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1. Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae)

   https://doi.org/10.1002/ece3.10025  

   Newton, Lacie G.; Starrett, James; Jochim, Emma E.; Bond, Jason E. (April 2023, Ecology and Evolution)

   Abstract Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population‐level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genusAptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, theAptostichus icenogleicomplex, which comprises the three sibling species,A. barackobamai,A. isabella, andA. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species‐based approach. We used genomic‐scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries withinA. icenoglei. 

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2. Removal of detritivore sea cucumbers from reefs increases coral disease

   https://doi.org/10.1038/s41467-024-45730-0  

   Clements, Cody S.; Pratte, Zoe A.; Stewart, Frank J.; Hay, Mark E. (December 2024, Nature Communications)

   Abstract Coral reefs are in global decline with coral diseases playing a significant role. This is especially true for Acroporid corals that represent ~25% of all Pacific coral species and generate much of the topographic complexity supporting reef biodiversity. Coral diseases are commonly sediment-associated and could be exacerbated by overharvest of sea cucumber detritivores that clean reef sediments and may suppress microbial pathogens as they feed. Here we show, via field manipulations in both French Polynesia and Palmyra Atoll, that historically overharvested sea cucumbers strongly suppress disease among corals in contact with benthic sediments. Sea cucumber removal increased tissue mortality ofAcropora pulchraby ~370% and colony mortality by ~1500%. Additionally, farmerfish that killAcropora pulchrabases to culture their algal gardens further suppress disease by separating corals from contact with the disease-causing sediment—functioning as mutualists rather than parasites despite killing coral bases. Historic overharvesting of sea cucumbers increases coral disease and threatens the persistence of tropical reefs. Enhancing sea cucumbers may enhance reef resilience by suppressing disease. 

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3. Population Genetics to Population Genomics: Revisiting Multispecies Connectivity of the Hawaiian Archipelago

   https://doi.org/10.3390/fishes10120623  

   Freel, Evan B; Conklin, Emily E; Knapp, Ingrid_S S; Kraft, Derek W; Johnston, Erika C; Forsman, Zac H; Coleman, Richard R; Whitney, Jonathan L; Iacchei, Matthew J; Bowen, Brian W; et al (December 2025, Fishes)

   Understanding connectivity between populations is key to identifying hotspots of diversity, dispersal sinks and sources, and effective management units for natural resources. Multi-species connectivity seeks to overcome species-specific idiosyncrasies to identify shared patterns that are most critical to spatial management. The linear Hawaiian archipelago provides an excellent platform to assess multi-species connectivity patterns, with shared boundaries to gene flow identified across a majority of the 41 coral reef species surveyed to date. Here, we evaluate genome-scale data by comparing consistency and resolution to previous connectivity studies using far fewer loci. We used pool-seq to genotype 22,503–232,730 single nucleotide polymorphisms per species (625,215 SNPs total) from the same individuals published in previous studies of two fishes, two corals, and two lobsters. Additionally, one coral species (Pocillopora meandrina) without previous archipelago-wide population genetic data was included. With greater statistical power, most genetic differences between pairwise comparisons of islands were significant (250 of 308), consistent with the most recent larval dispersal models for the Hawaiian Archipelago. These data reveal significant differentiation at a finer scale than previously reported using single-marker studies, yet did not overturn any of the conclusions or management implications drawn from previous studies. We confirm that population genomic datasets are consistent with previously reported patterns of multispecies connectivity but add a finer layer of population resolution that is pertinent to management. 

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4. Small‐scale genetic structure of coral populations in Palau based on whole mitochondrial genomes: Implications for future coral resilience

   https://doi.org/10.1111/eva.13509  

   Palumbi, Stephen R.; Walker, Nia S.; Hanson, Erik; Armstrong, Katrina; Lippert, Marilla; Cornwell, Brendan; Nestor, Victor; Golbuu, Yimnang (February 2023, Evolutionary Applications)

   Abstract The ability of local populations to adapt to future climate conditions is facilitated by a balance between short range dispersal allowing local buildup of adaptively beneficial alleles, and longer dispersal moving these alleles throughout the species range. Reef building corals have relatively low dispersal larvae, but most population genetic studies show differentiation only over 100s of km. Here, we report full mitochondrial genome sequences from 284 tabletop corals (Acropora hyacinthus) from 39 patch reefs in Palau, and show two signals of genetic structure across reef scales from 1 to 55 km. First, divergent mitochondrial DNA haplotypes exist in different proportions from reef to reef, causing Phi_STvalues of 0.02 (p = 0.02). Second, closely related sequences of mitochondrial Haplogroups are more likely to be co‐located on the same reefs than expected by chance alone. We also compared these sequences to prior data on 155 colonies from American Samoa. In these comparisons, many Haplogroups in Palau were disproportionately represented or absent in American Samoa, and inter‐regional Phi_ST = 0.259. However, we saw three instances of identical mitochondrial genomes between locations. Together, these data sets suggest two features of coral dispersal revealed by occurrence patterns in highly similar mitochondrial genomes. First, the Palau‐American Samoa data suggest that long distance dispersal in corals is rare, as expected, but that it is common enough to deliver identical mitochondrial genomes across the Pacific. Second, higher than expected co‐occurrence of Haplogroups on the same Palau reefs suggests greater retention of coral larvae on local reefs than predicted by many current oceanographic models of larval movement. Increased attention to local scales of coral genetic structure, dispersal, and selection may help increase the accuracy of models of future adaptation of corals and of assisted migration as a reef resilience intervention. 

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5. Biodiversity and biogeography of zooxanthellate soft corals across the Indo-Pacific

   https://doi.org/10.1038/s41598-025-98790-7  

   McFadden, Catherine S; Erickson, Katie L; Lane, Audra; Nassongole, Bibiana; Aguilar, Steven; Dunakey, Sabra K; Durkin, Kathleen M; Lalas, Jue_A A; Kushida, Yuka; Macrina, Laura; et al (May 2025, Scientific Reports)

   Documentation of biodiversity and its geographical distribution is necessary to understand the processes and drivers of evolutionary diversification as well as to guide conservation and management initiatives. Among the most emblematic patterns of biodiversity in the world’s oceans is the Coral Triangle (Indo-Australian Archipelago), widely recognized to be the center of species richness for a variety of marine life forms. The distribution of biodiversity remains incompletely documented, however, for a majority of reef-associated invertebrate taxa, including the zooxanthellate soft corals (Octocorallia) that dominate hard substrate on many Indo-Pacific reefs. We used a genetic approach to document the diversity of Indo-Pacific soft corals, sequencing two single-locus barcoding markers for > 4400 soft coral specimens and assigning individuals to molecular operational taxonomic units as proxies of species. We document two centers of species richness for zooxanthellate soft corals, one in the Indo-Australian Archipelago and a second, equally diverse center in the Western Indian Ocean. Centers of endemicity for soft corals are coincident with these centers of species richness, although the peripheral Red Sea and Hawaii also support high proportions of endemic taxa. The patterns documented here suggest that biogeographic distributions of soft coral families may be driven in part by larval dispersal potential: taxa with benthic larvae are absent from most oceanic islands of the central Pacific and are represented by higher proportions of endemic taxa in other geographic regions. Our findings demonstrate the distinct biogeographic patterns among reef taxa and underscore the need to document and analyze species distributions of more reef-associated invertebrate groups to derive a complete picture of reef biogeography. 

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