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1. Evidence supporting cryptic species within two sessile microinvertebrates, Limnias melicerta and L. ceratophylli (Rotifera, Gnesiotrocha)

   https://doi.org/10.1371/journal.pone.0205203  

   Azar Kordbacheh, Azar; Wallace, R.L.; Walsh, 2 (October 2018, PloS one)

   Munderloh, Ulrike Gertrud (Ed.)

   Microorganisms, including rotifers, are thought to be capable of long distance dispersal. Therefore, they should show little population genetic structure due to high gene flow. Nevertheless, substantial genetic structure has been reported among populations of many taxa. In rotifers, genetic studies have focused on planktonic taxa leaving sessile groups largely unexplored. Here, we used COI gene and ITS region sequences to study genetic structure and delimit cryptic species in two sessile species (Limnias melicerta [32 populations]; L. ceratophylli [21 populations]). Among populations, ITS region sequences were less variable as compared to those of the COI gene (ITS; L. melicerta: 0–3.1% and L. ceratophylli: 0–4.4%; COI; L. melicerta: 0–22.7% and L. ceratophylli: 0–21.7%). Moreover, L. melicerta and L. ceratophylli were not resolved in phylogenetic analyses based on ITS sequences. Thus, we used COI sequences for species delimitation. Bayesian Species Delimitation detected nine putative cryptic species within L. melicerta and four putative cryptic species for L. ceratophylli. The genetic distance in the COI gene was 0–15.4% within cryptic species of L. melicerta and 0.5–0.6% within cryptic species of L. ceratophylli. Among cryptic species, COI genetic distance ranged 8.1–21.9% for L. melicerta and 15.1–21.2% for L. ceratophylli. The correlation between geographic and genetic distance was weak or lacking; thus geographic isolation cannot be considered a strong driver of genetic variation. In addition, geometric morphometric analyses of trophi did not show significant variation among cryptic species. In this study we used a conservative approach for species delimitation, yet we were able to show that species diversity in these sessile rotifers is underestimated. 

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2. Population connectivity of the euphausiid, Stylocheiron elongatum , in the Gulf Stream (NW Atlantic Ocean) in relation to COI barcode diversity of Stylocheiron species

   https://doi.org/10.1093/icesjms/fsab158  

   Bucklin, Ann; Questel, Jennifer M; Blanco-Bercial, Leocadio; Frenzel, Alexandra; Smolenack, Sara B; Wiebe, Peter H (August 2021, ICES Journal of Marine Science)

   Grant, William (Ed.)

   Abstract The euphausiid genus Stylocheiron includes species with biogeographical distributions spanning multiple ocean basins. Despite their circumglobal distributions, the species show low levels of genetic diversity and little or no evidence of population structure based on the mitochondrial cytochrome oxidase I (COI) barcode region, with the exception of a possible cryptic species within Stylocheiron affine. Stylocheiron elongatum showed < 1% variation of the COI barcode region among populations in different ocean basins, but analysis of samples collected from the Florida Current (February, 1993) and Gulf Stream Meander Region (April, 1993) in the Northwest Atlantic Ocean revealed small-but-significant genetic differentiation between samples based on a different section of COI and mitochondrial cytochrome b (CYB). Both COI and CYB showed large haplotype and small nucleotide diversities, departures from neutral expectations, and haplotype networks consistent with persistent genetic structuring of the species population. These patterns of diversity indicate the presence of selection driving population divergence. We hypothesize that position-keeping by this deep-living, non-migrating euphausiid species may prevent genetic homogenization (panmixia) in the dynamic Gulf Stream System. This study demonstrates the importance of analyzing patterns of genetic diversity and structure at regional and global scales to understand the ecological and evolutionary processes impacting marine zooplankton. 

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3. Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes

   https://doi.org/10.1093/gbe/evac111  

   Drown, Melissa K; DeLiberto, Amanda N; Flack, Nicole; Doyle, Meghan; Westover, Alexander G; Proefrock, John C; Heilshorn, Sandra; D’Alessandro, Evan; Crawford, Douglas L; Faulk, Christopher; et al (August 2022, Genome Biology and Evolution)

   Costantini, Maria (Ed.)

   Abstract Genetic data from nonmodel species can inform ecology and physiology, giving insight into a species’ distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). These fish are found in shallow coastal waters and are frequently included in ecological models because they serve as abundant prey for commercially and ecologically important species. Despite their importance in sub-tropical and tropical ecosystems, little is known about their population connectivity and genetic diversity. Our A. stipes genome assembly is about 1.2 Gb with comparable repetitive element content (∼47%), number of protein duplication events, and DNA methylation patterns to other teleost fish species. Among five sampled populations spanning 43 km of South Florida and the Florida Keys, we find little population structure suggesting high population connectivity. 

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4. The landscape of structural variation in aye-ayes (Daubentonia madagascariensis)

   https://doi.org/10.1101/2024.11.08.622672  

   Versoza, Cyril J; Jensen, Jeffrey D; Pfeifer, Susanne P (November 2024, bioRxiv)

   Aye-ayes (Daubentonia madagascariensis) are one of the 25 most critically endangered primate species in the world. Endemic to Madagascar, their small and highly fragmented populations make them particularly vulnerable to both genetic disease and anthropogenic environmental changes. Over the past decade, conservation genomic efforts have largely focused on inferring and monitoring population structure based on single nucleotide variants to identify and protect critical areas of genetic diversity. However, the recent release of a highly contiguous genome assembly allows, for the first time, for the study of structural genomic variation (deletions, duplications, insertions, and inversions) which are likely to impact a substantial proportion of the species’ genome. Based on whole-genome, short-read sequencing data from 14 individuals, >1,000 high-confidence autosomal structural variants were detected, affecting ∼240 kb of the aye-aye genome. The majority of these variants (>85%) were deletions shorter than 200 bp, consistent with the notion that longer structural mutations are often associated with strongly deleterious fitness effects. For example, two deletions longer than 850 bp located within disease-linked genes were predicted to impose substantial fitness deficits owing to a resulting frameshift and gene fusion, respectively; whereas several other major effect variants outside of coding regions are likely to impact gene regulatory landscapes. Taken together, this first glimpse into the landscape of structural variation in aye-ayes will enable future opportunities to advance our understanding of the traits impacting the fitness of this endangered species, as well as allow for enhanced evolutionary comparisons across the full primate clade. 

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5. Population and genetic structure of a male-dispersing strepsirrhine, Galago moholi (Primates, Galagidae), from northern South Africa, inferred from mitochondrial DNA

   https://doi.org/10.1007/s10329-021-00912-y  

   Phukuntsi, Metlholo A.; Du Plessis, Morne; Dalton, Desiré L.; Jansen, Raymond; Sauther, Michelle L.; Cuozzo, Frank P.; Kotze, Antoinette (July 2021, Primates)

   The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into human settlements. To date, no intraspecific molecular genetic studies have been published on G. moholi. Here we estimate the genetic diversity and connectivity of populations of G. moholi using two mitochondrial gene regions, the cytochrome C oxidase subunit I gene (COI) and the displacement loop of the control region (D-loop). Samples from five localities in northern South Africa were obtained from archived collections. The two mitochondrial DNA gene regions were amplified and sequenced to provide population summary statistics, differentiation [proportion of the total genetic variation in a population relative to the total genetic variance of all the populations (FST), differentiation within populations among regions (ΦST)], genetic distance and structure. There was discernible genetic structure among the individuals, with two COI and six D-loop haplotypes belonging to two genetically different groups. There was population differentiation among regions (FST = 0.670; ΦST = 0.783; P < 0.01). However, there were low levels of differentiation among populations, as haplotypes were shared between distant populations. Adjacent populations were as divergent from each other as from distant populations. The results suggest that genetic introgression, most likely due to past migrations or recent unintentional translocations that include the animal trade, may have led to connectivity among populations. 

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