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Developments in Evolutionary Biology for 2001
This is a continuation of the Pandas Update series. The name has been changed to reflect the fact that subsequent creationist publications, such as Sarfati's Refuting Evolution and Wells' Icons of Evolution, cover essentially the same topics as Pandas and People which was the first Intelligent Design "textbook".
Begining with the year 1995, I began to summarize the year-to-year discoveries and advancements of science that have relevance to the subject matter of the book Of Pandas and People. Surveying all the published literature would have been a next to impossible task so I have relied heavily on certain weekly publications such as Nature, Science, Science News and New Scientist and various science magazines such as Natural History, Scientific American, American Scientist and Discover, along with a variety of newly published books, for my information. Herein are the new discoveries for the year 2001.
Chapter 1: The Origin of Life
Early lifeSeveral papers discuss the evolution of the earth's oxygen atmosphere (Copley 2001; Catling, Zahnle and McKay 2001; Hoehler, Bebout and Marais 2001; Sleep 2001). Dismukes and others (2001) describe an hypothesis for the step-wise evolution of photosynthesis. Several other papers (Orme and others 2001; Ribo and others 2001; Saghatellan and others 2001) discuss possible chiral mechanisms. Phoenix and others (2001) report that being mineralized in an iron-silica solution made cyanobacteria very resistant to the damaging effects of UV light. Supporting the RNA world concept, Johnson and others (2001) report on the creation of a ribozyme RNA polymerase while Netting (2001) reports on the creation of an RNA that binds to a specific amino acid (phenylalanine). Hazen (2001) discusses minerals as providing a scaffold for the assembly of biomolecules while Sowerby and others (2001) look at nucleic acid base absorption on crystalline graphite. Irion (2001) reports on research on self-assembling processes while Szostak, Bartel and Luisi (2001) look at the possibility of synthesizing life. Kintisch (2001) reports on the search for the smallest possible microbial genome.
Wilde, Valley, Peck and Craham (2001) provide evidence for the existence of continental crust and oceans 4.5 Gya. Grassineau and others (2001) and Shen, Buick and Canfield (2001) report on the antiquity of the biological sulfur cycle. Javaux, Knoll and Walter (2001) report that prerequisites for eukaryotic diversification were established nearly 1500 Mya. Eukaryotes may have arisen when a poxlike-virus ancestor provided a nucleus in symbiosis with an archaebacterium (Takemura 2001). Bell (2001) considers a similar hypothesis. Gibbs (2001) reports that the plans to penetrate Lake Vostok have been delayed.
The space connectionMuch of the water in the cold regions of molecular clouds may be sublimed and frozen on the surface of dust grains, which act as catalytic sites for the formation of complex organic molecules (Samuel 2001). Dworkin, Deamer, Sandford and Allamandola (2001) report the synthesis of a complex mixture of organics in laboratory interstellar ice analogs. Blake and Jenniskens (2001) report on a different kind of ice structure formed in space that could accumulate organics. Comets may have brought Earth its water, organic molecules and atmosphere (Delsemme 2001). Carbonaceous meteorites may also have contributed water (Robert 2001).
Cooper and others (2001) report on the discovery of sugar-related organics found in the Muchison and Murray meteorites. Extraterrestrial amino acids are found in the Orgueil and Ivuna meteorites (Ehrenfreund and others 2001). Experiments indicate that life building blocks from space could survive an earth impact (Gorman 2001).
Other worldsSpecial sections on astrobiology appeared in the Proceedings of the National Academy of Sciences (Coughlin 2001) and Nature (Gee 2001). Thomas-Keprta and others (2001) claims the magnetite crystals in the martian meteorite ALH84001 have a biological origin. Le Page (2001) hypothesizes that the 'nanobacteria' in the meteorite may be mineral deposits produced by larger iron-eating bacteria. Italian scientists claims to have grown alien microbes from meteorites (Abbott 2001). Chyba (2001) and Jones (2001) discuss life on Europa while Turtle (2001) claims Europa's ice shell may be 3 to 4 kilometers thick. Knight (2001), McCord (2001) and Schenk and others (2001) present evidence for an ocean on Ganymede. Ruiz (2001) discusses Callisto's ocean.
Kerr (2001) reports on a conference evaluating the evidence for water on Mars and the likelihood of panspermia. Hecht (2001) discusses a modern theory of panspermia. Other lines of evidence for water on Mars are presented by Cooper (2001), Mustard, Cooper and Rifkin (2001), Anonymous (2001) and for a deep internal source by McSween and others (2001) and Phillips and others (2001). Irion (2001) discusses the idea that Earth life came from Mars. Garlick (2001) dicusses a "galactic habitable zone" while Lunine (2001) discusses the role of Jovian planets in affecting the habitability of terrestrial planets in a planetary system. The literature on the birth of stars and planetary systems and the discovery of extra-solar planets is too large to be summarized here.
Chapter 2: Genetics and Evolution
MutationThe role of error-prone polymerases or mutases on the rate of evolution is reviewed by Chicurel (2001). Giraud and others (2001) look at the cost of high mutation rates. We may have attained our large brains by reducing our mutation rates (Svitil 2001). Harder (2001) and Massingham, Davies and Lio (2001) discuss malaria-protective mutations.
Natural selectionZimmer (2001) discusses detecting natural selection while Hoekstra and others (2001) and Kingsolver and others (2001) discuss natural selection in the wild. Brookfield (2001) discusses the concept of fitness. Emlen (2001) discusses the costs of exaggerated structures, in particular the production of horns in dung beetles, which reduces the size of neighboring morphological structures. Losos (2001) describes the evolution of anole lizards on Caribbean islands. Park, Buchanan and Evans (2001) consider the roles of natural and sexual selection in the evolution of tail streamers in barn swallows.
A number of articles deal with evolution of sexual selection and mate choice (Amundsen and Forsgren 2001, Engqvist and Sauer 2001, Gravilets, Arnqvist and Friberg 2001, Moore and others 2001). Several articles deal with genetic algorithms and test-tube evolution (Arnold 2001, Johnson 2001, Lemly 2001, Wakefield 2001).
SexAgrawal (2001) and Siller (2001) discuss how sexual selection can mitigate or even eliminate the cost of sex. Sexual reproduction functions to detect and remove genomic copy errors (Ridley 2001a, 2001b). It also functions to unlink favorable and unfavorable mutations allowing natural selection to preserve the favorable ones (Rice and Chippindale 2001). Brown and Casselton (2001) report on the unusual condition in mushrooms where there may be many different mating types. Jergalian and Lahn (2001) discuss the evolution of the mammalian X and Y chromosomes.
TransposonsKidwell and Lisch (2001) review the role of mobile elements in host genome evolution. Hughes and Coffin (2001) review human endogenous retroviruses which make up 8% of the human genome. Arkhipova and Morrison (2001) report that telomere-associated transposons protect chromosomes from degradation. Yu and others (2001) report on the birth of a gene resulting from retroposon activity.
GenomesThe big news this year is the announcement of the completion of the draft human genome both by Celera (Venter and others 2001) and the public consortium (International Human Genome Sequencing Consortium 2001). A number of other papers on the human genome that accompany these reports are not listed in the references. The low estimates of the number of genes (26K to 38K) prompted controversy (Kintisch 2001, Lee 2001). It was also reported that hundreds of these were derived by horizontal transfer from bacteria but others disagree (Ponting 2001). Other papers related to the project include Deloukas and others (2001), Helmuth (2001), Katsanis, Worley and Lupski (2001), Lynch (2001), Patil and others (2001) and Shields (2001).
Continuing work is reported on the Arabadopsis genome (Bebetzen 2001, Leyser 2001, Martienssen and McCombie 2001) and Drosophila (Karlin, Bergman and Gentles 2001). Gewolb (2001) discusses animals to be chosen for sequencing. Glausiusz (2001) reports on those being sequenced including the mouse (Butler 2001, Marshall 2001a), the rat (Marshall 2001b) and the chimp (Cyranoski 2001). Work will soon start on Anopheles (Balter 2001) and the banana (Coughlan 2001). Others that have been finished are rice (Davenport 2001), two species of puffer fish (Travis 2001), the marine tunicate Oikopleura (Seo and others 2001), a second yeast and two fungi (Pennisi 2001) and the symbiotic red algal nucleus of a cryptomonad alga (Douglas and others 2001). Microbial genomes are routinely being sequenced (about 20 in 2001) and these are no longer considered here.
Genome related researchPetrov (2001) discusses the evolution of genome size and the C-value paradox. Charlesworth, Charlesworth and McVean (2001) discuss the effect of all the genome sequences on evolutionary biology. Friedman (2001) reports on bacterial genomes. Kuhn, Hijiri and Sanders (2001) report on multiple genomes in arbuscular mycorrhizal fungi.
Pennisi (2001) reports on genome duplications as the raw material of evolution. Others investigate introchromosomal duplications in eukaryotes (Achaz, Netter and Coissc 2001), duplications in humans (Eicher 2001), the birth and death of duplicated genes (Wagner 2001), the functional divergence of duplicate genes (Massingham, Davies and Lio 2001, Van de Peer, Taylor, Braasch and Meyer 2001), and inversions in eukaryotes (Huynen, Snel and Bork 2001). Pseudogenes and junk DNA in Rickettsia genomes is reviewed by Andersson and Andersson (2001). Hirsch and Fraser (2001) investigate the rate of evolution in dispensible proteins in yeast.
The genetic codeAtkins and Gesteland (2001) review the discovery of the genetic code. Others investigate the evolution of redundancy (Ardell and Sella 2001), evolution of changes in the code - mostly in mitochondrial genomes (Knight, Landwebber and Yarus 2001), codon reassignment (O'Sullivan Davenport and Tuite 2001), and artificially expanding the code (Wang and others).
MacroevolutionCarroll (2001a) discusses the concepts of micro- and macro-evolution, the distinction being only descriptive, not mechanistic while Carroll (2001b) reviews the major events in evolution.
MiscellaneousComfort (2001) reviews the history of the gene concept. The role of introns is discussed by Duret (2001) and their origin by Fedorov and others (2001). Pietrokovski (2001) discusses intein spread and extinction. Benasson and others (2001) discuss mitrochondrial pseudogenes while Selosse, Albert and Godelle (2001) and Henze and Martin (2001) discuss how mitochondrial genes get transferred to the nucleus. Pennisi (2001) reports on extensive lateral transfer of genes between an archaean methanogen and a purple nonsulfur bacterium.
Barash (2001) discusses imperfections in evolutionary 'design'. Immigrants into a population will replenish genetic variation and reduce inbreeding depression, preventing the population's extinction (Ingvarsson 2001). Zimmer (2001) discusses junk DNA while Glausiusz (2001) reports on a coding error in 'junk' DNA linked with hyperactivity in rhesus monkeys. Weeks and others (2001) report on a mite species with haploid females probably caused by an undescribed endosymbiotic bacterium. Margulis and Sagan (2001) discuss symbiotic termite flagellates. Podos (2001) reports on correlated evolution of morphology and vocal signals in Darwin's finches.
Chapter 3: The Origin of SpeciesBarton (2001) introduces a special issue of Trends in Ecology and Evolution devoted to speciation with 11 separate articles on various aspects of the phenomenon including theoretical, genetic and chromosomal, sexual selection, ecological, sympatric speciation, and the fossil record. Harrison (2001) reviews the book Frogs, Flies & Dandelions: The Making of Species by Menno Schilthuizen. Irwin, Bensch and Price (2001) report a case of speciation in a ring in warblers where a chain of intergrading population encircles a barrier and the terminal forms coexist without interbreeding. Roco and others (2001) report genetic evidence for two species of elephants in Africa. Using genetic markers Martinsen and others (2001) find that hybrids can effectively filter gene flow between two species of cottonwood. Adaptation to microclimate overwhelms gene flow between two populations of Drosophila on opposite slopes of a canyon (Michalak and others 2001).
Gametic incompatibilities may lead to speciation in Drosophila (Alipaz, Wu and Karr 2001). Sperm-egg cytoplasmic incompatibility induced by Wolbachia (a cytoplasmically inherited bacterium) reduces the frequency of hybrid offspring between two species of wasp (Bordenstein, O'Hara and Werren (2001). Chromosomal inversions contribute to the hybrid sterility between Drosophila pseudoobscura and D. persimilis (Noor and other 2001). A chromosomal basis for speciation has also been found in mice (Corti and Rohlf 2001). Taylor, Peer and Meyer (2001) discuss a speciation model based on loss of different copies of a duplicated gene. Ritchie (2001) reports mtDNA evidence for allochronic speciation and reproductive character displacement in a new species of cicada. Swanson and others (2001) report natural selection driving the diversity of female reproductive proteins in mammals.
Hawthorne and Via (2001) report that ecological specialization can promote speciation if it is genetically linked to mate choice. Johannesson (2001) reviews studies emphasizing the role of ecological factors in sympatric speciation. Naisbit, Jiggins and Mallet (2001) report sexual selection against hybrids in two species of Heliconius butterflies, while Jiggins and others (2001) report assortative mating in Heliconius species based on shifts in mimicry color patterns. Divergent sexual selection enhanced reproductive isolation in sticklebacks (Boughman 2001).while Peichel and others (2001) look at the genetic basis for morphological differences in stickleback species. Butlin and Ritchie (2001) report on the genetic basis for divergent male sexual behaviors and female preferences in fruitflies and Doi and others (2001) find a locus for female discrimination behavior in Drosophila. Ting, Takahashi and Wu (2001) find sexual isolation based on multiple loci. On the other hand Veen and others (2001) find that apparent hybridization may be adaptive under some circumstances in flycatchers.
Kaufman (2001) and Meyer (2001) review The Cichlid Fishes: Nature's Grand Experiment in Evolution by GW Barlow. Research papers on cichilds discuss microsatellite species markers (Markert, Danley and Arnegard 2001), oldest fossil cichlids (Murray 2001), the role of lake level fluctuations in cichlid speciation (Sturnbauer and others 2001) while Fryer (2001) questions the drying out of Lake Victoria 12,000 years ago.
Chapter 4: The Fossil Record
New fossilsNew fossil finds include an exceptionally preserved vermiform mollusc (Sutton and others 2001a) and a three-dimensionally preserved polychaete (Sutton and others 2001b) from the Silurian of England, primitive deuterostomes from the Lower Cambrian of China considered a new phylum, the Ventulicolians (Shu and others 2001), an early Cambrian tunicate (Shu, Chen, Han and Zhang 2001), two early Cambrian crustaceans (Chen, Vannier and Huang 2001; Siveter, Williams and Wasloszek 2001), a primitive sarcopterygian fish from the Early Devonian of China (Zhu, Yu and Ahlberg 2001), hundreds of specimens, both larval and adult, of a Late Jurassic salamander from a Chinese pond deposit (Gao and Shubin 2001) and water lilies from the Early Cretaceous (Frils, Pedersen and Crane 2001).
Reptile material includes the earliest (260 Mya) terrestrial herbivore, a synapsid (Rybczynski and Reisz 2001), a procolophonoid parareptile from the Triassic of South Africa (Modesto, Sues and Damiani 2001), a brachiosaur tooth alongside a 110 to 125 Myo dinosaur trackway in South Korea (Perkins 2001a), a giant pterosaur (up to 12 m wingspan) from the Cretaceous of Spain (Perkins 2001b), a plesiosaur with stomach contents and gastroliths from the Late Cretaceous of Kansas (Cicimurri and Everhart (2001), a mosasaur with four advanced embryos (Caldwell and Lee 2001), a giant sauropod from the Upper Cretaceous of Egypt (Smith and others 2001), a coelurosaur and a herbivore from the mid-Cretaceous of North America (Schubert 2001), a giant 12 m long crocodile from the Cretaceous of Africa (Sereno and others 2001), the most complete titanosaurian sauropod yet found - from the Cretaceous of Madagascar (Rogers and Forster 2001), embryonic titanosaur skulls from Argentina (Chiappe, Salgado and Coria 2001), a small theropod from the Late Cretaceous of Madagascar with unusual lower dentition (Sampson Carrano and Forster 2001) and a small, long-armed velociraptor-like tyrannosaurid from the Isle of Wight (Stokstad 2001).
Mammalian finds include a tiny skull of an Early Jurassic mammal (Luo, Crompton and Sun 2001), the earliest with a fully mammalian jaw and middle ear, an Eocene fully quadrupedal sirenian representing a transitional form (Domning 2001), and a Late Cretaceous marsupial molar from Madagascar (Krauss 2001). Archibald, Averlanov and Ekdale (2001) report on Late Cretaceous eutherians.
The Cambrian ExplosionHackman and others (2001) report molecular data that suggests green algae and fungi were present 1000 Mya and land plants appeared by 700 Mya in the Precambrian. Holland and Chen (2001) discuss the origin and early evolution of vertebrates including recently discovered soft-bodied Cambrian forms. Lieberman (2001) reports that speciation rates of olenelloid trilobites were not unusually high during the Cambrian radiation. Kimura and Watanabe (2001) present chemical evidence for widespread oceanic oxygen deficiency immediately before the Cambrian explosion. Siveter, Williams and Waloszek (2001) descibe an exceptionally well-preserved crustacean from Lower Cambrian rocks of Shropshire, England.
BirdsJi and others (2001) report on the find of a dromaeosaurid dinosaur with unquestionable feathers. Xu, Zhou and Prum (2001) confirm the homology of Sinornithosaurus' integumentary appendages and primitive feathers. Perkins (2001) also discusses the origin of feathers. Prum and others (2001) question the feather-like nature of the integumentary structures of Longisquama. Rowe and others (2001) discuss the unfortunate Archaeoraptor forgery. The tail portion of that specimen is now described as that of a small bipedal dinosaur Microraptor zhaoianus. Galis (2001) discusses digit homology between dinosaurs and birds. A homeotic change may have affected digit identity in the wing of birds. Norell and Clarke (2001) report on the discovery of a new Late Cretaceous ornithurine bird. Cracraft (2001) presents evidence that modern birds originated in Gondwana prior to the K-T extinction event.
WhalesNew fossil material of terrestrial cetaceans (Gingerich and others 2001; Thewissen and others 2001) document the relationships of whales to artiodactyls. Thewissen and Bajpai (2001) provide an up-to-date summary of the whale fossil record as an example of macroevolution while Gatesey and O'Leary (2001) summarize the fossil and molecular data and the controversy over mesonichid versus artidactyl origins.
Mass extinctionsJoblonski (2001) and Erwin (2001) discuss the evolutionary role of mass extinctions. New fossil finds (Harder 2001) and possible rock-record bias (Smith, Gale and Monks 2001) may indicate some of the mass extinctions were not as great as previously thought.
Further discussion of the Snowball Earth hypothesis concerning widespread Precambrian glaciation is given by Kennedy, Christie-Blick and Prave (2001). Kennedy, Christie-Blick and Sohl (2001) believe these glaciations were ended by large-scale release of methane from solid gas hydrates. Hassler and Simonson (2001) report on evidence for Early Precambrian asteroid impacts. Kerr (2001) reports on the finding of meteorites in Ordovician strata.
The Permian-Triassic extinction was by far the largest such event (Wright 2001). Smith and Ward (2001) find a bed in the Karoo marked by a reddening of flood-plain mud rocks and a change from high- to low-sinuosity river channels and a catastrophic extinction of vertebrate taxa below this boundary and appearance of new taxa above it. Twitchett and others (2001) find evidence of rapid and synchronous collapse of marine and terrestrial ecosystems followed by a "dead zone" occupied by Permian plants (Looy and others 2001). Geochemical evidence of a Permian-Triassic impact event is presented by Becker and others (2001) and Kaiho and others (2001). Hotinski and others (2001) report end-Permian ocean stagnation and anoxia.
Retallack (2001) provides a 300 My long record of atmospheric CO2 levels based on fossil plant cuticles. Beerling, Osborne and Chaloner (2001) also correlate leaf anatomy with CO2 levels. Tanner and others report on CO2 levels across the Triassic/Jurassic boundary. Padden, Weissert and de Rafelis (2001) report evidence for a Late Jurassic release of methane while Erbacher and others (2001) and Wilson and Norris (2001) report on anoxia during the mid-Cretaceous accompanied by a massive expansion of marine archaeans (Kuypers and others 2001).
Mukhopadhyay, Farley and Montanari (2001) give geochemical evidence and Pearson and others (2001) give fossil evidence for an abrupt extinction event at the K-T boundary. Melosh (2001) looks at the anatomy of the Chicxulub crater. Evidence for the impact is found in SE Missouri (Perkins 2001) while Lubick (2001) discusses evidence that large impacts exacerbate volcanic eruptions.
MiscellaneousSteiner and Reitner (2001) suggest that some ediacarans were prokaryotic colonies! Stanley and Fautin (2001) postulate the origin of modern corals from soft-bodied mid-Triassic ancestors. The evolution of trees in the Devonian may have increased the O2 content of the atmosphere to nearly 40% (Simpson 2001). Jackson and Johnson (2001) discuss investigations into the diversity of animal life during the Phanerozoic (from about 500 Mya to the present). Bossuyt and Milinkovitch (2001) report a wide dispersal of frog lineages from India after it united with Eurasia.
Countering the creationist ideas that all crocodiles are alike, Naish (2001) reviews the wide variety of crocodilians. Cerrano and Wilson (2001) review fossil tetrapod tracks while Perkins (2001g) discusses other trace fossils. Diagnosing disease in fossils is treated by Perkins (2001b). A new population of coelacanths is found off Madagascar (Perkins 2001c) CT scans of eggs allow reconstruction of elephant bird embryos (Perkins 2001d). Norell, Makovicky and Currie (2001) investigate the beaks of ostrich dinosaurs. Niiler (2001) reports on a grooved theropod tooth that may have harbored deadly bacteria while Perkins (2001a) describes plant phytoliths trapped in cracks and pits of dino teeth giving clues to their diet. Sanz and others (2001) describe an Early Cretaceous coprolite containing tiny bird bones. Newly discovered skulls of juvenile Triceratops may reveal the growth patterns of their horns (Perkins 2001f).
Erickson, Rogers and Yerby (2001) investigate dino growth patterns and rapid avian growth rates. Dinos grew to their adult size relatively quickly, much as birds and mammals do today. Burness, Diamond and Flannery (2001) discuss why dinosaurs could grow so large. Powell (2001) reports that, because of heart limitations, Brontosaurus probably kept its neck more or less horizontal all the time. The evolution of alligator respiration is reviewed by Zimmer (2001) Witmer (2001) investigates nostril position in dinosaurs. Rayfield and others (2001) analyze the design and function of an allosaur skull. Luo, Cifelli and Kielan-Jawarowska (2001) discusss the possibility that tribosphenic mammals have a dual origin. Lister and Sher (2001) review the evolution of the woolly mammoth.
Rose (2001) and Wing (2001) describe Eocene ecosystems of Wyoming. Stokstad (2001a) discusses Utah fossil beds while Perkins (2001e) discusses fossil footprints in Utah. Stokstad (2001b) reviews all the recent Chinese fossils. Pringle (2001) recounts the discovery of a Middle Cretaceous ecosystem in New Mexico. Burdick (2001) descibes the fossil localities of Joggins and Cape Breton while Novacek (2001) describes fossil hunting in the Chilean Andes. Orndorff, Wieder and Filkorn (2001) discuss ichthyosaurs from Nevada strata. X-rays of an ichthyosaur skull suggest they were deaf (Anonymous 2001).
Buchholtz and Seyfarth (2001) recount the career of Tilly Edinger and the beginnings of paleoneurology. Zen (2001) introduces a special issue of the Journal of Geoscience Education devoted to Deep Time.
Chapter 4a: Human Evolution
ApesMarivaux and others (2001) report on a 30 Myo fossil lemur from Pakistan while Limons (2001) reports on the cranium on an Egyptian ape. Cantalupo and Hopkins (2001) report on Broca's area in the brain which may govern gestures in apes and became involved in speech in the human ancestral line. Wild chimps can learn hand gestures and copy the local customs when they join another group (Cohen 2001). Waal (2001) discusses pointing in primates. Blackmore (2001) describes some intelligent behavior in chimps. Baboons exhibit evidence for abstract thought (Motluk 2001). Whiten and Boesch (2001) review the culture exhibited by chimps. Small (2001) reports male chimps hunt and share spoils.
Pre-humansAiello and Collard (2001), Balter (2001), and Balter and Gibbons (2001) discuss the previous year's find of Orrorin and its place in our family tree. Haile-Selassie (2001) reports on a new Late Miocene find of the hominid Ardipithecus. Leakey and others (2001) report on a new genus Kenyanthropus from the Middle Pliocene of East Africa. Ainsworth (2001) reports that, in addition to Homo species, Paranthropus' brain size also increased between 1.5 and 2.6 Mya. Evidence for termite foraging by early hominds is presented by Blackwell and d'Errico (2001).
Ron and Levy (2001) conclude that hominids first left Africa between 1.7 and 2.0 Mya. Bower (2001) reports that H. erectus reached Java about 1.5 Mya. Shipman (2001) presents a detailed biography of Eugene Dubois and his discovery of Java Man. Boaz and Ciochon (2001) present the modern interpretation of the Peking Man Zhoukoudian site. Peking Man may have occasionally occupied the site, but the fossil remains indicated he was prey to giant hyenas. Manzi, Mallegni and Ascenzzi (2001) describe a European cranium representing a bridge between Homo ergaster/erectus and later Middle Pleistocene Homo heidelbergensis.
Maddox (2001) reviews Solly Zuckerman: A Scientist out of the Ordinary by John Peyton. Zuckerman is a favorite of creationists because he once denied the hominid character of Australopithecus.
NeanderthalsStringer and Davies (2001) report the latest views on the relations between Neanderthals and Cro-Magnons and their coexistence. Balter (2001) considers the extinction of the Neanderthals. Neanderthals were broad-based foragers exploiting a wide range of resources (Hardy and others 2001) but they apparently did not eat fish (Bower 2001c). They had greater grip strength than modern humans (Niewoehner 2001) but the similarity of their hands to us resulted in similarly made tools (Bower 2001a). They also took care of debilitated individuals (Lebel and others 2001). Ponce de Leon and Zollikofer (2001) report that the cranial and mandibular characters differentiating Neanderthals and modern humans arise early in development, perhaps prenatally. Comparison of Neanderthal and human children skeletons (and other hominids) is reported by Bower (2001b). Smith and others (2001) conclude that the successful recovery of Neanderthal DNA was made possible because the skeletons were preserved under cold conditions.
Modern HumansAnatomically modern humans existed in Africa by 100 Kya but they were behaviorally primitive until about between 50 and 40 Kya. Only then did they expand into Eurasia (Klein 2001). Analyses of dental development in fossil hominins suggest that our lengthy growth processes arose quite late in evolution (Dean and others 2001). Kirchweger (2001) discusses the evolution of skin color in humans while Rosenberg and Trevathan (2001) discuss the evolution of human birth. A pregnant woman's need for aid during labor may have evolved with upright walking. White (2001) reviews the evidence for cannibalism in the human fossil record.
Culotta, Sugden and Hanson (2001) introduce a special section on human migrations in the March 2 issue of Science. Zhu and others (2001) found 1.36 Myo stone artifacts in northeast Asia. Pavlov, Svendsen and Indrelid (2001) describe a 40 Kyo human site in the European arctic. Humans were in Britain by 400-500 Kya (Keys 2001). The first appearance of neolithic culture from central Italy to Portugal occurred around 5400 bce and is probably explained by maritime pioneer colonization (Zilhao 2001). Manning and others (2001) report on radiocarbon dating dating a 1599 year long tree ring chronology from Anatolia which will help resolve problems in Assyrian-Mesopotamian chronology.
With regard to the ancestors of New World humans, skulls unearthed in Brazil look more like modern Africans and Australians than Asians or native Americans (Bower 2001). Other craniofacial studies indicated that the first New World inhabitants resembled people from Japan and Polynesia (Brace and others 2001). The earliest archaeological maize from highland Mexico is dated to 6,250 ya (Piperno and Flannery 2001). The early New World urban center of Carel on the central coast of Peru is dated from 2627 bce to 1977 bce (Solis, Haas and Creamer 2001).
Language and the capacity for symbolic art may be what sets us apart from the Neanderthals (Tattersall 2001). Valladas and others (2001) reviews the chronology of cave art while Holden (2001) reports on skeletons found in Cussac Cave, a newly discovered cave art site. Harder (2001) reports on paleolithic burial sites. Alroy (2001) presents a computer simulation model indicating that humans could have been responsible for the Pleistocene megafauna extinctions. Roberts and others (2001) date the Australian megafauna die-off at about 45 Kya which rule out aridity at the Last Glacial Maximum as the cause. Miller (2001) discusses whether humans hunted mammoths to extinction or gave them lethal diseases.
Wolpoff, Hawks, Frayer and Hunley (2001) present evidence for their replacment theory. Soares (2001) discusses a Javan skull that supports the repacement theory. Svitil (2001) interviews Wolpoff.
DNALindahl (2001) reviews the book The Molecule Hunt by M. Jones which reviews the role of DNA research in archaeology. Genetic data based on the Y chromosome (Ke and others 2001), autosomes and mitochondria (Takahata, Lee and Satta 2001) support the Out-of-Africa hypothesis.
Zimmer (2001) discusses the Y chromosome and the human geneological tree. An odd genetic sequence taken from a 60 Kyo Australian 'modern' man does not necessarily contradict the Out-of-Africa theory, but reveal an extinct mtDNA lineage (Adcock and others 2001). Sykes (2001) reconstructs the development of European populations based on mtDNA sequences. DNA evidence hints that all humans descended from speakers of South African "click" languages (Travis 2001).
Hacia (2001) summarizes the known differences between human and ape genomes. Johnson and others (2001) document positive selection and diversification of a gene family on a duplicated section on human chromosome 16 during the emergence of humans and African apes. New research shows that the same genes are expressed differently in human and chimp brains (Normile 2001). McCollum and Sharpe (2001) reviews the evolution of hominid teeth in terms of the developmental genetics of dental patterning and the control of tooth specification. Humans have a low level of genetic diversity compared to apes (Kaessmann, Wiebe, Weiss and Paabo 2001).
Chapter 5: Homology and Development
HomologyMindell and Meyer (2001) discuss the criteria for defining the concept of homology. Dayton (2001) describes the extinction of the thylocine (marsupial wolf) while Su and others (2001) discuss the genetic diversity of red panda populations.
DevelopmentEach year there are more and more research publications in the field of evo-devo (evolution and development). I will only mention a highly selected few in this review. Three recent books (Carol, Grenier, Weatherbee 2001; Davidson 2001; Wilkins 2002) present the field of evolutionary developmental genetics and introduce the reader to selector genes, signaling pathways, transcription factors, and cis-regulatory regions of target genes that make up the network of factors controlling and directing the development of the organism. The binding sites on the cis-regulatory regions are short (4-8 base-pairs long) rendering the network susceptible to mutational changes that result in macroevolution. Thus evolution results, not from new regulatory genes, but from changes in the way the conserved ones interact. Carol, Grenier and Weatherbee is the most accessible to the non-specialist reader. Downward (2001) provides a general review of signaling pathways.
In addition to the two genome duplications believed to have occurred early in vertebrate evolution, several papers investigate the possiblity of a third duplication in the lineage leading to the teleost fishes (Malaga-Trillo and Meyer 2001; McClintock and others 2001; Robertson-Rechavi and Laudet 2001).
Pearson (2001) reports on how the two disciplines of development and cell biology are interacting. Kirk (2001) studies the genetic basis for germ-soma differentiation in Volvox. Randerson and Hurst (2001) investigates how gametes may have specialized into eggs and sperm. Popodi and Raff (2001) review Hox genes in radially symmetrical echinoderms.
Cnidarians reveal intermediate stages in the evolution of Hox genes (Finnerty 2001). This is one of nine papers in a symposium: HOX clusters and the Evolution of Morphology. Schilling and Knight (2001) report on Hox gene regulation in chordates. This is one of twelve papers in a theme issue of the journal devoted to: Evolution, development and genome analysis. McGonnell (2001) reports on a developmental mechanisms symposium.
Various reports deal with eye formation (Baker 2001), wing formation (Giss and others 2001), leg segmentation (Rauskolb 2001) and tracheae development (Llimargas and Lawrence 2001) in Drosophila. The latter concludes that retaining a number of similar control genes allows more subtle forms of control and flexibility in evolution.
Fishman (2001) introduces the zebrafish, one of the developmental biologists' favorite organisms. Arendt, Technau and Wittbrodt (2001) report on the genetic basis of the bilaterian larval foregut. Galis and Alphen and Metz (2001) explain why five is the standard for fingers and toes and Svitil (2001b) reports that polydactyly is linked with shortened bones of the limbs in mice, making movement very awkward. Wang, Hu, Meng, and Li (2001) present new evidence relevant to the orgin of the mammalian middle ear. The patterning of the pharyngeal arches is discussed by Graham and Smith (2001) Galis (2001) looks at the origin of vertebrate appendicular muscle. Martin (2001) looks at limb formation in vertebrates while Tabin and Johnson (2001) review the formation of vertebrate segments.
Svitil (2001a) reports on Arabidopsis genes that transform leaves into flowers. Arendt and Wittbrodt (2001) present a great deal of comparative information on animal eyes. Szathmary (2001) reports on computer models of developmental phenomena. Cohen (2001) suggests the possibility of resurrecting extinct forms by reactivating turned-off gene systems in present-day orgamisms. Such atavisms occur naturally resulting in three-toed horses and whales with hind limbs.
Lagos-Quintana and others (2001) report on the discovery of a new class of tiny (about 22 nucleotides long) regulatory RNAs.
Chapter 6: Biochemical Similarities
Biochemical structuresFeatures of algal photosystems are investigated by Grabowski, Cunningham and Gantt (2001) and Jordan and others (2001). The structure of the bacterial flagellar prototfilament is investigated by Samatey and others (2001) while Kalir and others (2001) look at the multiple steps of flagellar assembly. Guterman (2001) discusses how new enzymes evolve. Trifonov and others (2001) discuss protein evolution. The evolution of vertebrate steroid receptors is an example of the Darwinian evolution of an irreducibly complex biochemical system (Thornton 2001). Sambrano and others (2001) investigate the role of thrombin signalling in the blood clotting mechanism.
The detailed structure of the entire ribosome reported by Yusupov and others (2001) helps explain its function at the molecular level. Maquire and Zimmerman (2001) review research on the ribosome and its function. Ent, Amos and Lowe (2001) discover a bacterial precursor for the eukaryote cytoskeleton.
Molecular systematicsPennisi (2001) discusses the prospect of a project for a complete tree of life. Brown and others (2001) discuss universal trees (of domains, kingdoms and phyla) which are beyond the power of morphology while Dachs and Doolittle (2001) discuss the origin of the eukaryotes. King and Carroll (2001) present molecular data indicating a phylogenetic relationship between choanoflagellates and metazoons including possession by the former of a gene involved in animal development. Medina and others (2001) look at basal animal phylogenies based on large and small subunit rRNA. Borchiellini and others (2001) report that the sponges may be paraphyletic, the Calcarea being more related to Eumetazoa than to the siliceous sponges. Muller and others (2001) discuss genes shared by sponges and other metazoans. Miyata and Suga (2001) present evidence for two periods of gene duplication, one before and one after the Cambrian explosion. Neidart and others (2001) discuss genome duplications in early vertebrates.
Other molecular phylogenies include: bats (Nikaido and others 2001a; Lin and Penny 2001), murid rodents (Michaux, Reyes and Catzeflis 2001), teleosts (Miya, Kawaguchi and Nishida 2001), edentates (Delsuc and others 2001), early placentals (Murphy and others 2001), cetacean lineages (Nikaido and others 2001b), land snails (Wade, Mordan and Clarke 2001), arthropods (Giribet, Edgecombe and Wheeler 2001), amphibians (Zardoya and Meyer 2001) and australidelphian marsupials (Phillips and others 2001). Mammalian superfamial and interordinal clades are worked out by Liu and others (2001) and Dijk and others (2001). Mei Xu and Glazko (2001) estimate the divergence times of a number of groups: mice and rats (33 Mya), rodents and humans (96 Mya), eubacteria and eukaryotes (3 Bya), protists and other eukaryotes (1.7 Bya), plants, fungi and animals (1.3 Bya). Divergence times for major rodent groups are presented by Adkins and others (2001). Snakes exhibit high gene substitution rates (Hughes and Mouchiroud (2001).
DNA evidence suggests a Jurassic origin for angiosperms (Wikstrom, Savolainin and Chase 2001). The origin of flowering plants and their reproduction is reviewed by Friedman and Floyd (2001). Horsetails and ferns are the closest living relatives to seed plants (Pryer and others 2001), while the closest living relatives of land plants are the Charales (stoneworts) and Coleochaetales (Karol and others 2001). Lutzoni, Pagel and Reeb (2001) relate fungal ineages to lichen symbiotic ancestors.
Molecular data has elucidated the origin of many domestic animals including the horse (Vila and others 2001), cattle (Troy and others 2001), goats (Luikart and others 2001), pigs (Kijas and Anderson 2001), and llamas and alpacas (Kadwell and others 2001). Sato and others (2001) identify the grassquit Tiaris obscura as the nearest living relative of Darwin's finches.
Although much molecular systematics is done using ribosomal RNA and mitochondrial DNA, others have used various aspects of junk DNA. Thus Takahashi and others (2001a and b) base phylogeny of cichlid fishes on insertion patterns of SINES (short interspersed repetitive elements). Whelan and Goldman (2001) review the newest methods for analysing molecular data. Molecular data almost always supports and complements phylogenies based on morphological data, produces phylogenies among organisms with few morphological features or few such features in common, and dates divergences using molecular clocks. Zrzavy (2001) reviews one of the biggest discrepancies between morphological and molecular phylogenies - the relationship of the annelids to other invertebrates.
SummaryRibozymes that can reproduce RNA and combine with proteins, the first draft of the human genome, the discovery of feathered dinosaurs, new whale fossils documenting the origin of the group, the new hominids, Orrorin, and Kenyanthropus, and tiny RNA regulatory genes highlight the year's activities. The special issue of Trends in Ecology and Evolution (July 2001) on speciation and the three new books on developmental biology provide rich sources of information on these fields.
There are a number of additional books that are relevant to this review. Peter Bentley's Digital Biology (New York: Simon & Schuster; 2001) reviews research on computer experiments on evolution. It also provides a lucid description of the human immune system. The Book of Life, edited by Stephen Gould (New York: W. W. Norton & Co.; 2001) is an illustrated history of the evolution of life on earth. Ernst May's What Evolution Is (New York: Basic Books; 2001) is an authoritative introduction for the non-specialist and layman to all aspects of evolution. Ron Redfern's Origins: The Evolution of Continents, Oceans and Life (Norman OK: University of Oklahoma Press; 2001) is a wonderfully detailed and illustrated plate tectonics history of the earth. Carl Zimmer's Evolution: The Triumph of an Idea (New York: HarperCollins; 2001) is the companion to the recent PBS Series on evolution. Finally, Stephen Jones' Darwin's Ghost (New York: Ballantine Books; 1999) was overlooked in previous updates. Jones has rewritten The Origin of the Species utilizing modern research. This is an extremely useful and informative up-to-date summary of evolution.
REFERENCES: Chapter 1: The Origin of Life
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Copley J. The story of O. Nature 2001 Apr 19; 410: 862-864.
Catling DC, Zahnle KJ, McKay CP. Biogenic Methane, Hydrogen Escape, and the Irreversible Oxidation of Early Earth. Science 2001 Aug 3; 293: 839-843. See also: Kasting JF. The Rise of Atmospheric Oxygen. Science 2001 Aug 3; 293: 819-820.
Dismukes GC, and others. The origin of atmospheric oxygen on Earth: The innovation of oxygenic photosynthesis. Proceedings of the National Academy of Sciences 2001 Feb 27; 98(5): 2170-2175.
Gibbs WW. Out in the Cold. Scientific American 2001 Mar; 284(3): 16-17.
Grassineau NV and others. Antiquity of the biological sulphur cycle: evidence from sulphur and carbon isotopes in 2700 million-year-old rocks of the Belingwe Belt, Zimbabwe. Proceedings of the Royal Society of London Series B 2001 Jan 22; 268(1463): 113-119.
Hazen RM. Life's Rocky Start. Scientific American 2001 Apr; 285(4): 76-85.
Hoehler TM, Bebout BM, Marais DJDes. The role of microbial mats in the production of reduced gases on the early Earth. Nature 2001 Jul 19; 412: 324-327. See also: Jorgensen BB. Space for hydrogen. Nature 2001 Jul 19; 412: 286-289.
Irion R. Say the magic words. New Scientist 2001 Jun 9; 170(2294): 32-35.
Javaux E, Knoll AH, Walter MR. Morphological and ecological complexity in early eukaryotic ecosystems. Nature 2001 Jul 5; 412: 66-69.
Johnson WK and others. RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science 2001 May 18; 292: 1319-1325. See also: Davenport RJ. Making Copies in the RNA world. Science 2001 May 18; 292: 1278; Strobel SA. Repopulating the RNA world. Nature 2001 Jun 28; 411: 1003-1006; Anonymous. Life's first letters. New Scientist 2001 May 26; 170(2292): 27.
Kintisch E. Is Life that Simple? Discover 2001 Apr; 22(4): 66-71.
Netting J. RNA world gets support as prelife scenario. Science News 2001 Apr 7; 159(14): 212.
Orme CA and others. Formation of chiral morphologies through selective binding of amino acids to calcite surface steps. Nature 2001 Jun 14; 411: 775-779. See also: Addada L and Weiner S. Crystal, asymmetry and life. Nature 2001 Jun 4; 411: 753-756; Gorman J. Rocks May Have Given a Hand to Life. Science News 2001 May 5; 159(18): 276.
Phoenix VR and others. Role of biomineralization as an ultraviolet shield: Implications for Archean life. Geology 2001 Sep; 29(9): 823-826.
Ribo JM and others. Chiral Sign Induction by Vortices During the Formation of Mesophases in Stirred Solutions. Science 2001 Jun 15; 292: 2063-2066. See also: Feringa BL. A New Twist on Chirality. Science 2001 Jun 15; 292: 2021-2022; Matteson DS. Chiral Selection When Stirred, not Shaken. [letter] Science 2001 Aug 24; 293: 1435-1436.
Saghatellan A, and others. A chiroselective peptide replicator. Nature 2001 Feb 15; 409: 797-801. See also: Siegel JS. Single-handed cooperation. Nature 2001 Feb 15; 409: 777-778.
Shen Y, Buick R, Canfield DE. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 2001 Mar 1; 410: 77-81.
Sleep NH. Oxygenating the atmosphere. Nature 2001 Mar 15; 410: 317-319. See also: Anonymous. Bug Breath. New Scientist 2001 Feb 3; 169(2276): 21.
Sowerby SJ, and others. Differential adsorption of nucleic acid bases: Relevance to the origin of life. Proceedings of the National Academy of Sciences 2001 Jan 20; 98(3): 820-822.
Szostak JW, Bartel DP, Luisi PL. Synthesizing life. Nature 2001 Jan 18; 409: 387-390.
Takemura M. Poxviruses and the Origin of the Eukaryotic Nucleus. Journal of Molecular Evolution 2001 May; 52(5): 419-425.
Wilde SA, Valley JW, Peck WH, Graham CM. Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago. Nature 2001 Jan 11; 409: 175-178. See also: Mojzsis SJ, Harrison TM, Pidgeon RT. Oxygen-isotope evidence from ancient zircons for liquid water at the Earth's surface 4,300 Myr ago. Nature 2001 Jan 11; 409: 178-181; Halliday AN. In the beginning... Nature 2001 Jan 11; 409: 144-145; Anonymous. Primeval crystal. New Scientist 2001 Jan 13; 169(2273): 23.
(Life from space)
Blake DF, Jenniskens P. The Ice of Life. Scientific American 2001 Aug; 285(2): 44-51.
Cooper G, and others. Carbonaceous meteorites as a source of suger-related organic compounds for the early Earth. Nature 2001 Dec 20/27; 414: 879-883. See also: Sephton MA. Life's sweet beginnings? Nature 2001 Dec 20/27; 414: 857-858; Cowen R. Did Space Rocks Deliver Sugar? Science News 2001 Dec 22 & 29; 160(25&26): 388.
Delsemme AH. An Argument for the Cometary Origin of the Biosphere. American Scientist 2001 Sep-Oct; 89(5): 432-442. See also: Lunine JI. Cold Beginnings. [letter]. American Scientist 2001 Nov-Dec; 89(6): 484.
Dworkin JP and others. Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices. Proceedings of the National Academy of Sciences 2001 Jan 30; 98(3): 815-819. See also: Cowen R. Life's Housing May Come from Space. Science News 2001 Feb 3; 159(5): 68; Svitil KA. Interstellar seeds of life. Discover 2001 Jul; 23(7): 13; Spotts PN. Raw materials for life may predate Earth's formation. Christian Science Monitor (January 30, 2001).
Ehrenfreund P, and others. Extraterrestrial amino acids in Orgueil and Ivuna: Tracing the parent body of CI type carbonaceous chondrites. Proceedings of the National Academy of Sciences 2001 Feb 27; 98(5): 2138-2141. See also: Anonymous. Simple recipe. New Scientist 2001 Mar 10; 169(2281): 27.
Gorman J. Cosmic Chemistry Gets Creative. Science News 2001 May 19; 159(20): 317-319.
Robert F. The Origin of Water on Earth. Science 2001 Aug 10; 293: 1056-1058.
Samuel E. Frosty space dust may have seeded life. New Scientist 2001 Mar 3; 169(2280): 18.
Anonymous. Water on Mars. New Scientist 2001 Dec 15; 172(2321): 27.
Abbott A. Resuscitated 'alien' microbes stir up an Italian storm. Nature 2001 May 17; 411: 229.
Chyba CF, Hand KP. Life Without Photosynthesis. Science 2001 Jun 15; 292: 2026-2027.
Coughlin BC. Searching for an alien haven in the heavens. Proceedings of the National Academy of Sciences 2001 Jan 10; 98(3): 796.
Cooper M. Mars on ice. New Scientist 2001 Jun 23; 170(2296): 13.
Garlick MA. Ideal homes. New Scientist 2001 Apr 7; 170(2285): 18.
Gee H. Nature insight: Astrobiology. Nature 2001 Feb 23; 409: 1079.
Hecht J. Life will find a way. New Scientist 2001 Mar 17; 169(2282): 4.
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Jones N. In the pink. New Scientist 2001 Dec 8; 172(2320): 9.
Kerr RA. Rethinking Water on Mars And the Origin of Life. Science 2001 Apr 6; 292: 398-40.
Knight J. Deep waters. New Scientist 2001 Jan 6; 169(2272): 11.
Le Page M. Alien footprints. New Scientist 2001 Jun 2; 170(2292): 12.
Lunine JI. The occurrence of Jovian planets and the habitability of planetary systems. Proceedings of the National Academy of Sciences 2001 Jan 30; 98(3): 809-814.
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McSween HYJr and others. Geochemical evidence for magmatic water within Mars from pyroxenes in the Shergotty meteorite. Nature 2001 Jan 25; 487-490. See also: Cowen R. Ancient Mars water: A deep source? Science News 2001 Feb 24; 159(8): 123.
Mustard JF, Cooper CD, Rifkin MK. Evidence for recent climate change on Mars from the identification of youthful near-surface ground ice. Nature 2001 Jul 26; 412: 411-414.
Phillips RJ and others. Ancient Geodynamics and Global-Scale Hydrology on Mars. Science 2001 Mar 30; 291: 2587-2591. See also: Cowen R. Creating a warmer, wetter Mars. Science News 2001 Mar 24; 159(12): 184.
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Schenk PM and others. Flooding of Ganymede's bright terrains by low-viscosity water-ice lavas. Nature 2001 Mar 1; 410: 57-60. See also: Prockter LM. Icing Ganymede. Nature 2001 Mar 1; 25-27; McCook A. Otherworldly Ocean. Scientific American 2001 May; 284(5): 25.
Thomas-Keprta KL, and others. Truncated hexa-octahedral magnetite crystals in ALH84001: Presumptive biosignatures. Proceedings of the National Academy of Sciences 2001 Feb 27; 98(5): 2164-2169. See also: Friedmann EI, and others. Chains of magnetite crystals in the meteorite ALH84001: Evidence of biological origin. Proceedings of the National Academy of Sciences 2001 Feb 27; 98(5): 2176-2181; Lorenz R. Mars Attracts! New Scientist 2001 May 19; 179(2291): 38-40; Kerr RA. Are Martian 'Pearl Chains' Signs of Life? Science 2001 Mar 9; 291: 1875-1876; Cowen R. Debate over life in Mars rock rekindles. Science News 2001 Mar 10; 159(10): 150; Anonymous. Martian compasses. New Scientist 2001 Mar 3; 169(2280): 12.
For a dissenting opinion see:
Buseck PR, and others. Magnetite morphology and life on Mars. Proceedings of the National Academy of Sciences 2001 Nov 20; 98(24): 13490-13495.
Turtle EP, Pierazzo E. Thickness of a Europan Ice Shell from Impact Crater Simulations. Science 2001 Nov 9; 294: 1326-1328. See also: Kerr RA. Putting a Lid on Life on Europa. Science 2001 Nov 9; 294: 1258-1259; Hecht J. It's not unusual. New Scientist 2001 Mar 17; 169(2282): 10.
REFERENCES: Chapter 2: Genetics and Evolution
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Giraud A and others. Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut. Science 2001 Mar 30; 291: 2606-2609.
Harder B. The Seeds of Malaria. Science News 2001 Nov 10; 160(19): 296-298.
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Zimmer C. Alternative Life Styles. Natural History 2001b May; 110(4): 42-45.
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Brown AJ, Casselton LA. Mating in mushrooms: increasing the chances but prolonging the affair. Trends in Genetics 2001 Jul; 17(7): 393-400.
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Balter M. Sequencing Set for Dreaded Mosquito. Science 2001 Mar 9; 291: 1873.
Bennetzen JL Arabidopsis arrives. Nature Genetics 2001 Jan; 27(1): 3-5. See also Willmann MR. Arabidopsis enters the post-sequencing era. Trends in Ecology and Evolution 2001 Feb; 17(2): 72-73; Sanderfoot AA, Raikhel NV. Arabidopsis could shed light on human genome. Nature 2001 Mar 15; 410: 299.
Butler D. Mouse genome roars ahead with new map. Nature 2001 Oct 4; 413: 444.
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Cyranoski D. Japan's ape sequencing effort set to unravel the brain's secrets. Nature 2001 Feb 8; 409: 651-652.
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Deloukas P, and others. The DNA sequence and comparative analysis of human chromosome 20. Nature 2001 Dec 20/27; 414: 865-871. See also: Hattori M, Taylor TD. Part three in the book of genes. Nature 2001 Dec 20/27; 854-856.
Douglas S and others. The highly reduced genome of an enslaved algal nucleus. Nature 2001 Apr 26; 410: 1091-1096. See also: Gilson PR and McFadden GI. A grin without a cat. Nature 2001 Apr 26; 410: 1040-1041; Pearlman RE. Lessons from a small genome. Nature Genetics 2001 May; 28(1): 6-7.
Gewolb J. Animals Line Up to Be Sequenced. Science 2001 Jul 20; 293: 409-410.
Glausiusz J. A Garden of Genomes. Discover 2001 Mar; 22(3): 14.
Helmuth L. Map of the Human Genome 3.0. Science 2001 Jul 27; 293: 583-584.
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001 Feb 15; 409: 860-921.
Karlin S, Bergman A, and Gentles AJ. Annotation of the Drosophila genome. Nature 2001 May 17; 411: 259-260.
Katsanis N, Worley KC, Lupski JR. An evaluation of the draft human genome sequence. Nature Genetics 2001 Sep; 29(1): 88-91.
Kintisch E. So what's the score? New Scientist 2001 May 12; 170(2290): 16.
Lee C. The incredible shrinking Human Genome. Trends in Genetics 2001 Apr; 17(4): 187-188.
Leyser O. Summitting the Arabidopsis genome. Trends in Genetics 2001 Apr; 17(4): 185-187.
Lynch M. The molecular natural history of the human genome. Trends in Ecology and Evolution 2001 Aug; 16(8): 420-422.
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Marshall E. Rat Genome Spurs an Unusual Partnership. Science 2001b Mar 9; 291: 1872-1873.
Martienssen R, McCombie WR. The First Plant Genome. Cell 2001 Jun 1; 105(5): 571-574.
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Pennisi E. New Genomes Shed Light on Complex Cells. Science 2001 May 18; 292: 1280-1281.
Ponting CP. Plagiarized bacterial genes in the human book of life. Trends in Genetics 2001 May; 17(5): 235-237. See also: Salzberg SL and others. Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? Science 2001 Jun 8; 292: 1903-1906; Stanhope MJ and others. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 2001 Jun 21; 411: 940-944; Roelofs J, Van Haastert PJM. Genes lost during evolution. Nature 2001 Jun 28; 411: 1013-1014; Ainsworth C. Not so jumpy. New Scientist 2001 Jun 23; 170(2296): 15; Andersson JO, Doolittle WF, Nesbo CL. Are There Bugs in Our Genome? Science 2001 Jun 8; 292: 1848-1850.
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(Genome related research)
Achaz G, Netter P, Coissac E. Study of Intrachromosomal Duplications Among the Eukaryotic Genomes. Molecular Biology and Evolution 2001 Dec; 18(2): 2280-2288.
Andersson JO, Andersson SGE. Pseudogenes, Junk DNA, and the Dynamics of Rickettsia Genomes. Molecular Biology and Evolution 2001 May; 18(5): 829-839.
Charlesworth D, Charlesworth B, McVean AT. Genome sequences and evolutionary biology, a two-way interaction. Trends in Ecology and Evolution 2001 May; 16(5): 235-242.
Eichler EE. Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends in Genetics 2001 Nov; 17(11): 661-669.
Friedman R. Bacterial Revelations. Natural History 2001 Jun; 110(5): 52-57.
Hirsh AE, Fraser HB. Protein dispensability and rate of evolution. Nature 2001 Jun 28; 411: 1046-1049.
Huynen MA, Snel B, Bork P. Inversions and the dynamics of eukaryotic gene order. Trends in Genetics 2001 Jun; 17(6): 304-306.
Kuhn G, Hijri M, Sanders IR. Evidence for the evolution of multiple genomes in arbuscular mycorrhizal fungi. Nature 2001 Dec 17; 414: 745-748. For a general background on these fungi see: Bever JD and others. Arbuscular Mycorrhizal Fungi: More Diverse than Meets the Eye, and the Ecological Tale of Why. BioScience 2001 Nov; 51(11): 923-931.
Massingham T, Davies L, Lio P. Analysing gene function after duplication. BioEssays 2001 Oct; 23(10): 873-876.
Pennisi E. Genome Duplications: The Stuff of Evolution? Science 2001 Dec 21; 294: 2458-2460.
Petrov DA. Evolution of genome size: new approaches to an old problem. Trends in Genetics 2001 Jan; 17(1): 23-28.
Van de Peer Y, Taylor S, Braasch I, Meyer A. The Ghost of Selection Past: Rates of Evolution and Functional Divergence of Anciently Duplicated Genes. Journal of Molecular Evolution 2001 Oct/Nov; 53(4/5): 436-446.
Wagner A. Birth and death of duplicated genes in completely sequenced eukaryotes. Trends in Genetics 2001 May; 17(5): 237-239.
Ardell DH, Sella G. On the Evolution of Redundancy in Genetic Codes. Journal of Molecular Evolution 2001 Oct/Nov; 53(4/5): 269-281.
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For background on the evolution of the genetic code see:
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REFERENCES: Chapter 3: The Origin of Species
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REFERENCES: Chapter 4: The Fossil Record
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REFERENCES: Chapter 4a: Human Evolution
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REFERENCES: Chapter 5: Homology and development
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REFERENCES: Chapter 6: Biochemical Similarities
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