1. Recent SCI papers (2009-)

2013 (6)

(1)  Zhang H, Wu GG, Zhang H, Xie P*, Xu J*, Zhou Q. Role of body size and temporal hydrology in the dietary shifts of shortjaw tapertail anchovy Coilia brachygnathus (Actinopterygii, Engraulidae) in a large floodplain lake. Hydrobiologia (2012) 703:247–256 (*Correspondent author)

(2)    Zhao YY, Xie P*, Fan HH, Zhao SJ. Impairment of the mitochondrial OXPHOS system and oxidative stress in liver of crucian carp (Carassius auratus L) exposed to microcystins. Environ. Toxicol. (2013) (*Correspondent author)

(3)         Zhang X, Xie P*, Zhang XZ*, Zhou WS, Zhao SJ, Zhao Y Y, Cai Y. Toxic effects of microcystin-LR on HepG2 cell line under hypoxic and normoxic conditions. J Appl. Toxicol. (2013) (*Correspondent author)

(4)  Wu LY, Wang Q, Tao M, Chen J, Ma ZM, Xie P*.  Preliminary study of the distribution and accumulation of GSH/Cys metabolites of hepatotoxic microcystins-RR in common carp from a lake with protracted cyanobacterial bloom (Lake Taihu, China). B. Environ. Contam. Tox. 2013  (*Correspondent author)

(5)  Zhou WS, Zhang XZ, Xie P*, Liang HL, Zhang X*. The suppression of hematopoiesis function in Balb/c mice induced by prolonged exposure of microcystin-LR. Toxicol. Lett. (2013)

(6)  Zhang DW, Deng XW, Xie P*, Chen J, Guo LG. Risk assessment of microcystins in silver carp (Hypophthalmichthys molitrix) from eight eutrophic lakes in China. Food Chem. (2013)

2012（20篇）

(7)         Zhao YY, Xie P*, Fan HH. Genomic profiling of microRNAs and proteomics reveals an early molecular alteration associated with tumorigenesis induced by MC-LR in mice. Environ Sci. Technol. (2012) 46: 34–41 (*Correspondent author)

(8)         Deng XW,  Xie P, Qi M, Liang GD, Chen J*, Ma ZM, Jiang Y. Microwave-assisted purge-and-trap extraction device coupled with gas chromatography and mass spectrometry for the determination of five predominant odors in sediment, fish tissues, and algal cells. J Chromatogr A (2012) 1219: 75–82 (*Correspondent author)

(9)         Zhao SJ, Xie P*, Li GY, Cai Y, Xiong Q, Zhao YY. The proteomic study on cellular responses of the testes of zebra？sh (Danio rerio) exposed to microcystin-RR. Proteomics (2012) 12: 300–312 (*Correspondent author)

(10)     Tao M, Xie P*, Chen J, Qin BQ, Zhang DW, Niu Y, Zhang M, Wang Q, Wu LY. Use of a generalized additive model to investigate key abiotic factors affecting microcystin cellular quotas in heavy bloom areas of Lake Taihu. PLoS ONE (2012) 7: e32020

(11)     Yang Q, Xie P*, Shen H, Xu J, Wang PL, Zhang B. A novel flushing strategy for diatom bloom prevention in the lower-middle Hanjiang River. Water Res. (2012) 46: 2525-2534

(12)     Tan XY, Xie P*, Luo Z*, Lin H Z, Zhao Y H, Xi W Q. Dietary manganese requirement of juvenile yellow catfish Pelteobagrus fulvidraco, and effects on whole body mineral composition and hepatic intermediary metabolism. Aquaculture (2012) 326-329: 68–73 (*Correspondent author)

(13)     Zhang DW, Yang Q, Xie P, Deng XW, Chen J*, Dai M. Detoxification pathway of MC-LR in liver of bighead carp (Aristichthys nobilis): A field and laboratory study. Ecotoxicology (2012) 21: 244–252 (*Correspondent author)

(14)     Yuan GL, Xie P*, Zhang XZ, Tang R, Gao Y, Li DP, Li L. In vivo studies on the immunotoxic effects of microcystins on rabbit. Environ. Toxicol. (2011) 27: 83–89 (*Correspondent author)

(15)     Qiu T, Xie P, Li L, Guo LG, Zhang DW, Zhou Q. Nephrotoxic effects from chronic toxic cyanobacterial blooms in fishes with different trophic levels in a large Chinese lake. Environ. Toxicol. Pharm. (2012) 33: 252-261 (*Correspondent author)

(16)     Wang PL, Shen H, Xie P*. Can hydrodynamics change phosphorus strategies of diatoms? – Nutrient levels and diatom blooms in lotic and lentic ecosystems. Microbiol. Ecol. (2012) 63:369–382 (*Correspondent author)

(17)     Cai Y, Li HY, Hao L, Li GY, Xie P, Chen J*. Identificationof cda gene in bighead carp and its expression in response to microcystin-LR. Ecotoxicol. Environ. Saf. (2012) 79: 206–213 (*Correspondent author)

(18)     He J, Chen J*, Xie P, Zhang D W, Li G Y, Wu L Y, Zhang W, Guo X C, Li S C. Quantitatively evaluating detoxification of the hepatotoxic microcystins through the glutathione and cysteine pathway in the cyanobacteria-eating bighead carp. Aquat. Toxicol. (2012) 116–117: 61-68  (*Correspondent author)

(19)     Yuan JF, Su NA, Wang M, Xie, P, Shi ZL, Li, LJ. Down-regulation of heme oxygenase-1 by SVCV infection. Fish Shellfish Immun. (2012) 32: 301-306

(20)     Li H, Cai Y, Xie P*, Chen J, Hao L, Li G, Xiong Q. Identification and expression profile of Id1 in bighead carp in response to microcystin-LR. Environ. Toxicol. Pharmacol. (2012) 34: 324–333 (*Correspondent author)  

(21)     Yang H, Xie P, Ni LY, Flower R J. 2012. Pollution in the Yangtze. Science 337: 410

(22)  Sun XX, Tao M, Qin BQ, Qi M, Niu Y, Zhang J, Ma ZM, Xie P*. 2012. Large-scale field evidence on the enhancement of small-sized cladocerans by microcystis blooms in Lake Taihu, China. J. Plankton Res. 34: 853-863 (*Correspondent author)

(23)  Cai, YJ, Gong ZJ, Xie P. 1012. Community structure and spatiotemporal patterns of macrozoobenthos in Lake Chaohu (China). Aquat. Biol. 17: 35-46

(24)     Zou WS, Liang HL, Xie P*. Zhan XZ. 2012. Toxic effects of microcystin-LR on mice erythrocytes in vitro. Fresen. Environ. Bull. 21: 2274-2281

(25) Qi M, Chen J, Sun XX, Deng XW, Niu Y, Xie P*. Development of models for predicting the predominant taste and odor compounds in Taihu Lake, China. PLoS ONE (2012) 7(12): e51976. doi:10.1371/journal.pone.0051976 (*Correspondent author)

(26) He J, Chen J*, Wu LY, Li GY, Xie P*. Metabolic response to oral microcystin-LR exposure in the rat by NMR-based metabonomic study. J Proteme Res. (2012) 11 (12), pp 5934–5946 (*Correspondent author)

2011（20篇）

(27)     Li GY, Chen J, Xie P*, Jiang Y, Wu LY, Zhang XZ. Protein expression profiling in the zebrafish (Danio rerio) embryos exposed to the microcystin-LR. Proteomics (2011) 11: 2003–2018 (*Correspondent author)

(28)     Deng XW, Liang GD, Chen J, Qi M, Xie P*. Simultaneous determination of eight common odors in natural water body using automatic purge and trap coupled to gas chromatography with mass spectrometry. J Chromatogr A (2011) 1218: 3791–3798 (*Correspondent author)

(29)     Niu Y, Shen H, Chen J, Xie P*, Yang X, Tao M, Ma ZM, Qi M. Phytoplankton community succession shaping bacterioplankton community composition in Lake Taihu, China. Wat. Res. (2011) 45: 4169 -4182 (*Correspondent author)

(30)     Zhao YY, Xiong Q, Xie P*. Analysis of microRNA expression in embryonic developmental toxicity induced by MC-RR. PloS ONE (2011) 6: e22676 (*Correspondent author)

(31)     Yang H, Xie P, Ni LY, Flower RJ. Underestimation of CH4 emission from freshwater lakes in China. ES&T (2011) 45, 4203–4204

(32)     Zhang M, Wang ZQ, Xu J, Liu YQ, Ni LY, Cao T, Xie P. Ammonium, microcystins, and hypoxia of blooms in eutrophic water cause oxidative stress and C–N imbalance in submersed and floating-leaved aquatic plants in Lake Taihu, China. Chemosphere (2011) 82, 329-339.

(33)     Shen H, Niu Y, Xie P*, Tao M, Yang X. Morphological and physiological changes in Microcystis aeruginosa as a result of interactions with heterotrophic bacteria. Freshwat Biol (2011) 56: 1065–1080 (*Correspondent author)

(34)     Li GY, Xie P*, Li HY, Hao L, Xiong Q, Qiu T. Involment of p53, Bax, and Bcl-2 pathway in microcystins-induced apoptosis in rat testis, Environ. Toxicol. (2011) 26: 111–117 (*Correspondent author)

(35)     Li GY, Xie P*, Li HY, Hao L, Xiong Q, Qiu T & Ying Liu. Acute effects of microcystins on the transcription of 14 glutathione S-transferase isoforms in Wistar Rat. Environ. Toxicol. 26: 187–194 (2011) (*Correspondent author)

(36)     Liang GD, Xie P*, Chen J*, Yu T. Comparative studies on the pH dependence of DOW of microcystin-RR and -LR using LC-MS. TheScientificWorldJOURNAL (2011) 11, 20–26  (*Correspondent author)

(37)     Guo NC, Xie P*. A study on the effects of food quantity and quality on Glutathione S-transferase (GST) activity and growth rate parameters of Daphnia carinata varying in age. Aquat Ecol. (2011) 45:63–73 (*Correspondent author)  

(38)     Zhang M, Cao T, Ni LY, Xie P, Zhu GR, Zhong AW, Xu J, Fu H. Light-dependent phosphate uptake of a submersed macrophyte Myriophyllum spicatum L. Aquat. Bot. (2011) 94: 151–157

(39)     Xu J, Zhang M, Xie P*. Sympatric variability of isotopic baselines influences modeling of fish trophic patterns. Limnology (2011) 12: 107–115 (*Correspondent author)

(40)     Cao T, Ni LY, Xie P, Xu J, Zhang M. Effects of moderate ammonium enrichment on three submersed macrophytes under contrasting light availability. Freshwat Biol. (2011) 56, 1620–1629

(41)     Zhou Q, Xie P*, Xu J*, Liang X, Qin J, Cao T, Chen F. Seasonal trophic shift of littoral consumers in eutrophic Lake Taihu (China) revealed by a two-source mixing model. TheScientificWorldJournal (2011) 11, 1442–1454

(42)     Zhang XZ, Ji W, Zhan H, Zhang W, Xie P*. Studies on the toxic effects of microcystin-LR on the zebra？sh (Danio rerio) under different temperatures. J Appl Toxicol (2011) 31: 561–567 (*Correspondent author)

(43)     Li ZQ, Zhang M, Cao T, Zhang M, Ni LY, Xie P & Xu J. Variation in stable isotope signatures of the submersed macrophyte Vallisneria natans collected from several shallow lakes in China. J. Freshwat. Ecol. (2011) 26: 429-433

(44)     Zhang XZ, Xie P*, Li DP, Shi ZC, Wang J, Yuan GL, Zhao YY, Tang R. Anemia induced by repeated exposure to cyanobacterial extracts with explorations of underlying mechanisms. Environ. Toxicol. (2011) 26: 472–479 (*Correspondent author)

(45)     Xu J*, Yang Q, Zhang M, Zhang M, Xie P*, Hasson L. Preservation effects on stable isotope ratios and consequences for the reconstruction of energetic pathways. Aquat Ecol (2011) 45: 483–492 (*Correspondent author)

(46)     Xu J*, Cao T, Zhang M, Zhang M, Ni L & Xie P*. Isotopic turnover of a submersed macrophyte following transplant: the roles of growth and metabolism in eutrophic conditions. Rapid Commun. Mass Spectrom. (2011) 25: 3267–3273

2010

(47) Wu LY, Xie P*, Chen J*, Zhang DW, Liang GD. 2010. Development and validation of a liquid chromatography-tadem mass spectrometry assay for the simultaneous quantitation of microcystin-RR and its metabolites in fish liver. J Chromatogr A (2010) 1217， 1455-1462 (*Correspondent author)

(48)     Chen J, Xie P*, Ma ZM, Niu Y, Tao M, Deng XW, Wang Q. A systematic study on spatial and seasonal patterns of eight taste and odor compounds with relation to various biotic and abiotic parameters in Gonghu Bay of Lake Taihu, China. Sci Total Environ (2010) 409, 314–325 (*Correspondent author)

(49)     Zhang M, Cao T, Ni LY, Xie P & Li ZQ. Carbon, nitrogen and antioxidant enzyme responses of Potamogeton crispus to both low-light and high-nutrient stresses. Environmental and Experimental Botany (2009) 68: 44-50

(50)     Hao L, Xie P*, Li HY, Li GY, Xiong Q, Wang Q, Qiu T, Liu Y. Transcriptional alteration of cytoskeletal genes induced by microcystins in three organs of rats. Toxicon, (2010) 55: 1378-1386 (*Correspondent author).

(51)     Liu Y, Xie P* et al., Microcystin extracts induce ultrastructural damage and biochemical disturbance in male rabbit testis. Environ. Toxicol. (2010) 25, 9-17 (*Correspondent author)

(52)     Tan XY, Luo Z*, Xie P*, Li XD, Liu XJ, Xie WQ. Effect of dietary conjugated linoleic acid (CLA) on growth performance, body composition and hepatic intermediary metabolism in juvenile yellow catfish Pelteobagrus fulvidraco. Aquaculture (2010) 310  186–191  (*Correspondent author)

(53)     Wang Q, Niu Y, Xie P*, Chen J, Ma ZM, Tao M, Qi M, Wu LY, Guo LG. 2010. Factors affecting temporal and spatial variations of microcystins in Gonghu Bay of Lake Taihu, with potential risk of microcystin contamination to human health. TheScientificWorldJournal (2010) 10, 1795–1809 (*Correspondent author)

(54)     Xiong Q, Xie P*, Li HY, Hao, L, Li GY, Qiu T, Liu Y. Acute effects of microcystins exposure on the transcription of antioxidant enzyme genes in three organs (liver, kidney and testis) of male Wistar rats. J Biochem Mol Toxic (2010) (*Correspondent author) 24: 361-367

(55)     Li GY, Xie P*, Li HY, Chen J, Hao L, Xiong Q. Quantitative profiling of mRNA expression of glutathione S-transferase superfamily genes in various tissues of bighead carp (Aristichthys nobilis). J Biochem Mol Toxic (2010) 24, 250-259 (*Correspondent author)

(56)     Wen ZR, Xie P* and Xu J. Mussel isotope signature as indicator of nutrient pollution in a freshwater eutrophic lake: species, spatial, and seasonal variability. Environ Monit Assess. (2010). 163: 139-147(*Correspondent author)  

(57)     Li L, Xie P* et al., Antioxidant response in liver of the phytoplanktivorous bighead carp (Aristichthys nobilis) intraperitoneally-injected with extracted microcystins, Fish Physiol. Biochem., (2010) 36:165-172 (*Correspondent author)

(58)     Wang SB, Xie P*, Geng H. The relative importance of physicochemical factors and crustacean zooplankton as determinants of rotifer density and species distribution in lakes adjacent to the Yangtze River, China. Limnologica, (2009) 40：1-7(*Correspondent author)

(59)     Zhang DW, Xie P*, Chen J*. 2010. Effects of temperature on the stability of microcystins in muscle of fish and its consequences for food safety. Bull Environ Contam Toxicol (2010) 84：202-207 (*Correspondent author)

(60)     Li ZQ, Xu J, Cao T, Ni LY, Xie P*. Adaptive responses of a floating-leaved macrophyte, Nymphoides peltata, to a terrestrial habitat. J. Freshwat Ecol., (2010) 25: 481-486  (*Correspondent author)

(61)     Ke ZX, Xie P*, Huang LM, Xu J. Predation risk perception in Daphnia carinata induced by the milt of common carp (Cyprinus carpio). J. Freshwat Ecol., (2010) 25: 467-473  (*Correspondent author)

2009

(62) Chen J, Xie P*, Li L & Xu J, First identification of the hepatotoxic microcystins in the serum of a chronically exposed human population together with indication of hepatocellular damage, Toxicol. Sci., (2009) 108：81-89; (*Correspondent author)

(63)     Zhang DW, Xie P*, Chen J, Dai M, Qiu T, Liu YQ, Liang GD. Determination of microcystin-LR and its metabolites in snail (Bellamya aeruginosa), shrimp (Macrobrachium nipponensis) and silver carp (Hypophthalmichthys molitrix) from Lake Taihu, China, Chemosphere (2009) 7: 974-981 (*Correspondent author)

(64)     Qiu T, Xie P*, Liu Y, Li GY, Xiong Q, Hao L & Li HY, The profound effects of microcystin on cardiac antioxidant enzymes, mitochondrial function and cardiac toxicity in rat, Toxicology, 257 (2009), 86-94; (*Correspondent author)

(65)     Zhang D, Xie P*, Liu Y, Chen J, Wen Z, Spatial and temporal variations of microcystins in hepatopancreas of a freshwater snail from Lake Taihu. Ecotoxicol. Environ. Safety, 72 (2009), 466-472; (*Correspondent author)

(66)      Zhang DW, Xie P*, Liu YQ, Qiu T, Transfer, distribution and bioaccumulation of microcystins in the aquatic food web in Lake Taihu, China, with potential risks to human health, Sci. Total Environ., (2009), 407: 2191-2199; (*Correspondent author)

(67)     Chen J, Zhang DW, Xie P* & Ma ZM, Simultaneous determination of microcystin contaminations in various vertebrates (fish, turtle, duck and water bird) from a large eutrophic Chinese lake, Lake Taihu, with toxic Microcystis blooms, Sci. Total Environ.,  (2009), 407: 3317–3322; (*Correspondent author)

(68)     Zhao Y, Xie P* & Zhang XZ, Oxidative stress response after prolonged exposure of domestic rabbit to a lower dosage of extracted microcystins, Environ. Toxicol. Pharm., 27 (2009), 195-199; (*Correspondent author)

(69)     Qiu T, Xie P*, Guo LG & Zhang DW, Plasma biochemical responses of the planktivorous filter-feeding silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis) to prolonged toxic cyanobacterial blooms in natural waters, Environ. Toxicol. Pharm., (2009), 27: 350–356; (*Correspondent author)

(70)     Li H, Xie P*, Li G, Hao L and Xiong Q, In vivo study on the effects of microcystins extracts on the expression profiles of proto-oncogenes (c-fos, c-jun and c-myc) in liver, kidney and testis of male Wistar rats injected i.v. with toxins, Toxicon, 53 (2009), 169-175; (*Correspondent author)

(71)     Li H, Xie P*, Zhang D & Chen J, The first study on the effects of microcystin-RR on gene expression profiles of antioxidant enzymes and heat shock protein-70 in Synechocystis sp. PCC6803, Toxicon, (2009) 53: 595-601; (*Correspondent author)

(72)     Li DP, Xie P*, Zhang XZ & Zhao YY, Intraperitoneal injection of extracted microcystins results in hypovolemia and hypotension in crucian carp (Carassius auratus), Toxicon, (2009), 53: 638-644; (*Correspondent author)

(73)     Xiong Q, Xie P*, Li HY, Hao L, Li GY, Qiu T & Liu Y, Involvement of Fas/FasL system in apoptotic signaling in testicular germ cells of male Wistar rats injected i.v. with microcystins, Toxicon, (2009) 54: 1-7 (*Correspondent author)

(74)     Jiang Y, Xie P* & Liang GD, Distribution and depuration of the potentially carcinogenic malachite green in tissues of three freshwater farmed Chinese fish with different food habits, Aquaculture, 288 (2009), 1-6; (*Correspondent author)

(75)     Tan XY, Luo Z, Xie P*, Liu XJ. Effect of dietary n – 3 / n – 6 fatty acid ratios on growth performance, hepatic fatty acid profiles and intermediary metabolism for juvenile yellow catfish Pelteobagrus fulvidraco, Aquaculture (2009) 296: 96-101 (*Correspondent author)

(76)     Zhou Q, Xie P*, Xu J, Ke ZX & Guo LG, Seasonal variations in stable isotope ratios of two biomanipulation fishes and seston in a large pen culture in hypereutrophic Meiliang Bay, Lake Taihu, Ecol. Engin. (2009) 35: 1603-1609; (*Correspondent author)

(77)     Ke ZX, Xie P*, Guo LG, Impacts of two biomanipulation fishes stocked in a large pen on the plankton abundance and water quality during a period of phytoplankton seasonal succession, Ecol. Engin. (2009) 35: 1610-1618 (*Correspondent author)

(78)     Wu AP, Cao T, Wu SK, Ni LY & Xie P. Trends of Superoxide Dismutase and Soluble Protein of Aquatic Plants in Lakes of Different Trophic Levels in the Middle and Lower Reaches of the Yangtze River, China. J. Integrat. Plant Bio., (2009) 51: 414-422

(79)     Guo LG, Li ZJ, Xie P* & Ni LY, Assessment effects of cage culture on nitrogen and phosphorus dynamics in relation to fallowing in a shallow lake in China, Aquacult. Int., (2009) 17：229-241;

(80)     Zhou Q, Xie P*, Xu J, Ke ZX, Guo LG. Growth and food availability of silver and bighead carps: evidence from stable isotope and gut content analysis. Aquacul. Res., (2009) 40: 1616-1625 (*Correspondent author)

(81)     Li L, Xie P*. Hepatic histopathological characteristics and antioxidant response of phytoplanktivorous silver carp intraperitoneally injected with extracted microcystins. Biomedical and Environmental Sciences (2009) 22: 297-302

(82)     Gong ZJ, Li YL, Shen J, Xie P. Diatom community succession in the recent history of a eutrophic Yunnan Plateau lake, Lake Dianchi, in subtropical China. Limnology (2009) 10: 247-253

(83)     Liu Y, Xie P* & Wu XP, Grazing on toxic and non-toxic Microcystis aeruginosa PCC7820 by Unio douglasiae and Corbicula fluminea, Limnology, (2009) 10: 1-5;  (*Correspondent author)

(84)     Zhang XZ, Xie P*, Li DP, Tang R, Lei HH & Zhao YY, Time-dependent oxidative responses of crucian carp (Carassius auratus) to intraperitoneal injection of extracted microcystins, B. Environ. Contam. Tox., (2009), 82: 574–578; (*Correspondent author)

(85)     Cao T, Xie P, Li Z, Ni L, Zhang M and Xu J, Physiological stress of high NH ₄⁺ concentration in water column on the submersed macrophyte Vallisneria natans L., Bull. Environ. Contam. Toxicol., 82 (2009), 296-299;

(86)     Yu T, Xie P*, Dai M. and Liang GD. Determinations of MC-LR and [Dha7] MC-LR concentrations and physicochemical properties by liquid chromatography-tandem mass spectrometry. B. Environ. Contam. Tox., (2009) 83: 757-760, (*Correspondent author)  

(87)     Guo LG, Ke ZX, Xie P*, Ni LY, Food consumption by in situ pen-cultured planktivorous fishes and effects on an algal bloom in Lake Taihu, China, J. Freshwat. Ecol., 24 (2009), 135-143;  (*Correspondent author)

(88)     Wen ZR, Xie P*, Xu J. contributions of pelagic and benthic dietary sources to freshwater mussels: evidence from stable carbon isotope analysis, J. Freshwat. Ecol. (2009) 24: 425-430

- Books

All in Chinese language with English titles and captions for figures and tables.

1. Xie P., 2003. Silver carp and bighead, and their use in the control of algae blooms. Science Press, Beijing (in Chinese).

2. Xie P., 2006. Microsystins in aquatic animals with potential risk to human health. Science Press, Beijing (in Chinese).

3.  Xie P., 2007. A review on the causes of cyanobacterial blooms from an evolutionary, biogeochemical and ecological view of point. Science Press, Beijing (in Chinese).

4. Xie P., 2008. Historical development of cyanobacteria with bloom disaster in Lake Taihu-Why did water pollution incident occur in Gonghu Waterworks in 2007? After 30 years, can we succeed to rescue Lake Taihu from bloom disaster? Science Press, Beijing (in Chinese).

5.  Xie P., 2009. Reading about the histories of cyanobacteria, eutrophication and geological evolution in Lake Chaohu. Science Press, Beijing (in Chinese).

6. Xie P. 2013. Scaling Ecology to Understand Natural Design of Life Systems, Their Operations and Evolutions - Integration of Ecology, Genetics and Evolution through Reproduction. Science Press, Beijing (in Chinese).

- Contributions to books

The only author with full contributions to all above 6 books.

Scaling Ecology to Understand Natural Design of Life Systems, Their Operations and Evolutions

- Integration of Ecology, Genetics and Evolution through Reproduction

By Ping Xie (2013, Beijing: Science Press)

    There are millions of species living together on the earth, with a great variety of sizes, shapes and colors. How did life emerge and evolve? How did life grow in size from small bacteria to huge blue whale? How are organisms designed ecologically? Why are there so many species on the earth? Reproduction is an essential characteristic of all living creatures, and the ways of their reproductions can be broadly grouped into asexual and sexual reproductions. Sexual reproduction occurs in almost all animals and plants. Why is sex so widespread?

    Today, biologists understand the molecular mechanisms of sex fairly well. However, it is still a big mystery why new beings should be produced by the union of two sexual elements. “The why of sex” has been a puzzle to evolutionary biologists, including Darwin,for more than 150 years. At first glance, it seems very puzzling why sex systems of flowering plants are absolutely dominated by hermaphrodite, as few flowering plants (~10%) have unisexual flowers. Does selfing really cause depression?

    These questions are what I try to explore in this book. My efforts are to integrate ecology, genetics and evolution through reproduction, seeking for principles underlying natural design of life systems, their operations and evolutions. For this reason, I give a historical and critical review on the prevailing hypotheses. Most importantly,I defined two concepts:r- and K- reproductive strategies, and proposed two new theories - “Ecological Origin of Sex” and “Eco-Genetic Essence of Sexuality”. Therefore, this book  not only synthesizes our current understanding, but offers a subversive challenge totraditional theories, and presents new concepts and theories as well.

English Chapter Summary

Chapter 1 Seeking the Roots of Ecology: Its Early History and Diversification

This chapter gives a brief introduction to the concept, and early history of ecology. The term “Oecologie” was coined by the German zoologist Ernst Haeckel in 1859. He defined ecology as a science of the whole relations of organisms to their surrounding world. It is a very flexible, somewhat vague but also quite classic concept (even today it is still widely used). By this definition, ecology embraces all the experiences and interactions organisms have had. Afterwards, ecology has been defined in a variety of ways, by a variety of people, from a variety of disciplines. Meanwhile, the change of the definition reflects the growing understanding of this field of study, i.e., from individual to population, community, and ecosystem, from short responses to long-term changes, and from simple elements to structure and functions of complex ecosystems.

It is a challenging task to trace the origin of ecology or to know who established it. Ecology has undergone a series of developments, and it is no doubt that ecological thought is a historical product of human evolution and civilization. The most primitive form may be the instinctive ecological sense in the era of hunting and fishing. This was followed by the hazy ecological consciousness in the early period of human civilization. Eventually, a systematic ecological science emerged in the modern scientific era.

Scientific ecology is a developmental product of natural history, one branch of which later developed into evolutionary biology. Darwin could be a founder of ecology as there were numerous “ecological” descriptions in his classic book “The Origin of Species”, although he never used the term “ecology”. In the early period of ecology, scientists also coined several important ecological concepts, such as “biosphere”, “biocenosis”, “biogeography”, “niche”, “food chain” and “ecosystem”, which are still in widespread academic use today.

Ecology has diverged into a variety of branches. Why are there so many different kinds of ecology? Unquestionably, this isdue to the great diversity of its subjects: millions of species, numerous inter- and intraspecific interactions, extremely variable habitats or environments, etc. Unfortunately, though the roots of scientific ecology can be traced back to Darwin’s evolutionary biology, ecology later directed its way that is independent of evolutionary biology or indulging in self-admiration.

Chapter 2 Perspectives on thePrinciples of Organism Design from the Size Scales of Life

The living world is fascinating and complex, as there are millions of species living together on earth,with a great variety of sizes, shapes and colors. How did life grow in size from bacteria to blue whale? How are these organismsdesigned biologically or ecologically? These are important for understanding the existent (also evolutionary) patterns of various organisms. They are the key issues of this chapter.

An organism is characterized by a series oftraits that are biological (e.g. generation time, growth rate, feeding rate and metabolic rate) or ecological (e.g. movement speed, intrinsic rate of population growth, population density, range of activity, species richness). Macroscopically,it is accurate, to some extent, that nature has designed these traits along the size scale of life,. In other words, the functionally characterized traits of an organism are a product of macro-evolution, reflecting the complex interactions between its continuous adaptation to the environments and ceaseless natural selection by external forces. Of course, such processes are necessarily based on the design principles along the size scale of life.

   In general, there is an evolutionary tendency towards greatergenetic complexity and greater diversity of body types (particularly body size) in many linkages. Of course, such evolutionary processes have been shaped by various external forces, e.g. the abiotic climatic conditions and/or the biotic interspecific interactions. In this sense, characteristics of life are the evolutionary products of directional selection under certain survival circumstances. In other words, the sizescale of life has basically set up a species’ ecological (r- or K-) strategy, which is relevant to the understanding of both species evolution and successful ecosystem management.The size scale of life also determines the reproductive strategy of a species.

Chapter 3 Perspectives on the Operation of Life Systems from Dynamic Models

Dynamics is an essentialcharacteristic of all life processes in various living systems (or at different levels). But how to quantitatively describe the dynamic behaviors of these life processes? Can we integrate different models? This is what I try to explore in this chapter.

It is a fundamental characteristic that all living systems on earth have been organized into an inclusively and inter-connectively structured bio-system: cell→tissue→organ→individual→population→community→ecosystem→biosphere. It is an open self-organizing system interlaced with abiotic environments. In such system, various biotic components are interconnected by numerous complex processes as well as flows of information, energy and matter.

The commonly studied life-process models include those for enzymatic reactions, metabolic rate of organisms, individual growth and population dynamics. Firstly, it is interesting to note that rates of enzymatic reactions can be astonishingly high, e.g., enzymes can catalyze up to several million reactions per second! This is undoubtedly an important biochemical force to support agorgeous living world on the earth!

Regression models are widely used to study relations between metabolic rate and other factors. The mass-specific rate of metabolism is related negatively with body mass, but positively with temperature. Metabolic cost is the highest in endotherms, but the lowest in plants and algae.

S-curve models are frequently used to describe the dynamics of individual and population growths. Generally, von Bertalanffy model is used for individual growth, while Logistic model for population growth. Both models are similar to each other, i.e., in terms of trajectory, growth in both models starts exponentially, but ends finally at saturation.

Survival curve is a graph showing the proportion of a population living after a given age. A change in surviving curve can also significantly affect population dynamics (e.g. in humans), suggesting a possible direction for some species to increase their survival rates (K-strategy) in the ecological process of evolution.

Nature has provided biosystems at different organizational levels with quite unique (or relatively independent) tempos, dynamics, and rhythms, although it has designed an inclusively and inter-connectively structured bio-system. Unfortunately, at least until now, no one has succeeded in integrating these particular models into a synthesized one suitable for the whole bio-system.

Chapter 4 Perspectives on the Behaviors of Ecosystems from Stability, Resilience and Regimes Shift

Despite the importance of developing quantitative models for life processes, such models are usually less applicable in ecological practice, largely due to the unexpected complexity, non-linear interactions, as well as the numerous feedback mechanisms in the ecosystems. Therefore, in recent decades, qualitative or semi-quantitative conceptual models were also developed to understand trends of ecological processes. Several principle concepts are mentioned in this chapter.

Stability, resilience and regime shift have been widely used to describe the states or behaviors of various ecosystems. They were attempted to support the ecosystem management strategy of humans. For example, to restore a damaged ecosystem, it is of practical importance to artificially decrease hysteresis. However, such studies focused almost only on ecological processes at short or medium time scales.

Why can not we use the theory of multiple steady states to study biological phenomena at a longer time scale? For example, vegetational successions (primary or secondary) can be taken as a kind of regime shift between different plant communities (steady states). Also, at an evolutionary time scale, quantitative accumulation of minor variations may eventually lead to emergence of a new species. In terms of system behavior, this looks like a transition from quantitative to qualitative changes. Therefore, it seems interesting to extend the concepts of stability, resilience and regime shift into the fields of vegetational successions and evolutionary biology.

Of course, it would be more difficult to describe dynamics of ecological processes at a geological time scale. First, geological movements are almost unpredictable, unrepeatable and quite random. Second, temporal scales are proportionally related to spatial scales. Therefore, geo-ecological processes are inevitably affected or controlled by the very complex and unpredictable historicalclimatic patterns and geological processes.

Even so, it is still of importance to comparatively view the states, behaviors and dynamics of various life systems at multiple scales, and to integrate the dynamic interactions of various life systems at different temporal and spatial scales. With this, we may able to understand the principles underlying the operations and evolution of the whole life systems on the earth.

Chapter 5 Geographic Patterns of Vegetation: the Ecological Principles for the Design of Plant Communities

Green plants are the sources of all life on earth. Botanists coined a series of names to describe an assemblage of plants living in a certain space: plant community, life form, vegetation, biome, flora, and so on. They are interconnective concepts. The term vegetation refers to the ground cover provided by plants, and it is understandable to the non-botanists as its classification is based on physiognomic characters. The term biome refers to the major regional patterns of plant (as well as animal) assemblages discernible at a geographic or even global scale. The purposes of this chapter are to review geographic patterns of vegetation and to discuss how plant communities are designed ecologically.

There are various types of vegetations, e.g. tundra, temperate broadleaf and mixed forest, temperate steppe, subtropical rainforest, Mediterranean, tropical and subtropical moist broadleaf forests, desert, dry shrubland, dry steppe, grass savanna, tropical and subtropical dry forest, tropical rainforest, alpine tundra, and montane forests. A large number of evidences indicate that there is certain predictability of vegetational characteristics at regional and global scales.

The current geographic patterns of vegetation are not only a reflection of the present climatic (mainly temperature and precipitation) patterns, but also a product of interactions between climatic changes and life systems in the long evolutionary history or geological processes. The intrinsic relations between climatic and geographic vegetational patterns also suggest that evolutionary and distributional patterns of species as well as communities could have not been so random, i.e., they have been generally determined by patterns and histories of regional climates. Of course, these processes were inevitably accompanied with or affected by some local or transient randomness.  

In conclusion, at a geographic scale, climates have almost completely shaped or determined the large spatial pattern of vegetation. This is particularly important for evolutionary biology, as it has, to a great extent, affected or determined the evolutionary directions as well as the basic patterns of populations, communities and ecosystems, although necessarily based on certain background characteristics in bio-geological history.

Chapter 6 Vegetational Succession: an End-Result Reaction of Plants to Their Surviving Trajectories during Geological History

Succession, a key concept in the early period of ecology, is used to explain the mechanisms for the phenomenon or process by which a plant community undergoes orderly and directional changes or replacement. This chapter describes various types of successions, and it certainly is an example-filled chapter.

It is often debated whether succession is directional or whether its trajectory is predictable. It is likely that if we disregard temporal and spatial scales, all these debates will be meaningless. This is because modality and trajectory of the succession are closely related to temporal and spatial scales. In general, vegetational succession very likely tends to approach a regional climatic climax at a short or medium temporal scale. On a geological time scale, however, it is difficult to find regular or accurate cyclic patterns of species replacements.

The dynamic characteristics of succession are also dependent on temporal and spatial scales. With increasing temporal and spatial scales, vegetational succession tends to progress from determinacyand reversibility to randomicity and irreversibility. Such irreversibility of vegetational succession at geological scale was in well agreement with the historic fact that almost all species became extinct in each of the five major extinction events, as evidenced by fossils.

Therefore, vegetational succession is essentially a climate-dependent or end-result reaction or response of plants to their surviving trajectories at various periods of geologic history. However, these processes were also significantly affected by evolutionary randomness as well as mass extinction events.

    Succession is a dynamic evidence for the important role of climates in shaping geographical vegetational patterns, macro-evolution of plant community as well as speciation and extinction of various plants. Such macro processes also strongly influence the biological/ecological/reproductive characteristics or strategies of many plant species. In other words, succession can be a best evidence for directional macro-evolution.

Chapter 7 Geographic Patterns of Biodiversity: the Ecological Principles for the Design of Species

Species is a basic unit for survival, reproduction and evolution, and the currently known number of species has been over 1.7 million. However, the distribution of species is not uniform geographically. This chapter is aimed to describe geographic patterns of species richness in relation to major environmental factors. The purpose is to understand how biodiversity has been designed ecologically at a geographic scale.

It is important to know why there are so many different species on earth or how species were created. There have been a variety of theories on the mechanisms of speciation. Lamarck emphasized the importance of use and disuse, and inheritance of acquired traits, imagining a mysterious "tendency to perfection". Darwin believed that new species came about accumulative processes of random variation and natural selection (caused by struggles for existence). While, some scientists recommended saltational speciation, a process by which species rapidly diverges into more than one species, due to chromosome mutation, and genetic and physical isolation.

Unfortunately, all these theories focused more on micro-processes rather than macro-processes of speciation. On a macroscopic view, however, species is more likely a historical product of regional ecological processes despite the presence of randomness in speciation. It is only by regional ecological processes that an ultimate geographic pattern of species diversity could be formed.

    From an ecological viewpoint, species richness to a great extent is a natural product of rain and heat. In other words, distributional patterns of rain and heat have basically shaped the macro (or geographical) patterns of species diversity. For instance, tropical rain forests are located in the hottest and wettest regions where there are highest primary productivity and fastest speciation, and consequently richest species diversity. The geographical patterns of species diversity have been continuously sculptured by some key abiotic environmental factors (e.g., latitude, altitude and moisture). Therefore, they are the products of the complex interactions among ecological, evolutionary, geological and climatic processes.

Global climatic types affect macro-ecological processes (of course under the necessary control of micro-speciation mechanisms), and, consequently, they have not only determined the spatial distributions and successional modes of vegetation, but also shaped the geographical patterns of species diversity. This on one hand indicates the macro-direction in the evolution of species, and on the other hand suggests possible presence of quite different flora in the same region due to shift of climatic types between different geological periods. This very likely leaves us with a discontinuous impression of fossil distributions, and is even used as “reliable” evidences by paleobiologists to support their hypothesis of salutatory evolution.  

Chapter 8 Evolution of Genomes: the Eco-Genetic Principles for the Design of Species

Genes are full of secrets and mysteries. Undoubtedly, they are at the core of all life processes, being the spirit of all living things. Genes are able to precisely control the growth, behavior, development and reproduction of all organisms. Such properties essentially distinguish the living world from the non-living world. Therefore, the evolution of life must have been reasonably based on the evolution of genomes. This chapter aims to review how various organisms undergo genome evolution so as to understand how species are designedeco-genetically.

Macroscopically, genomes tend to evolve from simple to complex in the processes of inheritance and evolutionary development. Genes are especially adept at creating new species mainly through repeated addition or modification of existing genes, eventually leading to the change of genome from simple and concise to luxurious and wasteful (plenty of 'junk' DNA). While, the increasing size and complication of genome will inevitably enlarge cell size, prolong cell division, and extend life span.

Gene is also changeable due to spontaneous or induced mutation. It is known that rates of spontaneous gene mutation are generally similar among eukaryotes. However, it is observed that plants with larger genomes are less tolerant to induced mutation of radiation.

To our surprise,the evolution and renewal of genes and species showed completely different trajectories and modes. During the Archaean (3 billion years ago), the ancient prokaryotes intensively undertook evolutionary innovation, and completed creation of a series of gene families that perform basic living activities such as life construction, energy use and adaptation to biosphere oxidation. It is only after this that Cambrian (0.5 billions ago) explosion in species diversity of eukaryotes could have occurred. Since Cambrian, plenty of duplicated genes and orphan genes have been gradually added into the eukaryotic genomes. The evolution of eukaryotic genomes reflects a unique mode of gene innovation: combination, deposition and repair of existing genes by sexual reproduction.

Chapter 9 From Existence to Evolution: An Overview on Reproduction of Various Organisms

Reproduction is an essential characteristic of all living creatures.It is the basisfor survival, development and evolution of all species. This chapter overviews theexistence and evolution ofvarious reproductions in the major groups of organisms, especially from an ecological viewpoint. I particularly emphasize the relation between reproduction and dormancy.

Although over millions of species live together on earth, the ways of their reproductions can be broadly grouped into two basic types: asexual and sexual reproductions. Eukaryotes can undergo both asexual and sexual reproduction, but prokaryotes can only reproduce asexually. In asexual reproduction, offspring is produced from a single parent, and genetically will be an exact copy of the parent. It does not involve meiosis or fertilization. There are various types of asexual production: fission, budding, vegetative propagation, spore formation, fragmentation, parthenogenesis, etc.

In sexual reproduction, offspring is produced by combining the genetic material of two parents (male and female). It involves meiosis and fertilization. The simplest form of sexual reproduction is conjugation that involves the exchange of genetic material between two organisms of different mating type, e.g. through a bridge between the cytoplasms of two ciliate cells. This is a primitive type of sexual production, and is commonly observed in the unicellular ciliates. Syngamy is a more complex way in which two haploid gametes fuse permanently to produce a diploid zygote, and it can be iso, aniso and oogamy.

Unicellular organisms include both prokaryotes (e.g. bacteria, cyanobacteria) and eukaryotes (e.g. yeasts, many algae, protozoans). The unicellular eukaryotes reproduce asexually in most cases, but also occasionally perform sexual reproduction to produce dormant cells (e.g. akinetes in green algae) for overcoming unfavorable environments. This is very likely the first motive for sexual reproduction in eukaryotes. With the progress of evolution, sexual reproduction has tended to be fixed in the life cycles of many organisms. Overall, the unicellular organisms are a world dominated by asexuality.

Multicellular organisms include various plants and animals. Higher plants reproduce mostly sexually. In small moss, zygotes develop in the female gametagium that can provide effective protection for the embryo. Ferns (larger than moss in size) still rely on the use of small spores to spread populations, while seed plants have greatly increased the ability of dormancy and resistance to unfavorable conditions. The forms of dormancy in higher plants evolved from small spores (in moss and ferns) to relatively large and hard seeds (in flowering plants). Overall, higher plants are a world dominated by sexuality.

Sexual reproduction in flowering plants has to rely on a variety of pollinators such as wind, water, insects, birds, and bats. Pollination is the process by which pollen is transferred to enable the fertilization of different gametes (♀, ♂). Roughly, only 10% of flowering plants are pollinated without animal assistance. Coevolution of flowering plants with pollinating insects might have greatly speeded up the speciation of both.

There are several types of asexual reproduction in the lower invertebrates (fission, budding, fragmentation, parthenogenesis). In contrast to plants, hermaphroditism is extremely rare in animals, and only occasionally occurs in a few (mostly aquatic) invertebrates. In animals, there is usually a phenotypic difference between males and females of the same species (other than in the sex organs). This is called sexual dimorphism. Sexual dimorphism is seemingly more pronounced in higher animals than in lower animals. The primitive form of dormancy is resting eggs in some invertebrates. In birds and reptiles, eggs consist of protective eggshell. In mammals, the embryo develops inside the body of the mother, and egg dormancy is no longer needed.

Asexual (vegetative) reproduction is generally much more important for higher plants than for higher animals. It is a fast reproduction mode, and is quite common in aquatic vascular plants, especially in those invasive plants.

As prokaryotes can not reproduce sexually, how do they go to dormancy to overcome unfavorable conditions? Some bacteria can form a highly resistant, dormant structure called endospore, which is usually triggered by unfavorable conditions. Endospores can survive extreme environmental stresses, and may remain viable for millions of years. However, endospore is not a true spore, as it is not an offspring. The filamentous cyanobacteria can also form a thick-walled, dormant cell called akinete that derives from the enlargement of a vegetative cell in the filament. Such akinete has become a normal structure of the filament, production of which no longer needs stimuli of environmental stresses. This is suggestive of primitive cellular differentiation and fixation of dormancy in filamentous multicellular cyanobacteria.

Chapter 10 The Why of “Sex”: A Historical and Critical Review

“The why of sex” has been a puzzle to scientists for more than 150 years, from the eminent Darwin, Weismann, Fisher, Maynard Smith to many modern evolutionary biologists. They “truthfully” believed that sexuality is advantageous over asexuality. Until now, over 20 hypotheses have been proposed to supportthis. In spite of this, it still remains mysterious to biologists why reproduction mode shifted from asexuality to sexuality. This chapter gives ahistorical and critical review on the prevailing hypothesesregarding the why of sex. Especially, the complex sex systems of flowering plants cast doubt on the prevailing hypotheses, making me seriously reconsider the meaning of “sex”.

There are several prevailing hypotheses that have been put forth to explain the why of sex: 1) sex makes it possible to get genetic recombination, 2) asexual species will eventually go extinct, 3) asexual reproduction could not effectively adapt to environmental changes, 4) sexual reproduction provides powerful defense against parasites and pathogens, 5) sex became mandatory due to preference of sexiness, and 6) sex pays a two-fold cost. It is my efforts to refute these hypotheses one by one so as to build correct knowledge.

At first glance, it seems very puzzlingwhy sex systems of flowering plants are absolutely dominated by hermaphrodite. However, it seems reasonable for me to derive that if selfing had surely caused severe depression, there would have neither been so many self-pollination plants nor complete cleistogamy, and that if selfing was so harmful, it would have been not difficult for plants to completely eliminate hermaphrodite by natural selection or plants would have evolved towards complete dioecism.

However, what we are seeing in flowering plants are the extremelyvariable mating systemsthat might have been shaped by complex evolutionary interactions or forces. Why are there not only so many different combinations but also mostly hermaphrodite? Is not it perfectly clear that selective forces by cross-breeding are never strong? Rather, in my opinion, such mixed mating systems in flowering plants have well integrated different ecological strategies (r and K), perfectly reflecting the wisdom of nature.

Then, why is sex so widespread? Perhaps the genetic mysteries are hidden in the process of crossing over between homologous chromosomes in meiosis. However, the exchange of genetic information occurs never only in meiosis. Actually, sister chromatid exchanges (SCEs) also frequently occur during mitosis that is traditionally considered to be ‘faithful’. The effects of SCEs are seemingly non-hereditary, while those of crossing over between homologous chromosomes can be hereditary, probably leading to significant genetic and evolutionary consequences. Perhaps this is the reason why little attention is given to SCEs.

A unisexual flower is a flower with only stamens or only pistils. It is astonishing that few flowering plants (~10%) have unisexual flowers. This makes me strongly believe that the so called “selfing or inbreeding depression” could have been just a surmise. In other words, at least, this has been greatly exaggerated, or may completely be a non-existent effect.

Chapter 11 Environment-Dependent Modes of Reproduction: New Theories on the Ecological Origin, Evolution and Eco-genetic Essence of “Sex”

I believe that no one will deny thatcreation and developments of life systems on the earth have been undertaken or driven by the complex interactions of genetic, ecological and evolutionary forces. It is also a fact that such interactions would not have existed if there were no (sexual) reproduction. Therefore, sexual reproduction could never only be a tiresome genetic game. It is anevolutionary quintessence of eco-genetic processes and interactions. If we do not believe this, we may neverknow the real origin and the why of “sex”. For these reasons, in this chapter, I defined two new concepts, andproposednew theories on the ecological origin and eco-genetic essence of “sex”. Take a step farther, I use these concepts and theories to explain the puzzling sex systems of flowering plants and the widespread occurrence of sex. This is the most important chapter in this book, so I extended the English summary of this chapter.

It is a well-known fact that heredity is the passing of traits to offspring from the parents, but this is only part of the picture. Ecologically, heredity is also an internal process by which organisms strive to adapt to their living environments, at bothshort- and long-time scales. Therefore, evolution is a historic process ofthe interaction between heredity and environmental adaptation. In this sense, reproduction appears to be a fundamental force shaping the development of life systems on the earth through the coevolution of heredity, ecology and evolution.

1.     Modes of reproduction are strongly shaped by survival environments

Ecologically, millions of species can be broadly grouped into three functional groups: producer, decomposer, and consumer. They occupy two major types of habitats: lands and waters. Ecologically, morphology, physiology as well as modes of reproduction are all essentially dependent on the living environments of organisms.

(1) Decomposers

In contrary to the huge species number ofplants (producers) and animals (consumers), the enormous niches of decomposition in various ecosystems are almost only occupied by a small number of prokaryotic species (mostly bacteria). Apparently, this is most likely due to a strong selective pressure for fast rates of decomposition and multiplication that require maximizing the ratio of surface area to volume. The fast asexual reproductionis just suitable for these microorganisms. This may explain why only small asexual bacteria can occupy the vast niches of decomposition.

(2) Primary producers

Keepingfloating in surface water may be a key selective pressure for aquatic primary producers as light declines rapidly with depth, which inevitably favors the survival of those species with a large surface area to volume ratio. Of course, small size is also beneficial to absorption of dissolved nutrients in water (e.g. N, P, CO₂). These may explain why only very small planktonic algae completely occupy the niche of primary production in the vast ocean. These small algae consist ofprokaryotes and eukaryotes, both of which reproduce only or mainly asexually. The single-celled eukaryotic algae only occasionally reproduce sexually to produce resistant dormant cell. However, on land, to maximize the use of sunlight, plant communities have to diverge or diversify vertically as much as possible. Well, evolution and diversification of various vascular plants with sexual reproduction just meet these ecological requirements.

(3) Consumers

Forces driving the evolution ofanimal reproduction seem different fromthat of plants. Trophic relations (grazing or predation) are likely more important for the evolution of animal reproduction. In water, small planktonic invertebrates are the most abundant primary consumers as only they are able to filter the very small phytoplankton. These invertebrates reproduce mainly asexually, with only occasional sexual reproduction to produce resting eggs. In spite of their small size, they are an essential link in the complex food web of the ocean. However, the situation on land is somewhat different: besides the many invertebrates (mainly insects) that are important primary consumers, large-sized herbivorous animals are also very common or even more important. Coevolution between prey and predator generally increase the sizes of both, while large animals reproduce almost only sexually, and ecologically are typical K-strategists.

In short, decomposers are a microscopic asexual world; for primary producers, planktonic algae reproduce mainly asexually, but higher plants reproduce mainly sexually, i.e., asexuality dominates in water, but sexuality predominates on land; both terrestrial and aquatic consumers are a world dominated by sexuality. Ecologically, asexual organisms are small in size, and are representative or extreme r-strategists in general.

There is no doubt that the evolution of reproduction in various groups of organisms wellreflects the harmony oftheir structures, functions and survival environments. It is almost meaningless to discuss the advantage of sexuality or the disadvantage of asexuality if we disregard the survival environments and the corresponding ecological functions of the organisms. This is why I believe that we will never get the right answer for the so called “advantages” of sexuality if only based on some genetic mechanisms.

2.      Sex originated ecologically

Currently, no one knows with certainty where and how sex originated. Cellular or genetic hypotheses can depict imaginarymicro-processes (i.e., cellular or genetic details) of the possible origin of sexuality, but cannot explain the “why” of sex. So why can't we try a different approach for this? Chapter 9 gives a systematic review on the evolutionary histories of reproduction in various organisms, and from there I realize that ecologically, evolution of sex is likely more survival-oriented, instead of being only a so-called “advanced” reproductive mode.This greatly encouraged meto propose what Icall the “Ecological Origin of Sex” as follows:

No one can deny the fact that successful survival is a necessary preconditionfor the existence of any species. It is very likely that primitive sex first emerged and then developed in a series of adaptive processes that allowed eukaryotic animals and plants to overcome unfavorable environmental conditions. Some lower plants and animals only occasionally have “sex” (i.e., two haploid gametes fuse to produce a diploid zygote) for the purpose of producing dormant bodies (e.g. akinetes, resting eggs), which is likely the primitive motive of “sex”. Subsequently, evolution of dormancy completely diverged between animals and plants, i.e., higher plants, still “faithfully” along the direction of dormancy, evolved toward production of hard seeds to strengthen the abilityof dormancyand protection for the offspring, while animals (especially mammals) evolved towards viviparity where fates of both mother and embryo were closely interwoven. As embryo develops inside the body of the mother, viviparity is also highly protective for offspring. In this way, mammals have completely abandoned the primitive resting eggs that are still commonly used for dormancy by lower animals. In other words, for mammals, sex is no longer for dormancy purpose, and the original motive for sex was totally discarded. No matter plants or animals, they all evolved towards fixation and consolidation of sexuality or even with sex being the only one. In an ecological sense, evolution of sexual reproduction was initiated and driven for production, fixation and consolidation of dormancy to overcome unfavorable environmental conditions. This is the ecological origin of sex.

It is likely that production of dormant cell is not a necessary and sufficient condition for sexual reproduction. For example, bacteria can form resistant endospore without sexual reproduction. For the ancient eukaryotes, the association between production of dormant cell and sexual reproduction might have been just an accidentthat is extraordinarily favored by natural selection and they hence spread throughout the world rapidly.

3.      r- and K- reproductive strategies

Numerous facts indicate that reproductive strategy of a species is well interlaced with the ecological characteristics, and thus is an evolutionary product of its ecological strategy. I defined two concepts for two different reproductive strategies. Reproduction of all living things in nature can be divided into two basic types: asexual and sexual reproductions. These basically reflect two different reproductive strategies. Asexual reproduction, being ancient, simple and fast, dominates absolutely in small organisms (e.g. bacteria), and can be defined as a r-reproductive strategy. Sexual reproduction, being modern, complex and slow, originated from asexuality. It has become the only or main way to breed in higher plants and animals, and can be defined as a K-reproductive strategy.

How to distinguish the two strategies? Firstly, in terms of resources utilization, r-reproductive strategists are adept at utilizing resources quickly in local environments, but K-reproductive strategists tend to utilize resources at relatively stable levels in regional environments. Secondly, in terms of environmental tolerance, the r-reproductive strategists are likely more capable to survive in a wide fluctuation of abiotic environmental factors (e.g. climate), while K-reproductive strategists are likely more adaptive to relatively mild environments, especially to biotic interactions. Thirdly, sexual cost for reproduction is higher in K-strategy than in r-strategy, but it is reversed for survival, i.e., r-reproductive strategists seek for quantity of life, not caring about massive death, whereas K-reproductive strategists pursue quality of life, attempting to increase survival rate. Conclusively, r- and K-reproductive strategies are merely a reflection of relevant ecological strategies in reproductive characteristics.

4.      Eco-Genetic Essence of Sexuality

   Why is sex so dazzling? Or in other words, what is the essence of sexuality? If we do not understand the essence, and even if we have understood the detailed sexual process correctly, we may still never know the “why” of sex. Here, I propose what I call theEco-genetic Essence of Sexuality as follows.  

(1) Firstly, I define the gene pool of a species as the total genes within individual genomes, total genetic interactions among genes as well as total combinations of genes in individual genomes of the whole population. Then, sexuality is firsta process ofshuffling gene pool of a species through meiosis and homologous recombination during fusion of gametes from two parents. In this way, a eukaryotic species dynamically preserves its gene poolin total population(s) through sexual reproduction, i.e., the genes will be passed on from one generation to the next through the random combinations of all individuals. Therefore the total adaptation of a species to environments is stored in entirety in its gene pool.

(2) Is variation a cause or an effect of sex? It is a traditional belief that sex is designed to create genetic variations, which is even considered to be the “purpose of sex”. In my opinion, sex is merely a genetic operational process for the breeding and proliferation of a eukaryotic species. Therefore, variation is not the cause but the effect of sex! It is only the gene pool that contains a full record of that species' entire evolutionary history and that could determine the diversity of genotype/phenotype as well as adaptability of its population(s).

(3) Genetically, the genome of an individual is just a random combination from the gene pool of the population. Then, any individual genome of a sexual species can never be eternal, and must inevitably be fragmented or broken by repeated genetic recombination during the process of meiosis from generation to generation, eventually vanishing into the huge gene pool.

(4) Ecologically, the gene pool of a sexual species is also changeable due to a series of biotic and/or abiotic factors such as competition for existence, geographical isolation, eco-physiological interactions or other environmental changes. As a result, the gene pool of a species may extend, shrink or split, respectively leading to complication, degradation or speciation of the species.

(5) Evolutionarily, a species tends to maintain a transient genetic stability. There is seemingly a conflict between accuracy and variability in the genetic process of a sexual species. A flourishing species will inevitably make its gene (therefore phenotype) pool become more and more variable or diverse, although this usually occurs very slowly. This is likely due to the fundamental characteristics of meiosis: frequent genetic combination and variation. However, an ever-increasing variation may also increase the risk of unsuccessful copulation between individuals (e.g., rate of human infertility can be over 5%). Therefore, in the evolutionary history, a sexual species have to continuously balance the processes of genetic (phenotypic) diversity, successful breeding and environmental adaption by natural selection.

(6) How did a new biological species arise? It appears that speciation was driven by the interactions of genetic and ecological processes at an evolutionary time scale. As no speciescan increase the size of its gene pool unlimitedly, it is likely that the higher the genetic diversity, the greater the split probability of species' gene pool. Splitting of a gene pool (indicated by reproductive isolation or hybridization barriers) may consequently leads to speciation. In such process, the daughter and parent species usually have a quite overlapping gene pool, with only minor divergency. For example, humans and chimps share a surprising 98.8 percent of their DNA. Thus, it seems that a species is alwaysin a ceaseless cycle ofaccumulation-splitting-accumulation of its gene pool. In such a way, sexual reproduction through an incremental accumulation of genetic variations along time has inevitably led to an accelerated process of speciation, therefore contributing to a ceaseless emergence of new eukaryotic species on the earth.

It is this essence of sexuality that makes sex so dazzling. Also, in this sense, sex would have led endless emergence of new species as well as endlessextinction of old species. In other words, no species can be eternal, and all species will be doomed to perish or will change into more new species. In fact, our earth has witnessed a generally increasing tendencyin species richness, interspecific interactions, and ecological niches. Conclusively, the eco-genetic essence of sexuality may explain why there are so many species on the earth and also why all species have been more or less connected phylogenetically.

5. New insights into sex systems of flowering plants and the widespread occurrence of sex

The sex systems of flowering plants look very puzzling, as most of them are hermaphrodite and selfing is also very common. It seems not difficult to explain this if we base on the Eco-Genetic Essence of Sexuality as well as the Laws of Segregation and Independent Assortment by Mendal. In my opinion, inbreeding or selfing of a sexual species can be taken as an asexual “tool” of sexual reproduction (or like a mosaic of asexual and sexual reproduction), and can increase homozygosity of genes in local (or sub-) populations. The plant can also mix individual genomes between sub-populations through outcrossing. Therefore, the mixed mating systems of higher plants may have taken the advantages of both (r- and K-) reproductive strategies, which may be especially important for those higher plants lacking vegetative reproductive ability.

Why is sex so widespread?This has been a puzzling problem for over 150 years. To explain this satisfactorily, it is necessaryto integrate viewpoints of ecology, genetics and evolution, i.e., in the evolutionary processes, sexuality genetically meets the ecological requirements of plants and animals to adapt to their survival environments, and most importantly, it meets the requirements of plants and animals to increase their sizes. Firstly, terrestrial plants need to increase and diversify their body sizes to maximize the spatial use of light. For animals, coevolution of predators with preys can increase the sizes of both. Then, the increase in sizes of animals and plants will certainly promote their structural diversification and complication of the associated behavioral, physiological and biochemical cooperation and controls, which inevitably requires increased size and complexity of their genomes. Lastly, meiosis that operates sexual reproduction is just able to increase genome size by vigorous genetic exchange and recombination through synapsis and crossing over between homologous chromosomes, consequently meeting the need to increase both the size and complexity of genomes.

Chapter 12 Evolution of Earth's Environments: Great Inventions and Leaps of Life Systems

The earth is the mother of all life that occupy various habitatsor ecosystems. The global sum of all ecosystems is called biosphere, which is ecologically interlaced with lithosphere, hydrosphere, and atmosphere. So far, millions of species have been found. When did the first life emerge on earth? How did life and the earth environments co-evolve? These are what I want to sketch in this chapter.

Generally, species evolved through isolation, differentiation and hybridization during the geological history with breaking apart, drift and recombination of continental plates. Fundamentally, life is a natural product of the universe, or in other words, the current biosphere is a product of the interaction and coevolution between organisms and their physicochemical environments (water, atmosphere and landmass) in the long geological history. They affect (or modify) each other.

Approximately 3.8 billion years ago, life first emerged on earth after the hell of extremely hot and anaerobic environments. It is assumed that primordial seas gave rise to life. Then it lasted for a very long period of time that oxygen was released from the primordial seas as a byproduct of photosynthesis by cyanobacteria. Eventually, the accumulative effects of oxygenic photosynthesis by prokaryotes successfully converted the early reducing atmosphere into an oxidizing one. The aerobic atmosphere made it possible for life to come up onto land from ocean.

The ever-increasing aerobic atmospheric environments also caused gradual but significant modifications in physiological and ecological characteristics of the organisms. That is, increased oxygen levels were accompanied by structural complication and development of aerobic respiration of organisms, as well as complication of food webs. Eventually, there was aCambrian explosion around 530 million years ago when the rate of evolution was accelerated by an order of magnitude, i.e. rapid speciation and unprecedented flourishing of both plants and animals. Before Cambrian, most organisms were relatively simple, mainly composed of individual cells with only occasional organization into colonies. Apparently, evolution was not uniform in its rates along geological time.

  What resulted in such great leaps in the evolution of life systems? There are a series of key evolutionary inventions that greatly contributed to this: 1) a change of energy use from chemicals to sunlight, and from anoxygenic to oxygenic, 2) a change of cellular structure from prokaryote to eukaryote, 3) a change of individual structure from unicellular to multicellular (with close cellular connection), 4) a change of reproduction from asexual to sexual, 5) an increase of trophic levels from primary producers to sequential appearances of primary consumers, secondary consumers, and top predators, and 6) development of mutually beneficial relations between species (e.g. coevolution between flowering plants and pollinating insects).

Chapter 13 The Eternal Melody of Life: Creation, Evolution and Extinction

Life undergoes an endless cycle of creation, evolution and extinction, which is just like an eternal melody. However, the underlying agents, processes and modes are still the great natural mysteries of the world. This is what I want to explore in this last chapter.

How is an organism constructed physiologically? Life is skilled in using simplicity to assemble complexity for their microscopic construction or creation. This exists in a series of chemical and biological constructions, from elements to macro-molecular, gene, cell, individual and species. It is such a way of life design by assembling that enables us to recognize simple control principles behind the complex presentations and relations in the life world.

How did life evolve? Even today, the mechanisms for species evolution or speciation are still unsolved mysteries of our world. Evolutionism has witnessed a long debate between two great theories: Lamarckism (use and disuse, inheritance of acquired traits) and Darwinism (random variation, struggles for existence, and natural selection). Lamarckism claimed that environment gives rise to variation, while Darwinism believed that variations occur randomly. Paleontologists generally distrust Darwin's gradual evolution, but highly praise orthogenetic (a deformed Lamarckism) and abrupt evolutions. Geneticists believe in mutational evolution, and even declare that they have destroyed Lamarck’s theory (especially inheritance of acquired traits) by brandishing their complacent “weapons” – the germplasm theory by Weismann A, the genetic laws by Mendel GJ and the DNA central dogma by Crick F.

Is evolution directional? There have been two fundamentally different views on the direction of evolution. For Lamarckism, evolution is progressive and predictable, and is to produce a perfect fit. For Darwinism, evolution is neither purposive nor directional. In my humble opinion, neither view is completely wrong nor completely right, i.e., evolution is neither completely random nor completely directional, because directionality is hidden in random processes, and randomness is also interlaced with directional processes. In other words, there are internal and inseparable interactions between randomness and directionality. Genetically, this is very likely because of the unique way that species creation is deeply embedded in assembling and piling up of genes through meiosis.

What are the patterns of macroevolution and extinction? The earth’s environments are endlessly changing yet in an unpredictable way. In the macroevolution of life, species are renewed spontaneously, which is an essential character of all life on earth. In the geological history, life on earth has experienced several mass extinctions and great explosions, i.e. significant evolutionary renewal of species was undertaken by sudden and shocking extinctions. Such cyclic creation and extinction of species looked like whirligigs but with different trajectories.

It seems a paradox of adaptation that complex organisms easily go extinct but with simple species being more eternal. The evolutionary history of life never repeated itself simply. In other words, evolution of life was never simply a repaint of historical trajectories, but went up in a way of spiral. Life repeatedly opened up different paths of evolution, and undertook vigorous reconstruction and creation of living systems along with superposition of diversity and complexity.