Population genetic theory and empirical evidence indicate that deleterious alleles can be purged in small populations. However, this viewpoint remains controversial. It is unclear whether natural selection is powerful enough to purge deleterious mutations when wild populations continue to decline. Pheasants are terrestrial birds facing a long-term risk of extinction as a result of anthropogenic perturbations and exploitation. Nevertheless, there are scant genomics resources available for conservation management and planning. Here, we analyzed comparative population genomic data for the three extant isolated populations of Brown eared pheasant (Crossoptilon mantchuricum) in China. We showed that C. mantchuricum has low genome-wide diversity and a contracting effective population size because of persistent declines over the past 100,000 years. We compared genome-wide variation in C. mantchuricum with that of its closely related sister species, the Blue eared pheasant (C. auritum) for which the conservation concern is low. There were detrimental genetic consequences across all C. mantchuricum genomes including extended runs of homozygous sequences, slow rates of linkage disequilibrium decay, excessive loss-of-function mutations, and loss of adaptive genetic diversity at the major histocompatibility complex region. To the best of our knowledge, this study is the first to perform a comprehensive conservation genomic analysis on this threatened pheasant species. Moreover, we demonstrated that natural selection may not suffice to purge deleterious mutations in wild populations undergoing long-term decline. The findings of this study could facilitate conservation planning for threatened species and help recover their population size.

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 million years of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.

The utility of intratumour heterogeneity as a prognostic biomarker is the subject of ongoing clinical investigation. However, the relationship between this marker and its clinical impact is mediated by an evolutionary process that is not well understood. Here, we employ a spatial computational model of tumour evolution to assess when, why and how intratumour heterogeneity can be used to forecast tumour growth rate and progression‐free survival. We identify three conditions that can lead to a positive correlation between clonal diversity and subsequent growth rate: diversity is measured early in tumour development; selective sweeps are rare; and/or tumours vary in the rate at which they acquire driver mutations. Opposite conditions typically lead to negative correlation. In cohorts of tumours with diverse evolutionary parameters, we find that clonal diversity is a reliable predictor of both growth rate and progression‐free survival. We thus offer explanations—grounded in evolutionary theory—for empirical findings in various cancers, including survival analyses reported in the recent TRACERx Renal study of clear‐cell renal cell carcinoma. Our work informs the search for new prognostic biomarkers and contributes to the development of predictive oncology.

Remote sensing has greatly advanced our understanding of the land surface and the role of biology within it (Tucker and Sellers, 1986). But our ability to generate observations from remote sensing data at scales clearly aligned with biological processes has been limited. The problem is that biological processes like natural selection, metabolism, and resource allocation vary within and among individuals and change on scales of space and time that are finer than the granularity of traditional remote sensing measurements.Advances in technology are poised to overcome this problem by generating data from tower mounted, airborne and satellite sensors at scales of space and time aligned with biological understanding. Miniaturized sensor designs focus on lightweight instruments that can be carried by drones or operated on field platforms. And constellations of small sensors called cube-sats are now working together in space to image the entire land surface of our planet every day at resolutions fine enough to resolve individual plants.The quantitative step forward represented by these new technologies is significant, but the most important advance is conceptual. Measurements from remote sensing at ultra-high spatial and temporal resolution open the door to characterizing phenomena that have been beyond our grasp, including population dynamics Hubbell, 2017, 2018), high-spatial-resolution phenology (Wu et al., 2016), and physical quantities that can be related to organismal condition, like foliar chemistry, canopy temperature and solar-induced fluorescence (Daumard et al., 2010;Porcar-Castell et al., 2014). These new measurements cross thresholds of scale in space, time, and biological organization that are clearly aligned with decades of understanding in plant biology (Gamon et al., 1992;Demmig-Adams and Adams, 2006). HARNESSING DRONES TO ADVANCE REMOTE SENSING OF INDIVIDUAL PLANTSDrones operate at low altitude and can produce measurements at densities orders of magnitude greater than traditional airborne remote sensing (Kellner et al., 2019). These new measurements fundamentally alter our scope of inference by allowing us to work not with area-based summaries, but with individual plants. The cost of operating a drone is about an order of magnitude less than a traditional airborne program, which makes it possible to acquire measurements frequently, on demand. Lidar sensors record the return-time of emitted laser pulses to produce a physically accurate three-dimensional point cloud (Disney, 2019). Measurement densities from drone lidar are easily in the thousands of points per square meter (Fig. 1). This important distinction has allowed highdensity point clouds from drones to resolve branch and stem structure within individual trees, and to associate individual plants with remote sensing data (Brede et al., 2017;Trochta et al., 2017).Optical sensors on drones can produce pixels at the leaf level, resulting in many thousands of measurements within single trees from imaging spectrometers, multispectral cameras, and tradi...

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 million years of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.

Whole‐genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long‐read DNA sequencing can help clarify. Here, we report on whole‐genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue‐faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo‐Z chromosome by long‐read sequencing. Using short‐read genome‐wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3–1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo‐Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo‐Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination‐suppressed portion of the neo‐Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral‐Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long‐read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

Field measurements demonstrate a carbon sink in the Amazon and Congo basins, but the cause of this sink is uncertain. One possibility is that forest landscapes are experiencing transient recovery from previous disturbance. Attributing the carbon sink to transient recovery or other processes is challenging because we do not understand the sensitivity of conventional remote sensing methods to changes in aboveground carbon density (ACD) caused by disturbance events. Here we use ultra-high-density drone lidar to quantify the impact of a blowdown disturbance on ACD in a lowland rain forest in Costa Rica. We show that the blowdown decreased ACD by at least 17.6%, increased the number of canopy gaps, and altered the gap size-frequency distribution. Analyses of a canopy-height transition matrix indicate departure from steady-state conditions. This event will initiate a transient sink requiring an estimated 24–49 years to recover pre-disturbance ACD. Our results suggest that blowdowns of this magnitude and extent can remain undetected by conventional satellite optical imagery but are likely to alter ACD decades after they occur.

The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For J. copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020 Mbp/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795 Mbp/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 Mbp and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (> 59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for H. impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.