Editing Murray cod (section)

===Threats===
====Overfishing====
While extremely severe commercial and recreational overfishing in the 1800s and the early 1900s caused the first strong declines of Murray cod, [[overfishing]] by recreational fishermen, aided by inadequate fishing regulations, continues today and remains an extremely serious threat to Murray cod. The current size limit of 60&nbsp;centimetres in most states is inadequate now that scientific studies have documented average size at sexual maturity in Murray cod.<ref name=Nicol-et-al2005/> This and catch data and computer modelling exercises<ref name=Nicol-et-al2005/> on wild Murray cod stocks indicate measures such as raising the size limit to 70&nbsp;centimetres and reducing the bag and possession limits from 2 and 4 fish respectively to 1 fish are urgently needed to maintain the long-term viability of wild Murray cod populations. As of November 2014, the NSW Department of Fisheries has introduced a maximum size limit of 75&nbsp;cm for Murray Cod to provide protection for large breeding fish, as well as a new minimum size limit of 55&nbsp;cm.

Although angler effects are sometimes disregarded in the overall picture today, recent population studies have shown that while all year classes are well represented up to the minimum legal angling size (now 60&nbsp;centimetres in most states), above that size, numbers of fish are dramatically reduced almost to the point of non-existence in many waters.<ref name=Nicol-et-al2005/><ref name=Koehn2004/> Some emphasis has been made of the results of two small surveys which suggested a majority of Murray cod are released by anglers. However, there are valid questions as to the representativeness of these surveys: these surveys do not explain the dramatic disappearance of large numbers of young Murray cod at exactly the minimum size limit, and most importantly, any emphasis on these surveys miss the fundamental point — as a large, long-lived species with relatively low fecundity and delayed sexual maturity wild Murray cod populations are extremely vulnerable to overfishing, even with only modest angler-kill.<ref name=Nicol-et-al2005/><ref name=Koehn2004/> A tightening of fishing regulations for wild Murray cod, as referred to above, and a switch by fishermen to a largely [[catch and release]] approach for wild Murray cod would alleviate this problem.<ref name=Nicol-et-al2005/> Recognising these issues, in late 2014 the New South Wales and Victorian fishery departments amended their regulations so that a slot limit of 55 to 75&nbsp;cm now applies in these states. (i.e. only Murray cod between 55 and 75&nbsp;cm may be taken; those above and below this size range or "slot" must be released.) This measure should have positive effects for the Murray cod population by protecting and increasing the proportion of large breeding Murray cod.

Another issue is that Murray cod caught and released in winter, while developing their eggs, or in spring prior to spawning, resorb their eggs and do not spawn.<ref name=Rowland2005/><ref name=Lake1967/><ref name=Rowland1988>{{cite journal  | last = Rowland  | first = S. J.  | title = Hormone-induced spawning of the Australian freshwater fish Murray cod, ''Maccullochella peeli'' (Mitchell) (Percichthyidae)  | journal = Aquaculture  | volume = 70  | pages = 371–389  | year = 1988  | doi = 10.1016/0044-8486(88)90121-4  | issue = 4 | bibcode = 1988Aquac..70..371R }}</ref> This may be a minor issue compared to some of the other threats facing Murray cod, nevertheless, concerned fishermen try to avoid catching wild Murray cod at these times.<ref name=nfacod/> At this point in time a closed season is in place for the spring spawning period, during which anglers are not allowed to target Murray cod, even on a catch and release basis.

====Effects of river regulation====
The Murray River and southern tributaries originally displayed a pattern of high flows in winter, high flows and floods in spring, and low flows in summer and autumn. The breeding of Murray cod and other Murray-Darling native fish was adapted to these natural flow patterns. River regulation for irrigation has reversed these natural flow patterns, with negative effects on the breeding and recruitment of Murray cod. The Murray and most southern tributaries now experience high [[irrigation]] flows in summer and autumn and low flows in winter and spring. Small and medium floods including the once annual spring flood-pulse have been completely eliminated.<ref name=Allen-et-al2002/><ref name=McDowall1996/><ref name=Koehn2004>
{{Cite web |last=Koehn |first=J. D. |title=Threats to Murray cod |publisher=Murray Darling Basin Commission |date=2004 |url=http://www.mdbc.gov.au/__data/page/641/4_John_D._Koehn.pdf |access-date=4 October 2007 |url-status=dead |archive-url=https://web.archive.org/web/20070829102517/http://mdbc.gov.au/__data/page/641/4_John_D._Koehn.pdf |archive-date=29 August 2007}}</ref><ref name=sharing>{{cite book  | title = Sharing the Murray
  | publisher = Murray River Entitlements Committee  | year = 1997  | isbn = 0-7306-6797-9}}</ref>

It is estimated that flows at the river mouth by 1995 had declined to only 27% of natural outflows.<ref name=mdbcaudit1995>{{cite book |url=http://www.mdbc.gov.au/__data/page/101/WAM-Report-2004-05.pdf |title=Water Audit Monitoring Report 2004/05 |author=Murray-Darling Basin Commission| author-link=Murray-Darling Basin Commission|date=June 2006|isbn=1-921-038-93-4 |access-date=2007-09-28 |url-status=dead |archive-url=https://web.archive.org/web/20060906154918/http://www.mdbc.gov.au/__data/page/101/WAM-Report-2004-05.pdf |archive-date=2006-09-06 }}, retrieved 28 September 2007</ref> The probability of the bottom end of the Murray experiencing drought-like flows had increased from 5% under natural conditions to 60% by 1995.<ref name=mdbcaudit1995/>

[[Thermal pollution]] is the artificial reduction in water temperatures, especially in summer and autumn, caused when frigid water is released from the bottom of reservoirs for irrigation demands. Such temperature suppression typically extends several hundred kilometres downstream. Thermal pollution inhibits both the breeding of Murray cod and the survival of Murray cod larvae, and in extreme cases inhibits even the survival of adult Murray cod.<ref name=nfacod/>

The rare floods that do break free of the dams and weirs of the Murray-Darling system have their magnitude and duration deliberately curtailed by river regulators. Increasing research indicates this management practice is very harmful and drastically reduces the general [[ecosystem]] benefits and breeding and recruitment opportunities for Murray cod and other Murray-Darling native fish species these now rare floods can provide.<ref name=Allen-et-al2002/><ref name=McDowall1996/><ref name=Koehn2004/><ref name=sharing/>

====Blackwater events====
Blackwater events are emerging as a very serious threat to wild Murray cod stocks in lowland river reaches. Blackwater events occur when floodplains and ephemeral channels accumulate large quantities of [[leaf litter]] over a number of years and are then finally inundated in a flood event. The leaf litter releases large quantities of dissolved organic carbon, turning the water a characteristic black colour and inducing a temporary explosion in bacterial numbers and activity, which in turn consume dissolved oxygen, reducing them to levels harmful or fatal to fish. (Fish essentially asphyxiate.) Water temperature is a critical regulator of blackwater events as warmer water temperatures increase bacterial activity and markedly reduce the intrinsic oxygen carrying capacity of water; events that may be tolerable for fish in winter or early spring may be catastrophic in late spring or summer due to the increase in water temperature.<ref name="Whitworth et al. 2012">
{{Cite journal
  | last = Whitworth | first = K. L. |author2=Baldwin, D. S. |author3=Kerr, J. L.
  | title = Drought, floods and water quality: Drivers of a severe hypoxic blackwater event in a major river system (the southern Murray–Darling Basin, Australia)
  | journal = Journal of Hydrology
  | volume = 450–451
  | pages = 190–198
  | year = 2012
  | doi = 10.1016/j.jhydrol.2012.04.057| bibcode = 2012JHyd..450..190W }}
</ref>

Blackwater events are often described as "natural" events—while there are some historical records of relatively severe events in smaller, more ephemeral systems (e.g. lower Lachlan, upper Darling), there is no record of severe events in the Murray River and its largest southern tributaries before water extraction and river regulation. In the Murray and large southern tributaries, very severe large-scale blackwater events are a relatively new but recurring phenomenon and appear to be an effect of river regulation curtailing the winter/spring flood events that formerly swept [[leaf litter]] away annually, exacerbated by long-term declines in rainfall and recurring prolonged drought events.<ref name="Hladyz et al. 2011">
{{Cite journal
  | last = Hladyz | first = S. |author2=Watkins, S. C. |author3=Whitworth, K. L. |author4=Baldwin, D. S.
  | title = Flows and hypoxic blackwater events in managed ephemeral river channels
  | journal = Journal of Hydrology
  | volume = 401
  | pages = 117–125
  | year = 2011
  | doi = 10.1016/j.jhydrol.2011.02.014
  | issue = 1–2| bibcode = 2011JHyd..401..117H }}
</ref>

Flood events in 2010 and 2012 following the prolonged Millennium Drought (1997–2009) induced very severe blackwater events; while formal studies of these events were limited due to the relatively rapid response times required and logistical difficulties,<ref name="King et al. 2012">
{{Cite journal
  | last = King | first = A. J. |author2=Tonkin, A. |author3=Lieschke, J.
  | title = Short-term effects of a prolonged blackwater event on aquatic fauna in the Murray River, Australia: considerations for future events
  | journal = Marine and Freshwater Research
  | volume = 63
  | pages = 576–586
  | year = 2012
  | doi = 10.1071/MF11275
  | issue = 7 }}
</ref>
angler photographs and observations of extraordinary numbers of dead Murray cod during these events and plunging catch rates after these events show they induced extremely heavy Murray cod mortalities along extensive tracts of the Murray River.

====Physical barriers to fish movement====
Dams, [[weir]]s and other instream barriers block the migration of adult and juvenile Murray cod and prevent recolonisation of habitats and maintenance of isolated populations.<ref name=nfacod/> Additionally, recent study has proven approximately 50% of Murray cod larvae are killed when they pass through undershot weirs.<ref name=Baumgartner-et-al2006>
{{Cite journal
  | last = Baumgartner  | first = L. J. |author2=Reynoldson, N. |author3=Gilligan, D. M.
  | title = Mortality of larval Murray cod (''Maccullochella peelii peelii'') and golden perch (''Macquaria ambigua'') associated with passage through two types of low-head weirs
  | journal = Marine and Freshwater Research
  | volume = 57
  | pages = 187–191
  | year = 2006
  | doi = 10.1071/MF05098
  | issue = 2 }}
</ref>

====Habitat degradation / siltation====
Hundreds of thousands, perhaps more than a million, submerged timber "[[snags]]", mainly [[River Red Gum]], have been removed from lowland reaches of the Murray-Darling basin over the past 150 years.<ref name=MacNally-et-all2002>
{{Cite journal
  | last = MacNally  | first = R. |author2=Parkinson, A. |author3=Horrocks, G. |author4=Young, M.
  | title = Current Loads of Coarse Woody Debris on Southeastern Australian Floodplains: Evaluation of Change and Implications for Restoration
  | journal = Restoration Ecology
  | volume = 10
  | issue = 4
  | pages = 627–635
  | year = 2002
  | doi = 10.1046/j.1526-100X.2002.01043.x | bibcode = 2002ResEc..10..627M | s2cid = 84135006 }}
</ref> The removal of such a vast number of snags has had devastating impacts on Murray cod and river ecosystems. Snags are critical habitats and spawning sites for Murray cod. Snags are also critical for the functioning of lowland river ecosystems — as one of the few hard [[Substrate (marine biology)|substrates]] in lowland river channels composed of fine silts snags are crucial sites for [[biofilm]] growth, [[macroinvertebrate]] grazing and general in-stream productivity.<ref name=Koehn2004/><ref name=MacNally-et-all2002/>

Vegetation clearing and cattle trampling river banks create severe [[siltation]], which fill in pools, degrade river ecosystems and make rivers and streams uninhabitable for Murray cod.<ref name=McDowall1996/> This is exacerbated by removal of [[riparian]] (riverbank) vegetation which causes siltation and degrades river ecosystems in many ways.<ref name=nfacod/>

====Introduced carp====
There is serious competition for food between larval/early juvenile introduced carp and larval/early juvenile native fish.<ref name=Tonkin-et-al2006/> Introduced carp dominate the fish [[fauna]]s of lowland Murray-Darling rivers; the sheer amount of [[Biomass (ecology)|biomass]] carp now take up, and the large numbers of larvae carp produce, causes serious negative effects on river ecosystems and native fish.<ref name=Tonkin-et-al2006/> Carp are the main vector of the introduced ''[[Lernaea]]'' parasite (''[[Lernaea cyprinacea]]'') and serious vectors of the introduced Asian fish tapeworm (''[[Bothriocephalus acheilognathi]]'').

[[File:Lernaea parasite on a Murray cod.jpg|thumbnail|''Lernaea'' parasite on a murray cod]]

====Introduced pathogens====
Murray cod have soft skin and very fine scales that leave them particularly vulnerable to infection from exotic diseases and parasites. The following exotic diseases and parasites all seriously affect wild Murray cod; all have been introduced by imports of exotic fish.<ref name="Kaminskas 2020">{{cite journal|first1=S.|last1=Kaminskas|year=2020|title=Alien pathogens and parasites impacting native freshwater fish of southern Australia: a scientific and historical review|journal=Australian Zoologist|volume=41 |issue=4 |pages=696–730 |doi=10.7882/AZ.2020.039|s2cid=230643061 |doi-access=free}}</ref> ''Chilodonella'' is a single-celled, parasitic [[protozoa]] that infects the skin of Murray cod and has caused a number of serious kills of wild Murray cod.<ref name="Rowland and Ingram, 1991"/><ref name="Kaminskas 2020"/> ''[[Saprolegnia]]'' is a fungus-like oomycete or "water mould" that frequently infects Murray cod eggs and the skin of Murray cod that have been roughly handled through poor [[catch and release|catch and release technique]].<ref name="Rowland and Ingram, 1991"/><ref name="Kaminskas 2020"/> (It is essential that Murray cod intended for release only touch cool wet surfaces and are '''not''' put down on any hard, dry, rough or hot surfaces, e.g. boat gunwales, boat floors, dry grass, dry rocks, gravel banks, dry towels or mats, etc. Hands should also be wetted before touching them. They must not be hung vertically by the mouth or gill covers.) Wild Murray cod populations across their range suffer extremely severe infestations of ''Lernaea'' or "anchor worm", a parasitic [[copepod]] vectored by introduced [[carp]] and that burrows into the skin of Murray cod.<ref name="Rowland and Ingram, 1991">{{cite book|author1=Rowland SJ|author2=Ingram BA|title = Diseases of Australian native freshwater fishes with particular emphasis on the ectoparasitic and fungal diseases of Murray cod (Maccullochella peeli), golden perch (Macquaria ambigua) and silver perch (Bidyanus bidyanus)|publisher =NSW Fisheries, Sydney.|year =1991}}</ref><ref name="Kaminskas 2020"/><ref name="NSW Rivers Survey">{{cite book|author1=Harris JH|author2=Gehrke PC|title = Fish and Rivers in Stress — The NSW Rivers Survey|publisher =NSW Fisheries Conservation Office, Cronulla, Sydney|year =1997}}</ref> ''Lernaea'' puncture wounds are often secondarily infected by bacteria.<ref name="Khalifa and Post, 1976">{{cite journal|last1=Khalifa|first1=KA|last2=Post|first2=G|year=1976|title= Histopathological effect of Lernaea cyprinacea (a copepod parasite) on fish|journal= The Progressive Fish-Culturist|volume=38|issue=2|pages=110–113|doi=10.1577/1548-8659(1976)38[110:heolca]2.0.co;2}}</ref><ref name="Berry et al., 1991">{{cite journal|last1=Berry|first1=CR|last2=Babey|first2=GJ|last3=Shrader|first3=T|year=1991|title= Effect of Lernaea cyprinacea (Crustacea: Copepoda) on stocked rainbow trout (Oncorhynchus mykiss)|journal=Journal of Wildlife Diseases|volume=27|issue=2|pages=206–213|doi=10.7589/0090-3558-27.2.206|pmid=2067042|s2cid=28800550|doi-access=free}}</ref> Severe ''Lernaea'' infestations probably causes the death of many more adult Murray cod than commonly recognised.<ref name="Goodwin, 1999">{{cite journal|last1=Goodwin|first1=AE|year=1999|title= Massive Lernaea cyprinacea infestations damaging the gills of channel catfish Ictalurus punctatus polycultured with bighead carp Hypophthalmichthys nobilis|journal= Journal of Aquatic Animal Health|volume=11|issue=4|pages=406–408|doi=10.1577/1548-8667(1999)011<0406:mlcidt>2.0.co;2}}</ref><ref name="Kaminskas 2020"/> Ebner<ref name=Ebner2006/> reports a young adult Murray cod seemingly killed by severe ''Lernaea'' infestation.