Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse.

Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater's Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater's Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genomic components associated with the Z-chromosome influence the phenotype and thereby impact species limits among prairie grouse taxa despite ongoing contemporary gene flow.

Indirect effects of red imported fire ants on Attwater's prairie-chicken brood survival.

The invasive red imported fire ant (Solenopsis invicta) has negatively affected a host of taxonomic groups throughout its acquired North American range. Many studies have hypothesized indirect trophic impacts, but few documented those impacts. We evaluated invertebrate abundance as a factor limiting juvenile survival of the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri), and whether fire ants reduce invertebrate numbers and biomass. From 2009-2013, we monitored survival of Attwater's prairie-chicken broods (n = 63) with radio telemetry during the first 2 weeks post-hatch and collected daily invertebrate samples at brood sites. Broods located in areas with the highest median invertebrate count (338 invertebrates/25 sweeps) had a survival probability of 0.83 at 2 weeks post-hatch compared to 0.07 for broods located in areas with the lowest median invertebrate count (18 invertebrates/25 sweeps). During 2011-2012, we evaluated the reduction of fire ants on invertebrate numbers and biomass by aerially treating areas with Extinguish Plus™ in an impact-reference study design. Treated fields had 27% more individual invertebrates and 26% higher invertebrate biomass than reference fields. Our results clearly document that invertebrate abundance affects Attwater's prairie-chicken brood survival and that fire ants may indirectly contribute to low brood survival by suppressing invertebrate abundance. We posit that within the fire ant's acquired North American range, fire ants are likely contributing to declines of other insectivorous species. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Attacks on the endangered Attwater's Prairie-Chicken (Tympanuchus cupido attwateri) by black flies (Diptera: Simuliidae) infected with an avian blood parasite.

With fewer than 50 birds remaining in the wild, Attwater's Prairie-Chicken (Tympanuchus cupido attwateri) is critically endangered. Individuals of this species on the Attwater Prairie Chicken National Wildlife Refuge, Colorado Co., TX, have been attacked in successive winters, 2005-2006, by the blood-feeding black fly Cnephia ornithophilia. Attwater's Prairie-Chicken is a previously unreported host for Cnephia ornithophilia. Molecular screening indicated that about 15% of 13 blood-fed flies sampled from captured Attwater's Prairie-Chickens carried a parasite of the genus Leucocytozoon that can cause a debilitating avian malaria-like disease. If blood feeding or transmission of the disease agent becomes a threat to the birds, particularly in years of lean food supply or harsh weather, management of Cnephia ornithophilia should be considered.

Temporal changes in allele frequencies and low effective population size in greater prairie-chickens.

The number of greater prairie-chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo-likelihood approach that accounted for migration, estimates of Ne (15-32 prairie-chickens within each management area) were 10 times lower than census numbers from booming-ground counts. These low estimates of Ne are consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reduced Ne, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie-chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.

Genetic evaluation of a proposed introduction: the case of the greater prairie chicken and the extinct heath hen.

Population introduction is an important tool for ecosystem restoration. However, before introductions should be conducted, it is important to evaluate the genetic, phenotypic and ecological suitability of possible replacement populations. Careful genetic analysis is particularly important if it is suspected that the extirpated population was unique or genetically divergent. On the island of Martha's Vineyard, Massachusetts, the introduction of greater prairie chickens (Tympanuchus cupido pinnatus) to replace the extinct heath hen (T. cupido cupido) is being considered as part of an ecosystem restoration project. Martha's Vineyard was home to the last remaining heath hen population until its extinction in 1932. We conducted this study to aid in determining the suitability of greater prairie chickens as a possible replacement for the heath hen. We examined mitochondrial control region sequences from extant populations of all prairie grouse species (Tympanuchus) and from museum skin heath hen specimens. Our data suggest that the Martha's Vineyard heath hen population represents a divergent mitochondrial lineage. This result is attributable either to a long period of geographical isolation from other prairie grouse populations or to a population bottleneck resulting from human disturbance. The mtDNA diagnosability of the heath hen contrasts with the network of mtDNA haplotypes of other prairie grouse (T. cupido attwateri, T. pallidicinctus and T. phasianellus), which do not form distinguishable mtDNA groupings. Our findings suggest that the Martha's Vineyard heath hen was more genetically isolated than are current populations of prairie grouse and place the emphasis for future research on examining prairie grouse adaptations to different habitat types to assess ecological exchangeability between heath hens and greater prairie chickens.

Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens.

Greater prairie-chickens (Tympanuchus cupido pinnatus) were once found throughout the tallgrass prairie of midwestern North America but over the last century these prairies have been lost or fragmented by human land use. As a consequence, many current populations of prairie-chickens have become isolated and small. This fragmentation of populations is expected to lead to reductions in genetic variation as a result of random genetic drift and a decrease in gene flow. As expected, we found that genetic variation at both microsatellite DNA and mitochondrial DNA (mtDNA) markers was reduced in smaller populations, particularly in Wisconsin. There was relatively little range-wide geographical structure (FST) when we examined mtDNA haplotypes but there was a significant positive relationship between genetic (FST) and geographical distance (isolation by distance). In contrast, microsatellite DNA loci revealed significant geographical structure (FST) and a weak effect of isolation by distance throughout the range. These patterns were much stronger when populations with reduced levels of genetic variability (Wisconsin) were removed from the analyses. This suggests that the effects of genetic drift were stronger than gene flow at microsatellite loci, whereas these forces were in range-wide equilibrium at mtDNA markers. These differences between the two molecular markers may be explained by a larger effective population size (Ne) for mtDNA, which is expected in species such as prairie-chickens that have female-biased dispersal and high levels of polygyny. Our results suggest that historic populations of prairie-chickens were once interconnected by gene flow but current populations are now isolated. Thus, maintaining gene flow may be important for the long-term persistence of prairie-chicken populations.