Systematic Biology最新文献

Reconstructing phylogeny from morphological data remains mired in investigator biases, including subjective inclusion and discretisation of phenotypic variation. Geometric morphometrics and multivariate statistical analyses provide an alternative array of tools for studying variation in morphological traits. However, direct analysis of landmark data is often unreliable for phylogeny reconstruction. Morphological variation is typically highly correlated among nearby landmarks and may evolve saltationally between adaptive peaks instead of gradually, thereby violating the assumptions of typical continuous models. To address these concerns, we developed an approach to more objectively discretise morphometric data and applied it to 3D surface scans of mandibles and postcranial elements of Macropodiformes (kangaroos, bettongs and rat-kangaroos). The scanned elements were partitioned into sets of locally co-varying landmarks which approximate functional units. These subregions were discretised into "atomised" characters using novel approaches to combine the objectivity of continuous shape variation for delineating discrete states with the model flexibility offered for multistate and binary characters. This allows us to (1) potentially reduce the influence of non-independence among neighbouring landmarks, (2) accommodate multimodal variation from saltational evolution, (3) accommodate missing data, such as from fragmentary fossils, and (4) promote tree-search efficiency. We built discrete morphological character matrices using three alternative approaches: commonly used clustering algorithms (UPGMA, k-means, k-medoids, Gaussian mixture modelling), a minimum evolution branch length criterion, and a tree sampling procedure. Our phylogenetic analyses with these novel matrices generally succeeded in recovering genera and several deep-level macropodiform clades, but failed to accurately reconstruct intergeneric relationships within the rapid diversification of the macropodine sub-family; those relationships were also not recovered with continuous morphological data or traditionally discretised characters and are the most poorly resolved with DNA data. On balance, our atomised characters, which derive from only mandibular and three postcranial elements, show promise for improving objectivity, accuracy and clocklikeness in morphological phylogenetics and provide pathways for accommodating correlated homoplasy and for more accurately estimating rates of morphological evolution, and thereby better integrating phenotypic and genomic data for phylogenetic inference.

Explaining global species richness patterns is a major goal of evolution, ecology, and biogeography. These richness patterns are often attributed to spatial variation in diversification rates (speciation minus extinction). Surprisingly, prominent studies of birds, fish, and plants have reported higher speciation and/or diversification rates at higher latitudes, where species richness is lower. We hypothesize that these surprising findings are explained by the focus of those studies on relatively recent macroevolutionary rates, within the last ~20 million years. Here, we analyze global richness patterns among 10,213 squamates (lizards and snakes) and explore their underlying causes. We find that when diversification rates were quantified at more recent timescales, we observed mismatched patterns of rates and richness, similar to previous studies in other taxa. Importantly, diversification rates estimated over longer timescales were instead positively related to geographic richness patterns. These observations may help resolve the paradoxical results of previous studies in other taxa. We found that diversification rates were largely unrelated to climate, even though climate and richness were related. Instead, higher tropical richness was related to the ancient occupation of tropical regions, with colonization time the variable that explained the most variation in richness overall. We suggest that large-scale diversity patterns might be best understood by considering climate, deep-time diversification rates, and the time spent in different regions, rather than recent diversification rates alone.

Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank's Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.