Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics

Phenotypic correlates between clock genes and phenology among populations of Diederik cuckoo, Chrysococcyx caprius

The Diederik cuckoo, Chrysococcyx caprius, is a small Afrotropical bird in the family Cuculidae. It is taxonomically related to 13 other species within the genus Chrysococcyx and is migratory in sub-Saharan Africa. It has a unique breeding behaviour of being a brood parasite: Breeding pairs lay their eggs in the nests of a host species and hatchlings expel the eggs of the host species. The aim of the present study was to investigate diversity in two circadian clock genes, Clock and Adcyap1, to probe for a relationship between genetic polymorphisms and their role in circannual timing and habitat selection (phenology) in intra-African migrants. DNA extracted from blood was used for the PCR amplification and sequencing of clock genes in 30 Diederik cuckoos. Three alleles were detected for Clock with similar genotypes between individuals from the Northern and Southern breeding ranges while 10 alleles were detected for Adcyap1, having shorter alleles in the North and longer alleles in the South. Population genetic analyses, including allele frequency and zygosity analysis, showed distinctly higher frequencies for the most abundant Clock allele, containing 10 polyglutamine repeats, as well as a high degree of homozygosity. In contrast, all individuals were heterozygous for Adcyap1 and alleles from both regions showed distinct differences in abundance. Comparisons between both clock genes and phenology found several phenotypic correlations. This included evidence of a relationship between the shorter alleles and habitat selection as well as a relationship between longer alleles and timing. In both instances, evidence is provided that these effects may be sex-specific. Given that these genes drive some of the synchronicity between environments and the life cycles of birds, they provide valuable insight into the fitness of species facing global challenges including climate change, urbanisation and expanding agricultural practices.

Avian migration clocks in a changing world

Avian long-distance migration requires refined programming to orchestrate the birds' movements on annual temporal and continental spatial scales. Programming is particularly important as long-distance movements typically anticipate future environmental conditions. Hence, migration has long been of particular interest in chronobiology. Captivity studies using a proxy, the shift to nocturnality during migration seasons (i.e., migratory restlessness), have revealed circannual and circadian regulation, as well as an innate sense of direction. Thanks to rapid development of tracking technology, detailed information from free-flying birds, including annual-cycle data and actograms, now allows relating this mechanistic background to behaviour in the wild. Likewise, genomic approaches begin to unravel the many physiological pathways that contribute to migration. Despite these advances, it is still unclear how migration programmes are integrated with specific environmental conditions experienced during the journey. Such knowledge is imminently important as temporal environments undergo rapid anthropogenic modification. Migratory birds as a group are not dealing well with the changes, yet some species show remarkable adjustments at behavioural and genetic levels. Integrated research programmes and interdisciplinary collaborations are needed to understand the range of responses of migratory birds to environmental change, and more broadly, the functioning of timing programmes under natural conditions.

Genetics and Evolution of Bird Migration

Bird migration has long been a subject of fascination for humankind and is a behavior that is both intricate and multifaceted. In recent years, advances in technology, particularly in the fields of genomics and animal tracking, have enabled significant progress in our understanding of this phenomenon. In this review, we provide an overview of the latest advancements in the genetics of bird migration, with a particular focus on genomics, and examine various factors that contribute to the evolution of this behavior, including climate change. Integration of research from the fields of genomics, ecology, and evolution can enhance our comprehension of the complex mechanisms involved in bird migration and inform conservation efforts in a rapidly changing world.

Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies

Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.

Candidate gene polymorphisms are linked to dispersive and migratory behaviour: Searching for a mechanism behind the "paradox of the great speciators"

The "paradox of the great speciators" has puzzled evolutionary biologists for over half a century. A great speciator requires excellent dispersal propensity to explain its occurrence on multiple islands, but reduced dispersal ability to explain its high number of subspecies. A rapid reduction in dispersal ability is often invoked to solve this apparent paradox, but a proximate mechanism has not been identified yet. Here, we explored the role of six genes linked to migration and animal personality differences (CREB1, CLOCK, ADCYAP1, NPAS2, DRD4, and SERT) in 20 South Pacific populations of silvereye (Zosterops lateralis) that range from highly sedentary to partially migratory, to determine if genetic variation is associated with dispersal propensity and migration. We detected genetic associations in three of the six genes: (i) in a partial migrant population, migrant individuals had longer microsatellite alleles at the CLOCK gene compared to resident individuals from the same population; (ii) CREB1 displayed longer average microsatellite allele lengths in recently colonized island populations (<200 years), compared to evolutionarily older populations. Bayesian broken stick regression models supported a reduction in CREB1 length with time since colonization; and (iii) like CREB1, DRD4 showed differences in polymorphisms between recent and old colonizations but a larger sample is needed to confirm. ADCYAP1, SERT, and NPAS2 were variable but that variation was not associated with dispersal propensity. The association of genetic variants at three genes with migration and dispersal ability in silvereyes provides the impetus for further exploration of genetic mechanisms underlying dispersal shifts, and the prospect of resolving a long-running evolutionary paradox through a genetic lens.

PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses

Evolutionary processes happen gradually over time and are, thus, considered time dependent. In addition, several evolutionary processes are either adaptations to local habitats or changing habitats, otherwise restricted thereby. Since evolutionary processes driving speciation take place within the landscape of environmental and temporal bounds, several published studies have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species. Correct calibration is critical towards attributing evolutionary adaptations and speciation both to the time and paleogeography that contributed to it. Data from more than 4000 studies and nearly 1,50,000 species are available from a central TimeTree resource and provide opportunities of retrieving divergence times, evolutionary timelines, and time trees in various formats for most vertebrates. These data greatly enhance the ability of researchers to investigate evolution. However, there is limited functionality when studying lists of species that require batch retrieval. To overcome this, a PYTHON package termed Python-Automated Retrieval of TimeTree data (PAReTT) was created to facilitate a biologist-friendly interaction with the TimeTree resource. Here, we illustrate the use of the package through three examples that includes the use of timeline data, time tree data, and divergence time data. Furthermore, PAReTT was previously used in a meta-analysis of candidate genes to illustrate the relationship between divergence times and candidate genes of migration. The PAReTT package is available for download from GitHub or as a pre-compiled Windows executable, with extensive documentation on the package available on GitHub wiki pages regarding dependencies, installation, and implementation of the various functions.