irenenewton/Symbiosis_Papers

## Symbiosis_Papers
Symbiosis reviews
McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A. 2013;110(9):3229-36. doi: 10.1073/pnas.1218525110. PubMed PMID: 23391737; PMCID: PMC3587249.
Duron O, Hurst GDD. Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count. Bmc Biol. 2013;11. doi: Artn 45 10.1186/1741-7007-11-45. PubMed PMID: WOS:000317692700014.

Conflict and Cooperation in Symbiosis
Mushegian AA, Ebert D. Rethinking "mutualism'' in diverse host-symbiont communities. Bioessays. 2016;38(1):100-8. doi: 10.1002/bies.201500074. PubMed PMID: WOS:000371265200012.
Queller DC, Strassmann JE. Problems of multi-species organisms: endosymbionts to holobionts. Biol Philos. 2016;31(6):855-73. doi: 10.1007/s10539-016-9547-x. PubMed PMID: WOS:000389201100006.

Mechanisms of infection by symbionts

Batut J, Andersson SG, O'Callaghan D. The evolution of chronic infection strategies in the alpha-proteobacteria. Nat Rev Microbiol. 2004;2(12):933-45. doi: 10.1038/nrmicro1044. PubMed PMID: 15550939.
Dale C, Young SA, Haydon DT, Welburn SC. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proc Natl Acad Sci U S A. 2001;98(4):1883-8. doi: 10.1073/pnas.021450998. PubMed PMID: 11172045; PMCID: PMC29351.

Symbiont transmission strategies and host coevolution

Parratt SR, Frost CL, Schenkel MA, Rice A, Hurst GD, King KC. Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp. PLoS Pathog. 2016;12(6):e1005629. doi: 10.1371/journal.ppat.1005629. PubMed PMID: 27322651; PMCID: PMC4920596.
Koga R, Meng XY, Tsuchida T, Fukatsu T. Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface. P Natl Acad Sci USA. 2012;109(20):E1230-E7. doi: 10.1073/pnas.1119212109. PubMed PMID: WOS:000304369800008.
Clark MA, Moran NA, Baumann P, Wernegreen JJ. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution. 2000;54(2):517-25. PubMed PMID: 10937228.
Poulsen M, Bot ANM, Currie CR, Nielsen MG, Boomsma JJ. Within-colony transmission and the cost of a mutualistic bacterium in the leaf-cutting ant Acromyrmex octospinosus. Funct Ecol. 2003;17(2):260-9. doi: DOI 10.1046/j.1365-2435.2003.00726.x. PubMed PMID: WOS:000182457700013.
Watanabe K, Yukuhiro F, Matsuura Y, Fukatsu T, Noda H. Intrasperm vertical symbiont transmission. Proc Natl Acad Sci U S A. 2014;111(20):7433-7. doi: 10.1073/pnas.1402476111. PubMed PMID: 24799707; PMCID: PMC4034255.
Funkhouser LJ, Bordenstein SR. Mom knows best: the universality of maternal microbial transmission. PLoS Biol. 2013;11(8):e1001631. doi: 10.1371/journal.pbio.1001631. PubMed PMID: 23976878; PMCID: PMC3747981.
Longdon B, Jiggins FM. Vertically transmitted viral endosymbionts of insects: do sigma viruses walk alone? Proc Biol Sci. 2012;279(1744):3889-98. doi: 10.1098/rspb.2012.1208. PubMed PMID: 22859592; PMCID: PMC3427579.
Fitzpatrick BM. Symbiote transmission and maintenance of extra-genomic associations. Front Microbiol. 2014;5. doi: ARTN 46 10.3389/fmicb.2014.00046. PubMed PMID: WOS:000331931900001.


Endosymbiont genomic evolution

Jaenike J. Population genetics of beneficial heritable symbionts. Trends Ecol Evol. 2012;27(4):226-32. doi: 10.1016/j.tree.2011.10.005. PubMed PMID: 22104387.
Moran NA. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A. 1996;93(7):2873-8. PubMed PMID: 8610134; PMCID: PMC39726.
Gil R, Sabater-Munoz B, Latorre A, Silva FJ, Moya A. Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci U S A. 2002;99(7):4454-8. doi: 10.1073/pnas.062067299. PubMed PMID: 11904373; PMCID: PMC123669.
Wernegreen JJ. Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet. 2002;3(11):850-61. doi: 10.1038/nrg931. PubMed PMID: 12415315.
Moran NA, McCutcheon JP, Nakabachi A. Genomics and Evolution of Heritable Bacterial Symbionts. Annu Rev Genet. 2008;42:165-90. doi:
Degnan PH, Lazarus AB, Brock CD, Wernegreen JJ. Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. Syst Biol. 2004;53(1):95-110. PubMed PMID: 14965905.
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405(6784):299-304. doi: 10.1038/35012500. PubMed PMID: 10830951.

Endosymbiont adaptation to new hosts

Nakayama S, Parratt SR, Hutchence KJ, Lewis Z, Price TAR, Hurst GDD. Can maternally inherited endosymbionts adapt to a novel host? Direct costs of Spiroplasma infection, but not vertical transmission efficiency, evolve rapidly after horizontal transfer into D-melanogaster. Heredity. 2015;114(6):539-43. doi: 10.1038/hdy.2014.112. PubMed PMID: WOS:000354386700002.
Jiggins FM, Hurst GD, Yang Z. Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol. 2002;19(8):1341-9. doi: 10.1093/oxfordjournals.molbev.a004195. PubMed PMID: 12140246.

Evolution in extracellular symbionts

Barroso-Batista J, Demengeot J, Gordo I. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat Commun. 2015;6. doi: ARTN 8945 10.1038/ncomms9945. PubMed PMID: WOS:000366380400004.
Barroso-Batista J, Sousa A, Lourenco M, Bergman ML, Sobral D, Demengeot J, Xavier KB, Gordo I. The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. Plos Genet. 2014;10(3). doi: ARTN e1004182

Host adaptation by symbiosis

Lopez-Garcia P, Moreira D. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem Sci. 1999;24(3):88-93. PubMed PMID: 10203753.
Dunbar HE, Wilson ACC, Ferguson NR, Moran NA. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts. Plos Biology. 2007;5(5):1006-15. doi: ARTN e96 10.1371/journal.pbio.0050096. PubMed PMID: WOS:000246716700009.
Vorburger C. The evolutionary ecology of symbiont-conferred resistance to parasitoids in aphids. Insect Sci. 2014;21(3):251-64. doi: 10.1111/1744-7917.12067. PubMed PMID: WOS:000336463400002.
Bennett GM, Moran NA. Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole. P Natl Acad Sci USA. 2015;112(33):10169-76. doi: 10.1073/pnas.1421388112. PubMed PMID: WOS:000359738300039.
Douglas AE. Host benefit and the evolution of specialization in symbiosis. Heredity. 1998;81:599-603. doi: DOI 10.1038/sj.hdy.6884550. PubMed PMID: WOS:000077862700001.
Marquez LM, Redman RS, Rodriguez RJ, Roossinck MJ. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance (vol 315, pg 513, 2007). Science. 2007;316(5822):201-. PubMed PMID: WOS:000245654500020.

ANNA G. HIMLER, TETSUYA ADACHI-HAGIMORI, JACQUELINE E. BERGEN, AMARANTA KOZUCH, SUZANNE E. KELLY, BRUCE E. TABASHNIK, ELAD CHIEL, VICTORIA E. DUCKWORTH, TIMOTHY J. DENNEHY, EINAT ZCHORI-FEIN, MARTHA S. HUNTER. Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias. SCIENCE 08 APR 2011 : 254-256

The hologenome/phylosymbiosis controversy
Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TC, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR. Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes. mSystems. 2016;1(2). doi: 10.1128/mSystems.00028-16. PubMed PMID: 27822520; PMCID: PMC5069740.
Douglas AE, Werren JH. Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts. MBio. 2016;7(2):e02099. doi: 10.1128/mBio.02099-15. PubMed PMID: 27034285; PMCID: PMC4817262.
Moran NA, Sloan DB. The Hologenome Concept: Helpful or Hollow? PLoS Biol. 2015;13(12):e1002311. doi: 10.1371/journal.pbio.1002311. PubMed PMID: 26636661; PMCID: PMC4670207.
Brucker RM, Bordenstein SR. The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia. Science. 2013;341(6146):667-9. doi: 10.1126/science.1240659. PubMed PMID: WOS:000322884800042.
Bordenstein SR, Theis KR. Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol. 2015;13(8):e1002226. doi: 10.1371/journal.pbio.1002226. PubMed PMID: 26284777; PMCID: PMC4540581.
Rosenberg E, Zilber-Rosenberg I. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept. MBio. 2016;7(2):e01395. doi: 10.1128/mBio.01395-15. PubMed PMID: 27034283; PMCID: PMC4817260.
Brooks AW, Kohl KD, Brucker RM, van Opstal EJ, Bordenstein SR. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. Plos Biology. 2016;14(11). doi: ARTN e2000225 10.1371/journal.pbio.2000225. PubMed PMID: WOS:000392113500007.
	Symbiosis reviews
	McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Loso T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ. Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A. 2013;110(9):3229-36. doi: 10.1073/pnas.1218525110. PubMed PMID: 23391737; PMCID: PMC3587249.
	Duron O, Hurst GDD. Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count. Bmc Biol. 2013;11. doi: Artn 45 10.1186/1741-7007-11-45. PubMed PMID: WOS:000317692700014.

	Conflict and Cooperation in Symbiosis
	Mushegian AA, Ebert D. Rethinking "mutualism'' in diverse host-symbiont communities. Bioessays. 2016;38(1):100-8. doi: 10.1002/bies.201500074. PubMed PMID: WOS:000371265200012.
	Queller DC, Strassmann JE. Problems of multi-species organisms: endosymbionts to holobionts. Biol Philos. 2016;31(6):855-73. doi: 10.1007/s10539-016-9547-x. PubMed PMID: WOS:000389201100006.

	Mechanisms of infection by symbionts

	Batut J, Andersson SG, O'Callaghan D. The evolution of chronic infection strategies in the alpha-proteobacteria. Nat Rev Microbiol. 2004;2(12):933-45. doi: 10.1038/nrmicro1044. PubMed PMID: 15550939.
	Dale C, Young SA, Haydon DT, Welburn SC. The insect endosymbiont Sodalis glossinidius utilizes a type III secretion system for cell invasion. Proc Natl Acad Sci U S A. 2001;98(4):1883-8. doi: 10.1073/pnas.021450998. PubMed PMID: 11172045; PMCID: PMC29351.

	Symbiont transmission strategies and host coevolution

	Parratt SR, Frost CL, Schenkel MA, Rice A, Hurst GD, King KC. Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp. PLoS Pathog. 2016;12(6):e1005629. doi: 10.1371/journal.ppat.1005629. PubMed PMID: 27322651; PMCID: PMC4920596.
	Koga R, Meng XY, Tsuchida T, Fukatsu T. Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface. P Natl Acad Sci USA. 2012;109(20):E1230-E7. doi: 10.1073/pnas.1119212109. PubMed PMID: WOS:000304369800008.
	Clark MA, Moran NA, Baumann P, Wernegreen JJ. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution. 2000;54(2):517-25. PubMed PMID: 10937228.
	Poulsen M, Bot ANM, Currie CR, Nielsen MG, Boomsma JJ. Within-colony transmission and the cost of a mutualistic bacterium in the leaf-cutting ant Acromyrmex octospinosus. Funct Ecol. 2003;17(2):260-9. doi: DOI 10.1046/j.1365-2435.2003.00726.x. PubMed PMID: WOS:000182457700013.
	Watanabe K, Yukuhiro F, Matsuura Y, Fukatsu T, Noda H. Intrasperm vertical symbiont transmission. Proc Natl Acad Sci U S A. 2014;111(20):7433-7. doi: 10.1073/pnas.1402476111. PubMed PMID: 24799707; PMCID: PMC4034255.
	Funkhouser LJ, Bordenstein SR. Mom knows best: the universality of maternal microbial transmission. PLoS Biol. 2013;11(8):e1001631. doi: 10.1371/journal.pbio.1001631. PubMed PMID: 23976878; PMCID: PMC3747981.
	Longdon B, Jiggins FM. Vertically transmitted viral endosymbionts of insects: do sigma viruses walk alone? Proc Biol Sci. 2012;279(1744):3889-98. doi: 10.1098/rspb.2012.1208. PubMed PMID: 22859592; PMCID: PMC3427579.
	Fitzpatrick BM. Symbiote transmission and maintenance of extra-genomic associations. Front Microbiol. 2014;5. doi: ARTN 46 10.3389/fmicb.2014.00046. PubMed PMID: WOS:000331931900001.


	Endosymbiont genomic evolution

	Jaenike J. Population genetics of beneficial heritable symbionts. Trends Ecol Evol. 2012;27(4):226-32. doi: 10.1016/j.tree.2011.10.005. PubMed PMID: 22104387.
	Moran NA. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A. 1996;93(7):2873-8. PubMed PMID: 8610134; PMCID: PMC39726.
	Gil R, Sabater-Munoz B, Latorre A, Silva FJ, Moya A. Extreme genome reduction in Buchnera spp.: toward the minimal genome needed for symbiotic life. Proc Natl Acad Sci U S A. 2002;99(7):4454-8. doi: 10.1073/pnas.062067299. PubMed PMID: 11904373; PMCID: PMC123669.
	Wernegreen JJ. Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet. 2002;3(11):850-61. doi: 10.1038/nrg931. PubMed PMID: 12415315.
	Moran NA, McCutcheon JP, Nakabachi A. Genomics and Evolution of Heritable Bacterial Symbionts. Annu Rev Genet. 2008;42:165-90. doi:
	Degnan PH, Lazarus AB, Brock CD, Wernegreen JJ. Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia. Syst Biol. 2004;53(1):95-110. PubMed PMID: 14965905.
	Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405(6784):299-304. doi: 10.1038/35012500. PubMed PMID: 10830951.

	Endosymbiont adaptation to new hosts

	Nakayama S, Parratt SR, Hutchence KJ, Lewis Z, Price TAR, Hurst GDD. Can maternally inherited endosymbionts adapt to a novel host? Direct costs of Spiroplasma infection, but not vertical transmission efficiency, evolve rapidly after horizontal transfer into D-melanogaster. Heredity. 2015;114(6):539-43. doi: 10.1038/hdy.2014.112. PubMed PMID: WOS:000354386700002.
	Jiggins FM, Hurst GD, Yang Z. Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae. Mol Biol Evol. 2002;19(8):1341-9. doi: 10.1093/oxfordjournals.molbev.a004195. PubMed PMID: 12140246.

	Evolution in extracellular symbionts

	Barroso-Batista J, Demengeot J, Gordo I. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria. Nat Commun. 2015;6. doi: ARTN 8945 10.1038/ncomms9945. PubMed PMID: WOS:000366380400004.
	Barroso-Batista J, Sousa A, Lourenco M, Bergman ML, Sobral D, Demengeot J, Xavier KB, Gordo I. The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. Plos Genet. 2014;10(3). doi: ARTN e1004182

	Host adaptation by symbiosis

	Lopez-Garcia P, Moreira D. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem Sci. 1999;24(3):88-93. PubMed PMID: 10203753.
	Dunbar HE, Wilson ACC, Ferguson NR, Moran NA. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts. Plos Biology. 2007;5(5):1006-15. doi: ARTN e96 10.1371/journal.pbio.0050096. PubMed PMID: WOS:000246716700009.
	Vorburger C. The evolutionary ecology of symbiont-conferred resistance to parasitoids in aphids. Insect Sci. 2014;21(3):251-64. doi: 10.1111/1744-7917.12067. PubMed PMID: WOS:000336463400002.
	Bennett GM, Moran NA. Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole. P Natl Acad Sci USA. 2015;112(33):10169-76. doi: 10.1073/pnas.1421388112. PubMed PMID: WOS:000359738300039.
	Douglas AE. Host benefit and the evolution of specialization in symbiosis. Heredity. 1998;81:599-603. doi: DOI 10.1038/sj.hdy.6884550. PubMed PMID: WOS:000077862700001.
	Marquez LM, Redman RS, Rodriguez RJ, Roossinck MJ. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance (vol 315, pg 513, 2007). Science. 2007;316(5822):201-. PubMed PMID: WOS:000245654500020.

	ANNA G. HIMLER, TETSUYA ADACHI-HAGIMORI, JACQUELINE E. BERGEN, AMARANTA KOZUCH, SUZANNE E. KELLY, BRUCE E. TABASHNIK, ELAD CHIEL, VICTORIA E. DUCKWORTH, TIMOTHY J. DENNEHY, EINAT ZCHORI-FEIN, MARTHA S. HUNTER. Rapid Spread of a Bacterial Symbiont in an Invasive Whitefly Is Driven by Fitness Benefits and Female Bias. SCIENCE 08 APR 2011 : 254-256

	The hologenome/phylosymbiosis controversy
	Theis KR, Dheilly NM, Klassen JL, Brucker RM, Baines JF, Bosch TC, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR. Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes. mSystems. 2016;1(2). doi: 10.1128/mSystems.00028-16. PubMed PMID: 27822520; PMCID: PMC5069740.
	Douglas AE, Werren JH. Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts. MBio. 2016;7(2):e02099. doi: 10.1128/mBio.02099-15. PubMed PMID: 27034285; PMCID: PMC4817262.
	Moran NA, Sloan DB. The Hologenome Concept: Helpful or Hollow? PLoS Biol. 2015;13(12):e1002311. doi: 10.1371/journal.pbio.1002311. PubMed PMID: 26636661; PMCID: PMC4670207.
	Brucker RM, Bordenstein SR. The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia. Science. 2013;341(6146):667-9. doi: 10.1126/science.1240659. PubMed PMID: WOS:000322884800042.
	Bordenstein SR, Theis KR. Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol. 2015;13(8):e1002226. doi: 10.1371/journal.pbio.1002226. PubMed PMID: 26284777; PMCID: PMC4540581.
	Rosenberg E, Zilber-Rosenberg I. Microbes Drive Evolution of Animals and Plants: the Hologenome Concept. MBio. 2016;7(2):e01395. doi: 10.1128/mBio.01395-15. PubMed PMID: 27034283; PMCID: PMC4817260.
	Brooks AW, Kohl KD, Brucker RM, van Opstal EJ, Bordenstein SR. Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History. Plos Biology. 2016;14(11). doi: ARTN e2000225 10.1371/journal.pbio.2000225. PubMed PMID: WOS:000392113500007.