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Anthropogenic destruction and fragmentation of habitat restrict many species to small, isolated populations, which often experience high extirpation risk. Restoring connectivity through translocations is one approach for mitigating the demographic and genetic perils faced by small populations. However, translocation interventions often lack substantial postrelease monitoring, and thus important information including the performance of translocated individuals, the long-term impacts on the recipient population, and the extent to which management objectives are fulfilled over time are often poorly known. Here, we examined the establishment dynamics and long-term outcomes of translocations from multiple donor populations into an intensively monitored population of the federally threatened red-cockaded woodpecker. We found evidence that translocations contributed to population growth and led to genetic admixture within the population. The translocated birds provided direct demographic benefits through high rates of establishment, breeding, and survival. We found that the survival and lifetime reproductive success of individuals were positively related to their amount of translocation ancestry, indicating that demographic benefits extended beyond the direct performances of the translocated birds. The translocations diversified the population’s genetic composition with the ancestry of most individuals in the latter years of the study deriving from multiple translocation donor populations. We found marked heterogeneity in the genetic contributions of translocated individuals and cohorts, leading to disproportionate representation of certain lineages. Encouragingly, despite some accumulation of inbreeding during the study, the translocations thus far have not substantially contributed to inbreeding. Our findings illustrate in precise detail how translocations can be an effective approach for managing imperiled taxa. 

ABSTRACT Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high‐throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole‐genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re‐use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization—and the hypothesized processes by which it shapes diversification—and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life. 

Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3–4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1–2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.