Disclosure statement:Authors have nothing to disclose. Abstract (237) 1 2Hybridization is well recognized as a driver of speciation, yet it often remains difficult to parse 3 phylogenomically in that post-speciation gene flow frequently supersedes an ancestral signal. 4Here we examined how interactions between recombination and gene flow shaped the 5 phylogenomic landscape of red wolf to create non-random retention of introgressed ancestry. 6Our re-analyses of genomic data recapitulate fossil evidence by demonstrating red wolf was 7 indeed extant and isolated prior to more recent admixture with other North American canids. Its 8 more ancient divergence, now sequestered within low-recombinant regions on the X-9 chromosome (i.e., chromosomal 'refugia'), is effectively masked by multiple, successive waves 10 of secondary introgression that now dominate its autosomal ancestry. These interpretations are 11 congruent with more theoretical explanations that describe the manner by which introgression 12 can be localized within the genome through recombination and selection. They also tacitly 13 support the large-X effect, i.e., the manner by which loci that contribute to reproductive isolation 14 can be enriched on the X-chromosome. By contrast, similar, high recombinant regions were also 15 found as enriched within very shallow gene trees, thus reflecting post-speciation gene flow and a 16 compression of divergence estimates to 1/20 th of that found in recombination 'cold spots'. Our 17 results effectively reconcile conflicting hypotheses regarding the impact of hybridization on 18 evolution of North American canids and support an emerging framework within which the 19 analysis of a phylogenomic landscape structured by recombination can be used to successfully 20 address the macroevolutionary implications of hybridization. 21 22 23 24 precede introgression) can be depleted, and especially so in those lineages with a history of 48 secondary introgression. However, the parsing of genealogical histories is dependent on the 49 interactions between recombination, genetic drift, and selection (McGaugh et al. 2012; Schumer 50 et al. 2018). As such, branching patterns are often retained non-randomly, with reduced 51 permeability to gene flow found in those genomic areas with low recombination, where 52 introgression of deleterious alleles is restricted by an increased efficacy of linked selection 53 (Payseur and Rieseberg 2016; Runemark et al. 2018; Schumer et al. 2018). 54The interaction between selection and recombination through time allows fundamental 55 predictions to be made with regard to the stability of hybrids genomes, and this may promote the 56 role that hybridization plays in a given lineage. In the generations following a hybridization 57 event, recombination creates junction-points where ancestries transition from one parental 58 genome to another (Fisher 1954). Their densities along the length of a chromosome can be used 59 to find loci relating to hybrid fitness, because selection against incompatible loci w...

Replicated evolutionary patterns are often attributed to recurrent emergence following parallel selective pressures. However, similar genetic patterns (e.g., 'genomic islands') can also emerge following extensive homogenization in secondary contact, as a by-product of heterogeneous introgression. For example, within Himalayan tributaries of the Ganges/Brahmaputra rivers, drainage-specific mtDNA clades of polyploid snowtrout (Cyprinidae: Schizothorax) are partitioned as co-occurring morphological 'ecotypes,' hypothesized to represent parallel divergence among adjacent streams. To evaluate this scenario, we utilized a reduced-representation genomic approach (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs) applied to high-altitude Nepali/Bhutanese snowtrout (N=48 each). We unambiguously quantified ploidy levels by first deriving genome-wide allelic depths followed by ploidy-aware Bayesian models that produced genotypes statistically consistent with diploid/tetraploid expectations. When genotyped SNPs were clustering within drainages, the convergence of eco-phenotypes was sustained. However, subsequent partitioned analyses of phylogeny and population admixture instead identified subsets of loci under selection which retained genealogical concordance with morphology, with apparent patterns of parallel ecotype emergence instead driven by widespread genomic homogenization. Here, prior isolation is effectively masked by admixture occurring in secondary contact. We note two salient factors:1) Polyploidy has promoted homogenization in tetraploid Himalayan snowtrout; and 2) Homogenization varies across Himalayan tributaries, presumably in lockstep with extent of anthropogenic modification.

28Each year, millions of kilograms of insecticides are applied to crops in the US. While insecticide 29 use supports food, fuel, and fiber production, it can also threaten non-target organisms, a concern 30 underscored by mounting evidence of widespread insect decline. Nevertheless, answers to basic 31 questions about the spatiotemporal patterns of insecticide use remain elusive, due in part to the 32 inherent complexity of insecticide use, and exacerbated by the dispersed nature of the relevant 33 data, divided between several government repositories. Here, we integrate these public datasets 34 to generate county-level annual estimates of total 'insect toxic load' (honey bee lethal doses) for 35 insecticides applied in the US between 1997-2012, calculated separately for oral and contact 36 toxicity. To explore the underlying drivers of the observed changes, we divide insect toxic load 37 into the components of extent (area treated) and intensity (application rate x potency). We show 38 that while contact-based insect toxic load remained relatively steady over the period of our 39 analysis, oral-based insect toxic load increased roughly 9-fold, with reductions in application rate 40 outweighed by disproportionate increases in potency (toxicity/kg) and increases in extent. This 41 pattern varied markedly by region, with the greatest increases seen in Heartland and Northern 42Great Plains regions, likely driven by use of neonicotinoid seed treatments in corn and soybean. 43In this "potency paradox," US farmland has become more hazardous to insects despite lower 44 volumes of insecticides applied, raising serious concerns about insect conservation and 45 highlighting the importance of integrative approaches to pesticide use monitoring. 46 47 48 the potency (toxicity/kg) of insecticides applied and in the area treated; the volume of 56 insecticides applied declined. Toxic load increased most dramatically in regions where 57 neonicotinoid seed treatments for field crops are commonly used. 58 59 395