Transcriptomic analysis of immune response to bacterial lipopolysaccharide in zebra finch (Taeniopygia guttata).

BACKGROUND: Despite the convergence of rapid technological advances in genomics and the maturing field of ecoimmunology, our understanding of the genes that regulate immunity in wild populations is still nascent. Previous work to assess immune function has relied upon relatively crude measures of immunocompetence. However, with next-generation RNA-sequencing, it is now possible to create a profile of gene expression in response to an immune challenge. In this study, captive zebra finch (Taeniopygia guttata; adult males) were challenged with bacterial lipopolysaccharide (LPS) or vehicle to stimulate the innate immune system. 2 hours after injection, birds were euthanized and hypothalami, spleen, and red blood cells (RBCs) were collected. Taking advantage of the fully sequenced genome of zebra finch, total RNA was isolated, sequenced, and partially annotated in these tissue/cells. RESULTS: In hypothalamus, there were 707 significantly upregulated transcripts, as well as 564 and 144 in the spleen and RBCs, respectively, relative to controls. Also, 155 transcripts in the hypothalamus, 606 in the spleen, and 61 in the RBCs were significantly downregulated. More specifically, a number of immunity-related transcripts (e.g., IL-1ß, RSAD2, SOCS3) were upregulated among tissues/cells. Additionally, transcripts involved in metabolic processes (APOD, LRAT, RBP4) were downregulated. CONCLUSIONS: These results suggest a potential trade-off in expression of genes that regulate immunity and metabolism in birds challenged with LPS. This finding is consistent with a hypothermic response to LPS treatment in small birds. Unlike mammals, birds have nucleated RBCs, and these results support a novel transcriptomic response of avian RBCs to immune challenge.

Defining Populations and Predicting Future Suitable Niche Space in the Geographically Disjunct, Narrowly Endemic Leafy Prairie-Clover (Dalea foliosa; Fabaceae).

Conservation actions for rare species are often based on estimates of population size and number, which are challenging to capture in natural systems. Instead, many definitions of populations rely on arbitrarily defined distances between occurrences, which is not necessarily biologically meaningful despite having utility from a conservation management perspective. Here, we introduce a case study using the narrowly endemic and highly geographically disjunct leafy prairie-clover (Dalea foliosa), for which we use nuclear microsatellite loci to assess the current delimitations of populations and management units across its entire known range. We model future potential suitable niche space for the species to assess how currently defined populations could fare under predicted changes in climate over the next 50 years. Our results indicate that genetic variation within the species is extremely limited, particularly so in the distal portions of its range (Illinois and Alabama). Within the core of its range (Tennessee), genetic structure is not consistent with populations as currently defined. Our models indicate that predicted suitable niche space may only marginally overlap with the geology associated with this species (limestone glades and dolomite prairies) by 2070. Additional studies are needed to evaluate the extent to which populations are ecologically adapted to local environments and what role this could play in future translocation efforts.

Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae).

PREMISE OF THE STUDY: Microsatellites were developed for Astragalus bibullatus (Fabaceae), a federally endangered narrow endemic, to investigate reproductive ecology and species boundaries among closely related taxa. METHODS AND RESULTS: Next-generation sequencing was used to develop 12 nuclear microsatellite loci that amplify in A. bibullatus, as well as in A. crassicarpus var. trichocalyx, A. gypsodes, and A. tennesseensis. Identified loci were di- and trinucleotide repeats, with 1-15 alleles per locus. Observed and expected heterozygosities ranged from 0.000-0.938 and 0.000-0.860, respectively. Cross-amplification of three loci previously published in A. michauxii was also confirmed for the taxa included here. CONCLUSIONS: These data indicate the utility of novel microsatellite loci for conservation genetics and reproductive ecology in closely related Astragalus species.