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

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polytypic unit, with the proposed ‘threatened’ status under the U.S. Endangered Species Act of two elements being withdrawn.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 >22k 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 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.

Reproductive innovation enabled radiation in the deep sea during an ecological crisis

“…Although we resolve of the relationships of major lineages of anglerfishes, we find that a high degree of uncertainty underlies the relationships of major lineages of deep-sea ceratioids: the obligate sexual parasitic Linophrynidae, Neoceratias , Ceratiidae, and Centrophryne , and the temporary attachers and facultative parasites in Gigantactinidae, Thaumatichthys , Himantolophus , Oneirodidae, Diceratiidae and Melanocetus (Figure 1; Figure S5; Figure S9). The high magnitude of phylogenetic discordance among individual loci indicates the backbone of the ceratioid phylogeny is in the so-called anomaly zone (Figure 1, Figure S9, Figure S10) 38,46,47 , where variables such as large effective population size and rapid lineage divergence preclude adequate sorting of ancestral genetic variation and results in extensive incongruence among gene trees and the species tree. These results suggest a rapid pace of lineage divergence underlying early ceratioid evolution.…”

“…All nodes in the anomaly zone are reconstructed as ancestrally sexual parasites with varying degrees of support (Figure 1, Figure 3A). The lack of phylogenetic resolution may be the result of incomplete lineage sorting driven by a history of short intervals between divergence events 38,46,47 , suggesting that periods of rapid lineage origination were paired with innovation in reproductive mode in deep-sea anglerfishes.…”

“…However, such uncertainty is expected if anglerfishes radiated at the confluence of the Paleogene-Eocene Thermal Maximum. The extensive gene tree discordance and short branch lengths across the ceratioid phylogenomic backbone are indicative of ancestral polymorphism resulting from an ancestral large effective population size and relatively short intervals between speciation events 38,46,47 (Figure 1; Figure 2B, D). Rather than resulting from poor genetic sampling or methodological artifacts, the anomaly zone at the base of ceratioids appears to reflect an evolutionary history of relatively rapid lineage diversification.…”

“…To further interrogate our data and locate discordant regions of our generated phylogeny, we used custom scripts on the ASTRAL species tree to test for the presence of anomaly zones at particular regions of the tree. Anomaly zones (AZs) can be detected by checking whether branch lengths scaled to coalescent units fall within theoretical boundaries for AZs 38,46,47 ; we transformed branch lengths to coalescent units using quartet CFs before testing whether these branches were AZs using custom python code 46,47 .…”

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

“…Previous reports of empirical anomaly zones are from animal and plant phylogenies, including skink lizards (Linkem et al 2016), Ostariophysan fishes (Chakrabarty et al 2017), flightless birds (Cloutier et al 2019), the Gila robusta complex of fish species (Chafin et al 2021), the Trichophorae tribe of Cyperaceae plants (Léveillé-Bourret et al 2020), and amaranth plants (Morales-Briones et al 2021). Most likely, many other major lineages of the tree of life, including bacterial lineages, have also experienced extensive incomplete lineage sorting throughout their evolution as a result of radiations.…”