Reindeer, caribou, genetics and global warming

Reindeer (Rangifer tarandus tarandus) were domesticated probably around 20,000 years ago in northern Europe and Asia. They are still kept by many herders in the Eurasian Arctic, who derive their livelihood from their animals. Reindeer from Siberia were imported into Alaska in the late 19th century in an attempt to provide income for indigenous people. In the 1930s an estimated 600,000 reindeer existed in Alaska, but that number is now down to about 20,000. It seems that most people didn’t quite see the point of managing reindeer when all they had to do was go out and hunt its wild cousin, the caribou (Rangifer tarandus granti). One of the unforeseen consequences of this endeavor has been the migration of reindeer into caribou herds and until recently it was unknown to what extent this influx has had an impact on the genetic diversity of caribou. A recent analysis of microsatellite DNA in caribou and reindeer in Alaska, however, shows that very little genetic introgression seems to have taken place into either species and the authors think the reason could be that hybrid offspring may have a lower chance of survival. It is interesting to note that their study also indicates that the Alaskan/Russian reindeer and the Alaskan and Canadian caribou are much more closely related to each other than either is to the Scandinavian reindeer.

Caribou, which can be found throughout Alaska and the Canadian territories, migrate often in large herds between their summer and winter pastures. The porcupine herd, for example, numbers in excess of 100,000 animals and covers a distance of over 2000 km on its yearly route from the Yukon to the calving grounds on the Alaskan Arctic coast (the very same area the US government is trying to open up for oil exploration).  Many native people in Canada and Alaska still depend on these animals for their survival and they are becoming concerned that increasing human development and global warming may either affect the size of caribou herds or change their migration patterns.

From Michael Kubisch

Domestication

Michael’s post on water buffalo genetic diversity and domestication reminded me that I was intending to point you all in the direction of Dienekes’ Anthropology Blog. Although Dienekes mainly blogs about the genetic diversity and evolution of humans, he does occasionally link to papers on animal domestication and related issues. He has an RSS feed, which makes it easy to monitor his blog. In the past couple of years he has pointed to interesting papers on:

Incidentally, a great paper reviewing the use of genetics and archaeology to document domestication came out last year and you can see the abstract here. Now, what’s really needed is for someone to bring together the human, livestock and crop genetic data.

Water buffalo diversity

Michael Kubisch is a geneticist and reproductive physiologist working at the Tulane National Primate Research Center in the New Orleans area. He’s sent us his take on a recent paper on the genetics of the water buffalo. We really welcome this kind of contribution from our readers. Keep ’em coming! Here’s what Michael has to say:

Results of an interesting study by Chinese researchers have just been published, describing an extensive analysis of the genetics of Chinese swamp water buffalo (Bubalus bubalis). The Chinese swamp-type buffalo differs from the Indian river-type buffalo by the fact that it has 48 chromosomes compared to the 50 found in the latter. There is a third subspecies, the wild water buffalo, which may still exist in Southeast Asia, although its population size and genetic status are unknown and the animal is listed on the IUCN red list as being threatened. Based on analysis of mitochondrial DNA (which is solely inherited from one’s mother and consequently ideal for tracing maternal inheritance patterns), it appears that river and swamp buffalo split about 28,000 years ago with a further split in the swamp buffalo into two maternal lines taking place about 18,000 years ago. The genetic diversity varies between the two swamp buffalo matrilines in China and the authors suggest that the difference between the two lines might in part be due to the fact that occasional genetic introgression from wild swamp buffalo might have taken place into one of the lines. Interestingly, domestication of water buffalo seems to have occurred independently in India and China, most likely as a result of rice cultivation. Substantial numbers of water buffalo outside exist Asia, among other countries in Italy, where, as any cheese afficionado will know, their milk is used for the production of mozzarella.

Mapping underutilized genomes

It seems you can hardly open a newspaper these days — or open a news website — without reading that someone somewhere has mapped yet another genome, whether human, Neanderthal, sheep, mouse or bee. It hasn’t received any press coverage at all, but the taro (Colocasia esculenta) genome has now been added to the list. CIRAD scientists working in Vanuatu, in the South Pacific, and others just announced this at the recent meeting of the International Society for Tropical Root Crops held in Kerala, India.

One thing to note is that these are not all really genome mapping projects. Despite the many headlines to that effect, scientists are not mapping the Neanderthal genome. What they’re doing is sequencing it — or a small bit of it. There is a difference.

Sequencing means determining the (correct!) order of all the DNA bases — the letters of the genetic code — of an organism. Besides some very fancy hardware and software, you need the DNA of just one individual to do this. Mapping is both rather less and rather more. Less, because it only aims to determine the relative location of some major landmarks of the genome. That is, not the order of all the letters in the book of life, but rather the relative positions of the pages where some choice quotations can be found. More, because some of those genomic landmarks may be close to genes associated with predisposition to a disease or some other interesting trait. To find that out you need DNA from whole families, or populations, rather than a single individual — in the case of taro, the family was all the progeny from a couple of crosses between local ni-Vanuatu varieties. You trace the inheritance of the trait you’re interested in together with that of specific “markers” (any observable variation in the DNA sequence), and, hey presto, if you’re lucky you have a much more readily documented proxy for the trait.

With the new genome map, we now have genetic proxies for things like the yield and the dimensions of the underground corm of taro. This edible aroid is an important staple in Oceania and parts of South and South East Asia, Africa and the Caribbean, but there are few breeding programmes around the world, which is why it often ends up on lists of “neglected and underutilized species.” This map should make it easier to screen the hundreds of seeds that can result from crossing two varieties and select only the best individuals for further testing (this is called marker-assisted selection). It should therefore stimulate people to set up taro genetic improvement programmes.

These are much needed. Mainly vegetatively propagated by farmers, taro is genetically fairly uniform in many places, making it susceptible to pests and diseases. It was almost wiped out in the South Pacific country of Samoa in the mid-1990s by taro leaf blight, a fungal disease. It has recovered at least in part because a regional project (called TaroGen) was set up by Pacific countries with support from Australia to breed — in collaboration with farmers — and disseminate resistant varieties.

Biotechnology means GMOs to many people, but this is a case where biotechnology is facilitating conventional breeding — nothing to do with genetic engineering. It may not have made the news like other mapping projects, but the new genome map means taro breeding should prove a little bit easier in the future.

Seed Sources

Fork and Bottle, a “guide to eating, drinking and living”, recently updated its page of seed sources. The page offers personal experiences and recommendations from two dedicated growers in the USA.

I have added the link as an update to our page of Seed Exchanges; I’d be happy to add any others you send.