Cerebral palsy and genomics: an international consortium

Letter to the edito

Molecular and clinical characterization of de novo and familial cases with microduplication 3q29: guidelines for copy number variation case reporting

Microdeletions of 3q29 have previously been reported, but the postulated reciprocal microduplication has only recently been observed. Here, cases from four families, two ascertained in Toronto (Canada) and one each from Edinburgh (UK) and Leiden (Netherlands), carrying microduplications of 3q29 are presented. These families have been characterized by cytogenetic and molecular techniques, and all individuals have been further characterized with genome-wide, high density single nucleotide polymorphism (SNP) arrays run at a single centre (The Centre for Applied Genomics, Toronto). In addition to polymorphic copy-number variants (CNV), all carry duplications of 3q29 ranging in size from 1.9 to 2.4 Mb, encompassing multiple genes and defining a minimum region of overlap of about 1.6 Mb bounded by clusters of segmental duplications that is remarkably similar in location to previously reported 3q29 microdeletions. Consistent with other reports, the phenotype is variable, although developmental delay and significant ophthalmological findings were recurrent, suggesting that dosage sensitivity of genes located within 3q29 is important for eye and CNS development. We also consider CNVs found elsewhere in the genome for their contribution to the phenotype. We conclude by providing preliminary guidelines for management and anticipatory care of families with this microduplication, thereby establishing a standard for CNV reporting

Guiding conservation efforts in the Hantam–Tanqua–Roggeveld (South Africa) using diversity parameters

The Hantam–Tanqua–Roggeveld subregion falls within the Succulent Karoo and Fynbos Biomes, which are both recognised as global biodiversity hotspots that should be conserved. The objective of this study was to gather baseline biodiversity information that can be used to guide conservation efforts. A total of 40 Whittaker plots were surveyed in the subregion and the various diversity parameters calculated from the data were compared across the subregion and to available data for the Succulent Karoo and Fynbos Biomes. Species richness per 1000 m2 ranged from nine to 100 species across the subregion. Species richness for all plot sizes < 1000 m2 was significantly lower for the Tanqua Karoo than for both the Winter Rainfall Karoo and Mountain Renosterveld. The latter two areas did not differ significantly from each other with regard to species richness. Species richness was significantly higher only at the 1000 m2 scale in the Mountain Renosterveld compared to the Winter Rainfall Karoo. Evenness and Shannon and Simpson indices did not differ significantly between the Mountain Renosterveld and Winter Rainfall Karoo; however, these values were significantly higher than for the Tanqua Karoo. A principal coordinate analysis of species richness data at seven plot sizes produced three distinct clusters. One cluster represented the Tanqua Karoo, with low species richness, evenness, and Shannon and Simpson indices. Another cluster represented mostly Mountain Renosterveld vegetation, which was characterised by a high species richness, evenness, and Shannon and Simpson indices. The third cluster was formed by the remaining Mountain Renosterveld plots as well as the Winter Rainfall Karoo plots. The high species richness values found in the various vegetation units can add valuable information to the conservation planning arena by providing information on biodiversity parameters and their spatial distribution. This information can assist with conservation efforts in the Hantam, Tanqua and Roggeveld areas. Conservation implications: Conservation and development of the Hantam–Tanqua– Roggeveld subregion is hampered by a lack of information on floristic diversity. The results of the current study indicated areas of low diversity and contrasting areas of high diversity. These data can be used to guide effective conservation and management of the floristic diversity

Evaluating herbivore management outcomes and associated vegetation impacts

African savannas are characterised by temporal and spatial fluxes that are linked to fluxes in herbivore populations and vegetation structure and composition. We need to be concerned about these fluxes only when management actions cause the system to shift towards a less desired state. Large herbivores are a key attribute of African savannas and are important for tourism and biodiversity. Large protected areas such as the Kruger National Park (KNP) manage for high biodiversity as the desired state, whilst private protected areas, such as those adjacent to the KNP, generally manage for high income. Biodiversity, sustainability and economic indicators are thus required to flag thresholds of potential concern (TPCs) that may result in a particular set of objectives not being achieved. In large conservation areas such as the KNP, vegetation changes that result from herbivore impact, or lack thereof, affect biodiversity and TPCs are used to indicate unacceptable change leading to a possible loss of biodiversity; in private protected areas the loss of large herbivores is seen as an important indicator of economic loss. Therefore, the first-level indicators aim to evaluate the forage available to sustain grazers without deleteriously affecting the vegetation composition, structure and basal cover. Various approaches to monitoring for these indicators were considered and the importance of the selection of sites that are representative of the intensity of herbivore use is emphasised. The most crucial step in the adaptive management process is the feedback of information to inform management decisions and enable learning. Feedback loops tend to be more efficient where the organisation’s vision is focused on, for example, economic gain, than in larger protected areas, such as the KNP, where the vision to conserve biodiversity is broader and more complex. Conservation implications: In rangeland, optimising herbivore numbers to achieve the management objectives without causing unacceptable or irreversible change in the vegetation is challenging. This manuscript explores different avenues to evaluate herbivore impact and the outcomes of management approaches that may affect vegetation