Wednesday, October 28, 2015

How old are fireflies?

This is an "open lab notebook" detailing an analysis I did trying to figure out how old are fireflies.


Are fireflies - beetles who use light for courtship - more diverse than expected from the age of their lineage? Answering this question in part depends on knowing the age of the clades.

In this analysis, I come up with a very rough estimate that one firefly clade is 145 MY and another is 128 MY. Divergence time estimation is notoriously error-prone and these estimates are based on a number of assumptions. They should therefore be taken with a (large) grain of salt, ie be skeptical.

I began with the phylogeny of Martin et al. (2015). They concluded adult bioluminescence was originated twice in fireflies. One clade contains Lampyrinae+Photurinae, which I call ‘firefly1’. The other clade contains Pterotinae+Luciolinae - I call this the “firefly2” clade. This tree is based on 18S, 16S, and CO1, but did not do any divergence time analyses.


.

In order to estimate divergence times, I needed to include clades that could be constrained with fossils. I consulted Hunt et al. (2007), a phylogeny of all beetles, with divergence times. The closest clade to fireflies with a fossil constraint is their constraint “e”. This is Elaterophanes from 196.5 MY, used as a minimum age for the Elateridae. Hunt et al. (2007) used the same genes as Martin et al. (2015) (MEA), so I concatenated the MEA data set with elaterids from HEA. I also fixed beetles to be 285 MY, after Hunt et al. (2007). This is their estimate of divergence time for beetles. Using the fossil record could lead to a ‘maximum’ age of beetles as 411 (Rhynie Chert). But if I use 285 as a minimum and 411 as a maximum, the age gets pushed up to 411, which does not seem particularly realistic. Doing that raises the age estimates by some 40 MY-  for FF1 and FF2 to 186 and 164 MY, respectively.
I also included some other outgroups. First, I used a Hydroscaphidae because the MRCA of that clade and Lampyridae is the MRCA of all beetles. In addition, I used a non-beetle, Chrysopidae. These two taxa were the only species in HEA that had all 3 genes. For divtime analyses in r8s, I pruned the Chrysopidae to leave a rooted, fully resolved tree.

I required all 3 genes to be present for each species (using phylocatenator of Osiris (Oakley et al. 2014)). My tree had some differences with HEA and MEA:




  1. Elateridae are not monophyletic. With some different outgroups, I did get monophyly. HEA also consistently got monophyly. Perhaps adding Cantheridae (a closer sister to Lampyridae) would allow recovery of the expected monyphyly of elateridae. As a result, the divtime constraint is at the base of Elateridae AND Lampyridae, and could influence final results.
  2. Firefly 2 (red taxa) is not monophyletic as in MEA. Instead, I get Pollaclasis and Cyphonocerus within the Firefly2 clade. This could influence the time estimate for this clade. I could perhaps constrain monophyly here. Also other outgroups also could influence monophyly because Pterotus is the taxon changing places, and it is fairly long branch, and may be influenced by outgroups.








Data Files:

I used Osiris (Oakley et al. 2014) to build the phylogeny, which uses phytab format. That file is here.

I used r8s for the divergence time analysis, and that file is here:

#NEXUS


Begin TREES;

TREE 'Tree1' = ((((Oxynopterus_sp.:463.5249944,Agrypnus_murinus:526.2532825):58.07102708,(Panspaeus_guttatus:460.2987223,(Stenagostus_rhombeus:490.0649111,(Denticollis_linearis:345.0885786,Athous_haemorrhoidalis:348.234297):128.0768835):72.63022263):60.96422013):35.09443673,((((Phausis_reticulata:1662.289658,((((Lamprohiza_splendidula:544.0746241,Phosphaenus_hemipterus:229.7443014):285.1154906,Lucidota_atra:437.7055071):401.9635656,((((Photinus_australis:253.4245299,Photinus_tanytoxus:505.5902659):83.13503158,((Photinus_punctulatus:528.7843213,Photinus_pyralis:301.5064629):50.68180427,(Photinus_floridanus:473.4079674,(Ellychnia_californica:135.4824287,Ellychnia_aff._corrusca_KSH611:25.24849269):286.7912686):70.99285141):18.53357795):329.2700252,((Aspisoma_sp.:283.3096828,(Pyractomena_dispersa:29.67243287,(Pyractomena_palustris:31.23178185,(Pyractomena_angulata:517.0946069,Pyractomena_borealis:67.81801332):70.86493904):110.1146049):238.5808725):339.3010688,((Pleotomodes_needhami:426.6510094,Pleotomus_pallens:389.0211618):76.84583685,(Lampyris_noctiluca:477.2948781,((Diaphanes_formosus:371.9065228,Lychnuris_formosana:449.5272741):90.09984008,(Microphotus_angustus:406.2856534,Paraphausis_eximius:395.3158416):117.5049772):29.6282204):72.85630302):111.0228766):116.0625074):59.48984988,Micronaspis_floridana:558.9615698):107.7999852):229.3020886,(Vesta_sp.:561.4644596,(Bicellonycha_wickershamorum:491.2011309,((Photuris_tremulans:49.09336296,Photuris_aff._lucicrescens_KSH1:100.1688104):15.59686292,Photuris_quadrifulgens:50.11517938):457.7292255):121.0831356):150.8011019):163.8652632):66.19287172,((Brachylampis_blaisdelli:759.3860187,((Drilaster_axillaris:123.8337303,(Flabellotreta_sp.:171.4133031,Flabellotreta_obscuricollis:146.3672477):242.4682661):163.5674534,(Ceylonidrilus_sp.:422.4286714,(Drilaster_sp.:354.6668547,Drilaster_borneensis:394.0848821):241.6799973):72.15723681):351.5818484):270.4748514,((Luciola_sp.:326.8593145,((Luciola_parvula:576.0213995,(Curtos_okinawanus:182.2933313,Curtos_costipennis:220.7797732):214.4995191):130.4914738,Curtos_sp.:346.5873752):104.5451147):267.9094037,(Pterotus_obscuripennis:672.2005806,(Pollaclasis_bifaria:627.4316177,Cyphonocerus_ruficollis:348.7937363):198.7861435):41.84871305):52.94860049):62.12407915):680.5789337,Plateros_sp.:1002.688879):111.8242026,((Rhagophthalmus_ohbai:539.4926404,(Cebrioninae_sp.:547.7782899,Ampedus_balteatus:478.7696559):125.5329304):66.72017755,Cardiophorinae_sp.:883.3299248):39.872645):47.59526361):1043.317628,Hydroscaphidae:1499.20604);
End;

[** Beginning of the rates block containing commands for r8s **]

begin r8s;
blformat lengths=persite nsites=6417 ultrametric=no;

MRCA beetles Hydroscaphidae Drilaster_borneensis;
MRCA elateridae Cardiophorinae_sp. Panspaeus_guttatus;
MRCA firefly1 Phausis_reticulata Pleotomus_pallens;
MRCA firefly2 Pterotus_obscuripennis Luciola_parvula;


fixage taxon=beetles age=285;
#constrain taxon=beetles min_age=280 max_age=411;
constrain taxon=elateridae min_age=196.5;


divtime method=pl algorithm=tn [cvStart=0 cvInc=0.2 cvNum=8 crossv=yes];


describe plot=chrono_description;
showage shownamed=yes;

end;

References

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