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1. Extrinsically reinforced hybrid speciation within Holarctic ermine ( Mustela spp.) produces an insular endemic

   https://doi.org/10.1111/ddi.13234  

   Colella, Jocelyn P. ; Frederick, Lindsey M. ; Talbot, Sandra L. ; Cook, Joseph A. ; Brito, ed., José ( February 2021 , Diversity and Distributions)

   Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which experience dramatic fluctuations in connectivity in response to both lower sea levels during glacial events and increased fragmentation during glacial recession. We test whether extended refugial isolation has led to the divergence of genetically and morphologically distinct species within Holarctic ermine (Mustela erminea), a small cosmopolitan carnivore species that harbours 34 extant subspecies, 14 of which are insular endemics.

   Holarctic.

   We use genetic sequences (complete mitochondrial genomes, four nuclear genes) from >100 ermine (stoats) and geometric morphometric data for >200 individuals (27 of the 34 extant subspecies) from across their Holarctic range to provide an integrative perspective on diversification and endemism across this complex landscape. Multiple species delimitation methods (iBPP,bPTP) assessed congruence between morphometric and genetic data.

   Our results support the recognition of at least three species within theM. ermineacomplex, coincident with three of four genetic clades, tied to diversification in separate glacial refugia. We found substantial geographic variation within each species, with geometric morphometric results largely consistent with historical infraspecific taxonomy.

   Phylogeographic structure mirrors patterns of diversification in other Holarctic species, with a major Nearctic‐Palearctic split, but with greater intraspecific morphological diversity. Recognition of insular endemic speciesM. haidarumis consistent with a deep history of refugial persistence and highlights the urgency of mindful management of island populations along North America's North Pacific Coast. Significant environmental modification (e.g. industrial‐scale logging, mining) has been proposed for a number of these islands, which may elevate the risk of extinction of insular palaeoendemics.

    

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2. Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation

   https://doi.org/10.1093/sysbio/syad024  

   Wootton, Lara M ; Forest, Félix ; Verboom, G Anthony ( April 2023 , Systematic Biology)

   Yang, Ya (Ed.)

   Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).]

    

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3. Molecular and morphological differentiation among Torrent Duck ( Merganetta armata ) populations in the Andes

   https://doi.org/10.1111/zsc.12367  

   Gutiérrez‐Pinto, Natalia ; McCracken, Kevin G. ; Tubaro, Pablo ; Kopuchian, Cecilia ; Astie, Andrea ; Cadena, Carlos Daniel ( July 2019 , Zoologica Scripta)

   Birds living in riverine environments may show weak population structure because high dispersal abilities required to track habitat dynamics can result in gene flow over broad spatial scales. Alternatively, the configuration of river networks may result in restricted dispersal within river courses or basins, leading to high genetic structure. Although several bird species are riverine specialists in the Andes, no study has extensively evaluated the population genetic structure of any of them. We examined evidence from genetic and morphological data to address questions about the biogeography and taxonomy of the Torrent Duck (Merganetta armata), a riverine specialist bird with a broad distribution in Andean riverine habitats which certainly comprises different subspecies and may comprise more than one species. We found deep subdivisions of Torrent Duck populations from the northern, central and southern portions of the Andes. These lineages, which partly coincide with subspecies described based on plumage variation and body size, do not share mtDNA haplotypes, have private nuclear alleles and exhibit marked differences in morphometric traits. Some geographic barriers presumably restricting gene flow between groups partially coincide with those associated with major genetic breaks in forest species with similar distributions along the Andes, suggesting that bird assemblages including species occupying different habitats were likely affected by common biogeographical events. The three groups of Torrent Ducks may be considered different species under some species definitions and are distinct evolutionary lineages to be conserved and managed separately.

    

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4. Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird

   https://doi.org/10.1111/mec.14010  

   Walsh, Jennifer ; Lovette, Irby J. ; Winder, Virginia ; Elphick, Chris S. ; Olsen, Brian J. ; Shriver, Gregory ; Kovach, Adrienne I. ( February 2017 , Molecular Ecology)

   Understanding the processes that drive divergence within and among species is a long‐standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra‐ and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies ofA. nelsoniandA. caudacutususing a reduced‐representation sequencing approach to generate a panel of 1929SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish–water marsh habitats. These patterns support the current species‐level recognition but do not match the subspecies‐level taxonomy within each species—a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.

    

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5. Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes

   https://doi.org/10.1093/isd/ixab027  

   Williams, Jason L ; Zhang, Y Miles ; LaPolla, John S ; Schultz, Ted R ; Lucky, Andrea ( January 2022 , Insect Systematics and Diversity)

   Camacho, Gabriela P (Ed.)

   Abstract The ant genus Nylanderia Emery has a cosmopolitan distribution and includes 150 extant described species and subspecies, with potentially hundreds more undescribed. Global taxonomic revision has long been stalled by strong intra- and interspecific morphological variation, limited numbers of diagnostic characters, and dependence on infrequently collected male specimens for species description and identification. Taxonomy is further complicated by Nylanderia being one of the most frequently intercepted ant genera at ports of entry worldwide, and at least 15 globetrotting species have widespread and expanding ranges, making species-level diagnoses difficult. Three species complexes (‘bourbonica complex’, ‘fulva complex’, and ‘guatemalensis complex’) include globetrotting species. To elucidate the phylogenetic positions of these three complexes and delimit species boundaries within each, we used target enrichment of ultraconserved elements (UCEs) from 165 specimens representing 98 Nylanderia morphospecies worldwide. We also phased the UCEs, effectively doubling sample size and increasing population-level sampling. After recovering strong support for the monophyly of each complex, we extracted COI barcodes and SNPs from the UCE data and tested within-complex morphospecies hypotheses using three molecular delimitation methods (SODA, bPTP, and STACEY). This comparison revealed that most methods tended to over-split taxa, but results from STACEY were most consistent with our morphospecies hypotheses. Using these results, we recommend species boundaries that are conservative and most congruent across all methods. This work emphasizes the importance of integrative taxonomy for invasive species management, as globetrotting occurs independently across at least nine different lineages across Nylanderia. 

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