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Sun Mar 5, 2017, 02:59 PM

The Role of Declining Genetic Diversity in the Final Extinction of the Last Wooly Mammoths.

Although wooly mammoths went extinct on continental landmasses about 10,000 years ago, it appears that an isolated colony of these animals survived until relatively recent times - about 3,700 - years ago on Wrangle Island, which is off the coast of Siberia.

An interesting article in the open source journal PLOS Genetics details role that declining genetic diversity played in the ultimate extinction of this colony by comparison of the genetic map of a preserved specimen dating from around the time of the extinction with that of another preserved specimen from about 45,000 years ago.

The article is here: Excess of genomic defects in a woolly mammoth on Wrangel island (Rebekah L. Rogers, Montgomery Slatkin, PLoS Genet 13(3): e1006601.)

Some text from the full papers introduction:

Woolly mammoths (Mammuthus primigenius) were among the most populous large herbivoresin North America, Siberia, and Beringia during the Pleistocene and early Holocene [1].However warming climates and human predation led to extinction on the mainland roughly10,000 years ago [2]. Lone isolated island populations persisted out of human reach untilroughly 3,700 years ago when the species finally went extinct [3]. Recently, two complete high quality high-coverage genomes were produced for two woolly mammoths [4]. One specimens derived from the Siberian mainland at Oimyakon, dated to 45,000 years ago [4]. This sample comes from a time when mammoth populations were plentiful, with estimated effective population size of Ne = 13,000 individuals [4]. The second specimen is from Wrangel Island off the north Siberian coast [4]. This sample from 4,300 years ago represents one of the last known mammoth specimens. This individual comes from a small population estimated to contain roughly 300 individuals [4].

These two specimens offer the rare chance to explore the ways the genome responds to pre-extinction population dynamics. Nearly neutral theories of genome evolution predict that small population sizes will lead ton accumulation of detrimental variation in the genome [5]. Such explanations have previously been invoked to explain genome content and genome size differences across multiple species [6].


The article is, again, open source, so there is no need to quote anything more to the interested reader.

It is well known however that this issue is involved in the survival of many nearly extinct species that we haven't killed off yet. The most famous example is the Cheetah, which apparently survived a near extinction event about 12,000 years ago and is facing another such event presently.

A recent paper on the genetic diversity issues in Cheetahs and the poor quality of their sperm is here:

Continued decline in genetic diversity among wild cheetahs (Acinonyx jubatus) without further loss of semen quality (Terrell et al. Biological Conservation Volume 200, August 2016, Pages 192199)

An excerpt from the introduction to that paper, which may not be open sourced follows:

1. Introduction

Inbreeding is linked to negative fitness consequences across a diversity of mammal, bird, fish, reptile, amphibian, insect, and plant species in the wild (Allentoft and O'Brien, 2010, Frankham et al., 2002 and Keller and Waller, 2002). These negative effects are most profound in traits closely linked to reproductive success, including seminal quality and fecundity (Frankham et al., 2002). Species-level genetic diversity is correlated with semen quality among 20 mammals (Fitzpatrick and Evans, 2009), and analogous correlations have been documented at the individual level (i.e., within species) in the Iberian lynx (Lynx pardinus; ( Ruiz-Lopez et al., 2012), Mexican gray wolf (Canis lupus baileyi; ( Asa et al., 2007)), and Mohor gazelle (Gazella dama mhorr; ( Ruiz-Lopez et al., 2012)). Within Felidae, the link between genetic diversity and male reproductive traits is well established. A single generation of inbreeding reduces semen quality in the domestic cat (Felis catus; ( Neubauer et al., 2004)) and leopard cat (Prionailurus bengalensis; ( Wildt, 1994)), while free-ranging inbred lions (Panthera leo) produce higher proportions of malformed spermatozoa and have fewer seminiferous tubules compared to non-inbred counterparts ( Wildt et al., 1987). Consistent with this relationship, semen quality is relatively high among felid species with greater genetic diversity, including the ocelot (Leopardus pardalis), jaguar (Panthera onca), and African leopard (Panthera pardus pardus; ( Pukazhenthi et al., 2006b and Swanson et al., 1995)).

Although some natural populations have persisted over long periods with limited genetic diversity (Reed, 2010), most studies support a general relationship between inbreeding and population decline/extirpation (Keller and Waller, 2002). In particular, the Florida panther (Puma concolor coryi) provides a compelling example of the consequences of extreme inbreeding. Compared to other puma subspecies, the Florida panther is highly inbred, with a population size of < 100 individuals ( Johnson et al., 2010 and Roelke et al., 1993). Males experience severe reproductive defects, including an increased incidence of cryptorchidism, drastically reduced semen and testicular volumes, impaired sperm motility, and very high percentages (> 90%) of structurally-abnormal spermatozoa ( Mansfield and Land, 2002 and Roelke et al., 1993), which are known to be incapable of fertilization (Howard et al., 1993). Conversely, introgression of DNA from eight Texas pumas (Puma concolor stanleyana) increased heterozygosity in the Florida population and resulted in fewer reproductive defects and greater offspring survival ( Johnson et al., 2010). Aside from the Florida panther, the cheetah (Acinonyx jubatus) is perhaps the most thoroughly-studied wildlife model of inbreeding depression. The cheetah's lack of genetic diversity was originally detected by allozyme analysis and the ability of unrelated conspecifics to accept reciprocal skin grafts ( O'Brien et al., 1983


This planet is now experiencing a mass extinction comparable with say, a large meteor strike, since like a meteor strike, it is experienced a sudden (on a geological time scale) climate change event. We may think that by preserving a few individuals, we may - as the biblical literalist fools have it - have a Noah's Ark kind of situation. But we do not. Diversity is important, not only in making a truly great country - our greatness is about to go extinct - but in making a truly great population.

There are many nearly extinct great species for whom this is an issue, including but regrettably not even close to limited to, African elephants, Tasmanian devils, Siberian tigers, California Condors, Rhinos etc, and in the plant world, the species that most breaks my heart, the American Chestnut. (The chestnut is already effectively extinct, but genetically modified - by cross breeding - examples are currently being bred by the American Chestnut Society)

The scars on the strength of these species, without deliberate genetic modification, will not go away, and their long term survival is in question, even if we manage to preserve a few individual samples.

Enjoy the rest of the weekend.


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