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1. Elevational and oceanic barriers shape the distribution, dispersal, and diversity of Aotearoa’s Kapokapowai ( Uropetala ) dragonflies

   https://doi.org/10.1093/evolut/qpaf150  

   Tolman, Ethan_R; Beatty, Christopher_D; Goodman, Aaron; Ramchand, Priscilla; McAllister, Tara; Reyes, Kelly; Zahara, Akifa; Taveras, Kassandra; Wade, Vincent; Abbott, John; et al (July 2025, Evolution)

   Abstract Mountains and islands provide an opportunity for studying the biogeography of diversification and population fragmentation. Aotearoa (New Zealand) is an excellent location to investigate both phenomena due to alpine emergence and oceanic separation. While it would be expected that separation across oceanic and elevation gradients are major barriers to gene flow in animals, including aquatic insects, such hypotheses have not been thoroughly tested in these taxa. By integrating population genomic from subgenomic Anchored-Hybrid Enrichment sequencing, ecological niche modeling, and morphological analyses from scanning-electron microscopy, we show that tectonic uplift and oceanic vicariance are implicated in speciation and population structure in Kapokapowai (Uropetala) dragonflies. Although Te Moana o Raukawa (Cook Strait) is likely responsible for some of the genetic structure observed, speciation has not yet occurred in populations separated by the strait. We find that the altitudinal gradient across Kā Tiritiri-o-te-Moana (the Southern Alps) is not impervious, but it significantly restricts gene flow between the aforementioned species. Our data support the hypothesis of an active colonization of Kā Tiritiri-o-te-Moana by the ancestral population of Kapokapowai, followed by a recolonization of the lowlands. These findings provide key foundations for the study of lineages endemic to Aotearoa. 

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2. Segmentation of Glacier Area Using U-Net through Landsat Satellite Imagery for Quantification of Glacier Recession and Its Impact on Marine Systems

   https://doi.org/10.3390/jmse12101788  

   Robbins, Edmund; Breininger, Robert D; Jiang, Maxwell; Madera, Michelle; White, Ryan T; Kachouie, Nezamoddin N (October 2024, Journal of Marine Science and Engineering)

   Glaciers have experienced a global trend of recession within the past century. Quantification of glacier variations using satellite imagery has been of great interest due to the importance of glaciers as freshwater resources and as indicators of climate change. Spatiotemporal glacier dynamics must be monitored to quantify glacier variations. The potential methods to quantify spatiotemporal glacier dynamics with increasing complexity levels include detecting the terminus location, measuring the length of the glacier from the accumulation zone to the terminus, quantifying the glacier surface area, and measuring glacier volume. Although some deep learning methods designed purposefully for glacier boundary segmentation have achieved acceptable results, these models are often localized to the region where their training data were acquired and further rely on the training sets that were often curated manually to highlight glacial regions. Due to the very large number of glaciers, it is practically impossible to perform a worldwide study of glacier dynamics using manual methods. As a result, an automated or semi-automated method is highly desirable. The current study has built upon our previous works moving towards identification methods of the 2D glacier profile for glacier area segmentation. In this study, a deep learning method is proposed for segmentation of temporal Landsat images to quantify the glacial region within the Mount Cook/Aoraki massif located in the Southern Alps/Kā Tiritiri o te Moana of New Zealand/Aotearoa. Segmented glacial regions can be further utilized to determine the relationship of their variations due to climate change. This model has demonstrated promising performance while trained on a relatively small dataset. The permanent ice and snow class was accurately segmented at a 92% rate by the proposed model. 

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3. Incorporating the speciation process into species delimitation

   https://doi.org/doi.org/10.1371/journal.pcbi.1008924  

   Sukumaran, Jeet (May 2021, PLoS computational biology)

   Barraclough, Timothy G. (Ed.)

   The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself. 

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4. Population Genomics of Adaptive Radiation

   https://doi.org/10.1111/mec.17574  

   Combrink, Lucia_L; Golcher‐Benavides, Jimena; Lewanski, Alexander_L; Rick, Jessica_A; Rosenthal, William_C; Wagner, Catherine_E (December 2024, Molecular Ecology)

   ABSTRACT Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high‐throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole‐genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re‐use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization—and the hypothesized processes by which it shapes diversification—and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life. 

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5. Movement of transposable elements contributes to cichlid diversity

   https://doi.org/10.1111/mec.15685  

   Carleton, Karen L.; Conte, Matthew A.; Malinsky, Milan; Nandamuri, Sri Pratima; Sandkam, Benjamin A.; Meier, Joana I.; Mwaiko, Salome; Seehausen, Ole; Kocher, Thomas D. (November 2020, Molecular Ecology)

   Abstract African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids. 

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