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1. Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species ( Gila robusta Complex) in the Colorado River

   https://doi.org/10.1093/gbe/evab200  

   Chafin, Tyler K ; Douglas, Marlis R ; Bangs, Max R ; Martin, Bradley T ; Mussmann, Steven M ; Douglas, Michael E ( September 2021 , Genome Biology and Evolution)

   Holland, Barbara (Ed.)

   Abstract Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed “threatened” status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the “anomaly zone” of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level. 

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2. Molecular Phylogenetic Relationships and Unveiling Novel Genetic Diversity among Slow and Pygmy Lorises, including Resurrection of Xanthonycticebus intermedius

   https://doi.org/10.3390/genes14030643  

   Blair, Mary E. ; Cao, Giang T. ; López-Nandam, Elora H. ; Veronese-Paniagua, Daniel A. ; Birchette, Mark G. ; Kenyon, Marina ; Md-Zain, Badrul M. ; Munds, Rachel A. ; Nekaris, K. Anne-Isola ; Nijman, Vincent ; et al ( March 2023 , Genes)

   Genetic analysis of historical museum collections presents an opportunity to clarify the evolutionary history of understudied primate groups, improve taxonomic inferences, and inform conservation efforts. Among the most understudied primate groups, slow and pygmy lorises (genera Nycticebus and Xanthonycticebus) are nocturnal strepsirrhines found in South and Southeast Asia. Previous molecular studies have supported five species, but studies using morphological data suggest the existence of at least nine species. We sequenced four mitochondrial loci, CO1, cytb, d-loop, and ND4, for a total of 3324 aligned characters per sample from 41 historical museum specimens for the most comprehensive geographic coverage to date for these genera. We then combined these sequences with a larger dataset composed of samples collected in Vietnam as well as previously published sequences (total sample size N = 62). We inferred phylogenetic relationships using Bayesian inference and maximum likelihood methods based on data from each locus and on concatenated sequences. We also inferred divergence dates for the most recent common ancestors of major lineages using a BEAST analysis. Consistent with previous studies, we found support for Xanthonycticebus pygmaeus as a basal taxon to the others in the group. We also confirmed the separation between lineages of X. pygmaeus from northern Vietnam/Laos/China and southern Vietnam/Cambodia and included a taxonomic revision recognizing a second taxon of pygmy loris, X. intermedius. Our results found support for multiple reciprocally monophyletic taxa within Borneo and possibly Java. The study will help inform conservation management of these trade-targeted animals as part of a genetic reference database for determining the taxonomic unit and provenance of slow and pygmy lorises confiscated from illegal wildlife trade activities. 

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3. Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

   https://doi.org/10.1111/jbi.13748  

   Marques-Souza, Sergio ; Machado Pellegrino, Katia C. ; Oliveira Brunes, Tuliana ; Carnaval, Ana Carolina ; Pacheco Damasceno, Roberta ; Lima de Oliveira Borges, Manoela ; Candia Gallardo, Carlos ; Rodrigues, Miguel Trefaut ( December 2019 , Journal of Biogeography)

   To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.

   Central Amazonia, Brazil.

   Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

   We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).

   We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.

   Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

    

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4. Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes

   https://doi.org/10.1002/ece3.5538  

   Alza, Luis ; Lavretsky, Philip ; Peters, Jeffrey L. ; Cerón, Gerardo ; Smith, Matthew ; Kopuchian, Cecilia ; Astie, Andrea ; McCracken, Kevin G. ( August 2019 , Ecology and Evolution)

   To investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.

   Peruvian and Argentine Andes.

   Two subspecies of torrent duck (Merganetta armata).

   We sampled 156 individuals in Peru (M. a. leucogenis;Chillón River,n = 57 and Pachachaca River,n = 49) and Argentina (M. a. armata;Arroyo Grande River,n = 33 and Malargüe River,n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru,n = 10 and Argentina,n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.

   Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (Φ_STmtDNA = 0.82; Φ_STautosomal = 0.30; Φ_STZ chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using∂a∂i(isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.

   We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

    

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5. Notes from the taxonomic disaster zone: Evolutionary drivers of intractable species boundaries in an Australian lizard clade (Scincidae: Ctenotus )

   https://doi.org/10.1111/mec.17074  

   Prates, Ivan ; Hutchinson, Mark N. ; Singhal, Sonal ; Moritz, Craig ; Rabosky, Daniel L. ( July 2023 , Molecular Ecology)

   Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: theCtenotus inornatusspecies group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like theC. inornatusspecies group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization.

    

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