C. Scott Baker

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.

Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.

Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting.

Genetic diversity is the foundation for all biological diversity; the persistence and evolutionary potential of species depend on it. World leaders have agreed on the conservation of genetic diversity as an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, actions to protect genetic diversity are largely lacking. With only months left to the 2010-biodiversity target, when the 191 parties to the CBD have agreed on achieving a significant reduction of the rate of biodiversity loss, gene-level diversity is still not being monitored, and indicators and thresholds that can be used to devise strategies to conserve this important component of biodiversity are missing. Immediate action is needed to ensure that genetic diversity is not neglected in conservation targets beyond 2010.\nThe risks associated with depletion of genetic diversity were recognized in classic publications 4 decades ago (Frankel 1970, 1974), and this message has been repeatedly stressed ever since (e.g., Schonewald-Cox 1983; Ryman & Utter 1987; Frankham 1995; Allendorf & Ryman 2002; Hughes et al. 2008). In that time, a body of theory (Lynch & Lande 1993; Lande 1995; Lynch et al. 1995) and empirical work has emerged that demonstrates how populations and even species can collapse due to loss of genetic diversity (e.g., Newman & Pilson 1997; Briskie & Mackintosh 2004; Frankham 2005). Evidence supporting the importance of maintaining genetic variation to sustain species and ecosystems continues to accumulate (Wimp et al. 2004; Crutsinger et al. 2006; Whitham et al. 2006).\nGene-level biodiversity is recognized in the CBD (www.cbd.int) as one of three levels of diversity— ecosystems, species, and genes—that are to be conserved and sustainably used. Since its adoption in 1992, this convention has become the most important international political instrument for halting biodiversity loss. At present, 192 nations are parties to the CBD, representing every nation in the world except for Andorra, the Holy See (the Vatican), Somalia (party from mid December 2009), and the United States. Integral to the CBD is the task of “monitor[ing], through sampling and other techniques, the components of biological diversity” to “identify processes and categories of activities which have or are likely to have significant adverse impacts on the conservation and sustainable use of biological diversity, and monitor their effects.”\nIn 2002 parties to the CBD committed themselves to reduce significantly by 2010 the current rates of biodiversity loss at global, regional, and national levels as a “contribution to poverty alleviation and to the benefit of all life on Earth.” This 2010 biodiversity target was subsequently endorsed by the World Summit on Sustainable Development and the United Nations General Assembly and incorporated as a new target under the UN Millennium Development Goals (http://www.un.org/millenniumgoals/).\nTo evaluate progress toward the 2010 biodiversity target for genetic variation it is necessary to assess and monitor this critical level of diversity. The CBD is not a mandatory instrument; it is the responsibility of each country to develop and implement a National Biodiversity Strategy and Action Plan (NBSAP). To assess the extent to which genetic diversity is currently recognized in national biodiversity policy programs, we used information available at the convention’s website to review NBSAPs of a subset of countries party to the CBD (http://www.cbd.int; subheading: Countries; assessed January–March 2009). Our aim was to investigate whether individual parties state in their strategies and action plans that genetic variation of wild animals and plants is to be conserved in their country and whether they explicitly recognize the need for developing monitoring programs for this diversity.\nFor our analysis we selected every 10th country ranked according to its gross national product (GNP; http:// www.studentsoftheworld.info/infopays/rank/PN B2.html). If a country was not part of the CBD or not a sovereign nation, or if a document was missing, not searchable, or not in English, we chose the next country on the list. We reviewed 24 NBSAPs. Of these, 67% (16 countries) state that genetic variation should be conserved. Nevertheless, 38% (six) of these plans focus only on the genetic diversity of domesticated populations compared with 62% (10) that also recognize the genetic diversity of wild animals and plants as a conservation concern. Although most (90%; 21 countries) of the reviewed NBSAPs state that monitoring of biodiversity should be carried out, only 21% (five) explicitly acknowledge the need for developing means for monitoring diversity at the genetic level. These five countries all grouped in the upper 20% of the GNP ranking (i.e., larger countries with strong economic performance). In contrast, countries sharing the general goal of conserving genetic diversity represent the full spectrum of GNP ranks.