Species Come and Species Go

by Elio & Merry

Two Greek philoso­phers, Her­a­cli­tus and Dem­ocri­tus, found the hu­man con­di­tion vain and ridi­cu­lous, but Dem­ocri­tus al­ways ap­peared with a jeer­ing and laugh­ing coun­te­nance, whereas Hera­clitus com­mis­er­ated our con­di­tion with a sor­row­ful look and tears in his eyes.
 —Michel De Mon­taigne (1533–1592) 

While phi­los­o­phiz­ing about what is a species, should one laugh or cry? Maybe it mat­ters how you feel at the mo­ment. For me (Elio), that's the case. In my bil­ious mood, I de­spair about the chances for a use­ful, en­com­pass­ing, and con­sen­sual de­f­i­n­i­tion. But when I feel more jovial, I ap­plaud the con­tin­u­ous ef­forts of eru­dite bi­ol­o­gists to grap­ple with this, pos­si­bly the most in­tractable of all bio­logical predica­ments. Month by month, new ap­proaches are put for­ward, many borne out of newly ac­quired ge­nomic and eco­log­i­cal in­for­ma­tion, and their accompa­nying mind­sets. Per­haps the Holy Grail will one day be found. Mean­while, we re­cently of­fered some mirth.

We have thought about this is­sue of­ten, and what brought it up just now is a pa­per show­ing that two bac­te­r­ial species (al­low us to call them that) can not only di­verge from one an­other, but can, in fact, con­verge, pos­si­bly to be­come one again. Re­gardless of how you de­fine species, the pheno­me­non is in­ter­est­ing. The crea­tures in ques­tion are Campy­lobac­ter je­juni and C. coli, two dis­tinct gas­troen­teri­tis-caus­ing pathogens whose house­keeping genes have only an 85% se­quence iden­tity, well be­low the 94–97% cut-off point of­ten used to de­lin­eate bac­te­r­ial species. (Sal­mo­nella and E. coli, thought to have di­verged 120 mil­lion years ago, also dis­play about the same per­cent iden­tity.) It looks like C. coli ac­quired genes from C. je­juni on mul­ti­ple oc­ca­sions, which is blur­ring the species dif­fer­ence be­tween the two.

(above) Her­a­cli­tus, the "weep­ing philo­so­pher." (be­low) Dem­ocri­tus, the "laugh­ing philoso­pher." Both by Hen­drick ter Brug­ghen (1628)

The re­search re­ported is based on the multi lo­cus se­quence typ­ing (MLST) method widely used to type bac­terial strains. MLST in­volves PCR am­pli­fi­ca­tion and se­quencing of frag­ments of seven un­linked house­keep­ing genes, fol­lowed by as­sem­bly of the se­quences into 3309 base pair hap­lo­types. The MLST se­quences from sev­eral thou­sand iso­lates were al­ready avail­able in the Campy­lobacter data­base. These re­searchers set to work ana­lyzing this data. They found that more than 99% of the ha­plotypes fell neatly into one or the other of the two species. How­ever, there were some mixed "hy­brid" ha­plotypes, typ­i­cally C. coli that con­tained se­quences from C. je­juni. Most of these showed up within one of the three C. coli clades (clade 1).

More genes moved from C. je­juni to C. coli than went the other di­rec­tion. Since most of the gene ac­qui­si­tions were found in C. coli clade 1, the trans­fer oc­curred af­ter it di­verged from clades 2 and 3. Some of ac­qui­si­tions may have been quite re­cent, as many of the im­ported se­quences are iden­ti­cal to those in the donor pop­u­la­tion. Swaps of this sort lead­ing to "de­spe­ci­a­tion" hap­pened on mul­ti­ple oc­ca­sions, and at least four times more fre­quently than those lead­ing to di­ver­gence. As the au­thors state:"if main­tained over time, these rates would lead to pro­gres­sive ge­netic con­ver­gence. Well, if so, then at just what point should the re­cip­i­ent C. coli's be con­sid­ered "hy­brids" and no longer the orig­i­nal species?"

Il­lus­tra­tion of the ge­netic di­ver­gence and a sce­nario for de­spe­ci­a­tion of C. je­juni (gray) and C. coli clades 1 (blue), 2 (yel­low), and 3 (red). Be­tween time t_–2 and t_–1, Campy­lobac­ter split into two sep­a­rate species, C. je­juni and C. coli. Be­tween t_–1 and the present (t₀), C. coli fur­ther sepa­rated into three dis­tinct lin­eages repre­senting in­cip­i­ent species. At t₀ C. coli clade 1 starts to ac­cu­mu­late ge­netic ma­te­rial im­ported from C. je­juni, ow­ing to ex­pan­sion into a novel agri­cul­tural niche. By t₁, re­com­bi­na­tion has been suf­fi­cient to make strains with a clade 1 clonal ori­gin in­dis­tin­guish­able from C. je­juni. A more spec­u­la­tive pro­jec­tion would be that the change in en­vi­ron­men­tal con­di­tions could also have a sub­stan­tial ef­fect on clade 2 and clade 3 strains, with an ele­vated rate of ex­change with the cos­mopolitan and nu­mer­ous C. je­juni clade 1 bac­te­ria, which could lead to com­plete de­spe­ci­a­tion at the nu­cleotide level by time t₃. Source

An in­ter­est­ing point is that the im­ported C. je­juni genes are found more of­ten in C. coli strains iso­lated from do­mesticated cat­tle and birds, thus sug­gest­ing that hu­mans may have played a role in re­vers­ing the usual pat­tern of di­ver­gence by pro­vid­ing new hosts that are shared by both species. Maybe. What­ever the im­pe­tus, these two bac­te­ria do not be­have like good God-fear­ing species be­cause the ge­netic bar­ri­ers be­tween them are quite porous.

What to make of this? In prin­ci­ple, lat­eral gene trans­fer should be a two-way street, with genes able to travel in both directions—sometimes even back to the or­gan­ism they came from. So, are we wit­ness­ing some­thing new? Per­haps not in kind, but in an al­tered pat­tern due to our al­ter­ing the se­lec­tive pres­sures that op­er­ate on "species" se­lec­tion. The au­thors lament:"Hu­mans con­tinue to cause rapid and ex­ten­sive en­vi­ron­men­tal change. Pre­existing en­vi­ron­ments have been de­graded, and novel ones, such as in­ten­sive farms or acid mine drainage ar­eas, have been cre­ated that pro­vide a new adap­tive land­scape and op­por­tu­ni­ties for hy­brid forms to evolve."

Na­ture seems to be able to put Humpty Dumpty back to­gether again, a lively demon­stra­tion of the plas­tic­ity of the prokary­otic (and prob­a­bly also eu­kary­otic) species. In this game, noth­ing stays the same. As Her­a­cli­tus, the "weep­ing philoso­pher" of the paint­ing, said: Пάντα ρεΐ (panta rhei, every­thing is in flux). Is it ever!