[Paleopsych] SW: On Phylogeography

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Evolution: On Phylogeography

    The following points are made by B.C. Emerson and G.M. Hewitt (Current
    Biology 2005 15:R367):
    1) Phylogeography [1] is a young and fast-growing field that analyses
    the geographical distribution of genealogical lineages. It grew out of
    the new techniques of the 1980s that made it possible to determine DNA
    sequence variation from individuals across a species range, and hence
    to reconstruct gene genealogies. The spatial relationships of such
    genealogies may be displayed geographically and analyzed to deduce the
    evolutionary history of populations, subspecies and species. In
    particular, the technical accessibility of mitochondrial (mt)DNA
    sequences in animal species kindled and fueled this new field. Today,
    a range of DNA techniques, combined with new analytical methods and
    recent palaeoclimatic and geological studies are providing important
    insight into the distribution of genetic diversity around the globe,
    and how it evolved.
    2) Animal phylogeography is dominated by mtDNA, while plant
    phylogeography is dominated by chloroplast (cp)DNA. For both plants
    and animals, however, other DNA sequences and marker systems are
    available, and there is an increasing awareness of the rewards offered
    by these. Sex-specific markers within both plants and animals can help
    to shed light on any historical differences in demography between the
    sexes, and this has been a particularly informative approach for
    studies of human phylogeography. For deeper phylogenetic history, more
    slowly evolving sequences are needed, while for recent events, perhaps
    measured only in tens of thousands of years, more variable or more
    quickly evolving markers are required.
    3) To this end, the use of both microsatellites and amplified fragment
    length polymorphisms (AFLPs) can be extended beyond studies of
    population differentiation, and it may sometimes be possible to
    develop genealogies from these. Recent work [2] has complemented
    mitochondrial and nuclear DNA sequences with AFLPs to resolve the
    phylogeography of Lapaula crickets in the Hawaiian Islands, revealing
    the highest rate of speciation so far recorded for arthropods.
    4) Each DNA sequence has its own genealogy, and the evolutionary
    history of the organism is the sum of many different gene genealogies.
    The use of both mitochondrial and nuclear markers has demonstrated the
    potentially misleading conclusions that can be developed from a single
    marker if there has been historical hybridisation. Furthermore, the
    various methods of analysis probe different aspects of the molecular
    and spatial history. Consequently, to reconstruct a species
    phylogeographic history, one would ideally like to use a range of
    sequences, including nuclear, cytoplasmic, sex-linked, autosomal,
    conserved and neutral sequences, including examples with high and low
    mutation rates. Phylogeographic studies using genealogical data from
    several independent loci will help to provide a fuller and more
    reliable species history.[3-5]
    References (abridged):
    1. Avise, J.C. Phylogeography. (2000). Harvard University Press
    2. Mendelson, T.C. and Shaw, K.L. Sexual behavior: Rapid speciation in
    an arthropod. (2005). Nature 433, 375-376
    3. Posada, D. and Crandall, K.C. Intraspecific gene genealogies: trees
    grafting into networks. (2001). Trends Ecol. Evol. 16, 37-45
    4. Hewitt, G.M. Genetic consequences of climatic oscillations in the
    Quaternary. (2004). Philos. Trans. R. Soc. Lond. B Biol. Sci. 359,
    5. Gillespie, R.G. Community assembly through adaptive radiation in
    Hawaiian spiders. (2004). Science 303, 356-359
    Current Biology http://www.current-biology.com
    Related Material:
    Notes by ScienceWeek:
    In this context, the term "food web" refers in general to a
    description of who eats whom in an ecosystem.
    The following points are made by Peter Kareiva (Current Biology 2004
    1) The "global extinction crisis" has become a focus of concern and
    activism for conservationists [1]. We are currently in the middle of
    the sixth major extinction event in geologic history --this one almost
    entirely human induced. Current extinction rates are estimated to be
    100 to 1000 times higher than pre-human extinction rates [2]. This
    rapid loss of species has spurred researchers to examine what might be
    the consequences of losing such a large proportion of our
    2) Although ecosystems clearly would not function if all species went
    extinct, no one can really say what might be the impact of losing 80%
    of the species as opposed to only 20% of the species. In fact, even
    though we have seen many conspicuous species go extinct before our
    eyes, we know precious little about the consequences of those
    extinctions [3]. Recently, community ecologists have manipulated
    experimental communities by either removing one or two species or
    assembling communities of differing species richness [4]. These
    experiments teach us about the role of biodiversity and predation or
    competition, but have not provided a compelling picture of the
    consequences of extinction. The limitation of these targeted removals
    is their small scale and short duration.
    3) The weakness of our empirical insight regarding extinction has
    caused ecologists to rely heavily on metaphors and models. The purpose
    of these models is to anticipate what might happen if the predictions
    of massive species loss hold true [5]. Models that consider the
    consequences of extinction have tended to focus on either the
    reliability or the stability of ecosystems. Reliability models
    emphasize that the loss of species eliminates redundancy, so that at
    some point ecosystems may end up with only one or two species filling
    some critical function -- such as nitrogen sequestration or primary
    production -- leaving the ecosystems vulnerable to any catastrophe or
    stress that harms these now irreplaceable species. Stability models
    adopt a more traditional population dynamics framework, and ask how
    the loss of species alters either the ability to recover from
    disturbances, or the tendency towards fluctuations in the face of
    randomly varying environments. The general message of these many
    theoretical explorations of extinction is that species loss impairs
    both stability and reliability. But the theory is in no way complete:
    in particular, very few models consider food webs and highly
    structured trophic communities.
    References (abridged):
    1. Gibbs, W.W. (2001). On the termination of species. Sci. Am. 285,
    2. Pimm, S.L., Russell, G.J., Gittleman, J.L. and Brooks, T.M. (1995).
    The future of biodiversity. Science 269, 347-350
    3. Simberloff, D. (2003). Community and ecosystem impacts of
    single-species extinctions. In The Importance of Species. Kareiva, P.
    and Levin, S. eds. (Princeton: Princeton University Press), pp.
    4. Wootton, J.T. and Downing, A.L. (2003). Understanding the effects
    of reduced biodiversity: a comparison of two approaches. In The
    Importance of Species. Kareiva, P. and Levin, S. eds. (Princeton:
    Princeton University Press), pp. 85-103
    5. Pounds, J.A. and Puschendorf, R. (2004). Clouded futures. Nature
    427, 107-108
    Current Biology http://www.current-biology.com
    Related Material:
    The following points are made by J. Pastor and R.A. Moen (Nature 2004
    1) Sabre-toothed tigers, mastodons, woolly mammoths -- these and many
    other spectacular large mammals are generally thought to have become
    extinct about 10,000 years ago, at the end of the Pleistocene epoch,
    otherwise known as the last ice age. But it's becoming clear that some
    of these species clung on close to the present day. Thomas Jefferson's
    instruction to Meriwether Lewis and William Clark to search for live
    woolly mammoths in the American West in 1804 was perhaps a little
    optimistic. But the species survived on Wrangel Island in the
    northeastern Siberian Arctic until some 4000 years ago(1), making it
    contemporaneous with the Bronze Age Xia Dynasty in China. Stuart et
    al(2) have reported that another charismatic ice-age mammal that was
    thought to have become extinct 10,000 years ago -- the giant deer or
    Irish elk (Megaloceros giganteus) -- survived in western Siberia to
    the dawn of historic times. The finding lends weight to the idea that
    there is no one explanation for the so-called Pleistocene extinctions.
    2) The Irish elk must have cut an impressive figure, standing more
    than two meters high at the shoulder -- about the same as a bull
    moose, the largest living member of the deer family. But when and why
    did it become extinct? In their investigation, Stuart et al(2) began
    by carrying out radiocarbon dating of five skeletal specimens,
    including a complete skeleton of an antler-bearing male. By combining
    this information with maps of the specimens' locations, they
    demonstrated that Irish elk were widespread in Europe -- from Ireland
    to Russia, and from Scandinavia to the Mediterranean -- before 20,000
    years ago. But by the last glacial maximum 15,000 years ago, they may
    have been restricted to refuges in the shrub steppes of central Asia.
    From there, Irish elk apparently recolonized northwestern Europe
    following the retreat of the Alpine and Scandinavian ice sheets during
    a period of climatic warming. The European population made a last
    stand in the British Isles before dying out 10,500 years ago, but the
    Siberian population persisted for another 3000 years.
    3) What caused the extinction of so many large mammals 10,000 or so
    years ago? Human hunting(3), changes in climate or vegetation, or
    both(4), are often proposed to be causal factors. But the "ragged"
    nature of these Late Pleistocene extinctions, with isolated pockets of
    populations surviving for longer, suggests that the extinctions have a
    complex ecology, with no single mechanism responsible for the demise
    of every species in every location.
    4) Theories for both the expansion and the extinction of Irish elk
    populations, for instance, often focus on the animals' huge antlers,
    which weighed 40 kilograms and spanned 3.5 meters, making them 30%
    larger than those of modern moose. It has been suggested(5) that
    female Irish elk selected males with large antlers, as this might have
    signified an ability to find sufficient food to support building and
    shedding a rack each year. This ability would then be passed on to
    their male progeny. But the large antlers, which contained as much as
    8 kilograms of calcium and 4 kilograms of phosphate, would have posed
    a large annual nutritional burden on bulls. The antlers would also be
    physically unwieldy in dense forests. So both physical and nutritional
    constraints probably restricted the Irish elk to productive open
    environments, with relatively tall willow and birch shrubs that could
    be navigated but still supply sufficient calcium and phosphate for
    antler growth. An inability to balance sexual selection for large
    antlers with nutritional selection pressures for smaller antlers may
    have led to the Irish elk's demise in the British Isles, particularly
    as the climate cooled rapidly and caused the vegetation to change to
    short-statured and unproductive tundra.
    References (abridged):
    1. Vartanyan, S. L., Garrut, V. E. & Sher, A. V. Nature 362, 337-340
    2. Stuart, A. J., Kosintsev, P. A., Higham, T. F. G. & Lister, A. M.
    Nature 431, 684-689 (2004)
    3. Martin, P. S. in Quaternary Extinctions: A Prehistoric Revolution
    (eds Martin, P. S. & Klein, R. G.) 364-403 (Univ. Arizona Press,
    Tucson, 1984)
    4. Stuart, A. J. Biol. Rev. 66, 453-562 (1991)
    5. Geist, V. Nat. Hist. 95, 54-65 (1986)
    Nature http://www.nature.com/nature

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