This chapter from The Codex of the Endangered Species Act, Volume II: The Next Fifty Years describes how genetic information is used to inform decision-making for the Endangered Species Act. In one section of this chapter (page 4 of the PDF, page 162 of the book), the use of genomics to differentiate between subspecies of willow flycatcher (Empidonax traillii) is described.

This article describes how researchers discovered that southwestern willow flycatchers in southern California have evolved in response to climate change. Southwestern willow flycatcher (SWFL) populations are threatened by climate change and habitat loss. By sequencing DNA from historical SWFL samples and comparing these to modern samples, researchers determined that modern SWFL were more likely to have beneficial genes that help them cope with changing climate.

A look at the evolutionary response to climate change in the endangered southwestern willow flycatcher (Empidonax traillii extimus) using whole-genome comparisons between historic and modern specimens from California. While introgression led genomes of neighboring E. traillii extimus populations (California and Arizona) to become more similar, the specific loci linked to climate shifted in a way consistent with climate adaptation rather than becoming more similar to those of neighboring populations.

From the abstract:

An understanding of trait-environment relationships is particularly important in the case of invasive species which may alter abiotic conditions and available resources. This study is the first to measure the functional response of riparian plant communities to biocontrol of an invasive species.

Stahlke et al. developed a reference genome for tamarisk beetles (Diorhabda spp.) and reference panel of all four introduced parental species to monitor range expansion and hybridization across North America. They found a substantial genetic bottleneck among D. carinulata in N. America, although populations continue to establish and spread, possibly due to aggregation behavior. Among hybrids, they found that D. carinata, D. elongata, and D. sublineata hybridize in the field, especially in eastern New Mexico, with D. carinata × D.

To what extent has invasive riparian vegetation (IRV) treatment reversed channel narrowing and reduced dynamism trends? Paired treated and untreated reaches at 15 sites along 13 rivers were compared before and after treatment using repeat aerial imagery to assess long-term (~10 year) channel change due to treatment on a regional scale across the Southwest U.S. Wieting et al. found that IRV treatment significantly increased channel width and floodplain destruction.

Clark et al. evaluated theoretical predictions for evolution of reproductive life-history and dispersal traits in the range expansion of the tamarisk biological control agent, Diorhabda carinulata, or northern tamarisk beetle. With experiments run on field-collected populations, they found that females at the expansion front had increased fecundity and body mass, and reduced age at first reproduction; and that dispersal increased at the expansion front in males, especially when unmated and reared at low density.

Does hybridization among tamarisk beetles change the risk of non-target attack in the field? Clark et al. study the consequences of hybridization in  tamarisk beetles (Diorhabda). They paired laboratory phenotyping with genomics to assess changes in risk of non-target attack and body size and fecundity. Body size and early fecundity were similar in pure and hybrid females, indicating that hybridization is not detrimental to insect fitness or the biocontrol program and may provide variation that allows populations to become locally adapted.

What site conditions are associated with greater recovery and overall higher cover of willows? Goetz et al. performed a meta-analysis of tamarisk removal and willow (Salix) recovery across the southwest, compiling data from 260 sites where tamarisk was subject to active removal and/or biocontrol and 132 reference sures. Cut-stump method with biological control was the most effective method to improve native species dominance. Willow cover was generally highest in locations with low drought stress, as reflected by soil properties, distance to water, and climate.

  A Tale of Two Rivers:  The Role of Different Drought-Like Conditions in Promoting Vegetation Encroachment on the Lower Dolores River