Genetic evidence of multiple matrilineal lineages of the channel catfish, Ictalurus punctatus in North America

Using mitochondrial DNA control region (mtDNA CR) sequence data the present study evaluates the genetic status of the wild populations of channel catfish, Ictalurus punctatus, in North America. A total of 584 individuals representing 56 drainages across its distributional range in the United States were collected. There were 105 mtDNA CR haplotypes defined by 51 variable sites. Phylogenetic analyses have revealed the existence of six distinct matrilineal genetic lineages of channel catfish in the United States. Four of these lineages were restricted to southeast Gulf Coast, a region that never glaciated during the Pleistocene. While samples from the Mississippi river and its tributaries represent a single genetic lineage, samples from the southeast Atlantic coastal plain drainages formed a unique lineage. Each lineage should be regarded as an evolutionarily significant unit/management unit and therefore separate management and conservation strategies should be undertaken in order to conserve the genetic resources.     

Contrasting patterns of genetic diversity between the northern and southern populations of yellow bullhead catfish, Ameiurus natalis in North America

Environmental conditions have profound influence on the life history characteristics of a species, for instance, the yellow bullhead (Ameiurus natalis) population in its southernmost native range, South Florida was previously reported to be distinguished from other A. natalis populations in the United States by growth rates and feeding habits. Utilizing mitochondrial DNA control region sequence data, the present study sought to evaluate the patterns of intraspecific diversification of this North American freshwater catfish, A. natalis. The analyses have revealed the existence of four distinct matrilineal lineages (Mississippi, Gulf coast, Southeast Atlantic, and South Florida) with strong geographic specificity. Although all the lineages showed rapid demographic expansion, the South Florida lineage is shown to have greater genetic diversity than the remaining lineages. The persistence of more favorable environmental conditions and suitable habitats during the late-Pleistocene period in southern Florida could be the possible explanation for such genetic disparities among the lineages. However, taken together with the conclusion of previous studies, the present study predicted that the recurrent density-dependent process resulting from the altercation of hydrology in South Florida may cause the reduction in genetic diversity and put this species at risk in this region.     

Hydrologic variability in dryland regions: impacts on ecosystem dynamics and food security

Research on ecosystem and societal response to global environmental change typically considers the effects of shifts in mean climate conditions. There is, however, some evidence of ongoing changes also in the variance of hydrologic and climate fluctuations. A relatively high interannual variability is a distinctive feature of the hydrologic regime of dryland regions, particularly at the desert margins. Hydrologic variability has an important impact on ecosystem dynamics, food security and societal reliance on ecosystem services in water-limited environments. Here, we investigate some of the current patterns of hydrologic variability in drylands around the world and review the major effects of hydrologic fluctuations on ecosystem resilience, maintenance of biodiversity and food security. We show that random hydrologic fluctuations may enhance the resilience of dryland ecosystems by obliterating bistable deterministic behaviours and threshold-like responses to external drivers. Moreover, by increasing biodiversity and the associated ecosystem redundancy, hydrologic variability can indirectly enhance post-disturbance recovery, i.e. ecosystem resilience.     

Accurate prediction of interfacial residues in two‐domain proteins using evolutionary information: Implications for three‐dimensional modeling

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure–function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two‐domain proteins. We also use information from the three‐dimensional structures of individual domains of two‐domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (～85%) and specific (～95%) to the domain–domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain–domain interaction, rigid‐body docking was able to provide us with accurate full‐length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. Proteins 2014; 82:1219–1234. © 2013 Wiley Periodicals, Inc.     

Isolation by distance explains genetic structure of Buggy Creek virus,a bird-associated arbovirus

Many of the arthropod-borne viruses (arboviruses) show extensive genetic variability and are widely distributed over large geographic areas. Understanding how virus genetic structure varies in space may yield insight into how these pathogens are adapted to and dispersed by different hosts or vectors, the relative importance of mutation, drift, or selection in generating genetic variability, and where and when epidemics or epizootics are most likely to occur. However, because most arboviruses tend to be sampled opportunistically and often cannot be isolated in large numbers at a given locale, surprisingly little is known about their spatial genetic structure on the local scale at which host/vector/virus interactions typically occur. Here, we examine fine-scale spatial structure of two sympatric lineages of Buggy Creek virus (BCRV, Togaviridae), an alphavirus transmitted by the ectoparasitic swallow bug (Oeciacus vicarius) to colonially nesting cliff swallows (Petrochelidon pyrrhonota) and invasive house sparrows (Passer domesticus) in North America. Data from 377 BCRV isolates at cliff swallow colony sites in western Nebraska showed that both virus lineages were geographically structured. Most haplotypes were detected at a single colony or were shared among nearby colonies, and pair-wise genetic distance increased significantly with geographic distance between colony sites. Genetic structure of both lineages is consistent with isolation by distance. Sites with the most genetically distinct BCRV isolates were occupied by large numbers of house sparrows, suggesting that concentrations of invasive sparrows may represent foci for evolutionary change in BCRV. Our results show that bird-associated arboviruses can show genetic substructure over short geographic distances.     

Adaptive evolution of crustin antimicrobial peptides in decapods

Antimicrobial peptides (AMPs) are present in a wide range of taxonomic groups and played a crucial role in host adaptation to a diverse array of ever-changing pathogens. Crustin, a cysteine-rich cationic AMP, is known to exhibit antimicrobial activity against Gram-positive and Gram-negative bacteria in decapods. Given their important role in host-immune defense, a large proportion of amino acid substitutions in crustin AMPs are expected to be fixed by natural selection. Utilizing the complete coding nucleotide sequence data of crustin, the present study revealed the pervasive role of positive Darwinian selection in the evolution and divergence of crustin AMPs in decapods. Approximately, 20–35?% of codons in two phylogenetically distinct groups of closely related crustins in Penaeid shrimps are shown to have evolved under positive selection. Interestingly, several of these positively selected sites are located at the carboxyl-terminal region, the region that directly interacts with the invading pathogens. Pathogen-mediated selection pressure could be the likely cause for such an accelerated rate of amino acid substitutions and could have contributed to the structural and functional diversification of crustin AMPs in several taxa.