genetic bottlenecks or strong founder effects in all but four populations. This study deepens our understanding of the genetic past and present of this imperilled species, providing conservation suggestions for the future management of the species.