Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome.

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.

Mercury Concentration in Nestling Feathers Better Predicts Individual Reproductive Success than Egg or Nestling Blood in a Piscivorous Bird.

Piscivorous birds are at high risk of mercury exposure in aquatic food webs, and their reproductive success is sensitive to methylmercury exposure. Although effects are convincingly shown in a handful of lab studies, sublethal effects at environmentally relevant concentrations in the field, where there is a range of other natural stressors, are not well delineated. Part of that uncertainty arises because mercury concentration (hereafter, [Hg]) in adult tissues used to assess Hg risk can be influenced by Hg values in wintering grounds or other nonrelated areas. Several studies have used nestling tissues under the assumption that they better represent local risk to breeding since nestlings consume locally derived food. However, the correlation between [Hg] in nestling tissues and local breeding success remains unassessed. We analyzed great egret ( Ardea alba) breeding parameters collected over 3 years (2015-2017) in the Everglades (Florida, USA). The Everglades is a large contiguous wetland with geographically dispersed wading bird breeding sites exposed to variable and biologically relevant ranges of mercury concentrations. We examined mercury concentrations in albumen and nestling blood and feathers as predictors of 6 measures of reproductive success at individual nests. Albumen [Hg] did not correlate with reproductive end points, and correlations with blood [Hg] were weak. Feather [Hg] correlated negatively with all of the posthatching endpoints and explained 8.3% of the variance in the probability of a laid egg resulting in a fledged chick. However, most of the observed failures were hatching failures, which were not explained by albumen [Hg], and other nestling tissues could therefore not be evaluated. While our results support the use of nestling feathers as indicators of site-specific mercury exposure, we discuss both advantages and possible limitations of using nestling feathers as indicators of local mercury exposure.

Full lifetime perspectives on the costs and benefits of lay-date variation in tree swallows.

Animals must balance various costs and benefits when deciding when to breed. The costs and benefits of breeding at different times have received much attention, but most studies have been limited to investigating short-term season-to-season fitness effects. However, breeding early, versus late, in a season may influence lifetime fitness over many years, trading off in complex ways across the breeder's lifespan. In this study, we examined the complete life histories of 867 female tree swallows (Tachycineta bicolor) breeding in Ithaca, New York, between 2002 and 2016. Earlier breeders outperformed later breeders in short-term measures of reproductive output and offspring quality. Though there were weak indications that females paid long-term future survival costs for breeding early, lifetime fledgling output was markedly higher overall in early-breeding birds. Importantly, older females breeding later in the season did not experience compensating life history advantages that suggested an alternative equal-fitness breeding strategy. Rather, most or all of the swallows appear to be breeding as early as they can, and differences in lay dates appear to be determined primarily by differences in individual quality or condition. Lay date had a significant repeatability across breeding attempts by the same female, and the first lay date of females fledged in our population was strongly influenced by the first lay date of their mothers, indicating the potential for ongoing selection on lay date. By examining performance over the entire lifespan of a large number of individuals, we were able to clarify the relationship between timing of breeding and fitness and gain new insight into the sources of variability in this important life history trait.

Environmental DNA sampling reveals high occupancy rates of invasive Burmese pythons at wading bird breeding aggregations in the central Everglades.

The Burmese python (Python bivittatus) is now established as a breeding population throughout south Florida, USA. However, the extent of the invasion, and the ecological impacts of this novel apex predator on animal communities are incompletely known, in large part because Burmese pythons (hereafter "pythons") are extremely cryptic and there has been no efficient way to detect them. Pythons are recently confirmed nest predators of long-legged wading bird breeding colonies (orders Ciconiiformes and Pelecaniformes). Pythons can consume large quantities of prey and may not be recognized as predators by wading birds, therefore they could be a particular threat to colonies. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis-a genetic tool which detects shed DNA in water samples and provides high detection probabilities. We fitted multi-scale Bayesian occupancy models to test the prediction that pythons occupy islands with wading bird colonies at higher rates compared to representative control islands containing no breeding birds. Our results suggest that pythons are widely distributed across the central Everglades in proximity to active wading bird colonies. In support of our prediction that pythons are attracted to colonies, site-level python eDNA occupancy rates were higher at wading bird colonies (ψ = 0.88, 95% credible interval [0.59-1.00]) than at the control islands (ψ = 0.42 [0.16-0.80]) in April through June (n = 15 colony-control pairs). We found our water temperature proxy (time of day) to be informative of detection probability, in accordance with other studies demonstrating an effect of temperature on eDNA degradation in occupied samples. Individual sample concentrations ranged from 0.26 to 38.29 copies/µL and we generally detected higher concentrations of python eDNA in colony sites. Continued monitoring of wading bird colonies is warranted to determine the effect pythons are having on populations and investigate putative management activities.

Non-lethal sampling of avian indicators reveals reliable geographic signals of mercury despite highly dynamic patterns of exposure in a large wetland.

Mercury is a global contaminant with special relevance for aquatic food webs, where biomagnification can result in strong effects on apex predators. Non-lethal sampling of tissues such as blood and feathers is often used to assess mercury risk and spatiotemporal variability of mercury exposure on avian populations. However, the assumption that samples from individuals within a population are representative of local mercury exposure underpins those approaches. While this assumption may be justified, it is rarely expressed quantitatively. Further, the stability of the tissue/exposure relationship over time or space may depend on the sampling medium used, since some tissues and age classes may be better at reflecting local or short-term changes in exposure. Here, we present analyses of mercury concentrations from three tissues (albumen, blood and feathers) of the same individual great egret (Ardea alba) nestlings from breeding colonies in the Florida Everglades collected over three consecutive years. The interaction of year and colony location explained at least 50% of the observed variation in mercury concentration in all the sampled tissues. Annual colony-wide average Hg concentrations in any of the sampled tissues correlated with average Hg concentrations in the other two tissues from the same colony (R2 > 0.53 in every case), while concentrations in albumen, blood and feathers from the same individual correlated poorly (R2 < 0.23 in every case). We suggest that despite high variation between and within individuals of the same colony, annual colony-averaged mercury concentrations in albumen, nestling blood or feathers can be representative indicators of annual geographic differences in mercury exposure. These results support the use of non-lethal sampling of nestling tissues to reflect local mercury exposure over large spatial scales.