Museum genomics reveals the hybrid origin of an extinct crater lake endemic.

Crater lake fishes are common evolutionary model systems, with recent studies suggesting a key role for gene flow in promoting rapid adaptation and speciation. However, the study of these young lakes can be complicated by human-mediated extinctions. Museum genomics approaches integrating genetic data from recently extinct species are therefore critical to understanding the complex evolutionary histories of these fragile systems. Here, we examine the evolutionary history of an extinct Southern Hemisphere crater lake endemic, the rainbowfish Melanotaenia eachamensis. We undertook comprehensive sampling of extant rainbowfish populations of the Atherton Tablelands of Australia alongside historical museum material to understand the evolutionary origins of the extinct crater lake population and the dynamics of gene flow across the ecoregion. The extinct crater lake species is genetically distinct from all other nearby populations due to historic introgression between two proximate riverine lineages, similar to other prominent crater lake speciation systems, but this historic gene flow has not been sufficient to induce a species flock. Our results suggest that museum genomics approaches can be successfully combined with extant sampling to unravel complex speciation dynamics involving recently extinct species.

Phylogeny-based conservation priorities for Australian freshwater fishes.

Conservation scientists are increasingly interested in the question of how extinction prunes the tree of life. This question is particularly important for Australian freshwater fishes because there is a broad mix of ∼300 old and young species, many of which are severely threatened. We used a complete species-level phylogeny of Australian freshwater fishes to examine phylogenetic nonrandomness of extinction risk. We computed the potential loss of phylogenetic diversity by simulating extinction across the tree under a pattern weighted based on International Union for Conservation of Nature extinction risk category and compared this loss to projected diversity loss under a random null model of extinction. Finally, we calculated EDGE (evolutionary distinctiveness, global endangerment) scores for 251 freshwater and 60 brackish species and compiled a list of high-priority species for conservation actions based on their extinction risk and evolutionary uniqueness. Extinction risk was not random and was clustered in both diversity cradles (recently diversifying, species-rich clades, such as Galaxiidae and Percichthyidae) and museums (older, species-poor groups, such as freshwater chondrichthyans). Clustered extinction made little difference to the average expected loss of phylogenetic diversity. However, the upper bound of loss was higher under a selective model of extinction, particularly when the counts of species lost were low. Thus, the loss of highly threatened species would diminish the tree of life more than a null model of randomly distributed extinction.  High priority species included both widely recognized and charismatic ones, such as the Queensland lungfish (Neoceratodus forsteri), river sharks, and freshwater sawfishes, and lesser-known species that receive less public attention, including the salamanderfish (Lepidogalaxias salamandroides), cave gudgeons, and many galaxiids, rainbowfishes, and pygmy perches.

Prioridades de Conservación Basadas en la Filogenia para Peces de Agua Dulce de Australia Resumen Los científicos de la conservación cada vez están más interesados en el tema de cómo la extinción poda al árbol de la vida. Esta cuestión es particularmente importante para los peces de agua dulce de Australia ya que existe una mezcla amplia de ∼300 especies antiguas y recientes, muchas de las cuales se encuentran seriamente amenazadas. Usamos una filogenia completa a nivel de especie de los peces de agua dulce de Australia para examinar la no aleatoriedad filogenética del riesgo de extinción. Computamos la pérdida potencial de la diversidad filogenética mediante la simulación de la extinción en todo el árbol bajo un patrón ponderado con base en la categoría de riesgo de extinción de la Unión Internacional para la Conservación de la Naturaleza y la comparamos con la pérdida proyectada de diversidad bajo un modelo aleatorio nulo de la extinción. Por último, calculamos los puntajes EDGE (peculiaridad evolutiva, riesgo global) para 251 especies de agua dulce y 60 especies de agua salobre y recopilamos una lista de especies de alta prioridad para las acciones de conservación basada en su riesgo de extinción y su singularidad evolutiva. El riesgo de extinción no fue aleatorio y estuvo agrupado tanto en cunas de diversidad (clados ricos en especies con diversificación reciente, como Galaxiidae y Percichthyidae) como en museos (grupos más viejos con pocas especies, como los condrictios de agua dulce). La extinción agrupada no trajo grandes diferencias para la pérdida promedio esperada de la diversidad filogenética. Sin embargo, el límite superior de la pérdida fue más alto bajo un modelo selectivo de extinción, particularmente cuando los conteos de especies perdidas fueron bajos. Por lo tanto, la pérdida de especies en grave peligro de extinción disminuiría el árbol de la vida más que un modelo nulo de extinción distribuida aleatoriamente. Las especies de mayor prioridad incluyeron tanto a las más conocidas y carismáticas, como el pez pulmonado de Queensland (Neoceratodus forsteri), los tiburones de río y los peces sierra de agua dulce, como a las especies menos conocidas que reciben menos atención del público, incluyendo al pez salamandra (Lepidogalaxias salamandroides), los gobios de las cuevas y a muchos galaxiidos, peces arcoiris y percas pigmeas.

The evolution of egg colour and patterning in Australian songbirds.

To understand why avian eggs are so variable in colour and patterning, we investigated the characteristics of extant bird species that provide insight into the evolutionary transitions that occurred during the early radiation of the songbirds. We quantified egg colour and patterning from museum collections of 269 species of Australian passerine and collated it to nest type data (cup- or dome-nesting species). Using phylogenetically reconstructed trait data, we showed that the ancestral passerine egg was likely to be white, and to have been laid inside a domed nest. Egg colouration and nest type were both phylogenetically clustered, and there was evidence of correlated evolution between the two traits. As nests transitioned from domes to cups, there was an increase in the range of egg colours observed, presumably as a response to additional stressors. Finally, we found that egg colour changes occurred more than twice as frequently in cup-nesting species than in dome-nesting species. This suggests that colour may be an adaptive trait that compensates for the loss of the protective nest roof in cup-nesting species.

A fossil-calibrated time-tree of all Australian freshwater fishes.

Australian freshwater fishes are a relatively species-poor assemblage, mostly comprising groups derived from older repeated freshwater invasions by marine ancestors, plus a small number of Gondwanan lineages. These taxa are both highly endemic and highly threatened, but a comprehensive phylogeny for Australian freshwater fishes is lacking. This has hampered efforts to study their phylogenetic diversity, distribution of extinction risk, speciation rates, and rates of trait evolution. Here, we present a comprehensive dated phylogeny of 412 Australian fishes. We include all formally recognized freshwater species plus a number of genetically distinct subpopulations, species awaiting formal description, and predominantly brackish-water species that sometimes enter fresh water. The phylogeny was inferred using maximum-likelihood analysis of a multilocus data set comprising six mitochondrial and three nuclear genes from 326 taxa. We inferred the evolutionary timescale using penalized likelihood, then used a statistical approach to add 86 taxa for which no molecular data were available. The time-tree inferred in our study will provide a useful resource for macroecological studies of Australian freshwater fishes by enabling corrections for phylogenetic non-independence in evolutionary and ecological comparative analyses.