Р. Докинз. Рассказ Предка-28. Рекомендованное чтение. Библиография

 

27. Возвращение Хозяина

Ричард Докинз. Рассказ Предка
Часть 28

 

 

FURTHER READING
[Numbers in square brackets refer to sources listed in the bibliography]
 
BARLOW, GEORGE (2002) The Cichlid Fishes: Nature's Grand Experiment in Evolution. Perseus Publishing, Cambridge, Mass.
DIAMOND, JARED (1997) Guns, Germs and Steel: A Short History of Everybody for the Last 1 3,000 Years. Chatto & Windus. London.
FORTEY, RICHARD (1997) Life: An Unauthorised Biography. Harper Collins, London.
FORTEY, RICHARD (2004) The Earth: An Intimate History. Harper Collins. London.
LEAKEY, RICHARD (1994) The Origin of Humankind: Unearthing Our Family Tree. Science Masters series. Basic Books, New York.
MAYNARD SMITH, JOHN & SZATHMÀRY, EÔRS (1999). The Origins of Life: From the Birth of Life to the Origin of Language. Oxford University Press, Oxford. (See also (1891 for a more detailed treatment.)
QUAMMEN, DAVID (1996) The Song of the Dodo: Island Biogeography in an Age of Extinctions. Hutchinson. Oxford.
RIDLEY, MARK (2000) Mendel's Demon: Gene justice and the Complexity of Life. Weidenfeld & Nicolson, London.
RIDLEY, MATT (1999) Genome: The Autobiography of a Species in 23 Chapters. Fourth Estate, London.
SOUTHWOOD, RICHARD (2003) The Story of Life. Oxford University Press. Oxford.
TUDGE, COLIN (2000) The Variety of Life: A Survey and a Celebration of all the Creatures that Have Ever Lived. Oxford University Press, Oxford.
WEINER. JONATHAN (1994) The Beak of the Finch: A Story of Evolution in Our Time. Jonathan Cape, London.
WILSON, E. O. (1992) The Diversity of Life. Harvard University Press. Cambridge. Mass.
 
Advanced Reading
 
BRUSCA, RICHARD C. & BRUSCA, GARY J. (2002) Invertebrates. 2nd Edn. Sinauer Associates Inc. Sunderland, Mass.
CARROLL, ROBERT L. (1988) Vertebrate Paleontology and Evolution. W. H. Freeman, New York.
MACDONALD, DAVID (2001) The New Encyclopedia of Mammals. Oxford University Press, Oxford.
RIDLEY, MARK (2004) Evolution. 3rd Edn. Blackwell. Oxford.
NOTES TO THE PHYLOGENIES
YAN WONG
 
[Numbers in square brackets refer to sources listed in the bibliography]
Phylogeny Diagrams
The following notes outline the scientific basis for the phylogenies in this book, particularly in areas of major recent taxonomic revision and current debate. A good, relatively recent phylogenetic survey is given in Colin Tudge's The Variety of Life [289].
 
RENDEZVOUS 0 The Americas are omitted because evidence points to humans having arrived there recently from Asia. Concestor 0 must logically be at least as recent as any gene MRCA (such as Y-chromosome ‘Adam’), and even low levels of interbreeding are enough to result in a very recent MRCA of all humans [45], hence the recent date used here.
RENDEZVOUS 1 - 2 Phylogeny (as for the rest of the trees, the majority ‘vote’ among genes — see the Gibbon's Tale) supported by morphology [102] and molecules [20]. Divergence dates based on the molecular clock [105, 230].
RENDEZVOUS 3 Phylogeny and divergence dates based on morphological, fossil, and molecular data [102, 105, 273].
RENDEZVOUS 4 Gibbon phylogeny is unsure: this tree is based upon mtDNA data [246, fis 2c]. supplemented by molecular clock dates for the Concestor and Symphalangus/Hylobates nodes [105].
RENDEZVOUS 5 Conventional phylogeny. Divergence dates given by molecular and fossil data [105].
RENDEZVOUS 6 Phylogeny and dates taken directly or inferred from [105]. The position of the Aotinae is not very secure, and may change in the future.
RENDEZVOUS 7 Placement and dating [105] of the tarsier family agrees with molecular [254] and morphological data.
RENDEZVOUS 8 Within strepsirhines, lemur interrelationships are disputed, although the aye-aye is often considered basal. Order and dating of the four other families is from molecules [322], scaled to place basal primate divergence at 63 Mya [105, 207]. However, other calculations place this divergence at 80 Mya [281], moving Rendezvous 9, 10 and 11 backwards by up to 15 million years.
RENDEZVOUS 9 Placement of colugos and tree shrews is highly controversial (see accompanying tale), and is here based on recent molecular data [207]. Basal date then constrained by surrounding nodes to 63-75 Mya.
RENDEZVOUS 10 Placement of Glires from robust molecular evidence [207]. Rendezvous date constrained by molecular clock dating of Rendezvous 11 [207, 137], but maybe up to 10 My earlier [271]. Lagomorph placement uncontroversial [137, 207]. Rodent phylogeny debated. Hystricognath rodents (Hystricidae. Phiomorpha, Caviomorpha) generally accepted. Otherwise, 4 groups often found in molecular studies [e.g. 137, 202]: Muridae+Dipodidae, Aplodontidae+Sciuridae+Gliridae, Ctenodactylidae+hystricognaths, Heteromyidae+Geomyidae. Branching order and rough dating of these groups from mtDNA and rDNA 1202], but order is not robust [e.g. see 137].
RENDEZVOUS 11 - 12 Phylogeny and dating from recent revolutionary molecular studies [207, 271].
RENDEZVOUS 13 Phylogeny and dating from molecular data [107, 271]. Morphology [n?) and some molecules [205] agree on elephant/sirenian/hyrax split. However, there is uncertainty in the placement of the aardvark [205, 271], and morphological data may still conflict with the position of the Afrosoricida [177].
RENDEZVOUS 14 Rendezvous supported by old and recent data [208]. Placental-marsupial divergence at 140 Mya consistent with fossils and late molecular dates [7, 144]. Molecular studies find didelphids, then paucituberculates as sister to other marsupials [212, 272], consistent with morphology [251], Other branches variably supported by molecular data [212, 272]: position of monito del monte particularly uncertain, here interpreted as sister to Diprotodontia [251]. Divergence dates based on molecular clock data, but also constrained by Gondwanan biogeography [212].
RENDEZVOUS 15 Phylogeny and dating from recent molecular, morphological, and fossil data [208].
RENDEZVOUS 16 Date estimates for Rendezvous 16 average around 310 Mya [112], other early branch dates from fossil data [40]. Now-conventional branching within snakes and lizards [228]. Bird branching order from genetic studies [293] with dates from DNA hybridization [265]: many orders grouped as Neoaves due to uncertain relationships.
RENDEZVOUS 17 Although disputed by some palaeontologists [40], molecular and morphological data strongly support lissamphibian monophyly, and hint at order of branching shown here [325]. Basal date from palaeontological evidence [4], others from maximum likelihood trees of mtDNA [325].
RENDEZVOUS 18 - 19 Phylogeny and dating from molecular [294] and morphological/palaeontological [326] studies.
RENDEZVOUS 20 Rendezvous date generally accepted [209]. Ray-finned fish phylogeny is currently in a state of flux [141, 199], although the traditional view followed here [209] is broadly supported. Divergence dates based on fossil data [40.209]. Some groups deliberately omitted for simplicity, as phylogeny not robust.
RENDEZVOUS 21 Phylogeny based on morphological data [75, 263] [263], Divergence dates based on fossil data [209, 252].
RENDEZVOUS 22 Agnathan grouping based on genetic data [97, 279] which contradicts most fossil-based phylogenies (but these specialised groups show secondarily character lost, making morphological data difficult to use). Rendezvous date tightly constrained by fossil data [264]. Lamprey-hagfish divergence time suggested by molecular maximum likelihood trees [279].
RENDEZVOUS 23 Molecular clock data [315] places lancelet split close to basal deuterostome divergences here, estimated at 570 Mya according to medium-fuse dating of Cambrian Explosion (see the Velvet Worm's Tale).
RENDEZVOUS 24 Rendezvous date constrained by surrounding nodes. Possibly closer to ambulacrarians than to lancelets [315].
RENDEZVOUS 25 Ambulacrarian grouping and basal divergences from recent genetic data [32, 97, 31s], assuming medium fuse Cambrian explosion. Genetic studies also give deep-branching Xenoturbellida [28], although exact placement not robust. Echinoderm phylogeny and dating from genetic, morphological, and fossil data [176, 297].
RENDEZVOUS 26 Rendezvous date (about 590 Mya) from recent molecular clock studies [8, 10], and broadly consistent with fossil data [291]. Protostome phylogeny recently revised [3]: here a single broad scheme has been followed [103], based on genetics and morphology. Three branches consist of several phyla grouped together. These are: Cephalorhyncha [103], Gnathifera [162] (including Acanthocephala and Myzostomida), and Erachiozoa (phoronids and brachiopods). Edysozoan phylogeny relatively robust [103]: main uncertainties are the onychophore/arthropod grouping and basal inclusion of chaetognaths, here placed according to morphological/genetic data [224], Many ecdysozoan dates constrained by 'small-shelly' onychophore fossils (see the Velvet Worm's Tale). Lophotrochozoa branching order much more uncertain: annelid/mollusc/sipunculid group robust [224], nemerteans probably sister to this [290], branching order of others unsure.
RENDEZVOUS 27 Phylogeny based on molecular data [247, 283]. These often weakly support a paraphyletic Acoela, but morphological data strongly supports acoelomorph monophyly: divergence date thus arbitrary. Rendezvous date based on genetic distance estimates [247, 283]. assuming protostome/deuterostome split of 590 Mya and bilaterian/cnidarian split of 700 Mya.
RENDEZVOUS 28 - 29 Order of branching of cnidarians and ctenophores is still uncertain [35]. Certain molecular data weakly support the order used here [191]. Within cnidarian phylogeny now conventional, dates from genetic studies [so] calibrated to timescale used here.
RENDEZVOUS 30 Trichoplax placement unsure [35], but possibly near the base of the Metazoa [Peter Holland, pers. comm.].
RENDEZVOUS 31 Sponges generally interpreted as basal meta-zoans, although occasionally molecular data hint that they might be paraphyletic [191]. Rendezvous date of 800 Mya based on molecular clock data [211], recalibrated using protostome-deuterostome divergence of 590 Mya; this conflicts with absence of fossilised sponge spicules before the latest Precambrian, although these may represent a derived character.
RENDEZVOUS 32 & 33 Rendezvous dates roughly estimated from molecular trees [166, 191], assuming Rendezvous 31 at 800 and 34 at 1100 Mya. Position of Mesomycetozoea (Ichthyosporea) [231] based on mtDNA sequences [166], rather than (less extensive) rRNA [191].
RENDEZVOUS 34 Rendezvous date of roughly 1100 Mya commonly argued [91, 244] (but may not be particularly robust). Revised molecular studies now place Microsporidia in Fungi [149], possibly at the base [13]. Morphology and genetics place Ascomycota and Basidiomycota as closest relatives. rDNA additionally identifies Glomeromycota as sister to both [256], with previous 'zygomycetes' two (as shown here), or more paraphyletic branches. Divergence dates from molecular clock [133] reseated to fit rendezvous date used here.
RENDEZVOUS 35 Grouping of most amoebas and slime moulds as sister group to Metazoa+Fungi has substantial molecular support [13, 43], although unconventional rooting of the eukaryotic free may collapse Rendezvous 34, 35, 36, and 37 into one [43]. Divergence date arbitrarily placed halfway between two surrounding nodes.
RENDEZVOUS 36 Ribosomal RNA data grouping plants with animals and fungi now recognised as erroneous [13, 113]. As explained in the text of Rendezvous 37, the position of the plants in the eukaryotic phylogeny is uncertain, and the scheme adopted here is somewhat arbitrary. Rendezvous date constrained by 1200 Mya fossils [38 but see 42]; 1300 Mya broadly consistent with molecular clock studies (e.g. [91]). Within plants, phylogeny and relative dates from molecular data [203]. although inclusion of red algae sometimes disputed [214].
RENDEZVOUS 37 Branching order and divergence dates of major eukaryote groups uncertain [13] (hence polytomy shown). Ribosomal RNA studies erroneously place different groups as early branching lineages due to long branch attraction; amended frees only able to place eukaryotic branches far from the Archaea [113], implying much later divergence than Rendezvous 38: dates of Rendezvous 37-39 estimated to nearest 500 My. 
RENDEZVOUS 38 Rendezvous date uncertain; molecular clock data suggests roughly 2 billion years ago [eg. 91, but see 42]. Divergence dates and (conventional) phylogeny estimated from rRNA studies [e.g. 16].
RENDEZVOUS 39 Tree inherently difficult to root because there is no outgroup, and changes in mutation rate along different lineages obscure the 'centre' of the tree, It is often rooted between Archaea and Eubacteria (cross A), but other possibilities exist [42] (cross B), [113], and so is presented unrooted. Changes in rooting will affect overall branch lengths, so these cannot truly represent time and are thus somewhat arbitrary. Eubacterial phylogeny based on robust biochemical characteristics (e.g. cell wall glycoproteins) and rare genomic events (e.g. indels) [42, 117]; rRNA trees can have long branch attraction problems, but indicate that the divergences within the bacteria are deep [113]. Bacterial DNA exchange problematic for building a single tree, unless a core of unswapped genes exists [64].
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27. Возвращение Хозяина

Ричард Докинз. Рассказ Предка
Часть 28