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1. Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard ( Ctenotus pantherinus )

   https://doi.org/10.1093/zoolinnean/zlac076  

   Prates, Ivan; Doughty, Paul; Rabosky, Daniel L. (October 2022, Zoological Journal of the Linnean Society)

   Abstract Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies. 

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2. Intraspecific variation mediates density dependence in a genetically diverse plant species

   https://doi.org/10.1002/ecy.3502  

   Zaiats, Andrii; Germino, Matthew J.; Serpe, Marcelo D.; Richardson, Bryce A.; Caughlin, T. Trevor (September 2021, Ecology)

   Abstract Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco‐evolutionary dynamics through genotype‐mediated plant–plant interactions. However, few studies have examined how species‐wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long‐term common garden experiment that represents range‐wide diversity ofA. tridentata, we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant–plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long‐term consequences of plant–plant interactions. 

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3. Morphological-molecular incongruence in Sphagnum majus ssp. majus and ssp. norvegicum.

   Nieto-Lugilde, M.; Robinson, S.; Aguero, B.; Duffy, A.; Imwattana, K.; Hassel, K..; Flatberg, K.I.; Stenøien, H.K.; Shkurko, A.V.; Vladimir E.; et al (January 2022, The Bryologist)

   Species delimitation is problematic in many plant groups and among the mosses, Sphagnum is one of the more contentious genera because of high levels of morphological variation. The allopolyploid species, Sphagnum majus, comprises one such problematic complex. Two morphologically differentiated but overlapping subspecies have been described. We conducted morphometric and molecular analyses with samples from around the Northern Hemisphere to test for phenotypic and phylogenetic differentiation between the subspecies. Although field collections of the two species can be statistically differentiated morphologically, there is substantial overlap. Genome-scale molecular data do not suggest any differentiation between S. majus ssp. majus and ssp. norvegicum, including samples assigned to the two taxa from sympatric sites. Sequence data from the plastid genome were employed to infer parentage of allopolyploid S. majus. Our results support the hypothesis that S. annulatum is the paternal parent and S. cuspidatum is the maternal parent. We conclude that the morphological differences between them are either plastic responses to habitat heterogeneity or segregating genetic variation within a single taxon. Formal taxonomic recognition of two taxa is not supported by our molecular data. 

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4. Genome‐wide diversity and habitat underlie fine‐scale phenotypic differentiation in the rainbow darter ( Etheostoma caeruleum )

   https://doi.org/10.1111/eva.13135  

   Oliveira, Daniel R.; Reid, Brendan N.; Fitzpatrick, Sarah W. (October 2020, Evolutionary Applications)

   Abstract Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal‐limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold‐water species at‐risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine‐scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site‐specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake‐stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response. 

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5. Morphological and genetic data challenge species and subspecies in the Lerista microtis group (Squamata: Scincidae)

   https://doi.org/10.11646/ZOOTAXA.5437.3.2  

   FARQUHAR, JULES E; PRATES, IVAN; DOUGHTY, PAUL; RABOSKY, DANIEL L; CHAPPLE, DAVID G (April 2024, Zootaxa)

   The subspecies rank has been widely applied by taxonomists to capture infraspecific variation within the Linnaean classification system. Many subspecies described throughout the 20th century were recognised largely based on perceived variation in single morphological characters yet have since been found not to correspond to separately evolving population lineages, thus requiring synonymy or elevation to full species under lineage-based views of species. These modern lineage-based taxonomic resolutions have resulted from a combination of new molecular genetic techniques, improved geographical sampling of specimens, and more sophisticated analyses of morphological variation (e.g., statistical assessments rather than solely univariate descriptive ones). Here, we revisit the current taxonomic arrangement of species-level and subspecific taxa in the Lerista microtis (Gray) group, which is distributed along a narrow ~2000 km strip on the southern coast of Australia. From specimens of the L. microtis group, an additional species (Lerista arenicola) and two additional subspecies (L. m. intermedia and L. m. schwaneri) were described. We collected data on mensural, meristic, and colour pattern characters to explore morpho-spatial relationships among these taxa. Although our morphological analyses revealed some distinctiveness among specimens from locations assigned to each taxon, this variation is continuous along Australia’s southern coastline, assuming the form of a geographic cline rather than discrete forms. For many characters, however, spatial patterns were inconsistent with the original descriptions, particularly of the subspecies. Moreover, analysis of genome wide restriction-associated DNA loci revealed multiple instances of paraphyly among taxa, with phylogenetic clustering of specimens assigned to distinct species and subspecies. These emerging patterns provide no support for L. arenicola as a species evolving separately from L. microtis. Additionally, our findings challenge the presumed distinctiveness and coherence of the three subspecies of L. microtis. We thus synonymise L. arenicola and the L. microtis subspecies with L. microtis and provide a redescription of a single yet morphologically variable species—an arrangement that best reflects evolutionary history and the continuous nature of morphological variation across space. 

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