13 Oct 2013

Things we do for class - Bivalve dissection


Chama pacifica Chamidae

Just last week we did another dissection practical. This time, for bivalves! We got to dissect a Meretrix sp. ("La La", a heterodont), Nuculana sp. (which was really tiny, a protobranch), Anodonata sp. ("Mussel", family Mytillidae, a pteriomorph), Anadara sp. ("Blood Cockle", a heterodont).

Bivalves are molluscs that are laterally compressed and have a hinge, enclosing two hinged parts. The shell is made up of calcium carbonate secreted by the mantle lobes and mantle. The calcium carbonate can be either aragonitic (nacreous inner layer - sheet or lenticular, prismatic, cross lamellar structure - simple or complex) or calcitic (outer foliose, prismatic). The calcium carbonate of a shell is never entirely calcitic though, mostly it is a mix of aragonite and calcite. Certain bivalves though, like oysters have almost all calcitic. On the contrary, some families are entirely aragonitic.

Lima vulgaris Limidae with wholly aragonitic shells
They have a D-larva split into two stages, Prodissoconch I and Prodissoconch II which have the velum to help it with motility with the exception of the Paleoheterodonts which have glochidium/ lasidium larvae.

They are generally split into different clades based on gill type, presence of palps, type of stomach, fusion of mantle & siphon position (higher taxa); hinge teeth type (higher or lower taxa); foot size, position of adductor muscles (lower taxa):

(photographs were identified by Tan Siong Kiat in 2011 as part of Project Semakau: bivalve page)

- Protobranch (small group, 3 orders, considered 'ancient', small in size, bipectinate lamellae (simple) gills with palp probocoides (for Nuculidae and Nuculanidae), foot frilled with papillae, do not filter feed but scrape detritus or symbiotic with sulphur oxidising bacteria in gills (only Solemyida))
e.g. Nuculana

- Paleoheterodont (mostly in the family Unionidae but there are 6 other families; mostly are freshwater except one of which is salt-water - Trigoniidae)

- Heterodont (unequal hinge teeth, eulamellibranch gills, mantle edges are fused at the posterior end as an inhalant tube) and Anomalodesmatans (typically lack hinge teeth, aragonitic shells, long siphons, fourth pallial aperture, vestigial gill filaments; Septibranchia is carnivorous with a type II stomach)
e.g. Heart Cockle (Cartiidae), La La Siput (Veneridae), Meretrix (Veneridae)


Cordissum cardissa Cartiidae
Dosinia amphismoides Veneridae

Teredo sp. Terenidae
Tellina virgata Tellinidae


- Pteriomorphs  (reduced foot, filibranch gills (Oysters (orders Ostreida, Pectinida) are exceptions - they have eumellibranch gills with the exception of Plicatuloidea (superfamily)), mantle edges generally not fused, taxodont or dysodont hinge teeth)
 e.g. Green Mussel Perna sp. (Mytilidae), Hammer Oyster (Isognomonidae), See Hum Anadara sp. (Arcidae), File Shell (Limopsidae), Scallops (Pectinidae), Spiny Oysters (Spondylidae)

Lithophaga teres Mytilidae
Isognomon isognomon Isognomidae

Pinna bicolor Pinnidae

Spondylus niobarensis Spondylidae
A related species to Spondylus, the Comptopallium radula
Notes:
- filibranch is ancestral to eulamellibranch gills
- heterodont/schizodont/isodont/dysodont teeth is more derived than taxodont teeth


Important parts of the bivalves are:

Of the valves
- Hinge teeth: either cardinal or lateral; isodont/schizodont/heterodont/dysodont/taxodont

Taxodont hinge of Anadara antiquata Arcidae
- Umbo: a knobbly protuberance (determines dorsal)
- Lunule (typically anterior but the mouth position determines anterior/posterior)
- Estucheon (typically posterior)
- Periostracum - either secreted by the mantle edge or foot

- Pallial line, where the mantle edge is
- Pallial sinus, a groove where the siphons are retracted into

Anatomy
- Ligament: inner (lamellar), outer (fibrous); can be alivincular, duplivincular, parivincular, multivicular, either amphidetic (either side of the umbo; usually only for alivincular or dulivincular only) or opisthodetic (anterior of umbo; usually for parivincular or multivincular only); e.g. opisthodetic parivincular are typically of the heterodonts, multivincular opisthodetic are typically of the Isognomidae ("Hammer Oysters"), duplivincular amphidetic (Arcidae), alivincular amphidetic (Limopsidae),

- Gills: made up of lamellae with cillia (Protobranchs); when fused, form demibranches connected by tissue between lamella but not always so; might have cillary junctions (filibranch; Pteriomorphs); when filaments are fused with adjacent filaments, form interfilament junctions, exclusively NO cillary junctions (eulamellibranch; Heterodonts); typically one pair of ctenidia on each side of the visceral mass; each ctenidia with a descending and descending lamella for the eulamellibrach condition; Septibranch condition is a poorly-developed septum with vestigial gills but has tentacles on inhalant siphons to suck small prey up

- Adductor muscle - present most of the times in the anterior and posterior position (isomyarian/heteromyarian/monomyarian); typically one pair of adductor muscle(s) on each valve; for example, Green Mussels (Perna viridris) only has posterior adductor mussel, scallops have one large adductor (central) muscle (monomyarian)

Saccostrea cucullata Ostreidae with an adductor muscle scar

- Other retractor muscles 

- Mantle (inner, mid, outer folds; outer - secretory, may be sensory; mid - sensory, have tentacles, sometimes eyes; inner - muscular and attached to shells) with type A/B/C fusion

- Visceral mass which contains heart (2 auricles, 1 ventricle; open circulatory but certain families have haemoglobin and is 'bloody'), digestive organs (esophagus/ stomach - crystalline style, typhosole, sorting area/ intestines/ anus), reno-pericardial complex, gonads

- Periocardial complex
- Two ganglia (cerebro-pleural ganglia innervates palps, anterior adductor muscle, otocysts, part of mantle and visceral ganglia innervates gills, heart, pericardium, posterior adductor muscle, most mantle regions, siphons and pallial sense organs) 

- Byssus - secreted by foot typically
- Eyes - pallial (marginal or siphonal, innervated by mantle) or cephalic (inner demibranchs of ctenidia, innervated by cerebral ganglia)

- Siphon - for respiratory purposes/ suspension feeding

- Labial palps (2 pairs)/ palp probosoides (not always present)/ mouth; sometimes labial palps can be hypertrophied (such as in Scallops) to helps food items not 'fall out' while swimming


That was a spam of essential terms. Anyway, here're some photographs by Xin Rui during the practical.


Meretrix sp. ("La La") which is a heterodont. Photo source: Ong Xin Rui

The internal anatomy of the Meretrix sp. ("La La"), the same as above. For our practical session, we were required to draw the anatomy. Please note that the posterior and anterior ends should be exchanged. Photo source: Ong Xin Rui

Further reading
[1] About Glochidium/Lasidium larvae: http://mussel-project.uwsp.edu/evol/syst/larvae.html
[2] About hinge types: http://paleo.cortland.edu/tutorial/Bivalves/bivalvemorph.htm
[3] Pictures of bivalves: http://www.nmr-pics.nl/index.htm

I shall update this page again, after I have dug up my bivalve photographs. Everything makes more sense now after this class...

Please correct if you spot any errors. Information taken and summarized from Bivalve lecture notes.

4 Sept 2013

Things we do in class - Fish dissection

Figure 1 - The Tilapia (Osteichthyes: Actinopterygii: Teleostei: Perciformes: Cichlidae: Tilapiine), before dissection. Instruments of the trade
Today marks the first time dissecting an animal during a practical session in "Topics in Aquatic Biodversity". Have watched people do it, and have heard people do it but have never done it myself before because it was never compulsory during biology classes in Junior College and in university, until now. It was quite an interesting experience, albeit frightening at first because it was fish but it really was not so bad.

*****

Fishes, a general introduction


Fishes are a diverse group of animals, that both live in marine and freshwater environments.

They are generally split into these extant groups:
  • Hagfishes (Myxiniformes)
  • Lampreys (Pteromyzontiformes)
  • Jawed Fishes
    - Cartilagenous fishes
    - Bony fishes [ray finned - split into Sacropterygii and Actinopetrygii and lobe finned] 
Note: the Sacropterygii are further split into lungfishes, Tetrapods and Coelacanth; Actinopterygii further split into Neoptergyii and Chondrostei (bichirs, surgeons: which have some what ossification but are generally cartilagenous). Neopterygii is further split into gars (swim bladders function as lungs; heteroceral tail, ganoid scales), bowfins (similar to gars; which are actually able to breathe air, storing the air in its swim bladder connected to its digestive tract) and Teleostei
They are, however, paraphyletic, because any animal that "has a cranium, gill-bearing and lack limbs with digits" are lumped to this clade whereas the 'Tetrapods' are nested within this clade. Thus, it is not monophyletic.

Though, that is, besides the point. Most would be interested in fish as a commodity because it is important for food, which leads to problems of overfishing and is popular in the pet trade, which can lead to the proliferation of invasive animals, in the context of Singapore.

****

Morphology: the exterior and interior

note: the information presented here is learnt during lessons by Dr Tan Heok Hui

Just looking at the morphology of a fish can yield lots of interesting information. One can never divorce morphology from taxonomy and classification of fishes.

By looking at its exterior morphology (Figure 2), one can infer life history traits, habitat and food preferences about the fish based on certain generalizations -- but of course, there are always exceptions! Further, there are specialised structures, indicating some form of adaptations (e.g. barbels for sensory purposes).

1. Position of mouth: superior, terminal, inferior (and a whole suite of in-betweens)
2. Shape of body: torpedo, streamlined like the Tuna; oval shaped/ compressed laterally like the Mola Mola
3. Dentition: the type of teeth/ teeth plates (hooked, grazer-type, flesh-cutting, grinding; fused that is beak-like), the arrangement of the teeth (cartilagenous fishes have rows of teeth, unlike bony fishes), presence of pharyngeal teeth (to act as grips, not masticatory) which is located in the skull
4. Fins: shape of the five fins (ventral fins: pelvic, anal; dorsal fin(s); caudal fin, pectoral fins), whether it is fused or not; caudal fins can be truncate, emarginate, forked, deeply forked, rounded; pelvic fins can be fused; there can be one or two pectoral fins
5. Lateral line: can be complete or incomplete, from the top of the operculum to the (mid-) end of the peduncle; hyped-up lateral line systems with strong/weak voltage, the former for defense/finding prey and the latter for navigation.
6. Buccal cavity adaptations: in mudskippers it is used to store water, projectile expulsion in archer fishes, egg brooding in Osphronemidae/ Cichlidae/ Apogonidae/ Ariidae
7. Scales: Ctenoid/Cycloid (usually for higher fishes like the Teleostei; Ctenoid have a toothed outer edge, fishes with spiny rays as opposed to soft rays); Ganoid (garfishes, bichirs); Placoid (dermal/epidermal origins for Cartilagenous fishes)

Further, dissection to look at the internal morphology of the fish can further confirm the inferences (based on external morphology) such as the diet (gut content, length of gut), gender (male or female, by the gonads) and age (from otoliths in temperate fishes). Also, one can look at the gill rakers.

Figure 2 - Anatomy of a female fish. In a male fish, the ovary is replaced by the testicles.The bones are dorsal to the organs.
Source: http://en.wikipedia.org/wiki/Fish_anatomy

Figure 3 - Bamboo sharks (Chondrichthyes: Orectolobiformes: Hemiscylliidae), a male and a female. The males have a pair of claspers at the anal fins.

Figure 4 - Xin Rui's neat dissection area. She found two little crabs and one fish in the stomach of the predatory fish (second fish from the left).


27 Aug 2013

XR's fieldwork short notes

This page's purpose is to keep everyone updated on my fieldwork progress.

1 June 2013
Went to the site in Chestnut. Google maps was not functioning properly. Wasted a decent amount of time trying to locate the GPS coordinates of the central tree in both sites. Setup transect lines of the two grids with some hassle. Total time spent in the field was 5 hours. Longest ever. D:

3 June 2013
Went to the site in Bukit Timah, near Catchment Path. Site was easily accessed. No transect lines were done in one grid due to the frequent visits of researchers to this area.

4 June 2013
Went to the site in Bukit Batok. Both grid transects were located quite far apart and accessed via two different entrances. Terrain was quite hilly in the site near Meralodge. Illegal squatters were since but unoccupied. No fishing lines were done in both sites due to the presence of squatters.

6 June 2013
Went to the site along BKE (i.e. Bukit Timah East). Very easily accessible via the entrance near the army gate along the BKE (requires a vehicle). Terrain relatively flat. Good forest to work in.

13 June 2013
First ever setup of pitfall traps in Chestnut. Was done with very little hassle.

15 June 2013
Collected specimens from Chestnut's pitfall traps. Estimated to have about 5 species from this site. Pitfall traps that were baited with Sambar deer dung had no dung beetles at all. One pitfall trap baited with python dung had no dung beetles as well.

18 June 2013
BTNR Site. Slightly hazy conditions. Might affect the number of dung beetles captured in the traps.

20 June 2013
Relatively lesser dung beetles in BTNR site as compared to previous site in Chestnut. Possibly due to the haze. Requires comparison with second sampling round to prove this. Yet again, no dung beetles in Sambar deer dung baited traps.


27 June 2013
Bukit Batok Site. Pretty tough working on a slope and setting up the traps. Not to mention the mossies that are not deterred by any amount of repellent. Lots of bites and body aches. Good fun nonetheless. :)

29 June 2013
Collected specimens from the pitfall traps in Bukit Batok. Very low diversity of dung beetles in this site. Expected.


4 July 2013
BKE Site. The best site to work in due to its relatively open understory and flat terrain. Finished setting up traps with little hassle.

6 July 2013
Collected specimens from the BKE site. Lots of dung beetles captured but no Catharsius molossus at all. Perhaps they are just not common there. Hmm. One dung beetle in reticulated python trap and once again, no dung beetles in Sambar deer trap.

11 July 2013
First ever trip to the site in MacRitchie. Really dense forest with visibility of less than 5m (maybe even 2.. hmm). Flat terrain makes life much easier in the presence of spiny rattan and nibong palms. Did both transect setting and pitfall trap setup with the help of many great assistants. Barely escaped the thunderstorm. Thank God~ :D

13 July 2013
Collected specimens from MacRitchie. Pretty difficult to find the traps. Interesting finds from this plot. And there are finally dung beetles in the Sambar deer trap! :)

25 July 2013
Returned back to Bukit Timah Site to start my second round of sampling. Fieldwork was postpone for 30 min due to the heavy rain in the area. Had trouble finding the first plot. Blame it on my own poor navigation skills. Haha.


27 July 2013
Collected specimens from Bukit Timah. Got caught in the rain but it was alright. Good find from the site.

1 Aug 2013
Headed back to the site in Chestnut with many helpers! Had fun "bossing" people around. Saw the Giant millipede! Very cooling weather right after the rain. (:

3 Aug 2013
Fast and quick collection of specimens from Chestnut. Great weather.

8 Aug 2013
Back to BKE site to setup pitfall traps. Was slightly delayed due to the morning thundery showers.

11 Aug 2013
Lots of dung beetles collected from the BKE Site. (:


17 Aug 2013
Back to Bukit Batok to feed the mossies and setup pitfall traps. Saw a some animal paw prints along the stream. Cat? Dog? Always tough to setup traps on a hilly terrain.

19 Aug 2013
Forgot to bring covers along for one transect in Bukit Batok (dang). Had to improvise and use my latex gloves as temporary covers. As expected, very little dung beetles AGAIN. Saw a stray dog which is most likely responsible for those paw prints. One data logger had bite marks. -.-

24 Aug 2013
Back to MacRitchie. Although the forest is very dense with all the rattans n shrubs, it still beats working in Bukit Batok. :D

26 Aug 2013
Much lesser dung beetles as compared to the very first time I sampled this area. Could be due to the weather as there was no rain throughout the 48 hour sampling period. LAST SITE OF ROUND 2! HOORAY!!


(1 June 2013 to 26 Aug 2013... That's almost 3 months of fieldwork!!)

9 Aug 2013

Singapore dungabee fact #2

Paragymnopleurus maurus


Paragymnopleurus maurus
is perhaps the only dung beetle species in Singapore that rolls dung balls away from the dung source. Such rollers are also referred to as telocoprids, whereas the tunnelers are known as paracoprids [1].

Check out these long hind legs!

Rollers can be identified by their longer hind legs, which they use to roll dung balls away from its main source and bury them in another location for nesting purposes [1]. P. maurus is about 15mm in length, making it the second largest dung beetle in Singapore thus far.

Finally, please enjoy this short video (shot by Dave Ng) of this cool rolling "dungabee".



References:
[1] Hanski, I. & Cambefort, Y.  (1991) Dung Beetle Ecology. Princeton: Princeton University Press.

Photos by Zestin Soh


18 Jun 2013

Ants of Singapore #08 - Strumigenys (cf. koningsbergi)

Strumigenys

Species accounts


Strumigenys cf. koningsbergi


Strumigenys c.f. koningsbergeri
Strumigenys (Myrmicinae : Dacetini) is a small, cryptic, leaf-litter dwelling ant; they are otherwise known as Trap Jaw ants as well.

They are pretty numerous in the leaf litter and also nest in the crevices of dead logs. They are move slowly most of the time, unless when disturbed.

It is said that some species are specialist predators of springtails (Coembolla, which are arthropods with six legs but do not have wings [Entognatha]). Perhaps that is why they require trap-jaw like mandibles as well, to 'capture' these fast moving Coembollas!


17 Jun 2013

Ants of Singapore #07 - Cerapachys (undet.)

Cerapachys

Species accounts


sp. 1


Old World Army Ants Cerapachys sp.

The Old World Army Ants, Cerapachys are a diverse group of ants. Some of these ants are blind (i.e. they have no eye facets), while others are not. The one as shown above has only one eye facet (look at picture below), suggesting a subterranean or nocturnal lifestyle. It was actually seen attacking an earthworm at night, though no photographs to document that.


Cerapachys biroi, one of the species within the genus, is said to be very widespread and is considered a tramp ant [1] and was first described in Singapore by Forel in 1907, suggesting its origins in Asia as well. They are said to practice parthenogenesis [2] because workers can produce diploid eggs. They are also entirely subterranean which also suggests dispersal by exported soil perhaps. This might be an interesting article for those who wish to read more.

Alright, good day ahead.


References

[1] Wetterer et al.. 2012. Worldwide spread of Cerapachys biroi (Hymenoptera: Formicidae: Cerpachyinae). Myrmecological News 17: 1-4.
[2] Kronaeur et al.. 2012. Asexual reproduction in introduced and native populations of Cerapachys biroi. Molecular Ecology 21(21): 5221-5225.



15 Jun 2013

Ants of Singapore #06 - Pheidologeton (diversus)

Pheidologeton

Species accounts


Pheidologeton diversus 


Recently Pheidologeton was synonymised under Carebara (Fisher, 2014). I will still recognize Pheidologeton for the sake of this blog.

Pheidologeton diversus, otherwise known as the Maurauder Ant. 

These ants are commonly seen, in the day and in the night, where there is a dead carcass. They are quick to recruit, and are the dominant insects at a particular dead carcass, often excluding other competitors. Maybe that's why they're relatively common insects.

Dominating at a carcass

They are polymorphic (come in various sizes), and sometimes the minor ants can be seen to be riding on the major ants, a behaviour similar to the leaf cutter ants whose minors ride on the leaves carried by the major workers. Not many are sure why this behaviour is so, but it has been hypothesized that perhaps it prevents phorid flies from laying eggs on their head.



They look similar to the Pheidole ant, another genus but can be distinguished based on the number of antennal clubs (Pheidologeton has 2, Pheidole has 3).