| References |
|
|
Anderson JO
(2010)
Gene transfer diversification of microbial eukaryotes.
Annual Review of Microbiology
63:
177193 (DOI 10.1146/annurev.micro091208.073203).
|
|
|
Arnold ML and
Fogarty ND
(2009)
Reticulate evolution and marine organisms: the final frontier?
International Journal of Molecular Sciences
10:
38363860 (DOI 10.3390/ijms10093836).
|
|
|
Bapteste E,
O¢Malley MA,
Beiko RG et al.
(2009)
Prokaryotic evolution and the tree of life are two different things.
Biology Direct
4:
34 (DOI 10.1186/1745-6150-4-34).
|
|
|
Bapteste E,
Susko E,
Leigh J et al.
(2008)
Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny.
Molecular Biology and Evolution
25:
8391 (DOI 10.1093/mlbev/msm229).
|
|
|
Boussau B,
Guéguen L and
Gouy M
(2008)
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria.
BMC Evolutionary Biology
8:
272 (DOI 10.1186/1471-2148-8-272).
|
|
|
Chan CX,
Beiko RG,
Darling AE and
Ragan MA
(2009)
Lateral transfer of genes and gene fragments in prokaryotes.
Genome Biology and Evolution
2009:
429438 (DOI 10.1093/gbe/evp044).
|
|
|
Cohen O and
Pupko T
(2010)
Inference and characterization of horizontally transferred gene families using stochastic mapping.
Molecular Biology and Evolution
27:
703713 (DOI 10.1093/molbev/msp240).
|
|
|
Dagan T,
Artzy-Randrup Y and
Martin W
(2008)
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution.
Proceedings of the National Academy of Sciences of the USA
105:
1003910044 (DOI 10.1073/pnas.0800679105).
|
|
|
book
Darwin C
(1859)
On the Origin of Species by means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life.
London: Murray.
|
|
|
Doolittle WF
(1999)
Phylogenetic classification and the universal tree.
Science
284:
21242128 (DOI 10.1126/science.284.5423.2124).
|
|
|
Doolittle WF and
Bapteste E
(2007)
Pattern pluralism and the tree of life hypothesis.
Proceedings of the National Academy of Sciences of the USA
104:
20432049 (DOI 10.1073/pnas.0610699104).
|
|
|
Doolittle WF and
Logsdon JM Jr
(1998)
Do Archaea have a mixed heritage?
Current Biology
8:
R209R211 (DOI 10.1016/S0960-9822(98)70127-7).
|
|
|
Embley TM and
Martin W
(2006)
Eukaryotic evolution, changes and challenges.
Nature
440:
623630 (DOI 10.1038/nature04546).
|
|
|
Galtier N and
Daubin V
(2008)
Dealing with incongruence in phylogenetic analyses.
Philosophical Transactions of the Royal Society B
363:
40234029 (DOI 10.1098/rstb.2008.0144).
|
|
|
Gladyshev EA,
Meselson M and
Arkhipova IR
(2008)
Massive horizontal gene transfer in bdelloid rotifers.
Science
320:
12101213 (DOI 10.1126/science.1156407).
|
|
|
Gogarten JP,
Doolittle WF and
Lawrence JG
(2002)
Prokaryotic evolution in light of gene transfer.
Molecular Biology and Evolution
19:
22262238.
|
|
|
Gogarten JP and
Townsend JP
(2005)
Horizontal gene transfer, genome innovation and evolution.
Nature Reviews. Microbiology
3:
679687 (DOI 10.1038/nrmicro1204).
|
|
|
Goldenfeld N and
Woese C
(2007)
Biology's next revolution.
Nature
445:
369 (DOI 10.1038/445369a).
|
|
|
Gophna U,
Charlebois RL and
Doolittle WF
(2004)
Have archaeal genes contributed to bacterial virulence?
Trends in Microbiology
12:
213219 (DOI 10.1016/j.tim.2004.03.002).
|
|
|
Gribaldo S and
Brochier C
(2009)
Phylogeny of prokaryotes: does it exist and why should be care?
Research in Microbiology
160:
513521 (DOI 10.1016/j.resmic.2009.07.006).
|
|
|
Guljamow A,
Jenke-Kodama H,
Saumweber H et al.
(2007)
Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium.
Current Biology
17:
R757R759 (DOI 10.1016/j.cub.2007.06.063).
|
|
|
Hilario E and
Gogarten JP
(1993)
Horizontal gene transfer of ATPase genes the tree of life becomes a net of life.
BioSystems
31:
111119 (DOI 10.1016/0303-2647(93)90038-E).
|
|
|
Hotopp JCD,
Clark ME,
Oliveira DCSG et al.
(2007)
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes.
Science
317:
17531756 (DOI 10.1126/science.1142490).
|
|
|
Huang J and
Gogarten JP
(2006)
Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
Trends in Genetics
22:
361366 (DOI 10.1016/j.tig.2006.05.004).
|
|
|
Huang J and
Gogarten JP
(2008)
Concerted gene recruitment in early plant evolution.
Genome Biology
9:
R109 (DOI 10.1186/gb-2008-9-7-r109).
|
|
|
Jain R,
Rivera MC and
Lake JA
(1999)
Horizontal gene transfer among genomes: the complexity hypothesis.
Proceedings of the National Academy of Sciences of the USA
96:
38013806.
|
|
|
Kanhere A and
Vingron M
(2009)
Horizontal gene transfer in prokaryotes show differential preferences for metabolic and translational genes.
BMC Evolutionary Biology
9:
9 (DOI 10.1186/1471-2148-9-9).
|
|
|
Keeling PJ and
Palmer JD
(2008)
Horizontal gene transfer in eukaryotic evolution.
Nature Reviews. Genetics
9:
605618 (DOI 10.1038/nrg2386).
|
|
|
Koonin EV,
Makarova AS and
Aravind L
(2001)
Horizontal gene transfer in prokaryotes. Quantification and classification.
Annual Review of Microbiology
55:
709742.
|
|
|
Koonin EV and
Wolf YI
(2009a)
Is evolution Darwinian or/and Lamarckian?
Biology Direct
4:
42 (DOI 10.1186/1745-6150-4-42).
|
|
|
Lane CE and
Archibald JM
(2008)
The eukaryotic tree of life: endosymbiosis takes its TOL.
Trends in Ecology and Evolution
23:
268275 (DOI 10.1016/j.tree.2008.02.004).
|
|
|
Lapierre P and
Gogarten JP
(2009)
Estimating the size of the bacterial pan-genome.
Trends in Genetics
25:
107110 (DOI 10.1016/j.tig.2008.12.004).
|
|
|
Lercher MJ and
Pál C
(2008)
Integration of horizontally transferred genes into regulatory interaction networks takes many million years.
Molecular Biology and Evolution
25:
559567 (DOI 10.1093/molbev/msm283).
|
|
|
Lovell HC,
Mansfield JW,
Godfrey SAC et al.
(2009)
Bacterial evolution by genomic island occurs via DNA transformation in planta.
Current Biology
19:
15861590 (DOI 10.1016/j.cub.2009.08.018).
|
|
|
Marri PR and
Golding GB
(2008)
Gene amelioration demonstrated: the journey of nascent genes in bacteria.
Genome
51:
164168 (DOI 10.1139/G07-105).
|
|
|
Nakamura Y,
Itoh T,
Matsuda H and
Gojobori T
(2004)
Biased biological functions of horizontally transferred genes in prokaryotic genomes.
Nature Genetics
36:
760766 (DOI 10.1038/ng1381).
|
|
|
Oliver KR and
Greene WK
(2009)
Transposable elements: powerful facilitators of evolution.
Bioessays
31:
703714 (DOI 10.1002/bies.200800219).
|
|
|
Ragan MA
(2001)
Detection of lateral gene transfer among microbial genomes.
Current Opinion in Genetics and Development
11:
620626 (DOI 10.1016/S0959-437X(00)00244-6).
|
|
|
Rannala B and
Yang Z
(2008)
Phylogenetic inference using whole genomes.
Annual Review of Genomics and Human Genetics
9:
217231 (DOI 10.1146/annurev.genom.9.081307.164407).
|
|
|
Rest JS and
Mindell DP
(2003)
Retroids in archaea: phylogeny and lateral origin.
Molecular Biology and Evolution
20:
11341142 (DOI 10.1093/molbev/msg135).
|
|
|
Richards TA,
Dacks JB,
Jenkinson JM,
Thornton CR and
Talbot NJ
(2006)
Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms.
Current Biology
16:
18571864 (DOI 10.1016/j.cub.2006.07.052).
|
|
|
Rivera MC and
Lake JA
(2004)
The ring of life provides evidence for a genome fusion origin of eukaryotes.
Nature
431:
152155 (DOI 10.1038/nature02848).
|
|
|
Rumpho ME,
Worful JM,
Lee J et al.
(2008)
Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica.
Proceedings of the National Academy Sciences of the USA
46:
1786717871 (DOI 10.1073/pnas.0804968105).
|
|
|
Sorek R,
Zhu Y,
Creevey CJ et al.
(2007)
Genome-wide experimental determination of barriers to horizontal gene transfer.
Science
318:
14491452 (DOI 10.1126/science.1147112).
|
|
|
Syvanen M
(1985)
Cross-species gene transfer: Implications for a new theory of evolution.
Journal of Theoretical Biology
112:
333343.
|
|
|
Tettelin H,
Masignani V,
Cieslewicz MJ et al.
(2005)
Genome analysis of multiple pathogenic isolates of Streptococus agalactiae: implications for the microbial pan-genome.
Proceedings of the National Academy of Sciences of the USA
102:
1395013955 (DOI 10.1073/pnas.0506758102).
|
|
|
Wagner A and
De la Chaux N
(2008)
Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences.
Molecular Genetics and Genomics
280:
397408 (DOI 10.1007/s00438-008-0373-y).
|
|
|
Woese CR,
Kandler O and
Wheelis M
(1990)
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Proceedings of the National Academy of Sciences USA
87:
45764579.
|
|
|
Zhaxybayeva O,
Gogarten JP,
Charlebois RL,
Doolittle WF and
Papke RT
(2006)
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events.
Genome Research
16:
10991108 (DOI 10.1101/gr.5322306).
|
|
|
Zhaxybayeva O,
Swithers KS,
Lapierre P et al.
(2009)
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.
Proceedings of the National Academy of Sciences of the USA
106:
58655870 (DOI 10.1073/pnas0901260106).
|
| Further Reading |
|
|
Andersson JO
(2005)
Lateral gene transfer in eukaryotes.
Cellular and Molecular Life Sciences
62:
11821197 (DOI 10.1007/s00018-005-4539-z).
|
|
|
Bock R
(2010)
The give-and-take of DNA: horizontal gene transfer in plants.
Trends in Plant Science
15:
1122 (DOI 10.1016/j.tplants.2009.10.001).
|
|
|
Boto L
(2010)
Horizontal gene transfer in evolution: facts and challenges.
Proceedings of the Royal Society B
277:
819827 (DOI 10.1098/rspb.2009.1679).
|
|
|
Koonin EV and
Wolf YI
(2009b)
The fundamental units, processes and patterns of evolution, and the tree of life conundrum.
Biology Direct
4:
33 (DOI 10.1186/1745-6150-4-33).
|
|
|
Kuo C-H and
Ochman H
(2009)
The fate of new bacterial genes.
FEMS Microbiological Reviews
33:
3843 (DOI 10.1111/j.1574-6976.2008.00140.x).
|
|
|
Kurland CG
(2005)
What tangled web: barriers to rampant horizontal gene transfer.
Bioessays
27:
741747 (DOI 10.1002/bies.20258).
|
|
|
Ragan MA and
Beiko RG
(2009)
Lateral genetic transfer: open issues.
Philosophical Transactions of the Royal Society B
364:
22412251 (DOI 10.1098/rstb.2009.0031).
|
|
|
Rocha EPC
(2008)
Evolutionary patterns in prokaryotic genomes.
Current Opinion in Microbiology
11:
454460 (DOI 10.1016/j.mib.2008.09.007).
|
|
|
Whitaker JW,
McConkey GA and
Westhead DR
(2009)
Prediction of horizontal gene transfers in eukaryotes: approaches and challenges.
Biochemical Society Transactions
37:
792795 (DOI 10.1042/BST037092).
|