More Like this

1. Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

   https://doi.org/10.1093/isd/ixad005  

   Sandoval-Arango, Stephania; Branstetter, Michael G; Cardoso, Carolina F; López-Uribe, Margarita M (March 2023, Insect Systematics and Diversity)

   Lozier, Jeffrey (Ed.)

   Abstract Coloration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Müllerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes Eulaema meriana and Eulaema bombiformis (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that E. atleticana and E. niveofasciata are subspecies of E. meriana and E. bombiformis, respectively, and not different species as previously suggested. Therefore, we recognize Eulaema meriana atleticanacomb. n. and Eulaema bombiformis niveofasciatacomb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts. 

   more » « less
2. Why are red flowers so rare? Testing the macroevolutionary causes of tippiness

   https://doi.org/10.1111/jeb.13381  

   Ng, Julienne; Smith, Stacey D. (October 2018, Journal of Evolutionary Biology)

   Abstract Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short‐term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red‐flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE(Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSEmodel when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population‐level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone. 

   more » « less
3. Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards

   https://doi.org/10.1093/sysbio/syae040  

   Barley, Anthony J; Nieto-Montes_de_Oca, Adrián; Manríquez-Morán, Norma L; Thomson, Robert C (July 2024, Systematic Biology)

   Carstens, Bryan (Ed.)

   Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a 2 species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology. 

   more » « less
4. Widespread reticulate evolution in an adaptive radiation

   https://doi.org/10.1093/evolut/qpad011  

   DeBaun, Dylan; Rabibisoa, Nirhy; Raselimanana, Achille P.; Raxworthy, Christopher J.; Burbrink, Frank T. (January 2023, Evolution)

   Abstract A fundamental assumption of evolutionary biology is that phylogeny follows a bifurcating process. However, hybrid speciation and introgression are becoming more widely documented in many groups. Hybrid inference studies have been historically limited to small sets of taxa, while exploration of the prevalence and trends of reticulation at deep time scales remains unexplored. We study the evolutionary history of an adaptive radiation of 109 gemsnakes in Madagascar (Pseudoxyrhophiinae) to identify potential instances of introgression. Using several network inference methods, we find 12 reticulation events within the 22-million-year evolutionary history of gemsnakes, producing 28% of the diversity for the group, including one reticulation that resulted in the diversification of an 18 species radiation. These reticulations are found at nodes with high gene tree discordance and occurred among parental lineages distributed along a north-south axis that share similar ecologies. Younger hybrids occupy intermediate contact zones between the parent lineages showing that post-speciation dispersal in this group has not eroded the spatial signatures of introgression. Reticulations accumulated consistently over time, despite drops in overall speciation rates during the Pleistocene. This suggests that while bifurcating speciation rates may decline as the result of species accumulation and environmental change, speciation by hybridization may be more robust to these processes. 

   more » « less
5. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

   https://doi.org/10.1038/s44320-025-00118-0  

   Feng, Bo; Li, Yonglin; Xu, Biyang; Liu, Hongyue; Steenwyk, Jacob_L; David, Kyle_T; Tian, Xiaolin; Gonçalves, Carla; Opulente, Dana_A; LaBella, Abigail_L; et al (May 2025, Molecular Systems Biology)

   Abstract Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family evolution differs from that of plants, animals, and filamentous ascomycetes, and is characterized by smaller overall gene numbers yet larger gene family sizes for a given gene number. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses—commensurate with a narrowing of metabolic niche breadth—but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages. 

   more » « less