Academic literature on the topic 'Trait-Dependent biogeography models'

Abstract The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.

Abstract The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has shown an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. To explore whether assuming no dependence on traits leads to bias in inference on island dynamics, we extend an island biodiversity model, DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) to include trait-dependent diversification simulations, and evaluate the robustness of the inference model which ignores this trait-dependence. Our results indicate that when the differences between colonization, extinction and speciation rates between trait states are moderate, the model shows negligible error for a variety of island diversity metrics, suggesting that island diversity dynamics can be accurately estimated without the need to explicitly model trait dependence. We conclude that for many biologically realistic scenarios with trait-dependent diversification and colonization, this simple trait-less inference model is informative and robust to trait effects on colonization, speciation and extinction. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.

The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The New World hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.

Abstract Background and Aims The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny, and interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. Methods New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, estimated then the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analyzed using CAFE and InterProScan. Key Results Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of ‘bisexual climbers’ comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual-flowered clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (Psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined, increased then through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as heat shock protein, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. Conclusions Our results improve our understanding of aroid phylogeny using the large number of single/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.

Quantifying trophic relationships of marine species is fundamental to the construction and performance of ecosystem models, development of effective ecosystem-based fisheries management strategies, and support of trait-based approaches to ecological risk assessment. Accounting for food web dynamics in taxonomically diverse ecosystems, such as the California Current Large Marine Ecosystem (CCLME), is especially challenging because of the sheer number of trophic linkages and their inherent variability. Consequently, analyses that can inform the most appropriate means of aggregating species or other taxonomic groups into assemblages or guilds are critical to reducing system complexity for modeling and management, particularly when data are limited. To provide a methodological approach that is globally applicable in such cases, we define trophic guilds within biogeographic regions of the CCLME, compare results among these regions, and discuss ecological and management implications. Within each biogeographic region, predator guilds were clearly demarcated by foraging habitat (benthic, nearshore pelagic, offshore pelagic), scale of foraging movements, and trophic position. Furthermore, trophic guilds were distinctive for each region, with species composition and the noted ecological characteristics largely driving guild structure. Predator species that are reliant on continental slope and offshore foraging habitat, such as adult Pacific Hake, have diets that are representative of these areas and are similar throughout the CCLME. Generally, larger, more mobile predators that typically feed in deeper offshore waters, including swordfish, sea lions, and sharks clustered together in multiple bioregions along the coast; all reliant primarily on fishes and squids. Throughout bioregions, groundfishes preyed on benthic invertebrates (e.g., decapods, amphipods, polychaetes), while shelf-oriented pelagic predators, including smaller salmon, preyed on pelagic invertebrates (e.g., euphausiids, copepods, gelatinous zooplankton). A large number of forage taxa that are well represented in this study have dynamics largely dependent on oceanographic conditions at a regional scale (e.g., decapods), basin scale (e.g., copepods), or a combination of both (e.g., euphausiids, Northern Anchovy). Such distinctions indicate that spatial and temporal scales of coherence of predators and prey also must be considered in development of ecosystem models and evaluation of management strategies. Our study quantifies the spatial coherence of predator guilds integrated over decades within and across bioregions of the CCLME, providing an improved understanding of regional ecosystem functioning. The analytical approach we developed may be easily extended to address similar ecological and ecosystem based fisheries management priorities in other marine regions.