Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea.

Accurate identification of evolutionarily significant units of rare and threatened organisms provides a foundation for effective management and conservation. Up to seven subspecies of the critically endangered Yellow-crested Cockatoo (Cacatua sulphurea) have been described, four of which were commonly recognised pre-2014. In the absence of genotypic data, C.

Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data.

Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity.

Parallel evolution despite low genetic diversity in three-spined sticklebacks.

When populations repeatedly adapt to similar environments they can evolve similar phenotypes based on shared genetic mechanisms (parallel evolution). The likelihood of parallel evolution is affected by demographic history, as it depends on the standing genetic variation of the source population. The three-spined stickleback () repeatedly colonized and adapted to brackish and freshwater.

An evolutionarily distinct ringed seal in the Ilulissat Icefjord.

The Earth's polar regions are low rates of inter- and intraspecific diversification. An extreme mammalian example is the Arctic ringed seal (Pusa hispida hispida), which is assumed to be panmictic across its circumpolar Arctic range. Yet, local Inuit communities in Greenland and Canada recognize several regional variants; a finding supported by scientific studies of body size variation.

Condition- and context-dependent variation of sexual dimorphism across lizard populations at different spatial scales.

The evolution of sexual dimorphism (SD) is driven by intricate interplays between sexual and natural selection. When it comes to SD variation within populations, however, environmental factors play a major role. Sexually selected traits are expected to be strongly dependent on individual body condition, which is influenced by the local environment that individuals experience.

Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation.

The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after.

Cast away in the Adriatic: Low degree of parallel genetic differentiation in three-spined sticklebacks.

The three-spined stickleback (Gasterosteus aculeatus) has repeatedly and independently adapted to freshwater habitats from standing genetic variation (SGV) following colonization from the sea. However, in the Mediterranean Sea G. aculeatus is believed to have gone extinct, and thus the spread of locally adapted alleles between different freshwater populations via the sea since then has been highly unlikely.

Population Structure Limits Parallel Evolution in Sticklebacks.

Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e.

Biases in Demographic Modeling Affect Our Understanding of Recent Divergence.

Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (Ne) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice.

The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae).

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China.

On the causes of geographically heterogeneous parallel evolution in sticklebacks.

The three-spined stickleback (Gasterosteus aculeatus) is an important model system for the study of parallel evolution in the wild, having repeatedly colonized and adapted to freshwater from the sea throughout the northern hemisphere. Previous studies identified numerous genomic regions showing consistent genetic differentiation between freshwater and marine ecotypes but these had typically limited geographic sampling and mostly focused on the Eastern Pacific region. We analysed population genomic data from global samples of the three-spined stickleback marine and freshwater ecotypes to detect loci involved in parallel evolution at different geographic scales.

The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus.

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs).

Estimating uncertainty in divergence times among three-spined stickleback clades using the multispecies coalescent.

Incomplete lineage sorting (ILS) can lead to biased divergence time estimates. To explore if and how ILS has influenced the results of a recent worldwide phylogeny of three-spined sticklebacks (Gasterosteus aculeatus), we estimated divergence times among major clades by applying both a concatenation approach and the multispecies coalescent (MSC) model to single-nucleotide polymorphisms. To further test the influence of different calibration strategies, we applied different calibrations to the root and to younger nodes in addition to the ones used in the previous study.

A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius.

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data.

Cryptic temporal changes in stock composition explain the decline of a flounder ( spp.) assemblage.

Unobserved diversity, such as undetected genetic structure or the presence of cryptic species, is of concern for the conservation and management of global biodiversity in the face of threatening anthropogenic processes. For instance, unobserved diversity can lead to overestimation of maximum sustainable yields and therefore to overharvesting of the more vulnerable stock components within unrecognized mixed-stock fisheries. We used DNA from archival (otolith) samples to reconstruct the temporal (1976-2011) genetic makeup of two mixed-stock flounder fisheries in the Åland Sea (AS) and the Gulf of Finland (GoF).

Worldwide phylogeny of three-spined sticklebacks.

Stickleback fishes in the family Gasterosteidae have become model organisms in ecology and evolutionary biology. However, even in the case of the most widely studied species in this family - the three-spined stickleback (Gasterosteus aculeatus) - the worldwide phylogenetic relationships and colonization history of the different populations and lineages remain poorly resolved. Using a large collection of samples covering most parts of the species distribution range, we subjected thousands of single nucleotide polymorphisms to coalescent analyses in order to reconstruct a robust worldwide phylogeny of extant G.

Extraordinarily rapid speciation in a marine fish.

Divergent selection may initiate ecological speciation extremely rapidly. How often and at what pace ecological speciation proceeds to yield strong reproductive isolation is more uncertain. Here, we document a case of extraordinarily rapid speciation associated with ecological selection in the postglacial Baltic Sea.

Effects of temperature, salinity and composition of the dinoflagellate assemblage on the growth of Gambierdiscus carpenteri isolated from the Great Barrier Reef.

Increases in reported incidence of ciguatera fish poisoning (hereafter ciguatera) have been linked to warmer sea temperatures that are known to trigger coral bleaching events. The drivers that trigger blooms of ciguatera-causing dinoflagellates on the Great Barrier Reef (GBR) are poorly understood. This study investigated the effects of increased temperatures and lowered salinities, often associated with environmental disturbance events, on the population growth of two strains of the potentially ciguatera-causing dinoflagellate, Gambierdiscus carpenteri (NQAIF116 and NQAIF380).

Genetic structure and signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos).

With overfishing reducing the abundance of marine predators in multiple marine ecosystems, knowledge of genetic structure and local adaptation may provide valuable information to assist sustainable management. Despite recent technological advances, most studies on sharks have used small sets of neutral markers to describe their genetic structure. We used 5517 nuclear single-nucleotide polymorphisms (SNPs) and a mitochondrial DNA (mtDNA) gene to characterize patterns of genetic structure and detect signatures of selection in grey reef sharks (Carcharhinus amblyrhynchos).

Connectivity in grey reef sharks (Carcharhinus amblyrhynchos) determined using empirical and simulated genetic data.

Grey reef sharks (Carcharhinus amblyrhynchos) can be one of the numerically dominant high order predators on pristine coral reefs, yet their numbers have declined even in the highly regulated Australian Great Barrier Reef (GBR) Marine Park. Knowledge of both large scale and fine scale genetic connectivity of grey reef sharks is essential for their effective management, but no genetic data are yet available. We investigated grey reef shark genetic structure in the GBR across a 1200 km latitudinal gradient, comparing empirical data with models simulating different levels of migration.

The diversity of Coolia spp. (Dinophyceae Ostreopsidaceae) in the central great barrier reef region.

Background: Dinoflagellates are important primary producers, crucial in marine food webs. Toxic strains, however, are the main causative agents of non-bacterial seafood poisoning, a major concern for public health worldwide. Despite their importance, taxonomic uncertainty within many genera of dinoflagellates is still high.

Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae).

The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish.

Classic approach revitalizes genomics: Complete characterization of a candidate gene for thermal adaptation in two coral reef fishes.

Lactate dehydrogenase-B (ldh-b) encodes a metabolic enzyme (LDH-B) which plays an important role in maintaining aerobic performance and in thermal acclimation and/or adaptation of fish. As the first step in understanding the effect this enzyme has on the ability of tropical coral reef fishes to cope with thermal stress, we characterized both coding and non-coding regions of ldh-b in two congeneric perciformes, Plectropomus leopardus and Plectropomus laevis. Ldh-b was 4666 and 4539bp in length in P.