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1. Does island ontogeny dictate the accumulation of both species richness and functional diversity?

   https://doi.org/10.1111/geb.13420  

   Kraemer, Andrew C. ; Roell, Yannik E. ; Shoobs, Nate F. ; Parent, Christine E. ( October 2021 , Global Ecology and Biogeography)

   The accumulation of functional diversity in communities is poorly understood. Conveniently, the general dynamic model of island biogeography (GDM) makes predictions for how such diversity might accumulate over time. In this multiscale study of land snail communities on 10 oceanic archipelagos located in various regions of the globe, we test hypotheses of community assembly in systems where islands serve as chronosequences along island ontogeny.

   Ten volcanic archipelagos.

   From 23 Ma to the present.

   Endemic land snails.

   Initially, we assembled geological island characteristics of area, isolation and ontogeny for all studied islands. We then characterized island‐scale biotic variables, including the species diversity and functional diversity of snail communities. From these data, we assessed relationships between island and snail community variables as predicted by the GDM, focusing initially on the islands of the Galápagos archipelago and thereafter with a broader analysis of 10 archipelagoes.

   As in other studies of island assemblages, in Galápagos we find a hump‐shaped curve of species richness, with depauperate snail faunas on early‐ontogeny islands, increasing species richness on mid‐ontogeny islands and low species richness on islands in late ontogeny. We find exceptionally low functional diversity on early‐ontogeny islands that increases through mid‐ontogeny, whereas late‐ontogeny islands exhibit a range of functional diversity. The analysis including all 10 archipelagos indicates a major role of archipelago‐specific factors. In both sets of analyses, functional diversity is exceptionally low on early‐ontogeny islands, and island ontogeny is a significant predictor of morphology.

   Consistent patterns of functional diversity across island ontogeny on all examined archipelagos indicate a common role for habitat filtering, ecological opportunity and competition in a diversity of systems, leading to predictable changes in functional diversity and average morphology through island ontogeny, whereas patterns of species richness appear subject to archipelago‐specific factors.

    

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2. Genomic novelty within a “great speciator” revealed by a high-quality reference genome of the collared kingfisher ( Todiramphus chloris collaris )

   https://doi.org/10.1093/g3journal/jkac260  

   Eliason, Chad M. ; Hains, Taylor ; McCullough, Jenna ; Andersen, Michael J. ; Hackett, Shannon J. ; Baldwin, ed., M. ( September 2022 , G3 Genes|Genomes|Genetics)

   Islands are natural laboratories for studying patterns and processes of evolution. Research on island endemic birds has revealed elevated speciation rates and rapid phenotypic evolution in several groups (e.g. white-eyes, Darwin’s finches). However, understanding the evolutionary processes behind these patterns requires an understanding of how genotypes map to novel phenotypes. To date, there are few high-quality reference genomes for species found on islands. Here, we sequence the genome of one of Ernst Mayr’s “great speciators,” the collared kingfisher (Todiramphus chloris collaris). Utilizing high molecular weight DNA and linked-read sequencing technology, we assembled a draft high-quality genome with highly contiguous scaffolds (scaffold N50 = 19 Mb). Based on universal single-copy orthologs, we estimated a gene space completeness of 96.6% for the draft genome assembly. The population demographic history analyses reveal a distinct pattern of contraction and expansion in population size throughout the Pleistocene. Comparative genomic analysis of gene family evolution revealed that species-specific and rapidly expanding gene families in the collared kingfisher (relative to other Coraciiformes) are mainly involved in the ErbB signaling pathway and focal adhesion. Todiramphus kingfishers are a species-rich group that has become a focus of speciation research. This draft genome will be a platform for future taxonomic, phylogeographic, and speciation research in the group. For example, target genes will enable testing of changes in sensory structures associated with changes in vision and taste genes across kingfishers.

    

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3. Two centuries of settlement and urban development in the United States

   https://doi.org/10.1126/sciadv.aba2937  

   Leyk, Stefan ; Uhl, Johannes H. ; Connor, Dylan S. ; Braswell, Anna E. ; Mietkiewicz, Nathan ; Balch, Jennifer K. ; Gutmann, Myron ( June 2020 , Science Advances)

   Over the past 200 years, the population of the United States grew more than 40-fold. The resulting development of the built environment has had a profound impact on the regional economic, demographic, and environmental structure of North America. Unfortunately, constraints on data availability limit opportunities to study long-term development patterns and how population growth relates to land-use change. Using hundreds of millions of property records, we undertake the finest-resolution analysis to date, in space and time, of urbanization patterns from 1810 to 2015. Temporally consistent metrics reveal distinct long-term urban development patterns characterizing processes such as settlement expansion and densification at fine granularity. Furthermore, we demonstrate that these settlement measures are robust proxies for population throughout the record and thus potential surrogates for estimating population changes at fine scales. These new insights and data vastly expand opportunities to study land use, population change, and urbanization over the past two centuries. 

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4. Phylogenomic Data Reveal Widespread Introgression Across the Range of an Alpine and Arctic Specialist

   https://doi.org/10.1093/sysbio/syaa071  

   Funk, Erik R ; Spellman, Garth M ; Winker, Kevin ; Withrow, Jack J ; Ruegg, Kristen C ; Zavaleta, Erika ; Taylor, Scott A ( September 2020 , Systematic Biology)

   Smith, Stephen (Ed.)

   Abstract Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. Although simple population models produce predictable results, how these processes balance in taxa with patchy distributions and complicated natural histories is less certain. These types of populations might be highly connected through migration (gene flow), but can experience stronger effects of genetic drift and inbreeding, or localized selection. Although different signals can be difficult to separate, the application of high-throughput sequence data can provide the resolution necessary to distinguish many of these processes. We present whole-genome sequence data for an avian species group with an alpine and arctic tundra distribution to examine the role that different population genetic processes have played in their evolutionary history. Rosy-finches inhabit high elevation mountaintop sky islands and high-latitude island and continental tundra. They exhibit extensive plumage variation coupled with low levels of genetic variation. Additionally, the number of species within the complex is debated, making them excellent for studying the forces involved in the process of diversification, as well as an important species group in which to investigate species boundaries. Total genomic variation suggests a broadly continuous pattern of allele frequency changes across the mainland taxa of this group in North America. However, phylogenomic analyses recover multiple distinct, well supported, groups that coincide with previously described morphological variation and current species-level taxonomy. Tests of introgression using D-statistics and approximate Bayesian computation reveal significant levels of introgression between multiple North American taxa. These results provide insight into the balance between divergent and homogenizing population genetic processes and highlight remaining challenges in interpreting conflict between different types of analytical approaches with whole-genome sequence data. [ABBA-BABA; approximate Bayesian computation; gene flow; phylogenomics; speciation; whole-genome sequencing.] 

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5. A multivariate approach reveals diversity of ontogenetic niche shifts across taxonomic and functional groups

   https://doi.org/10.1111/fwb.13463  

   Rudolf, Volker H. W. ( December 2019 , Freshwater Biology)

   Shifts in the fundamental and realised niche of individuals during their ontogeny are ubiquitous in nature, but we know little about what aspects of the niche change and how these changes vary across species within communities. However, this knowledge is essential to predict the dynamics of populations and communities and how they respond to environmental change.

   Here I introduce a range of metrics to describe different aspects of shifts in the realised trophic niche of individuals based on stable isotopes. Applying this multi‐variate approach to 2,272 individuals from 13 taxonomic and functional distinct species (Amphibia, Hemiptera, Coleoptera, Odonata) sampled in natural pond communities allowed me to: (1) describe and quantify the diversity of trophic niche shift patterns over ontogeny in multi‐dimensional space, and (2) identify what aspects of ontogenetic shifts vary across taxa, and functional groups.

   Results revealed that species can differ substantially in which aspects of the trophic niche change and how they change over ontogeny. Interestingly, patterns of ontogenetic niche shifts grouped in distinct taxonomic clusters in multi‐variate space, including two distinct groups of predators (Hemiptera versus Odonata). Given the differences in traits (especially feeding mode) across groups, this suggests that differences in ontogenetic niche shifts across species could at least partially be explained by variation in traits and functional roles of species.

   These results emphasise the importance of a multivariate approach to capture the large diversity of trophic niche shifts patterns possible in natural communities and suggest that differences in ontogenetic niche shifts follow general patterns.

    

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