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1. 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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2. The role of dominant species in community organization and aboveground production in semiarid grasslands

   https://doi.org/10.1002/ecy.70164  

   Ohlert, Timothy J; Hallmark, Alesia; Rudgers, Jennifer A; Peters, Debra_P C; Collins, Scott L (August 2025, Ecology)

   Abstract Dominant species play a key role in plant communities, influencing the abundance and richness of subordinate species through competitive and facilitative interactions. However, generalizations about the effects of dominant plant species in grasslands can be difficult due to the many differences among communities, such as abiotic conditions and regional species pools. To overcome this issue, we conducted a dominant species removal experiment in two semiarid grassland communities at the Sevilleta National Wildlife Refuge in central New Mexico. These communities had different dominant species but similar abiotic conditions and regional species pools. We studied the effects of removing dominant species on community composition, diversity, and aboveground net primary production (ANPP) over a 23‐year period. Our results showed that dominant grasses suppressed both richness and abundance of subordinate species. In the Chihuahuan Desert grassland, the loss ofBouteloua eriopodawas only partially compensated for by subordinate species, while in the Great Plains grassland, the loss ofBouteloua graciliswas fully compensated for after 16 years. Despite increased species richness, removing dominant species reduced ANPP and resulted in a negative relationship between species richness and ANPP in both grasslands. These results have important implications for ecosystem management and conservation, highlighting the potential impact of losing dominant species on subordinate species and community dynamics. 

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3. Interspecific competition affects resource use by three cryptic freshwater species of Hyalella Smith, 1874 (Amphipoda: Hyalellidae)

   https://doi.org/10.1093/jcbiol/ruab019  

   Mercer, Arissa A; Cothran, Rickey D (June 2021, Journal of Crustacean Biology)

   null (Ed.)

   Abstract Species that use the same resources present a paradox for understanding their coexistence. This is especially true for cryptic species because they are phenotypically similar. We examined how competition affects food-resource use in three cryptic species of Hyalella Smith, 1874, a freshwater-amphipod genus. We hypothesized that competitively inferior species would use high-quality algae patches when alone and competitively superior species would displace inferior species to low-quality patches. We compared use of foraging patches varying in algal content (i.e., quality) when species were alone or with another species. Our results showed that the competitively inferior species spent more time on the low-quality patch in the presence of the competitively superior species, but the behavior of the competitively superior species was independent of heterospecifics. This study provides insight into the role of interspecific competition in shaping resource use and patterns of coexistence in nature. 

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4. A revision of the wilsoni species group in the millipede genus Nannaria Chamberlin, 1918 (Diplopoda, Polydesmida, Xystodesmidae)

   https://doi.org/10.3897/zookeys.1096.73485  

   Hennen, Derek A.; Means, Jackson C.; Marek, Paul E. (April 2022, ZooKeys)

   Although many new species of the millipede genus Nannaria Chamberlin, 1918 have been known from museum collections for over half a century, a systematic revision has not been undertaken until recently. There are two species groups in the genus: the minor species group and the wilsoni species group. In this study, the wilsoni species group was investigated. Specimens were collected from throughout its distribution in the Appalachian Mountains of the eastern United States and used for a multi-gene molecular phylogeny. The phylogenetic tree recovered Nannaria and the two species groups as monophyletic, with Oenomaea pulchella as its sister group. Seventeen new species were described, bringing the composition of the wilsoni species group to 24 species, more than tripling its known diversity, and increasing the total number of described Nannaria species to 78. The genus now has the greatest number of species in the family Xystodesmidae. Museum holdings of Nannaria were catalogued, and a total of 1,835 records used to produce a distribution map of the species group. Live photographs, illustrations of diagnostic characters, ecological notes, and conservation statuses are given. The wilsoni species group is restricted to the Appalachian region, unlike the widely-distributed minor species group (known throughout eastern North America), and has a distinct gap in its distribution in northeastern Tennessee and adjacent northwestern North Carolina. The wilsoni species group seems to be adapted to mesic microhabitats in middle to high elevation forests in eastern North America. New species are expected to be discovered in the southern Appalachian Mountains. 

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5. Comparing single- and mixed-species groups in fruit flies: differences in group dynamics, but not group formation

   https://doi.org/10.1093/jhered/esab041  

   Girardeau, Anna R; Foley, Brad R; Saltz, Julia B (August 2021, Journal of Heredity)

   Hughes, Kim (Ed.)

   Abstract Mixed-species groups describe active associations among individuals of 2 or more species at the same trophic level. Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation, and research that ignores the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected. Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species groups form. Furthermore, insects have been almost completely ignored in the study of mixed-species groups, despite their taxonomic importance and relative prominence in the study of single-species groups. Here, we measured group formation processes in Drosophila melanogaster and its sister species, Drosophila simulans. Each species was studied alone, and together, and one population of D. melanogaster was also studied both alone and with another, phenotypically distinct D. melanogaster population, in a nested-factorial design. This approach differs from typical methods of studying mixed-species groups in that we could quantitatively compare group formation between single-population, mixed-population, and mixed-species treatments. Surprisingly, we found no differences between treatments in the number, size, or composition of groups that formed, suggesting that single- and mixed-species groups form through similar mechanisms of active attraction. However, we found that mixed-species groups showed elevated interspecies male–male interactions, relative to interpopulation or intergenotype interactions in single-species groups. Our findings expand the conceptual and taxonomic study of mixed-species groups while raising new questions about the mechanisms of group formation broadly. 

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