An Overview of Speciation and Species Limits in Birds

Accurately determining avian species limits has been a challenge and a work in progress for most of a century. It is a fascinating but difficult problem. Under the biological species concept, only lineages that remain essentially independent when they are in sympatry are clearly species. Otherwise, there is no clear line yet found that marks when a pair of diverging lineages, e.g., in allopatry, become different enough to warrant full biological species status. Also, with more data, species limits often require re-evaluation. The process of divergence and speciation is itself very complex and is the focus of intense research. Translating what we understand of that process into taxonomic names can be challenging. A series of issues are important. Single-locus criteria are unlikely to be convincing. Genetic independence is not a species limits requirement, but the degree of independence (gene flow) needs to be considered when there is opportunity for gene flow and independence is not complete. Time-based species (limits determined by time of separation) are unsatisfactory, though integrating time more effectively into our datasets is warranted. We need to disentangle data signal due to neutral processes versus selection and prioritize the latter as the main driver of speciation. Assortative mating is also not likely to be an adequate criterion for determining species limits. Hybridization and gene flow are more important than ever, and there is a condition not being treated evenly in taxonomy: evolutionary trysts of two or more lineages stuck together through gene flow just short of speciation over long periods. Comparative methods that use what occurs between good species in contact to infer species limits among allopatric forms remain the gold standard, but they can be inaccurate and controversial. Species-level taxonomy in birds is likely to remain unsettled for some time. While the study of avian speciation has never been more exciting and dynamic, there is no silver bullet for species delimitation, nor is it likely that there will ever be one. Careful work using integrative taxonomy in a comparative framework is the most promising way forward.

Winker, K. 2021. An overview of speciation and species limits in birds. Ornithology in press.

Demographic Consequences of Foraging Ecology Explain Genetic Diversification in Neotropical Birds

Comparisons of divergence among 58 lineages of Middle American birds reveal that diet is the most important driver, with insectivore and mixed-diet populations diverging more than plant-dependent species (mostly fugivores and nectivores). We propose and test a model for why this occurs and find support for dispersal and demographic expansion periodically reuniting plant-dependent species across this geographic space. Thus, local ecological and demographic factors here scale up to macroevolutionary phenomena.

Miller, M. J., E. Bermingham, B. L. Turner, S. E. Lipshutz, J. C. Touchon, A. B. Johnson, and K. Winker. 2021. Demographic consequences of foraging ecology explain genetic diversification in Neotropical bird species. Ecology Letters In press. https://doi.org/10.1111/ele.13674


Population Genomics of Trans-Beringian Birds

Contrasts of UCE-based genomic estimates of divergence and demographic processes in co-distributed high-latitude taxa having divergence levels from populations to full species show that gene flow is a predominant factor in avian speciation in this region. In addition, these taxa are discontinuously distributed on the speciation continuum, showing two clusters in a divergence space defined by FST and gene flow.

McLaughlin, J. F., B. C. Faircloth, T. C. Glenn, and K. Winker. 2020. Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds. Molecular Ecology 29: 3526-3542. https://doi.org/10.1111/mec.15574 .


Sample Size Effects on Population Demographic Estimates in Birds using Ultraconserved Elements (UCEs)

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergencewith-gene-flow models optimized with full datasets, we subsampled at sequentially
smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefm). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

McLaughlin, J. F., and K. Winker. 2020. An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data. PeerJ 8:e9939 DOI 10.7717/peerj.9939

Ooooh, shiny!

It’s finally time to update my web site. It was looking pretty dated (but it loaded fast and delivered information effectively to people with low bandwidth). I’ll keep up the details on the “Old School” page. Just use your browser’s search function there to find what you want. I’ll peck away at bringing other attributes to bear over time.