SUMMARY A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e. ‘supergenes’ [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3–5]. Morph is determined by alternative alleles at a balanced >100Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole genome sequencing coupled with population- and phylo-genomic data, to show that alternate supergene alleles are highly divergent at over 1,000 genes, that these alleles originated prior to the split of Z. albicollis from its sister species, and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the ‘white' allele may be degrading, similar to neo-Y/Wsex chromosomes. We further show that the ‘tan’ allele has surprisingly low levels of genetic diversity, yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism.

Ecological mismatches between reproductive events and seasonal resource peaks are frequently proposed to be a key driver of population dynamics resulting from global climate change. Many local populations are experiencing reduced reproductive success as a consequence of mismatches, but few mismatches have led to species-level population declines. To better understand this apparent paradox, we investigated the breeding phenology and chick survival of two disjunct populations of Hudsonian godwits Limosa haemastica breeding at Churchill, Manitoba and Beluga River, Alaska. Only one population experienced a mismatch: godwits bred nearly one week after the onset of the invertebrate peak at Churchill because of asynchronous climatic change occurring throughout their annual cycle. However, chicks were not uniformly aff ected by the mismatch -growth rates and survival of young chicks were not correlated with invertebrate abundance, but older chicks tended to suff er lower survival rates on days of low invertebrate abundance. Ecological mismatches thus resulted in a complex array of consequences, but nonetheless contributed to reductions in chick survival. In contrast, godwits at Beluga River hatched their chicks just before the invertebrate peak, such that the period of highest energetic need coincided with the period of highest invertebrate abundance. As a result, growth rates and survival of godwit chicks were unaff ected by invertebrate abundance. Godwits at Beluga River were able to properly time their reproduction because of predictable rates of climatic change and strong selection imposed by high predation on late-hatched chicks. Taken together, our results suggest that population-specifi c, local-scale selection pressures play a critical role in determining the degree and severity of ecological mismatches. Th e potential for global climate change to induce species-level population declines may therefore be mediated by the spatial variation in the selection pressures acting across a species ' range.

No abstract

Nearly 20% of all bird species migrate between breeding and nonbreeding sites annually. Their migrations include storied feats of endurance and physiology, from non-stop trans-Pacific crossings to flights at the cruising altitudes of jetliners. Despite intense interest in these performances, there remains great uncertainty about which factors most directly influence bird behaviour during migratory flights. We used GPS trackers that measure an individual's altitude and wingbeat frequency to track the migration of black-tailed godwits () and identify the abiotic factors influencing their in-flight migratory behaviour. We found that godwits flew at altitudes above 5000 m during 21% of all migratory flights, and reached maximum flight altitudes of nearly 6000 m. The partial pressure of oxygen at these altitudes is less than 50% of that at sea level, yet these extremely high flights occurred in the absence of topographical barriers. Instead, they were associated with high air temperatures at lower altitudes and increasing wind support at higher altitudes. Our results therefore suggest that wind, temperature and topography all play a role in determining migratory behaviour, but that their relative importance is context dependent. Extremely high-altitude flights may thus not be especially rare, but they may only occur in very specific environmental contexts.

Examining physiological traits across large spatial scales can shed light on the environmental factors driving physiological variation. For endotherms, flexibility in aerobic metabolism is especially important for coping with thermally challenging environments and recent research has shown that aerobic metabolic scope [the difference between maximum thermogenic capacity (Msum) and basal metabolic rate (BMR)] increases with latitude in mammals. One explanation for this pattern is the climatic variability hypothesis, which predicts that flexibility in aerobic metabolism should increase as a function of local temperature variability. An alternative explanation is the cold adaptation hypothesis, which predicts that cold temperature extremes may also be an important driver of variation in metabolic scope. To determine the thermal drivers of aerobic metabolic flexibility in birds, we combined data on metabolic scope from 40 bird species sampled across a range of environments with several indices of local ambient temperature. Using phylogenetically‐informed analyses, we found that minimum winter temperature was the best predictor of variation in avian metabolic scope, outperforming all other thermal variables. Additionally, Msum was a better predictor of latitudinal patterns of metabolic scope than BMR, with species inhabiting colder environments exhibiting increased Msum over their counterparts in warmer environments. Taken together, these results suggest that cold temperature extremes drive latitudinal patterns of metabolic scope via selection for enhanced thermogenic performance in cold environments, supporting the cold adaptation hypothesis. Temperature extremes may therefore be an important selective pressure driving macrophysiological trends of aerobic performance in endotherms.

Small temperate birds reversibly modify their aerobic performance to maintain thermoregulatory homeostasis under seasonally changing environmental conditions and these physiological adjustments may be attributable to changes in the expression of genes in the underlying regulatory networks. Here, we report the results of an experimental procedure designed to gain insight into the fundamental mechanisms of metabolic flexibility in the dark-eyed junco (Junco hyemalis). We combined genomic transcriptional profiles with measures of metabolic enzyme activities and wholeanimal thermogenic performance from juncos exposed to four 6-week acclimation treatments that varied in temperature (cold, 3°C; warm, 24°C) and photoperiod (short day, 8 h light:16 h dark; long day, 16 h light:8 h dark). Cold-acclimated birds increased thermogenic capacity compared with warm-acclimated birds, and this enhanced performance was associated with upregulation of genes involved in muscle hypertrophy, angiogenesis, and lipid transport and oxidation, as well as with catabolic enzyme activities. These physiological changes occurred over ecologically relevant timescales, suggesting that birds make regulatory adjustments to interacting, hierarchical pathways in order to seasonally enhance thermogenic capacity.

Few studies have been able to directly measure the seasonal survival rates of migratory species or determine how variable the timing of migration is within individuals and across populations over multiple years. As such, it remains unclear how likely migration is to affect the population dynamics of migratory species and how capable migrants may be of responding to changing environmental conditions within their lifetimes. To address these questions, we used three types of tracking devices to track individual black-tailed godwits from the nominate subspecies (Limosa limosa limosa) throughout their annual cycles for up to 5 consecutive years. We found that godwits exhibit considerable inter-and intra-individual variation in their migratory behavior across years. We also found that godwits had generally high survival rates during migration, although survival was reduced during northward flights across the Sahara Desert. These patterns differ from those observed in most other migratory species, suggesting that migration may only be truly dangerous when crossing geographic barriers that lack emergency stopover sites and that the levels of phenotypic flexibility exhibited by some populations may enable them to rapidly respond to changing environmental conditions.

In a study of almost 16 000 nest records from seven swallow species across the entire Western Hemisphere, clutch sizes decline with relative laying date in each population, but the slope of this decline grows steeper with increasing distance from the equator. Late-laying birds at all latitudes lay clutches of similar sizes, suggesting that latitudinal differences may be driven primarily by earlier-laying birds. Focused comparisons of site-years in North America with qualitatively different food availability indicate that food supply significantly affects mean clutch size but not the clutch size-lay date regression. Other studies on the seasonality of swallow food also indicate that steeper clutch size-lay date declines in the North are not caused by steeper earlier food peaks there. The distribution of lay dates grows increasingly right-skewed with increasing latitude. This variation in lay-date distributions could be due to the predominance of higher quality, early-laying (and large-clutched) individuals among populations at higher latitudes, resulting from latitudinal variation in mortality rates and the intensity of sexual selection. Our results underscore the importance of studying clutch size and lay date in tandem and suggest new research into the causes of their joint geographic variation.