A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts

Genetic affinities within a large global collection of pathogenic <i>Leptospira</i>: implications for strain identification and molecular epidemiology

Leptospirosis is an important zoonosis with widespread human health implications. The non-availability of accurate identification methods for the individualization of different Leptospira for outbreak investigations poses bountiful problems in the disease control arena. We harnessed fluorescent amplified fragment length polymorphism analysis (FAFLP) for Leptospira and investigated its utility in establishing genetic relationships among 271 isolates in the context of species level assignments of our global collection of isolates and strains obtained from a diverse array of hosts. In addition, this method was compared to an in-house multilocus sequence typing (MLST) method based on polymorphisms in three housekeeping genes, the rrs locus and two envelope proteins. Phylogenetic relationships were deduced based on bifurcating Neighbor-joining trees as well as median joining network analyses integrating both the FAFLP data and MLST based haplotypes. The phylogenetic relationships were also reproduced through Bayesian analysis of the multilocus sequence polymorphisms. We found FAFLP to be an important method for outbreak investigation and for clustering of isolates based on their geographical descent rather than by genome species types. The FAFLP method was, however, not able to convey much taxonomical utility sufficient to replace the highly tedious serotyping procedures in vogue. MLST, on the other hand, was found to be highly robust and efficient in identifying ancestral relationships and segregating the outbreak associated strains or otherwise according to their genome species status and, therefore, could unambiguously be applied for investigating phylogenetics of Leptospira in the context of taxonomy as well as gene flow. For instance, MLST was more efficient, as compared to FAFLP method, in clustering strains from the Andaman island of India, with their counterparts from mainland India and Sri Lanka, implying that such strains share genetic relationships and that leptospiral strains might be frequently circulating between the islands and the mainland

Double-digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles.

The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double-digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded adapters and incorporates universal indexes for multiplexing. We tested for reproducibility and functionality by comparing shared loci from sample replicates and assessed the effects of numbers of ambiguous sites and clustering thresholds on coverage depths, number of shared loci among samples, and phylogenetic reconstruction. Errors between technical replicates were minimal. Relaxing the quality-filtering criteria increased the mean coverage depth per locus and the number of loci recovered within a sample, but had little effect on the number of shared loci across samples. Increasing clustering threshold decreased the mean coverage depth per cluster and increased the number of loci recovered within a sample but also decreased the number of shared loci across samples, especially among distantly related species. The combination of low similarity clustering (70%) and relaxed quality-filtering (allowing up to 30 ambiguous sites per read) performed the best in phylogenetic analyses at both recent and deep genetic divergences. Hence, this method generated sufficient number of shared homologous loci to investigate the evolutionary relationships among divergent fungal lineages with small haploid genomes. The greater genetic resolution also revealed new structure within species that correlated with ecological traits, providing valuable insights into their cryptic life histories

Genetic Toolkit for Assessment and Prediction of Population-Level Impacts of Bridge Construction on Birds

Recent studies have highlighted alarming rates of declines in bird populations across the country. The State of California is home to over 650 resident and migrant avian species. Legislation for protecting these species has existed for over a century now, yet tools for identifying populations and understanding seasonal movement remain limited. Recently, genetic and genomic tools have provided a method for understanding population structure, allowing for more informed delineation of management units. The goal of this project was to create a genetic toolkit for identifying breeding populations and assigning individuals to those populations. Ultimately, such tools could be used to assess population-level impacts when there are conflicts with birds at infrastructure construction sites. As a test case, we sequenced entire genomes for 40 individual Anna’s hummingbirds (Calypte anna) from across the state. Based on this initial data, we found low levels of differentiation between sampled locations, suggesting that C. anna in California are not subdivided into different population units. However, there was a weak signal of geography suggesting there may be localized genetic differences in a small proportion of the genome. Follow-up work will focus on a broader sampling across the state of California to clarify any possible population subdivision or geographical patterns of differentiation.View the NCST Project Webpag

Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

Abstract Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris , the progenitor of common bean ( P. vulgaris ), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for ∼20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris . As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean. Author Summary The ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from ∼35° N. Lat. to ∼35° S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method – outlier detection – was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method – genome-wide association – was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans

Drilling down hotspots of infraspecific diversity to bring them into on-ground conservation of threatened species

Unprecedented rates of biodiversity loss raise the urgency for preserving species ability to cope with ongoing global changes. An approach in this direction is to target intra-specific hotspots of genetic diversity as conservation priorities. However, these hotspots are often identified by sampling at a spatial resolution too coarse to be useful in practical management of threatened species, hindering the long-appealed dialog between conservation stakeholders and conservation genetic researchers. Here, we investigated the spatial and temporal variation in species presence, genetic diversity, as well as potential risk factors, within a previously identified hotspot of genetic diversity for the endangered Apennine yellow-bellied toad Bombina pachypus. Our results show that this hotspot is neither a geographically homogeneous nor a temporally stable unit. Over a time-window spanning 10–40 years since previous assessments, B. pachypus populations declined in large portions of their hotspot, and their genetic diversity levels decreased. Considering the demographic trend, genetic and epidemiological data, and models of current and future climatic suitability, populations at the extreme south of the hotspot area still qualify for urgent in-situ conservation actions, whereas northern populations would be better managed through a mix of in-situ and ex-situ actions. Our results emphasize that identifying hotspots of genetic diversity, albeit an essential step, does not suffice to warrant on-ground conservation of threatened species. Hotspots should be analyzed at finer geographic and temporal scales, to provide conservation stakeholders with key knowledge to best define conservation priorities, and to optimize resource allocation to alternative management practices

Fine-scale population structure and asymmetrical dispersal in an obligate salt-marsh passerine, the Saltmarsh Sparrow (Ammodramus Caudacutus)

Understanding the spatial scale of gene flow can yield valuable insight into the ecology of an organism and guide conservation strategies. Fine-scale genetic structure is uncommon in migratory passerines because of their high vagility and presumed high dispersal abilities. Aspects of the behavior and ecology of some migratory species, however, may promote structure on a finer scale in comparison to their mobility. We investigated population genetic structure in the Saltmarsh Sparrow (Ammodramus caudacutus), a migratory passerine that breeds along the northeastern coast of the United States, where it is restricted exclusively to a narrow strip of patchily distributed tidal marsh habitat. Using genotyping with 10 microsatellite loci, we detected weak but significant population structure among Saltmarsh Sparrows from nine marshes on the breeding grounds between Scarborough, Maine, and Oceanside, New York. Genetic variation among marshes was largely consistent with a pattern of isolation by distance, with some exceptions. One inland marsh was genetically divergent despite its proximity to other sampled marshes, which suggests that mechanisms besides geographic distance influence population genetic structure. Bayesian clustering, multivariate analyses, and assignment tests supported a population structure consisting of five groups. Estimates of migration rates indicated variation in gene flow among marshes, which suggests asymmetrical dispersal and possible source-sink population dynamics. The genetic structure that we found in Saltmarsh Sparrows may result from natal philopatry and breeding-site fidelity, combined with restricted dispersal due to obligate dependence on a patchy habitat. Our findings suggest that fine-scale population structure may be important in some migratory passerines. Received 12 July 2011, accepted 1 February 2012

Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand the functional organization of cells. In this review, we discuss the key contributions of computational methods developed till date (approximately between 2003 and 2015) for identifying complexes from the network of interacting proteins (PPI network). We evaluate in depth the performance of these methods on PPI datasets from yeast, and highlight challenges faced by these methods, in particular detection of sparse and small or sub- complexes and discerning of overlapping complexes. We describe methods for integrating diverse information including expression profiles and 3D structures of proteins with PPI networks to understand the dynamics of complex formation, for instance, of time-based assembly of complex subunits and formation of fuzzy complexes from intrinsically disordered proteins. Finally, we discuss methods for identifying dysfunctional complexes in human diseases, an application that is proving invaluable to understand disease mechanisms and to discover novel therapeutic targets. We hope this review aptly commemorates a decade of research on computational prediction of complexes and constitutes a valuable reference for further advancements in this exciting area.Comment: 1 Tabl

Network analysis identifies weak and strong links in a metapopulation system

The identification of key populations shaping the structure and connectivity of metapopulation systems is a major challenge in population ecology. The use of molecular markers in the theoretical framework of population genetics has allowed great advances in this field, but the prime question of quantifying the role of each population in the system remains unresolved. Furthermore, the use and interpretation of classical methods are still bounded by the need for a priori information and underlying assumptions that are seldom respected in natural systems. Network theory was applied to map the genetic structure in a metapopulation system by using microsatellite data from populations of a threatened seagrass, Posidonia oceanica, across its whole geographical range. The network approach, free from a priori assumptions and from the usual underlying hypotheses required for the interpretation of classical analyses, allows both the straightforward characterization of hierarchical population structure and the detection of populations acting as hubs critical for relaying gene flow or sustaining the metapopulation system. This development opens perspectives in ecology and evolution in general, particularly in areas such as conservation biology and epidemiology, where targeting specific populations is crucial