I. the origin of species by means of natural selection

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

/pdf/whole-genome-analyses-resolve-early-branches-in-the-tree-of-2wufsv5juy.pdf

Whole-genome analyses resolve early branches in the tree of life of modern birds

People depend on benefits provided by ecological systems. Understanding how these ecosystem services – and the ecosystem properties underpinning them – respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species’ effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms – which both depend on combinations of functional traits – correlate across species and how they are arranged on the species’ phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.

/pdf/functional-traits-the-phylogeny-of-function-and-ecosystem-3nld3ytwb7.pdf

Functional traits, the phylogeny of function, and ecosystem service vulnerability.

Recent phylogeographic studies have overturned three paradigms for the origins of marine biodiversity. (i) Physical (allopatric) isolation is not the sole avenue for marine speciation: many species diverge along ecological boundaries. (ii) Peripheral habitats such as oceanic archipelagos are not evolutionary graveyards: these regions can export biodiversity. (iii) Speciation in marine and terrestrial ecosystems follow similar processes but are not the same: opportunities for allopatric isolation are fewer in the oceans, leaving greater opportunity for speciation along ecological boundaries. Biodiversity hotspots such as the Caribbean Sea and the Indo-Pacific Coral Triangle produce and export species, but can also accumulate biodiversity produced in peripheral habitats. Both hotspots and peripheral ecosystems benefit from this exchange in a process dubbed biodiversity feedback.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(13)00035-9.pdf

The origins of tropical marine biodiversity

The process of adaptive radiation—the proliferation of species from a single ancestor and diversification into many ecologically different forms—has been of great interest to evolutionary biologists since Darwin. Since the middle of the last century, ecological opportunity has been invoked as a potential key to understanding when and how adaptive radiation occurs. Interest in the topic of ecological opportunity has accelerated as research on adaptive radiation has experienced a resurgence, fueled in part by advances in phylogenetic approaches to studying evolutionary diversification. Nonetheless, what the term actually means, much less how it mechanistically leads to adaptive diversification, is currently debated; whether the term has any predictive value or is a heuristic useful only for post hoc explanation also remains unclear. Recent recognition that evolutionary change can occur rapidly and on a timescale commensurate with ecological processes suggests that it is time to synthesize ecological and evo...

Ecological Opportunity and Adaptive Radiation

Ecological opportunity – through entry into a new environment, the origin of a key innovation or extinction of antagonists – is widely thought to link ecological population dynamics to evolutionary diversification. The population-level processes arising from ecological opportunity are well documented under the concept of ecological release. However, there is little consensus as to how these processes promote phenotypic diversification, rapid speciation and adaptive radiation. We propose that ecological opportunity could promote adaptive radiation by generating specific changes to the selective regimes acting on natural populations, both by relaxing effective stabilizing selection and by creating conditions that ultimately generate diversifying selection. We assess theoretical and empirical evidence for these effects of ecological opportunity and review emerging phylogenetic approaches that attempt to detect the signature of ecological opportunity across geological time. Finally, we evaluate the evidence for the evolutionary effects of ecological opportunity in the diversification of Caribbean Anolis lizards. Some of the processes that could link ecological opportunity to adaptive radiation are well documented, but others remain unsupported. We suggest that more study is required to characterize the form of natural selection acting on natural populations and to better describe the relationship between ecological opportunity and speciation rates.

/pdf/ecological-opportunity-and-the-origin-of-adaptive-radiations-xyl3zeq0ai.pdf

Ecological opportunity and the origin of adaptive radiations

Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.

Hybridizing salamanders experience accelerated diversification

/pdf/hybridizing-salamanders-experience-accelerated-pylcwdf1tj.pdf

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Ecological opportunity and the origin of adaptive radiations

Hybridizing salamanders experience accelerated diversification

Hybridizing salamanders experience accelerated diversification