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The twenty-first century has witnessed an explosion in research on animal migration, in large part due to a technological revolution in tracking and remote-sensing technologies, along with advances in genomics and integrative biology. We now have access to unprecedented amounts of data on when, where, and how animals migrate across various continents and oceans. Among the important advancements, recent studies have uncovered a surprising level of variation in migratory trajectories at the species and population levels with implications for both speciation and the conservation of migratory populations. At the organismal level, studies linking molecular and physiological mechanisms to traits that support migration have revealed a remarkable amount of seasonal flexibility in many migratory animals. Advancements in the theory for why animals migrate have resulted in promising new directions for empirical studies. We provide an overview of the current state of knowledge and promising future avenues of study.

Bio-loggers are widely used for studying the movement and behavior of animals. However, some sensors provide more data than is practical to store given experiment or bio-logger design constraints. One approach for overcoming this limitation is to utilize data collection strategies, such as non-continuous recording or data summarization that may record data more efficiently, but need to be validated for correctness. In this paper we address two fundamental questions—how can researchers determine suitable parameters and behaviors for bio-logger sensors, and how do they validate their choices? We present a methodology that uses software-based simulation of bio-loggers to validate various data collection strategies using recorded data and synchronized, annotated video. The use of simulation allows for fast and repeatable tests, which facilitates the validation of data collection methods as well as the configuration of bio-loggers in preparation for experiments. We demonstrate this methodology using accelerometer loggers for recording the activity of the small songbird Junco hyemalis hyemalis.

Colonization of a novel environment by a few individuals can lead to rapid evolutionary change, yet there is scarce evidence of the relative contributions of neutral and selective factors in promoting divergence during the early stages of colonization. Here we explore the role of neutral and selective forces in the divergence of a unique urban population of the dark-eyed junco (Junco hyemalis), which became established on the campus of the University of California at San Diego (UCSD) in the early 1980s. Previous studies based on microsatellite loci documented significant genetic differ-entiation of the urban population as well as divergence in phenotypic traits relative to nearby montane populations, yet the geographical origin of the colonization and the contributing factors remained uncertain. Our genome-wide single nucleotide polymorphism data set confirmed the marked genetic differentiation of the UCSD population, and we identified the coastal subspecies pinosus from central California as its sister group instead of the neighbouring mountain population. Demographic infer-ence recovered a separation from pinosus as recent as 20–32 generations ago after a strong bottleneck, suggesting a role for drift in genetic differentiation. However, we also found significant associations between habitat variables and genome-wide variants linked to functional genes, some of which have been reported as potentially adaptive in birds inhabiting modified environments. These results suggest that the interplay between founder events and selection may result in rapid shifts in neutral and adaptive loci across the genome, and reveal the UCSD junco population as a case of contemporary evolutionary divergence in an anthropogenic environment., Funding was provided by grants CGL-2011-25866 and CGL-2015-66381 from Spain’s Ministerio de Ciencia e Innovación to B.M., and USA National Science Foundation IOS-1257527 to T.J.G.

Billions of animals migrate between breeding and non-breeding areas worldwide. Partial migration, where both migrants and residents coexist within a population, occurs in most animal taxa, including fish, insects, birds and mammals. Partial migration has been hypothesised to be the most common form of migration and to be an evolutionary precursor to full migration. Despite extensive theoretical models about partial migration and its potential to provide insight into the ecology and evolution of migration, the physiological mechanisms that shape partial migration remain poorly understood. Here, we review current knowledge on how physiological processes mediate the causes and consequences of avian partial migration, and how they may help us understand why some individuals migrate and others remain resident. When information from birds is missing, we highlight examples from other taxa. In particular, we focus on temperature regulation, metabolic rate, immune function, oxidative stress, telomeres, and neuroendocrine and endocrine systems. We argue that these traits provide physiological pathways that regulate the ecological and behavioural causes and/or consequences of partial migration, and may provide insight into the mechanistic basis of wintering decisions. They may, thus, also help us to explain why individuals switch strategies among winters. We also highlight current gaps in our knowledge and suggest promising future research opportunities. A deeper understanding of the physiological mechanisms mediating the causes and consequences of partial migration will not only provide novel insights into the ecology and evolution of migration in general, but will also be vital to precisely modelling population trends and predicting range shifts under global change.

Reproductive allochrony presents a potential barrier to gene flow and is common in seasonally sympatric migratory and sedentary birds. Mechanisms mediating reproductive allochrony can influence population divergence and the capacity of populations to respond to environmental change. We asked whether reproductive allochrony in seasonally sympatric birds results from a difference in response to supplementary or photoperiodic cues and whether the response varies in relation to the distance separating breeding and wintering locations as measured by stable isotopes. We held seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco hyemalis) in a common garden in early spring under simulated natural changes in photoperiod and made measurements of reproductive and migratory physiology. On the same dates and photoperiods, sedentary juncos had higher testosterone (initial and gonadotropin-releasing hormone induced), more developed cloacal protuberances, and larger testes than migrants. In contrast, migratory juncos had larger fat reserves (fuel for migration). We found a negative relationship between testis mass and feather hydrogen isotope ratios, indicating that testis growth was more delayed in migrants making longer migrations. We conclude that reproductive allochrony in seasonally sympatric migratory and sedentary birds can result from a differential response to photoperiodic cues in a common garden, and as a result, gene flow between migrants and residents may be reduced by photoperiodic control of reproductive development. Further, earlier breeding in response to future climate change may currently be constrained by differential response to photoperiodic cues.

Every year, billions of wild diurnal songbirds migrate at night. To do so, they shift their daily rhythm from diurnality to nocturnality. In captivity this is observed as a gradual transition of daytime activity developing into nocturnal activity, but how wild birds prepare their daily rhythms for migration remains largely unknown. Using an automated radio-telemetry system, we compared activity patterns of free-living migrant and resident European blackbirds (Turdus merula) in a partially migratory population during the pre-migratory season. We found that activity patterns between migrant and resident birds did not differ during day and night. Migrants did not change their daily rhythm in a progressive manner as has been observed in captivity, but instead abruptly became active during the night of departure. The rapid shift in rhythmicity might be more common across migratory songbird species, but may not have been observed before in wild animals due to a lack of technology.

Every year, billions of wild diurnal songbirds migrate at night. To do so, they shift their daily rhythm from diurnality to nocturnality. In captivity this is observed as a gradual transition of daytime activity developing into nocturnal activity, but how wild birds prepare their daily rhythms for migration remains largely unknown. Using an automated radio-telemetry system, we compared activity patterns of free-living migrant and resident European blackbirds (Turdus merula) in a partially migratory population during the pre-migratory season. We found that activity patterns between migrant and resident birds did not differ during day and night. Migrants did not change their daily rhythm in a progressive manner as has been observed in captivity, but instead abruptly became active during the night of departure. The rapid shift in rhythmicity might be more common across migratory songbird species, but may not have been observed before in wild animals due to a lack of technology.

Stable isotope ratios of hydrogen (δD) and carbon (δ13C) in feathers collected from Painted Buntings ( Passerina ciris (L., 1758)) breeding in the midwestern United States revealed a surprising degree of variation in δD, as well as a clear bimodal signal in δ13C in the innermost primary feather. Because this population does not molt on the breeding grounds, we reasoned that these observations could be due (i) to birds migrating to two (or possibly more) distinct molting areas or (ii) to differences in the timing of molt (as opposed to molt location) relative to arrival at the stopover site. To evaluate these hypotheses, we collected feathers at a molting location in northwestern Mexico, which revealed patterns similar to those from the birds in the US (favoring the second hypothesis above). We suspect that some birds arrive at stopover sites and begin molting before their body tissues equilibrate to the new isoscape so that the first feathers grown represent a blend of materials from the breeding and stopover locations. Other birds may delay molt after arriving at the molting site, allowing them to equilibrate with the local isoscape and produce feathers with isotope signatures of the molting location.

The potential reproductive rate (PRR, the rate at which each sex could reproduce if given unlimited mates) has proven to be a useful tool in predicting the direction and strength of sexual selection. We conducted a 2-month study of the PRR in the polyandrous gulf pipefish, Syngnathus scovelli, a year-round breeder. In this sex-role reversed species, the female transfers eggs to a male's brood pouch during mating and thus renders him unavailable to mate for 2 weeks. We predicted females would have a higher PRR than males and that the rates in both sexes would change over successive breeding bouts in relationship to previous reproductive output. Females did have a higher overall PRR than males for the entire study period. However, PRR was not constant across individual breeding bouts. For each sex, the PRRs from the first and third bouts of mating were significantly higher than the PRR of second mating bout. Our results are consistent with individuals making trade-offs between current and future reproductive investment. We also discuss how ovarian morphology may contribute to elevated female PRR in this species. To our knowledge, this is the first study of PRR in a North American pipefish.

Comparative equilibration has been proposed as a methodological approach for determining the hydrogen isotopic composition (δD) of non-exchangeable hydrogen in complex organic materials, from feathers to blood and soils. This method depends on using homogenized standards that have been previously calibrated for their δD values of non-exchangeable H, that are compositionally similar to unknown samples, and that span an appropriate isotopic range. Currently no certified organic reference materials with exchangeable H exist, and so isotope laboratories have been required to develop provisional internal calibration standards, such as the keratin standards currently used in animal migration studies. Unfortunately, the isotope ratios of some samples fall outside the range of keratin standards currently used for comparative equilibration. Here we tested a set of five homogenized keratin powders as well as feathers from Painted Buntings and Dark-eyed Juncos to determine the effects of extrapolating comparative equilibration normalization equations outside the isotopic range of keratin standards. We found that (1) comparative equilibration gave precise results within the range of the calibration standards; (2) linear extrapolation of normalization equations produced accurate δD results to ∼40‰ outside the range of the keratins standards used (−187 to −108); and (3) for both homogenized keratin powders and heterogeneous unknown samples there was no difference in variance between samples within and outside the range of keratin standards. This suggested that comparative equilibration is a robust and practical method for determining the δD of complex organic matrices, although caution is required for samples that fall far outside the calibration range. Copyright © 2009 John Wiley & Sons, Ltd.

Comparative equilibration has been proposed as a methodological approach for determining the hydrogen isotopic composition (deltaD) of non-exchangeable hydrogen in complex organic materials, from feathers to blood and soils. This method depends on using homogenized standards that have been previously calibrated for their deltaD values of non-exchangeable H, that are compositionally similar to unknown samples, and that span an appropriate isotopic range. Currently no certified organic reference materials with exchangeable H exist, and so isotope laboratories have been required to develop provisional internal calibration standards, such as the keratin standards currently used in animal migration studies. Unfortunately, the isotope ratios of some samples fall outside the range of keratin standards currently used for comparative equilibration. Here we tested a set of five homogenized keratin powders as well as feathers from Painted Buntings and Dark-eyed Juncos to determine the effects of extrapolating comparative equilibration normalization equations outside the isotopic range of keratin standards. We found that (1) comparative equilibration gave precise results within the range of the calibration standards; (2) linear extrapolation of normalization equations produced accurate deltaD results to approximately 40 per thousand outside the range of the keratins standards used (-187 to -108); and (3) for both homogenized keratin powders and heterogeneous unknown samples there was no difference in variance between samples within and outside the range of keratin standards. This suggested that comparative equilibration is a robust and practical method for determining the deltaD of complex organic matrices, although caution is required for samples that fall far outside the calibration range.