How do fish get their colors?

It’s no secret that minnows, suckers (as I found out tonight), and loaches are extremely popular in the aquarium trade. Part of this is due to the hardiness of (some of) these species, but more so due to their extremely amazing color patterns. Some species have horizontal stripes running the length of their bodies (e.g., North American minnows) whereas others have stripes running from the dorsal to ventral side of the body (e.g. clown loach; Chromobotia maracanthus). Some species have similar spots all over their body while others have spots of various sizes (e.g., imperial flower loach, Leptobotia elongata). Some have red, yellow, blue/purple, and black pigments all the time while only males develop these colors during the breeding season in other species. This amazing variation in pigmentation patterns is what drives a lot of the interest in this group in the aquarium trade.

A new article entitled “Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish” is hot off the press in Science. The authors of this paper developed a protocol whereby they could track in developing zebrafish (Danio rerio) the development of three types of cells associated with color production in fishes: xanthophores (yellow/red pigment), iridiophores (reflective), and melanophores (black pigment). It has long been known that these pigments contribute to color patterns in fishes, but how they do from embryo to adult has long remained a mystery. If you think about how small each cell is and the fact that it has be tracked throughout development to determine their embryonic origin, you can figure out why studying these cells have been difficult for so many years. Although difficult, if we knew how these cells formed, we could then understand the striking patterns of color patterns in fishes.

Danio rerio Photo: Pogrebnoj-Alexandroff

So what did they find? Well, read the paper for the exact details, but the xanthophores first arrive on these scene and form the layer of xanthophores as observed in adults. The iridiophores and melanophores ultimately arrive on the scene taking different cellular routes to arrive. Once the iridiophores arrive, the yellow xanthophores form a dense layer over the iridiophores producing the yellow inter-stripe. The black “zebra” stripes are formed by melanophores with a loose, scatter of xanthophores over the top of it. Why is it necessary for the xanthophores to densely cover the iridiophores and only loosely cover the melanophores? According to the authors, it produces and sharpens the characteristic yellow/black zebra pattern.

If you do a thought experiment, you can see how lacking xanthophores over the melanophores would probably produce a more “monotonous” color pattern. Think about how something changes when you put (a little) glitter on it. It adds some “flare” to whatever you put the glitter on. …I know this analogy isn’t perfect, but hopefully it gets the point across.

So, where do we go from here? Well, this is very exciting. If we understand how such color patterns are formed in one species, we can then ask questions about more complex color patterns as well as distribution of underlying mechanisms — i.e., does the same underlying mechanism produce color patterns in all fishes or are there multiple development mechanisms (convergent evolution). Although this is HUGE step, I still think we have other questions to address. What signals are these cells using? What genes are involved in the recruitment of these cells and how does their expression influence the production of color patterns? There has been a lot of interest in the evolution of genes associated with color production (Kelsh et al. 2004Braasch et al. 2007Braasch et al. 2008Braasch et al. 2009) and even in the expression of these genes (Salzburger et al. 2007; Henning et al. 2010Gunter et al. 2011). Now, the role of these genes can be much more thoroughly assessed using the various pigmentation mutants of zebrafish (e.g., Watanbe et al. 2006). So, stay tuned. I’m sure there will be more studies in the not too distant future that shed more light on the molecular development of pigmentation patterns in fishes!


Braasch I, Schartl M, Volff J-N (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evolutionary Biology 7(74) doi: 10.1186/1471-2148-7-74.

Braasch I, Volff J-N, Schartl M (2008) The evolution of teleost pigmentation and the fish-specific genome duplication. Journal of Fish Biology 73(8):1891-1918.

Braasch I, Brunet F, Volff J-N, Schartl M (2009) Pigmentation pathway evolution after whole-genome duplication in fish. Genome Biology and Evolution 1:479-493.

Gunter HM, Clabaut C, Salzburger W, Meyer A (2011) Identification and characterization of gene expression involved in the coloration of cichlid fish using microarray and qRT-PCR approaches. Journal of Molecular Evolution 72:127-137.

Henning F, Renz AJ, Fukamachi S, Meyer A (2010) Genetic, comparative genomic, and expression analyses of the Mc1r locus in the polychromatic Midas cichlid fish (Teleostei, Cichlidae, Amphilophus sp.) species group. Journal of Molecular Evolution 70:405-412.

Kelsh, K (2004) Genetics and evolution of pigment patterns in fish. Pigment Cell Research 17:326-336.

Mahalwar P, Walderich B, Singh AP, Nusslein-Volhard C (2014) Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish. Science doi: 10.1126/science.1254837.

Salzburger W, Braasch I, Meyer A (2007) Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes. BMC Biology 5(51), doi: 10.1186/1741-7007-5-51.

Watanbe M, Iwashita M, Ishii M, Kurachi Y, Kawakami A, Kondo S, Okada K (2006) Spot pattern of leopard Danio is caused by mutation in zebrafish connexin41.8 gene. EMBO Reports 7(9):893-897.

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A conservation success story?

Some of you may have seen the headline “Endangered Nevada Fish Makes Comeback” from the Las Vegas Review-Journal. 

Could it be? Could the endangered Moapa Dace (Moapa coriacea) really make a come back and get off the endangered species list? If you aren’t familiar with this species, it is a thermophilic minnow endemic – meaning they don’t occur anywhere else in the world – to the Muddy River and the warm, thermal springs associated with this system in Clark County, Nevada.

Being endemic to specific reaches of a single river drainage, this species may be prone to extinction naturally. But what really is hurting this species? Historically, there were probably a few things. The river this species is endemic to, the Muddy (or Moapa) River, was dammed in 1935 by the Hoover Dam to build Lake Mead. Because this species has such narrow habitat requirements, converting a river channel to a large, flooded area with little to no water flow isn’t ideal for this species. Further, this completely goes against the thermophilic requirements of this fish. This species also has had to deal with introduced species including the shortfin molly (Poecilia mexicana), channel catfish (Ictalurus puncatus), common carp (Cyprinus carpio), fathead minnow (Pimephales promelas), black bullhead catfish (Ameirus melas) (US Fish and Wildlife Service 2014). It also faces parasites that were introduced with these species so it may still be an uphill battle for this species to get off the endangered list. And I didn’t touch much on it, but water withdrawals by humans will certainly have negative impacts on this species (Hatten et al. 2013). 

So, what is the big news about? Recent surveys informed managers that the population is made up of at least 2,248 individuals, a count up by almost 33% from the count a year ago (Brean 2014). Obviously, this is positive news and the population is trending up. For them to be downgraded from “endangered” to “threatened,” there must be at least 4,500 Moapa dace counted (Brean 2014). To be “delisted”, the population must be a minimum of 6,000 individuals and at least 75% of the fish’s native habitat must be restored (Brean 2014). It’s tough to imagine this species not receiving some level of protection given it’s small native range, but if it was downgraded to “threatened”, that would certainly represent additional progress in the right direction. 


Brean H. 2014. Endangered Nevada fish makes comeback. Las Vegas Review-Journal. Available at

Hatten JR, Batt TR, Scoppettone GG, Dixon CJ. 2013. An ecohydraulic model to identify and monitor Moapa Dace habitat. PLoS One, DOI: 10.1371/journal.pone.00055551.

Moapa Dace. 2014. US Fish and Wildlife Service. Available at

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Can aquarists and scientists collectively form a better scientific community?

The reason I started this blog is two-fold. First, there are a lot of aquarists who care for minnows, suckers, and loaches. When I say alot, I mean A LOT. It is highly likely that many of these aquarists have abundant information about the natural history, behavior, or diet that isn’t in the scientific literature or is extremely difficult to find in the literature. Second, there is a lot of information in the scientific literature that may of value or interest to aquarists who otherwise would not have access to it. By starting this blog, my goal was to begin building (or extending) the bridge between aquarists and scientists.

Yesterday, I went by a local pet store in Norman and saw three loach species: clown loaches (Chromobotia macracanthus), dojo loaches (Botia almorhae), and zebra loaches (Botia striata). In addition to these loaches, there were an abundance of minnows, probably 6-8 species realistically.

Clown loaches, dojo loach, and zebra loaches from a local pet shop.

Clown loaches, dojo loach, and zebra loaches from a local pet shop.


Of these, I was particularly interested in the zebra loach. So, when I arrived home, I searched for zebra loaches just to learn a little about them. Where are they native to? What habitat do they live in? Standard stuff, I suppose. Of course, when you search loaches, some of the top hits are in fact, not scientific articles (in the sense of published literature), but aquarists websites. To me, this is interesting because it suggests that in fact, this species is abundant in the aquarium trade. This isn’t surprising because this species is beautiful and apparently, somewhat hardy for a loach. I searched additional sites and found that this species is listed as endangered by the International Union for the Conservation of Nature:

“Botia striata is assessed as Endangered because the species is a habitat specialist and is inferred to have an area of less than 400 km2. Further the species is known from only four fragmented locations. The habitat of the species is severely threatened because of deforestation leading to siltation, recreational activities on the mountain tops and pollution of the hill streams.”

So, this species is listed as endangered because it has a very small distribution (approximately 1/10th the size of Rhode Island) and is threatened by future human activities. So, how does it end up in the aquarium trade? This is at least partially due to a lack of enforcement of local laws and regulations (Raghavan et al. 2013) and until this changes, it is difficult to think that much will be done to prevent sale of threatened and endangered species — it is important to note that the problem with the sale of endangered species is that they are removed from their native habitat thereby reducing already small population sizes (we also can’t full resolve the taxonomy and systematics of these fishes if we don’t know what species are where or how many species there are). 

Given that these endangered fishes – B. striata is not the only one, but I am simply using it as an example – are already in the aquarium trade, can we turn a negative into a positive? I think so and let me suggest a few ways this can be done.

  1. Any information you have on these fishes can easily be published online for free (for example, Google Sites). How big is your fish? Where does it hang out in the tank? What is your tank setup? What do you feed him/her? Did he/she reproduce? If so, did you notice any difference between the male and female? How does the fish behave? Did he/she produce sounds that you could hear outside the tank? These things sound so trivial, I know, but believe me, they are invaluable. If you don’t publish these things online, then the reality is we may never know these things about some species. It’s not easy to get all of these data when you are snorkeling and watching a fish in the field.
  2. If your fish breed, take note of EVERYTHING you can. What were the conditions in the tank? pH? temperature? What were you feeding the fish? What time of day did they spawn? At what point in the year did this occur? Did they perform any courtship behaviors prior to spawning? Did they defend the nest? What other fish were in the tank? Did they eat the eggs? For a species such as Botia striata, little to none of this information is known. It would be even better to have a video that can readily be uploaded to YouTube to supplement this information, but obviously it is difficult to catch fish in the act! Wouldn’t it be nice to know how to breed these fish in the event that a captive breeding program needs to be started? Of course, it would.
  3. When the fish dies, save it. What? Ridiculous, I know. But for many species, we do not not have museum voucher specimens or tissue samples. By preserving these fish, we can collect invaluable information and in some cases, determine if it is a new species. Now, preserving fish is tricky (if you don’t preserve it, your house will smell like hog-heaven and the specimen will ultimately be worthless). Traditionally, ichthyologists preserve fish in formaldehyde, but this is not readily available to most people. The cheapest and easiest method may be to throw the specimen in a plastic bag and into the freezer. By throwing them in the freezer, a tissue can still be collected and most diagnostic characters can still be used to identify the fish. This is probably the best method available to most people. Of course, follow this up by collecting an ichthyologist (such as myself) that would be interested in the specimen and using it for scientific purposes. 

I just touched on a few ways here that I think any information from the aquarists could be useful to the scientific community. It’s too easy to share information globally to not share it with others who may find it extremely useful. As a quick aside, please do not take this post as my support to purchase threatened or endangered species. I don’t. Publishing information for any captive fish, especially those that are threatened or endangered and still in the aquarium trade, however, is extremely useful and may contribute significantly to the scientific community.


Raghavan R, N Dahanukar, MF Tlusty, AL Rhyne, KK Kumar, S Molur, and AM Rosser. 2013. Uncovering an obscure trade: Threatened freshwater fishes and the aquarium pet markets. Biological Conservation 164:158-169.


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Why do several species of minnows breed over the same nest?

For those unaware, I was on a brief hiatus to the Joint Meeting of Ichthyologists and Herpetologists annual meeting in Chatanooga, TN! There were numerous exciting talks, especially those pertaining to minnows, and it seems in the near future, there may be some resolution of the systematics of minnows, suckers, and loaches (see Part III of my first post if you think we understand the systematics of this group!). Stay tuned as I will update the blog as new studies are published!

One of the many amazing things about Tennessee relative to Oklahoma (where I currently live) is the clarity of the water. In Oklahoma, water clarity is extremely low (due to high turbidity) throughout most of the state with the exception of systems to the east (e.g., the Blue River). In Tennessee, several of the rivers are cool and clear and provide unique snorkeling opportunities. If you jump in the waters in Tennessee in May or June, you may see HUGE aggregation of small fishes on top of a large gravel nest (Freshwaters Illustrated has some excellent pictures of nest associations). What is this? Aren’t individuals supposed to mate only with individuals from their species?

These large spawning aggregations are known as nest associations and are well documented in the scientific literature. Essentially, male Nocomis or Campostoma build nests by gathering small stones in their mouth and bring them back to a designated area for nest building — as a quick aside, minnows may also spawn over sunfish (Centrarchidae: Lepomis) nests. After building the nest for spawning, other minnows will come to these nests and spawn over the nest. By spawning over the nest, the eggs from these minnows are fertilized and fall into the nest of the Nocomis

What minnows may spawn over the nests of Nocomis? Frankly, the minnows documented to spawn over such nests are pretty diverse. Several species of Notropis spawn over nests although most of these species may be in the subgenus Hydrophlox (Cashner et al. 2011). Other species of Chrosomus, Dionda, Lythrurus, Luxilus, Notemigonus, Notropis, and even Cyprinella – a crevice spawner – have been documented as nest associates (Shao 1997; Cashner and Bart 2010; Phillips et al. 2011Mattingly and Black 2013). I think this is representative of the minnows that are nest associates, but this list is unlikely to include all species that are actual nest associates. What do all these species have in common? They have demersal eggs which sink to the substrate so that they can be protected by the host male. Other species, such as those with pelagic eggs (e.g., Hybognathus amarus) or those that guard their eggs (e.g., Pimephales spp.), have life-history traits that prevent them from taking advantage of nest associations. 

As an evolutionary biologist, one of the more intriguing questions is: how have nest associations evolved? Step out of your human mindset and remind yourself that evolutionary speaking, every organism’s goal is to pass on their genes such that their offspring will reproduce in the future and pass on their genes (and so on). One may expect that for these associations to evolve, they must benefit both species – i.e., they are mutualistic. Not surprisingly, several studies support this notion and find that both species benefit largely as a result of the dilution effect (Wallin 1992; Johnston 1994a; Johnston 1994b; Shao 1997). By not 1, but 2 or 3 or 4 species depositing their eggs in the same nest, the number of eggs in a nest increases significantly (potentially by several magnitudes depending on the species of nest associates). As a result, the chance of the eggs of the host species (e.g., Nocomis) being eaten in any particular predation event is reduced. The nest associates depositing their eggs in the host’s nest may suffer from increased predation, but benefit from the parental care they receive by the guarding male (Johnston 1994b).

Although more in-depth studies are needed, it does seem that some species may be nest associates more frequently than other species. In fact, minnow species that are “strong” nest associates of Nocomis have ranges largely overlapping with Nocomis species whereas “weak” nest associates don’t exhibit such a pattern (Pendleton et al. 2012). Further, “strong” nest associates were much more rare than “weak” nest associates. This relationship is worth a further look as it may have important implications for the loss of biodiversity – i.e., if we lose Nocomis, will we lose its “strong” nest associates? That may be too much of a generalization, but this is something certainly worth pondering and investigating.

So, the next time you are you in a nearby stream in mid-summer, grab a mask and snorkel and look underwater. Maybe you won’t see anything. Maybe you will see just a few fish swimming around. But maybe, just maybe, you will see a large conglomerate of minnows swimming around and spawning over the nest of a Nocomis, Campostoma, or Lepomis. Hopefully then, you will understand the true beauty of such nest associations!


Cashner MF, and HL Bart Jr. 2010. Reproductive ecology of nest associates : use of RFLPs to identify cyprinid eggs. Copeia 2010(4):554-557.

Cashner, MF, KR Piller, and HL Bart Jr. 2011. Phylogenetic relationships of the North American subgenus HydrophloxMolecular Phylogenetics and Evolution 59(2011):725-735.

Johnston CE. 1994a. Nest association in fishes: evidence for mutualism. Behavioral Ecology and Sociobiology 35(6):379-383.

Johnson CE. 1994b. The benefit to some minnows of spawning in the nests of other species. Environmental Biology of Fishes 40(2):213-218.

Mattingly HT, and TR Black. 2013. Nest association and reproductive microhabitat of the threatened blackside dace, Chrosomus cumberlandensis. The Southeastern Naturalist 12(4):49-63.

Pendleton RM, JJ Pritt, BK Peoples, and EA Frimpong. 2012. The strength of Nocomis nest association contributes to patterns of rarity and commoness among New River, Virginia cyprinids. The American Midland Naturalist 168(1):202-217.

Phillips CT, RJ Gibson, and JN Fries. 2008. Spawning behavior and nest association by Dionda diabolii in the Devils River, Texas. The Southwestern Naturalist 56(1):108-112.

Shao B. 1997. Effects of golden shiner (Notemigonus crysoleucas) nest association on host pumpkinseeds (Lepomis gibbosus): evidence for a non-parasitic relationship. Behavioral Ecology and Sociobiology 41(6):399-406.

Wallin JE. 1992. The symbiotic nest association of yellowfin shiners, Notropis lutipinnis, and bluehead chubs, Nocomis leptocephalus. Environmental Biology of Fishes 33(3):287-292.


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Part III: What are Cypriniforms and why does anyone care?

Welcome to the Part III of “my first blog post!” Part I provided insight into what a Cypriniform is and the distribution of species )across families. Part II focused more on what these fish look like and the final episode of my first post, Part III, will focus on the evolutionary history of this group (or at least what we know to this point)! Before we jump into the evolutionary history of this group, it is worth briefly this question: What is a phylogeny? A phylogeny is a hypothesis of evolutionary relationships among some organismal groups of interest (e.g., populations, species, families, etc.). It essentially assess how these groups are related based on some aspects of the genome, morphology, physiology, behavior, or any other trait that can be qualified/quantified. Depending on the type of data (e.g., genomic vs. morphology), different techniques and algorithms (e.g., parsimony, likelihood, Bayesian) can be used to build the hypotheses. One important point to remember is that a phylogeny is only a hypothesis. It can change with the addition of new evidence. If the concept of a phylogeny still isn’t clear, check out this site from Berkley or just google “what is a phylogeny.” Plenty of web sites will emerge. It’s probably best to first take a look at the broader evolutionary history of Cypriniforms (e.g., what are they closely related to? how long ago did they diverge?) before talking about loaches, suckers, and minnows! So, how did Cypriniforms come to be? Cypriniforms are part of a well-defined group known as Ostariophysi, a group that includes Gonorynchiforms (milkfish, et al.), Cypriniforms (loaches, minnows, and suckers), Gymnotiforms (South American knifefish), Characiforms (characins), and Siluriforms (catfishes) (look here; Betancur-R et al. 2013). Using a series of fossil calibrations and analytical techniques, Betancur-R et al. (2013) estimated the Cypriniforms to have last shared a common ancestor with all other Ostariophsyi at about 170 +/- 25 million years ago (MYA). This basically means that the lineage of little fish we classify as Cypriniforms showed up on earth around 170 MYA. Let that sink in… … 170 MILLION years ago.  Do you know what was roaming the earth then that isn’t alive today? Dinosaurs. Yep, these bad ass little fish survived whatever catastrophes wiped out teeth gnashing Tyrannosaurus and ginormous Argentinosaurus, a 30+ meter, 80+ tonne dinosaur. That’s pretty spectacular, right??!?! Agreed!! With regard to Cypriniforms, the other inference we can draw from this paper is that minnows (Cyprinoidei) diverged from loaches and suckers (Cobitoidei) around 100 +/- 30 MYA. So, before dinosaurs ever went extinct, there were two lineages of Cypriniforms, one that ultimately led to loaches and suckers and one that led to minnows. One interesting question that hasn’t been answered yet: what caused the split of the minnow lineage with the lineage that led to loaches and suckers? Good question and honestly, I haven’t seen a good answer although I will venture to take a guess. If you read my last post, I mentioned that loaches are uniquely adapted to high flow habitats – they have (generally) flat ventral bases for adhering to the substrate, smooth streamlined dorsal sides, and large paired fins attached on a horizontal plane – whereas minnows are (generally) more adapted to living off the substrate – they have laterally compressed bodies and paired appendages on a more vertical (or diagonal) plane. So, one might hypothesize that suckers and loaches evolved to live on the substrate (termed benthic fish) whereas minnows adapted to life in the water column (termed pelagic fish). Specifically, adaptation to each environment drove reproductive isolation and ultimately led to speciation. Now, obviously this isn’t adequate to explain all the diversity in this group, but it is a starting hypothesis that needs more data to be thoroughly accepted or rejected. OK, so let’s take a more in-depth look at evolutionary relationships within each of the two suborders. The most thorough look at morphology in loaches was published in 1982 (Sawada 1982). If you are interested in loaches, you should give it a read. Mayden et al. (2009) also provided insight into phylogenetic relationships of Cobitoidei using four (out of thousands) nuclear genes and thirteen (out of thirteen) mitochondrial genes. Generally, they recover relationships as shown in the picture with a few exceptions: Mayden et al. (2009) didn’t sample Serpenticobiditidae or Ellopostomatidae, but they did sample Botiidae (recognized as a subfamily of Cobitidae in the Catalog of Fishes); the locations of Balitoridae and Nemacheilidae are switched.

Phylogenetic hypothesis for Cypriniformes Photo: Gerhard Ott

Phylogenetic hypothesis for Cypriniformes
Photo: Gerhard Ott

After posting this blog, one of my colleagues pointed out a paper I glaringly missed (thanks Milton!) which is perhaps the most thorough attempt at resolving major relationships among the lineages of Cypriniforms (Mayden and Chen 2010).

The authors used six nuclear genes and with regard to loaches, largely found the same results among the sampled families as Mayden et al. (2009). Although not included in this phylogenetic hypothesis, the authors previously suggested Ellopostomatidae was sister to Nemacheilidae (Chen et al. 2009).  As far as I know, Serpenticobitidae and Gastromyzontidae haven’t given a phylogenetic treatment (yet). Nonetheless, studies like Sawada (1982)Mayden et al. (2009), and Mayden and Chen (2010) (among others I haven’t referenced here for time sake) have laid the foundation of our understanding of how suckers and loaches diversified — shown in the figure above –over the last 100 million years . What about Cyprinoidei? Well, that’s a whole ‘nother story. As I mentioned earlier, there are at least 2,960 species in this suborder and at least 14 subfamilies. At least. Given that we don’t have a good idea of the diversity and how it all will be taxonomically filed, it’s impossible to come up with a good phylogenetic hypothesis to explain this diversity. One (potential) attempt to explain evolutionary relationships among most of the subfamilies was based on skeletal characteristics and seems like it could be an excellent starting point (Xiang-Lin et al. 1984). Other attempts to resolve the relationships have been made based on single genes (He et al. 2008). As with Cobitoidei, the most thorough treatment of Cyprinoidei may be by Mayden and Chen (2010). These authors sampled 14 subfamilies of Cyprinoidei and recovered relatively strong support for their relationships (again, based on six nuclear genes).

Phylogenetic hypothesis for Cyprinoidei from Mayden and Chen 2010

Phylogenetic hypothesis for Cyprinoidei from Mayden and Chen 2010

The recovered relationships are shown above with me using subfamily names (rather than the elevated family names as they used in the paper). The support for most of these groups is relatively high although additional subfamilies still need to be sampled. One particularly interesting findings it that Psilorynchidae is sister to Cyprininae. This is interesting because it would seem to suggest that Psilorynchidae (a taxonomic rank of family) should be demoted to Psilorynchinae subfamily) in order to keep Cyprinidae monophyletic. Realistically, Cyprinidae and Psilorynchidae will probably remain as families although Cyprinidae likely will be broken into multiple families (e.g., as suggested in Mayden and Chen 2010). Only time and more data will tell! Nonetheless, this paper provides an excellent starting point for additional work on this group. It’s worth noting that relationships within even some of the subfamilies have been difficult to resolve. For example, the Notropis radiation within the subfamily Leuciscinae has proven excessively difficult to resolve. Some subgenera (Notropis species classified into smaller taxonomic groups) have been delineated (e.g., Hydrophlox; Cashner et al. 2011), but relationships among Notropis are largely unresolved. So why do phylogenetic relationships matter? Because our goal is to understand and explain the patterns that generated the amazing diversity around us. Without phylogenetic relationships, it is next to impossible to do. In other words, without a good understanding of the evolutionary relationships of Cypriniforms, we can’t understand why there are so many little bad ass minnows that survived catastrophes even the dinosaurs couldn’t!


Betancur-R R, RE Broughton, EO Wiley, K Carpenter, JA Lopez, C Li, NI Holcroft, D Arcila, M Sanciangco, JC Cureton II, F Zhang, T Buser, MA Campbell, JA Ballesteros, A Roa-Varon, S WIllis, WC Borden, T Rowley, PC Reneau, DJ Hough, G Lu, T Grande, G Arratia, G Orti. 2013. The tree of life and a new classification of bony fishes. PLOS Currents Tree of Life, doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.

Cashner MF, Piller KR, Bart HL. 2011. Phylogenetic relationships of the North American subgenus HydrophloxMolecular Phylogenetics and Evolution 59:725-735.

Chen WJ, Lheknim V, and Mayden RL. 2009. Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes. Journal of Fish Biology 75(9):2197-2208.

He S, Mayden RL, Wang X, Wang W, Tang KL, Chen W-J, Chen Y. 2008. Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: Further evidence from a nuclear gene of the systematic chaos in the family. Molecular Phylogenetics and Evolution 46:818-829.

Mayden RL, WJ Chen, HL Bart, MH Doosey, AM Simons, KL Tang, RM Wood, MK Agnew, L Yang, MV Hirt, MD Clements, K Saitoh, T Sado, M Miya, and M Nishida. 2009. Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes-order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome. Molecular Phylogenetics and Evolution 51:500-514

Mayden RL, Chen WJ. 2010. The world’s smallest vertebrate species of the genus Paedocypris: a new family of freshwater fishes and the sister group to the world’s most diverse clade of freshwater fishes (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution 57:152-175.

Sawada, Y. 1982. Phylogeny and zoogeography of the superfamily Cobitoidea (Cyprinoidei; Cypriniformes). Memoirs of the Faculty of Fisheries Hokkadio University 28(2):65-223.

Xiang-Lin C, Pei-Qi Y, Een-Duan L. 1984. Major groups within the family Cyprinidae and their phylogenetic relationships. Acta Zoological Sinica 1984(4): ??

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Part II: What are Cypriniforms and why does anyone care?

Welcome to the Part II of “my first blog post!” Part I provided insight into what a Cypriniform is and the distribution of species across families. Part II will focus more on what these fish look like – i.e., what makes a Cobitid a Cobitid and a Cyprinid a Cyprinid. Part III will then focus on the evolutionary history of this group, how the families are related to each other, and what the implications are for the evolution of Cypriniform diversity!

If you remember from my previous post, there are 11 families that contain 4,182 species! There were at least two interesting points about this diversity:

  1. Cyprinidae is an exceptionally large family. It contains almost five times as many species as the next largest family. It’s fair to wonder if Cyprinidae, ultimately, will be broken down into multiple families at some point in the future, but that is an issue for another post.
  2. The diversity is distributed a bit funny with Cyprinidae containing the majority of species followed by some families with a large number of species, a few families with a moderate number of species, and a few families with only a few species.

So, with those patterns in mind, let’s take a more in-depth look at each family. When possible, I will post a picture of a representative species for each family. Unfortunately, I don’t have pictures of most of these families right now (and will link to pictures of them). If you have a good picture of species for any of the groups for which I don’t have a picture and you don’t mind them being posted to my blog, I will post them with photo credit to you!

OK, let’s take a look at the major divisions of Cypriniforms (now grouped by suborders):

COBITOIDEI (loaches)

The majority of families (8 of the 11) are in the suborder Cobitoidei and are commonly known as loaches. Loaches are small, benthic fish that have a very characteristic set of body shapes. Generally speaking, they are vermiform (worm-like) although they usually have a relatively flat ventral side. And their paired fins (the pectoral and pelvic fins) are typically on a somewhat horizontal plane. Why?

HINT: Think about where they live (ahem…Generally, they live in fast flowing rivers and streams across Europe, Asia, and a few species in Africa. …ahem).

By having a flat ventral side, large pectoral and pelvic fins, and a streamlined dorsal side, the fish are well adapted to live in fast flowing streams. They are able to cling to the substrate without “much” effort because their pectoral and pelvic fins can help adhere to rocks and such in the habitat. Wanna see? Check out this photograph:

Homalopterula ripleyi Photo: Gerhard Ott,

Homalopterula ripleyi
Photo: Gerhard Ott,

Despite this generalization, there are some very peculiar looking loaches: check out the look of Tarimichthys bombifrons, pretty wild!

To me, there are some other peculiar things about loaches (relative to other Cypriniforms). A lot of loaches tend to have barbels, which are the sensory organs around the mouth. Most people, at least from where I am from in the southern US, call them whiskers and usually only talk about them when we catch a catfish.They are thought to be involved in foraging (Kasumyan and Sidorov 2010; Kasumyan et al. 2010) although the diversity of barbels across loaches almost certainly warrants a thorough investigation. Theoretically, they could be involved in other functions such as acquiring mates and sexual selection. Anecdotally, loaches frequently tend to have vertical stripes more frequently than horizontal stripes. I assume these are probably involved in camoflauge considering that we see vertical stripes serve as crypsis in several benthic North American fishes (Barlow 1972Armbruster and Page 1996).

It’s somewhat easier to take a look at loach taxonomy because of the recent publication of a manuscript addressing the state of taxonomy of the loaches (Kottelat 2012). As mentioned in this paper, there are likely hundreds of additional undescribed species that will be described (hopefully) over the next few years. They place the valid species in ten families, the eight below plus Gastromyzontidae and Botiidae (Botiinae is recognized as a subfamily in the Catalog of Fishes).

  • Gryinocheilidae (3 species)
  • Vaillantellidae (3 species)
  • Cobitidae (245 species)
  • Ellopostomatidae (2 species)
  • Barbuccidae (2 species)
  • Balitoridae (230 species)
  • Nemacheilidae (627 species)
  • Serpenticobitidae (3 species)
  • Catostomidae (83 species)***

It is worth taking a look at how species from each of these families look. You can see a lot of excellent pictures in Kottelat 2012 so I would suggest starting there – by using this paper, you also can assure you are looking at the species you think you are looking at.


Within this suborder, Cyprinidae clearly constitutes the majority of species: Psilorhynchidae constitutes less than 1% of the species in this suborder. So, what made the minnows so successful relative to their loach relatives? Well, at this point, I’m not sure anyone knows. Generally speaking, there are quite a few differences that can be seen with the idea. Perhaps the most notable difference is body shape. They tend to have laterally compressed shape relative to their loach counterparts.

Luxilus chrysocephalus

Luxilus chrysocephalus

Look at the Luxilus pictured above relative to the Homalopterula pictured above. See how the Luxilus has a much deeper body that is somewhat symmetrical along the horizontal plane? Now, that isn’t to say that there aren’t cyprinids that have flattened ventral sides. Some do. Look at Cyprinus carpio. They have flattened ventral sides and barbels, but are cyprinids, not loaches! As a quick side note, Psilorhynchus also exhibit these characteristics and not surprisingly, is probably closely related to these species (He et al. 2008). Why is this cool? Because if this is the case, this suggest that the body plan evolved likely only once in the minnow clade. Anyways, we can talk more about this later.

Barbels also seems to be less frequent in minnows relative to their loach and sucker counterparts. Several minnow genera do have barbels – Macrhybopsis, Cyprinus, etc – and they likely serve a similar function in foraging. Additionally, and again generally, it seems that minnows much more frequently have horizontal stripes rather than vertical stripes. This could be a visual bias for me: I see North American minnows much more frequently than minnows in other portions of the world and I simply could be generalizing the stripe-pattern too broadly. If I’m wrong, someone should let me know.

The taxonomy of these two families is much more difficult to tackle. For example, within Cyprinidae, there at least fourteen – YES, F-O-U-R-T-E-E-N – subfamilies according to the Catalog of Fishes. I suspect that is a minimum number and we are only recently beginning to understand relationships among these subfamilies.

  • Cyprinidae (2960 species)
  • Psilorhynchidae (24 species)

Given these taxonomic concerns, there hasn’t been a recent publication on the taxonomy of these two families. It makes it difficult to publish such a beast when we understand so little about their diversity. Nonetheless, multiple researchers are working on resolving this problem although it may be several more years before we thoroughly understand Cyprinidae.

As a quick side note, you will note that I use “generally” a lot when referring to morphological characters. This is due to the fact that it is difficult to make a definitive claim about some aspect of morphology when talking about such a diverse group of fishes. This is largely the result of convergent evolution – i.e., evolution should lead to similar morphological traits in species that inhabit similar environments. I will cover this more in a later post, but I just wanted to make a quick note of why I use “generally” so frequently. 

In my next post, I will address how loaches and minnows are related, evolutionarily speaking. It should be an interesting post to look at the phylogenetics of this group and try to make heads or tails of the diversification of this group!


Armbruster, J. W., and L. M. Page. 1996. Convergence of a cryptic saddle pattern in benthic freshwater fishes. Environmental Biology of Fishes 45:249-257.

Barlow, G. W. 1972. The attitude of fish eye lines in relation to body shape and to stripes and bars. Copeia 1972(1):4-12.

He, S., Gu, X., Mayden, R. L., Chen, W. J., Conway, K. W., and Y. Chen. 2008. Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniforms): evidence from the mitochondrial genome. Molecular Phylogenetics and Evolution 47(1):419-425.

Kasumyan, A. O., Sidorov, S. S., and E. A. Marusov. 2010. Taste preferences and behavior of testing gustatory qualities of food in stone loach Barbatula barbatula (Balitoridae, Cypriniforms). Journal of Ichthyology 50(8):682-693.

Kasumyan, A. O., and S. S. Sidorov. 2010. Taste preferences and feeding behavior of the stone loach Barbatula barbatula (Balitoridae, Cypriniforms) after partial deprivation of circum-mouth external gustatory and tactile receptors. Journal of Ichthyology 50(11):1021-1029.

Kottelat, M. 2012. Conspectus cobitidum: an inventory of the loaches of the world (Teleostei: Cyprniforms: Cobitoidei). The Raffles Bulletin of Zoology 26:1-199.

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PART I: What are Cypriniforms and why does anyone care?

Minnows, carps, loaches, and their relatives – known as Cypriniforms – are an exceptionally diverse group of fishes (4,182 currently valid species according to the Catalog of Fishes) that come in a wide range of sizes, shapes, and colors . Their overall small size and aesthetic variation has made them appealing to the aquarists (does the clown loach [Chromobotia macracanthus] look familiar?)! In fact, aquarists are some of the most knowledgeable people on these species!

Just as interesting is that Cypriniforms can be found across multiple continents in a variety of habitats with unique foraging, locomotive, and reproductive patterns and morphologies and fill a variety of ecological roles (e.g., predatory and prey). For example, the fathead minnow, known scientifically as Pimephales promelas (Check out this blog post by Liz Marchio for an excellent explanation of scientific names!) develops excessively large tubercles on a really dark, swollen head during the breeding season (see some images here). There are THOUSANDS of other interesting species. Just hit up Google and start searching!

As an evolutionary biologist, I am interested in understanding and conserving patterns of phenotypic diversity and novelty: How did what’s here get here and how can we keep it here? I think the best approach is to look at what we know about Cypriniform diversity and what we know about the evolution of that diversity, first. That is, how are those 4,182 species distributed across groups and how are those groups related to each other. Accordingly, I am splitting “my first blog post” into a three-part series. Part I will provide insight into what a Cypriniform is and the distribution of species across families. Part II will focus more on each family and what makes a Cobitid a Cobitid and a Cyprinid a Cyprinid. Part III will then focus on the evolutionary history of this group, how the families are related to each other, and what the implications are for the evolution of Cypriniform diversity! After that, my goal is really to blog about anything I find interesting for minnows – recent research using a particular minnow species, a pretty new species I saw at a pet shop, an update on the taxonomy of a particular group. Really, pretty much anything Cypriniformish.

First, what is a Cypriniform? I’m sure you think this should be an easy question to answer, right? It’s a small fish that goes in my aquarium…or that I see at the edge of the lake…or…OK, not really. It is actually difficult to answer this question in a way that makes most people go “aha, I understand!” Given this problem, let’s stick with defining a Cypriniform as any fish with a kinethmoid. What?!?!? OK, the kinethmoid is a tiny bone used in jaw protrusion (e.g., eating) and is found only in species that are considered Cypriniforms. Makes sense, right? What does it look like? Check out this photograph:

(Photo: Gerhard Ott,

Photo: Gerhard Ott,

This photograph is a dorsal  view – standing over the fish and looking down on its mouth – of the the jaw bones from a cleared-and-stained specimen of Homaloptera ripleyi (from Ott 2009). The five bones labelled are the maxillary (Mx), premaxillary (Pmx), anterior process of prexmaxillary (anP), ascending process of the premaxillary (asP), and the, wait for it…kinethmoid (Ke)! It may take some Googling and a brief review of your anatomy to identify each of these bones and understand the kinethmoid, but now you know the kinethmoid is a legitimate bone in Cypriniforms (read more in Staab et al. 2012). For the future purpose of this blog, we will assume that any species classified as a Cypriniform is appropriately classified and has a…kinethmoid!

Now, let’s look at the distribution of that diversity, taxonomically speaking. Although still debated and it may change, there are currently 11 recognized families of Cypriniforms according to the Catalog of Fishes (listed in no particular order):

  • Cyprinidae (2960 species)
  • Psilorhychidae (24 species)
  • Cobitidae (245 species)
  • Balitoridae (230 species)
  • Nemacheilidae (627 species)
  • Serpenticobitidae (3 species)
  • Vaillantellidae (3 species)
  • Ellopostomatidae (2 species)
  • Barbuccidae (2 species)
  • Gryinocheilidae (3 species)
  • Catostomidae (83 species)

There are a few quick observations that we can make here:

  1. The family Cyprinidae is exceptionally diverse relative to all other families of Cypriniformes. This family is an order of magnitude larger than the diversity in all other families. The next most diverse family contains only 627 species (Nemacheilidae), only 15% of the diversity observed in Cyprinidae!
  2. The disparity of taxonomic diversity is unusual. There is one exceptionally diverse family (Cyprinidae), four families with moderate diversity (Cobitiidae, Balitoridae, Nemacheilidae, Catostomidae), and six families with low diversity (Psilorhynchidae, Serpenticobitidae, Vaillantellidae, Ellopostomatidae, Barbuccidae, Gyrinocheilidae). It’s an unusual pattern worth exploring more.

What do you think? Are there any patterns about the distribution of diversity in this order that you notice? Next time, I will focus on what species in each of these families look like and provide some information about each of these groups!



Ott, G. 2009. Redescription of Homaloptera ripleyi (Fowler, 1940) from Sumatra, Indonesia (Teleostei: Balitoridae). Bulletin of Fish Biology 11(1/2):73-86.

Staab, K. L. 2012. Comparative kinematics of cypriniform premaxillary protrusion. Zoology 115(2):65-77.

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