Rapid evolution of recombination landscapes during the divergence of cichlid ecotypes in Lake Masoko.

Variation of recombination rate along the genome is of crucial importance to rapid adaptation and organismal diversification. Many unknowns remain regarding how and why recombination landscapes evolve in nature. Here, we reconstruct recombination maps based on linkage disequilibrium and use subsampling and simulations to derive a new measure of recombination landscape evolution: the Population Recombination Divergence Index (PRDI).

Haemoglobin Gene Repertoire in Teleost and Cichlid Fishes Shaped by Gene Duplications and Genome Rearrangements.

Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high-quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids).

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past.

The genetics of niche-specific behavioral tendencies in an adaptive radiation of cichlid fishes.

Behavior is critical for animal survival and reproduction, and possibly for diversification and evolutionary radiation. However, the genetics behind adaptive variation in behavior are poorly understood. In this work, we examined a fundamental and widespread behavioral trait, exploratory behavior, in one of the largest adaptive radiations on Earth, the cichlid fishes of Lake Tanganyika.

Genome-wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides.

Little is known about when and how planktonic species arise and persist in the open ocean without apparent dispersal barriers. Pteropods are planktonic snails with thin shells susceptible to dissolution that are used as bio-indicators of ocean acidification. However, distinct evolutionary units respond to acidification differently, and defining species boundaries is therefore crucial for predicting the impact of changing ocean conditions.

The history and organization of the Workshop on Population and Speciation Genomics.

With the advent of high-throughput genome sequencing, bioinformatics training has become essential for research in evolutionary biology and related fields. However, individual research groups are often not in the position to teach students about the most up-to-date methodology in the field. To fill this gap, extended bioinformatics courses have been developed by various institutions and provide intense training over the course of two or more weeks.

Drivers and dynamics of a massive adaptive radiation in cichlid fishes.

Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains unclear in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika.

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes.

Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution.

Movement of transposable elements contributes to cichlid diversity.

African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates.

Dsuite - Fast D-statistics and related admixture evidence from VCF files.

Patterson's D, also known as the ABBA-BABA statistic, and related statistics such as the f -ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only small subsets of the available statistics, and are impractical to evaluate all gene flow hypotheses across data sets with many populations or species due to computational inefficiencies. Here, we present a new software package Dsuite, an efficient implementation allowing genome scale calculations of the D and f -ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file.

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.

RADpainter and fineRADstructure: Population Inference from RADseq Data.

Powerful approaches to inferring recent or current population structure based on nearest neighbor haplotype "coancestry" have so far been inaccessible to users without high quality genome-wide haplotype data. With a boom in nonmodel organism genomics, there is a pressing need to bring these methods to communities without access to such data. Here, we present RADpainter, a new program designed to infer the coancestry matrix from restriction-site-associated DNA sequencing (RADseq) data.

Feasibility of using the National Marine Mammal Tissue Bank for retrospective exploratory studies of perfluorinated alkyl acids.

Perfluorinated alkyl acids (PFAAs) have been used for 50+ years in materials such as stain-resistant treatments for paper and clothing, lubricants, and foam fire extinguishers. PFAAs are characterized by a fully fluorinated alkyl chain with a terminal acid group. Their long half-lives and ubiquitous environmental distribution create considerable concern for wildlife and human exposure.

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology.

The genomic substrate for adaptive radiation in African cichlid fish.

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.

3D CT spine data segmentation and analysis of vertebrae bone lesions.

A method is presented aiming at detecting and classifying bone lesions in 3D CT data of human spine, via Bayesian approach utilizing Markov random fields. A developed algorithm for necessary segmentation of individual possibly heavily distorted vertebrae based on 3D intensity modeling of vertebra types is presented as well.

Novel registration-based framework for CT angiography in lower legs.

Proper subtraction and visualization of contrast-enhanced blood vessels in lower extremities using computed tomography angiography (CTA) is based on precise masking of all non-contrasted structures in the area, and it is the main prerequisite for correct diagnosis and decision on treatment for peripheral arterial occlusive disease (PAOD). Because of possible motion of patients during the CTA examination, precise elimination of non-contrasted tissues, including bones, calcifications, and soft tissue, is still very challenging for lower legs, that is, from knees to toes. We propose novel registration-based framework for detection and correction of the motion in lower legs, which typically occurs between and during CTA pre-contrast and post-contrast acquisitions.

Registration of FA and T1-weighted MRI data of healthy human brain based on template matching and normalized cross-correlation.

In this work, we propose a new approach for three-dimensional registration of MR fractional anisotropy images with T1-weighted anatomy images of human brain. From the clinical point of view, this accurate coregistration allows precise detection of nerve fibers that is essential in neuroscience. A template matching algorithm combined with normalized cross-correlation was used for this registration task.