Bulletin of the Society of Systematic Biologists

Seeing the Network for the Trees: Methodological and Empirical Advances in Reticulate Evolution

2025-03-21T08:41:34+00:00

This special collection includes topics related to the development of novel methods for reconstructing phylogenetic networks from different mathematical, statistical, and computational approaches that highlight the challenges of network reconstruction and the needs of contemporary genomic data. In addition, the collection broadcasts diverse applications of phylogenetic networks on a wide variety of organisms across the Tree of Life.

What Is an Eared Nightjar? Ultraconserved Elements Clarify the Evolutionary Relationships of Eurostopodus and Lyncornis Nightjars (Aves: Caprimulgidae)

2025-03-05T06:17:05+00:00

Nightjars (Aves: Caprimulgidae) are a species-rich family of birds, with the “eared nightjars” (Eurostopodinae) being an early-branching group endemic to the Indo-Pacific. While much research has focused on species-rich nightjar genera and their higher-level relationships, the evolutionary history of Eurostopodinae (Eurostopodus, Lyncornis) remains understudied. We generated a genome-scale dataset to produce the first fully sampled phylogeny of all Eurostopodus and one Lyncornis species, including sequencing two type specimens of critically endangered and extinct species. Tree-building methods inferred concordant, well-resolved topologies that reveal intriguing biogeographic patterns within Eurostopodus. Our results show Eurostopodus as sister to all other nightjars, while Lyncornis, previously considered related, is more closely allied with other caprimulgids. We propose that the term “eared nightjars” should apply only to the two Lyncornis species, which should be classified within the subfamily Caprimulginae. Accordingly, since only Eurostopodus species remain in Eurostopodinae, we recommend renaming this subfamily “Indo-Pacific nightjars” to reflect their geographic distribution in this significant region.

Global Integration of Phylogenomic Data and Fine-Scale Partitioning Strategies Refine the Evolutionary Tree of Adephaga Beetles

2025-02-01T06:53:06+00:00

Over the past decade, genomic-scale data has revolutionized insect phylogenetics by allowing the generation of increasingly comprehensive genomic and taxonomic datasets. However, because different approaches have been used, it is often difficult to understand to what extent these data can be integrated to reconstruct evolutionary trees. In this study, we focus on the beetle suborder Adephaga to explore whether genomic data produced in the past decade can be combined to reconstruct the largest phylogenomic tree of this clade to date. To that end, we collected publicly-available transcriptomes, genomes, and target sequence capture data of Adephaga beetles to generate a global dataset. Taking advantage of a newly developed bioinformatic pipeline, we demonstrate the overall compatibility of data types, especially of ultraconserved elements and exon-capture data. We also examined the impact of factors such as the treatment of off-target flanking genomic regions, data trimming regimes and partitioning, as well as varying levels of taxonomic and genomic sampling on phylogenomic inference. Using a matrix of 2,471 loci, we inferred the most comprehensive fossil-based evolutionary tree of Adephaga beetles. Our results confirm the independent colonization of aquatic ecosystems by two lineages. We also reconstruct Hygrobiidae as sister to Amphizoidae and a paraphyletic Aspidytidae, supporting the evolutionary convergence of prothoracic glands in both Hygrobiidae and Dytiscidae. Our results suggest an origin of Adephaga in the Carboniferous, with subsequent diversification of major lineages in the mid-Permian. Future efforts should focus on expanding the taxonomic sampling in Geadephaga, this clade of terrestrial beetles being the most diverse lineage in Adephaga and paradoxically one of the least sampled. To that end, we introduce a new ultraconserved element probe set tailored for Geadephaga beetles that will help generate compatible genomic data to further refine the Adephaga tree of life.

The Evidence for New Species Across the Tree of Life: Morphology Still Rules the Largest Kingdoms

2025-04-01T05:57:25+00:00

Over the past ~20 years, several forces have converged to potentially create a seismic shift in how new species are described. These forces include: (1) pleas for DNA-based taxonomy, (2) large-scale genomic datasets for species delimitation, (3) new statistical methods for molecular species delimitation, (4) the discovery of hundreds of cryptic species hiding within morphology-based species, (5) the possibility that most morphologically distinct species are already described, and (6) the putative decline of morphology-based taxonomy. But has a major shift towards molecular-based taxonomy actually happened? Here, we examined newly described species from 9 major groups across the Tree of Life and the evidence used to delimit them. We found five major results. First, in the largest groups, most new species were still described based on morphological data alone, including arthropods, mollusks, and plants (groups collectively including ~90% of all known species). Second, in other groups, most new species were described based on both molecular and morphological evidence, including chordates, fungi, bacteria, and archaeans. Third, species described based only on molecular data remain rare. Fourth, within animals, the majority of species descriptions that incorporated molecular data included only mitochondrial sequences. Fifth, molecular data were typically used to build a tree and generate genetic distances, rather than being used for statistical delimitation methods. Our results suggest that many new developments in species delimitation are underutilized by taxonomists (e.g. genomics), likely because these developments do not offer the fastest way to describe new species before they become extinct. Our results also suggest that many morphologically distinct species (and cryptic species) remain to be described.