Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation

<p>Abstract</p> <p>Background</p> <p>Adaptive radiation, the evolution of ecological and phenotypic diversity from a common ancestor, is a central concept in evolutionary biology and characterizes the evolutionary histories of many groups of organisms. One such group is the Mustelidae, the most species-rich family within the mammalian order Carnivora, encompassing 59 species classified into 22 genera. Extant mustelids display extensive ecomorphological diversity, with different lineages having evolved into an array of adaptive zones, from fossorial badgers to semi-aquatic otters. Mustelids are also widely distributed, with multiple genera found on different continents. As with other groups that have undergone adaptive radiation, resolving the phylogenetic history of mustelids presents a number of challenges because ecomorphological convergence may potentially confound morphologically based phylogenetic inferences, and because adaptive radiations often include one or more periods of rapid cladogenesis that require a large amount of data to resolve.</p> <p>Results</p> <p>We constructed a nearly complete generic-level phylogeny of the Mustelidae using a data matrix comprising 22 gene segments (~12,000 base pairs) analyzed with maximum parsimony, maximum likelihood and Bayesian inference methods. We show that mustelids are consistently resolved with high nodal support into four major clades and three monotypic lineages. Using Bayesian dating techniques, we provide evidence that mustelids underwent two bursts of diversification that coincide with major paleoenvironmental and biotic changes that occurred during the Neogene and correspond with similar bursts of cladogenesis in other vertebrate groups. Biogeographical analyses indicate that most of the extant diversity of mustelids originated in Eurasia and mustelids have colonized Africa, North America and South America on multiple occasions.</p> <p>Conclusion</p> <p>Combined with information from the fossil record, our phylogenetic and dating analyses suggest that mustelid diversification may have been spurred by a combination of faunal turnover events and diversification at lower trophic levels, ultimately caused by climatically driven environmental changes. Our biogeographic analyses show Eurasia as the center of origin of mustelid diversity and that mustelids in Africa, North America and South America have been assembled over time largely via dispersal, which has important implications for understanding the ecology of mustelid communities.</p

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata).

Differences in color vision can play a key role in an organism's ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this variation results from variation in color vision caused by plasticity in opsin expression. Specifically, we asked about the role of dietary carotenoid availability, because carotenoids (1) are the precursors for vitamin A, which is essential for the creation of photopigments and (2) have been linked to variation in female mate choice. We raised guppies on different carotenoid-level diets and measured opsin expression. Guppies raised on high-carotenoid diets expressed higher levels of long wavelength sensitive opsin (LWS) opsins than those raised on lower levels of carotenoids. These results suggest that dietary effects on opsin expression represent a previously unaccounted for mechanism by which ecological differences across populations could lead to mate choice differences

Data from: Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata)

Differences in color vision can play a key role in an organism’s ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this variation results from variation in color vision caused by plasticity in opsin expression. Specifically, we asked about the role of dietary carotenoid availability, because carotenoids (1) are the precursors for vitamin A, which is essential for the creation of photopigments and (2) have been linked to variation in female mate choice. We raised guppies on different carotenoid-level diets and measured opsin expression. Guppies raised on high-carotenoid diets expressed higher levels of long wavelength sensitive opsin (LWS) opsins than those raised on lower levels of carotenoids. These results suggest that dietary effects on opsin expression represent a previously unaccounted for mechanism by which ecological differences across populations could lead to mate choice differences

Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata).

Differences in color vision can play a key role in an organism's ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this variation results from variation in color vision caused by plasticity in opsin expression. Specifically, we asked about the role of dietary carotenoid availability, because carotenoids (1) are the precursors for vitamin A, which is essential for the creation of photopigments and (2) have been linked to variation in female mate choice. We raised guppies on different carotenoid-level diets and measured opsin expression. Guppies raised on high-carotenoid diets expressed higher levels of long wavelength sensitive opsin (LWS) opsins than those raised on lower levels of carotenoids. These results suggest that dietary effects on opsin expression represent a previously unaccounted for mechanism by which ecological differences across populations could lead to mate choice differences

R File of Stats

This is the R file of the statistics run

Opsin Expression Relative to Housekeeping

Expression level for each opsin relative to a housekeeping gene

Proportional Opsin Expression

Expression of each opsin as a proportion of total opsin expression. (See manuscript for justification)

Mišljenja i komentari: Čovjek od mramora

H America (blue) or South America (green). Proportional likelihood values and associated significance levels for ancestral area reconstructions are presented in Additional file . Taxa are colored according to their coding states (see legend). * = occurs in Eurasia and North America; + = occurs in North America and South America; # = occurs in Africa and Eurasia.<p><b>Copyright information:</b></p><p>Taken from "Multigene phylogeny of the Mustelidae: Resolving relationships, tempo and biogeographic history of a mammalian adaptive radiation"</p><p>http://www.biomedcentral.com/1741-7007/6/10</p><p>BMC Biology 2008;6():10-10.</p><p>Published online 14 Feb 2008</p><p>PMCID:PMC2276185.</p><p></p