Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes

Hox genes are key regulators of anterior-posterior axis patterning and have a major role in hindbrain development. The zebrafish Hox4 paralogs have strong overlapping activities in hindbrain rhombomeres 7 and 8, in the spinal cord and in the pharyngeal arches. With the aim to predict enhancers that act on the hoxa4a, hoxb4a, hoxc4a and hoxd4a genes, we used sequence conservation around the Hox4 genes to analyze all fish:human conserved non-coding sequences by reporter assays in stable zebrafish transgenesis. Thirty-four elements were functionally tested in GFP reporter gene constructs and more than 100 F1 lines were analyzed to establish a correlation between sequence conservation and cis-regulatory function, constituting a catalog of Hox4 CNEs. Sixteen tissue-specific enhancers could be identified. Multiple alignments of the CNEs revealed paralogous cis-regulatory sequences, however, the CNE sequence similarities were found not to correlate with tissue specificity. To identify ancestral enhancers that direct Hox4 gene activity, genome sequence alignments of mammals, teleosts, horn shark and the cephalochordate amphioxus, which is the most basal extant chordate possessing a single prototypical Hox cluster, were performed. Three elements were identified and two of them exhibited regulatory activity in transgenic zebrafish, however revealing no specificity. Our data show that the approach to identify cis-regulatory sequences by genome sequence alignments and subsequent testing in zebrafish transgenesis can be used to define enhancers within the Hox clusters and that these have significantly diverged in their function during evolution.     

Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

The origin of cultivated tree peonies, known as the ‘king of flowers'' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.     

Contractual National Parks and the Makuleke Community

Contractual national parks in South Africa are established on land owned either by the state or by a group of private individuals, but managed by South African National Parks (SANP) according to the terms of a joint management agreement drawn up by a joint management committee consisting of representatives from SANP and the landowners. Since majority rule in 1994, contractual national parks have been seen as a model through which the country's conservation as well as development objectives can be met, particularly where landowners are previously disadvantaged communities. This study looks at the Makuleke region of Kruger National Park in order to ascertain how successful the contractual national park model is in meeting conservation, social, and economic objectives for the area.     

Vicariance and endemism in a Neotropical savanna hotspot: distribution patterns of Cerrado squamate reptiles

Aim To test predictions of the vicariance model, to define basic biogeographical units for Cerrado squamates, and to discuss previous biogeographical hypotheses. Location Cerrado; South American savannas south of the Amazon, extending across central Brazil, with marginal areas in Bolivia and Paraguay and isolated relictual enclaves in adjacent regions. Methods We compiled species occurrence records via field sampling and revision of museum specimens and taxonomic literature. All species were mapped according to georeferenced locality records, and classified as (1) endemic or non‐endemic, (2) typical of plateaus or depressions, and (3) typical of open or forested habitats. We tested predictions of the vicariance model using biotic element analysis, searching for non‐random clusters of species ranges. Spatial congruence of biotic elements was compared with putative areas of endemism revealed by sympatric restricted‐range species. Effects of topographical and vegetational mosaics on distribution patterns were studied according to species composition in biotic elements and areas of endemism. Results We recorded 267 Cerrado squamates, of which 103 (39%) are endemics, including 20 amphisbaenians (61% endemism), 32 lizards (42%) and 51 snakes (32%). Distribution patterns corroborated predictions of the vicariance model, revealing groups of species with significantly clustered ranges. An analysis of endemic species recovered seven biotic elements, corroborating results including non‐endemics. Sympatric restricted‐range taxa delimited 10 putative areas of endemism, largely coincident with core areas of biotic elements detected with endemic taxa. Distribution patterns were associated with major topographical and vegetational divisions of the Cerrado. Endemism prevailed in open, elevated plateaus, whereas faunal interchange, mostly associated with forest habitats, was more common in peripheral depressions. Main conclusions Our results indicate that vicariant speciation has strongly shaped Cerrado squamate diversity, in contrast to earlier studies emphasizing faunal interchange and low endemism in the Cerrado vertebrate fauna. Levels of squamate endemism are higher than in any other Cerrado vertebrate group. The high number of recovered endemics revealed previously undetected areas of evolutionary relevance, indicating that biogeographical patterns in the Cerrado were poorly represented in previous analyses. Although still largely undocumented, effects of vicariant speciation may be prevalent in a large fraction of Cerrado and Neotropical biodiversity.     

Allozyme variation and population structure of the very narrow endemic Seseli farrenyi (Apiaceae)

Analyses have been made of allozyme variation of the narrow endemic species Seseli farrenyi Molero & J. Pujadas (Apiaceae), which has only three known populations in Catalonia with a total of around 2000 individuals. All three populations were sampled and subjected to starch gel electrophoresis. Nine enzymes were resolved and 14 loci were interpreted. We detected high values of polymorphism ( P = 83.3%, A = 3.0, H _e = 0.297), far exceeding those expected for endemic species ( P = 26.3%, A = 1.39, H _e = 0.063). Genetic diversity was greater within populations than among populations, and the value of gene flow was very high ( Nm = 5.85). Most loci showed deviations from Hardy– Weinberg equilibrium, possibly due to the presence of subpopulations. The main threats to this species are human activities (tourism, fires), while natural threats are minimal due to its high genetic diversity. Finally, we propose some conservation measures which include both in situ and ex situ strategies. © 2000 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 305–314.     

Evidence of a genetically distinct population of Vrljika softmouth trout Salmo obtusirostris Heckel evolved by vicariance

Mitochondrial DNA haplotypes (control region, partial cytochrome b and ATPase6 genes) indicate a sister relationship between Vrljika and Neretva softmouth (Adriatic) trout Salmo obtusirostris . This relationship was supported by a tree of individuals based on microsatellite results [allele sharing distances ( D _AS)], which revealed three distinctive clusters, corresponding to Jadro softmouth, Neretva brown trout Salmo trutta and Neretva softmouth trout. Within the latter taxon, Vrljika trout are clearly separated from other trout. The genetic results contradict the synonymy of Jadro with Vrljika softmouth trout, as recently proposed in the Red Book of Freshwater Fish in Croatia. Vrljika softmouth trout appear to have originated from a vicariance that split a common ancestor into large (Neretva) and small (Vrljika) fragmented populations 135 000–270 000 years ago. Vrljika softmouth trout can be distinguished by an array of derived phenotypic and molecular character states. For conservation, this population should be recognized formally at the same taxonomic level as the other geographically separated populations of softmouth trout.