Jeff Prendergast | USGS Science

USGS2023

A highly-contiguous and annotated genome assembly of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus).

The Lesser Prairie-Chicken ( Tympanuchus pallidicinctus ; LEPC) is an iconic North American prairie grouse, renowned for ornate and spectacular breeding season displays. Unfortunately, the species has disappeared across much of its historical range, with corresponding precipitous declines in contemporary population abundance, largely due to climatic and anthropogenic factors. These declines led to a 2022 US Fish and Wildlife decision to identify and list two distinct population segments (DPSs; i.e., northern and southern DPSs) as threatened or endangered under the 1973 Endangered Species Act. Herein, we describe an annotated reference genome that was generated from a LEPC sample collected from the southern DPS. We chose a representative from the southern DPS because of the potential for introgression in the northern DPS, where some populations hybridize with the Greater Prairie-Chicken ( Tympanuchus cupido ). This new LEPC reference assembly consists of 206 scaffolds, an N50 of 45 Mb, and 15,563 predicted protein-coding genes. We demonstrate the utility of this new genome assembly by estimating genome-wide heterozygosity in a representative LEPC and in related species. Heterozygosity in a LEPC sample was 0.0024, near the middle of the range (0.0003–0.0050) of related species. Overall, this new assembly provides a valuable resource that will enhance evolutionary and conservation genetic research in prairie grouse.

Genome Biology and Evolution↗

USGS2023

Ring-necked Pheasant brood habitat selection and movements in an intensive agricultural landscape

Management of row crops can greatly influence wildlife populations in an agriculturally intensive landscape. Many upland gamebird populations, including Phasianus colchicus L. (Ringnecked Pheasant; hereafter pheasant) are experiencing contemporary population declines in such landscapes throughout the Midwest United States. Reduced availability of quality brood habitat may be a factor in these declines. Alternative practices, such as spring cover crops, may increase brood survival and benefit local pheasant populations. Our objectives were to follow radio-tagged females and assess pheasant brood 1) movements among available habitat patches within landscapes including spring cover crops and Conservation Reserve Program (CRP) fields, 2) relative use of available cover types within a landscape, 3) selection of vegetation structure, vegetation composition, and invertebrate community structure by brood-rearing hens in landscapes dominated by row-crop agriculture, and 4) survival rates. Broods were found primarily in grassy areas (native grass, pasture, train track right-of-way, and grass strips) and spring cover crop fields even though cover crops were the least common cover type in all study areas. Brood movements were limited with broods staying near nest locations for 30 days after hatch. Though movements were small, broods were found in multiple cover types, averaging 2.8 out of 6 available cover types. There was no difference between used and random locations for invertebrate metrics including total counts, biomass, and richness; order-specific biomass; and order-specific counts. Visual obstruction and vegetation composition were similar between used and random locations. Across our study sites, we found little support for point-site selection (i.e., within-patch 4th order selection) but significant support for patch-site selection by female pheasants attending broods. Spring cover crops (<5%) and CRP (<15%) comprised a small percentage of the landscape area, but were selected by females attending broods as each contained approximately 25% of brood locations. Apparent survival of pheasant broods was low compared to other studies. Female pheasants selected for spring cover crops and CRP when attending broods, both are alternatives to current row-crop farming practices. As pheasants continue to respond to changes in western Kansas landscapes, homogeneity of cover types found in agricultural landscapes can be detrimental if practices continue to shift from quality pheasant habitat but can be advantageous if practices shift towards favorable management practices.

Kansas↗