The example of hummingbird hemoglobin must be one of the most striking cases of molecular convergence (and parallelism), because there were at least 17 independent changes at two amino acid positions of the beta-hemoglobin subunit, and there is a near perfect relationship between altitude and the genotype at those two sites. (Full disclosure: this is the system I study!).

Article Repeated elevational transitions in hemoglobin function duri...

You can also check out this review paper by Harold Zakon: https://www.researchgate.net/publication/11181943_Convergent_evolution_on_the_molecular_level?ev=prf_pub

Article Convergent Evolution on the Molecular Level

Thank you Simon and Heather.  These are both very interesting and speak exactly to my question. I will definitely be including prestin in my cladistics lectures.

Hi

As my investigations in Poaceae Family; Triticum boeoticum and T. monococcum are the distinct ones. they have been mentioned two separate species in many references such as Flora Iranica but in my molecular researches, their populations nested among each other and they illustrated kind of convergence. it can be considered that gene flow is one of the reasons of this convergence.

Another great case of convergence was recently published in Science "Genomic basis for the convergent evolution of electric organs":

http://www.sciencemag.org/content/344/6191/1522

It always depends on the scale you are searching for.

The most frequent examples will be shared nucleotide biases in clearly unrelated taxa, I would expect.

But I guess the examples mentioned by Simon & Heather may better fit into what you were looking for.

The example of hummingbird hemoglobin must be one of the most striking cases of molecular convergence (and parallelism), because there were at least 17 independent changes at two amino acid positions of the beta-hemoglobin subunit, and there is a near perfect relationship between altitude and the genotype at those two sites. (Full disclosure: this is the system I study!).

Article Repeated elevational transitions in hemoglobin function duri...

Hello Christopher,

Wow! This is amazing research; you have my sincere admiration. I think you have shown that, at least in this phenotypic domain, the adaptive landscape is much more constrained than we might have imagined. Going forward it will be interesting to learn how general such apparent constraints are; equally good evidence from other trait spaces will be needed. Nevertheless this result is fundamentally interesting. Sincere congrats for your vision and ingenuity.

Since you clearly have pondered related issues, how molecularly constrained do you think a heredity molecule might be? I do want to live long enough to see extra-terrestrial life, for this one reason.

Best regards,

Steven

Are there examples among marine invertebrates ?

Lots indeed. The simple fact that there are only four possible character states in DNA (five if you add presumptive deletions) means there are many, many convergent bases in the same positions. ON the larger scale, check out the work from the Andrew Johnson lab at the University of Nottingham. He works on the evolution of primordial germ cell determination mechanisms and he has identified several genes that are convergent for the mechanisms, such as Oct4/Pou5, dazl, and vasa. 

This may be a day late and a dollar short, but there was recently an interesting finding that crickets on two separate islands in Hawaii are now silent, selection in response to a parasitizing fly. The cool part about this example is that while the morphological outcome is the same (silent males, no cricket songs) the molecular pathways are different on each island. Makes for a fun example of apparent convergence in response to the same pressure, but in actuality non-homologous routes to get there. 

http://phenomena.nationalgeographic.com/2014/05/29/the-silence-of-the-crickets-the-silence-of-the-crickets/

Hi Heather,

Thank you.  That is an interesting case of convergent adaptation. What I was originally going after with my question was this: Can taxonomists avoid being fooled into thinking that convergent species are closely related if they look below the level of the surface phenotype at the underlying molecular and (ultimately) DNA underpinning of the traits? The answer seems to be generally, yes, they can.  However the roads of geneland may be narrower in some regions than others, and the possible solutions to particular adaptive problems may be more constrained than we would have imagined. Simon J. Goodman's prestin example and Christopher C. Witt's hemoglobin example (both with links to the primary research in their answers) are compelling examples of apparently constrained adaptive spaces.

A protein in cat dander/saliva Fel d 1 is infamous allergen. Nearly identical protein appears in skin secretions of slow loris (Krane et al. Naturwissenschaften). May be anti-arthropod defensive agent.

Another striking example of convergent evolution is the emergence of C4 photosynthesis pathway in plants. This occurred more than 60 times during evolution. And some of the components are also under selective pressure under convergent evolution, the most studied being the Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Generally, to avoid the problem of convergence when reconstructing the history of species, researchers use multiple genes to build a phylogenetic tree.

Some papers:

Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis.

Christin PA, Salamin N, Muasya AM, Roalson EH, Russier F, Besnard G.

http://www.ncbi.nlm.nih.gov/pubmed/18695049

Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato.

Kapralov MV, Smith JA, Filatov DA.

http://www.ncbi.nlm.nih.gov/pubmed/23285238

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

Studer RA, Christin PA, Williams MA, Orengo CA.

http://www.ncbi.nlm.nih.gov/pubmed/24469821

In the last paper, we mapped the stability effects on the RubisCO tree. This is visible in page 7 of the supp data:

http://www.pnas.org/content/suppl/2014/01/24/1310811111.DCSupplemental/pnas.201310811SI.pdf

This is an excellent example and paper:

Evidence for an ancient adaptive episode of convergent molecular evolution

Castoe, TA (Castoe, Todd A.)[ 1 ] ; de Koning, APJ (de Koning, A. P. Jason)[ 1 ] ; Kim, HM (Kim, Hyun-Min)[ 1 ] ; Gu, WJ (Gu, Wanjun)[ 1 ] ; Noonan, BP (Noonan, Brice P.)[ 2 ] ; Naylor, G (Naylor, Gavin)[ 3 ] ; Jiang, ZJ (Jiang, Zhi J.)[ 4,5 ] ; Parkinson, CL (Parkinson, Christopher L.)[ 4,5 ] ; Pollock, DD (Pollock, David D.)[ 1 ]

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106 (22): 8986-8991

DOI:10.1073/pnas.0900233106

Published: JUN 2 2009

Abstract

Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions ( primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamid lizards. We estimate that approximate to 44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from non-neutral causes-a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that non-neutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of non-neutral convergent sequence evolution.

One of the classic studies was by Jim Bull et al. in the late 1990s, published in Science I think, involving thermal tolerance in multiple lineages of bacteriophage.

another clear example of convergent evolution is the presence of spines on cactus (cactaceae) and that on euphorbia (euphorbiaceae). there is no common ancestor but this phenomena is for ecological adaptation. this caharacter considered as analogous feature as a result of homoplasy not homology. i hope this example is good for you Gaulin, S. J. C.

Gordon W Schuett's example from the work of Todd Castoe is 100% on topic and a very impressive example of molecular convergence that dramatically disrupts the presumably correct phylogenetic tree.  This is just the kind of example I was seeking.  Thank you!  I recommend it to the other commentators on this question.

It certainly opened my eyes and answered some big questions regarding squamate relationships.

Glad it was helpful.

Early example by Caro-Beth Stewart, Allan Wilson and colleagues - late 1980s.  Lysozyme in primates and ruminates.  

How about http://www.nature.com/nature/journal/v502/n7470/full/nature12511.html

This could be a really fun lab exercise. If you're interested I can send you some data.

There are papers on the C4 photosynthesis of grasses.

http://www.sciencedirect.com/science/article/pii/S0960982207015734

Christin, Pascal-Antoine, et al. " C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes." Current Biology 17.14 (2007): 1241-1247.

Thank you Magdalena.  This in another excellent example that  is new to me.  It speaks directly to the point that phylogenetic signals can be distorted by such precise molecular convergence.

I have another one based on microRNA and phylogenetic analysis

Estimating Phylogeny from microRNA Data: A Critical Appraisal

R Thomson, D Plachetzki, L Mahler, B Moore - bioRxiv, 2014 - biorxiv.org

Significance

As progress toward a highly resolved tree of life continues, evolutionary relationships that defy resolution continue to be identified. Recently, the presence/absence of microRNA families has emerged as a potentially ideal source of information to resolve these difficult phylogenetic problems, and these data have been used to address several long-standing problems in the metazoan phylogeny. To our knowledge, this study performs the first rigorous statistical assessment of the phylogenetic utility of microRNAs and finds that a high incidence of homoplasy and sampling error renders published phylogenies based on microRNA data highly biased or uncertain. This study casts serious doubt on the central phylogenetic conclusions of several previous analyses of microRNA datasets.

A striking example IMO is S.Mirceta cs 2013 Evolution of mammalian diving capacity traced by myoglobin net surface charge, Science doi 10.1126/science.1234192: "Evolution of extended breath-hold endurance enables the exploitation of the aquatic niche by numerous mammalian lineages and is accomplished by elevated body oxygen stores and morphological and physiological adaptations that promote their economical use. High muscle myoglobin concentrations in particular are mechanistically linked with an extended dive capacity phenotype, yet little is known regarding the molecular and biochemical underpinnings of this key specialization. We modeled the evolutionary history of this respiratory pigment over 200 million years of mammalian evolution to elucidate the development of maximal diving capacity during the major mammalian land-to-water transitions." (if you want, I can send you the article, m_verhaegen at skynet.be).

These myoglobin changes strongly correlate with deep diving (max dive time) & long aquatic history. I'm very much interested in this particular case because our early-Pleistocene ancestors & relatives (genus Homo), who dispersed as far as Indonesia, Georgia, the Rift & Algeria (fossil or archeological sites c 1.8 Ma), IMO did so, not running over open plains ("savanna") but along African & Eurasian coasts (& from there inland along rivers & wetlands), where they (at least partly) must have beach-combed, waded bipedally & dived for shallow aquatic & waterside foods (M.Verhaegen 2013 The aquatic ape evolves: common misconceptions and unproven assumptions about the so-called Aquatic Ape Hypothesis, Hum.Evol.28:237-266). The absence of such myoglobin changes in humans suggest that possible diving episodes in human evolution at most were brief (esp.during glacials??), and/or that our ancestors at most were shallow divers & perhaps only parttime divers. www.researchgate.net/profile/Marc_Verhaegen  independent.academia.edu/marcverhaegen  

http://www.sciencemag.org/content/337/6102/1634

http://www.sciencemag.org/content/344/6185/738.short

Two interesting cases in the insect group summarized here

http://news.sciencemag.org/biology/2014/05/evolution-predictable