Planned intervention: On Wednesday April 3rd 05:30 UTC Zenodo will be unavailable for up to 2-10 minutes to perform a storage cluster upgrade.
Published October 20, 2020 | Version v1
Dataset Open

Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification

  • 1. University of Groningen
  • 2. Center for Environmental Economics in Montpellier in Montpellier*
  • 3. University of Stirling

Description

One of the primary goals of macroevolutionary biology has been to explain general trends in long-term diversity patterns, including whether such patterns correspond to an up-scaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity-dependent diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time-dependence without diversity-dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time-dependent, but diversity-independent model that matches the expected diversity through time of a diversity-dependent model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity-dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity-dependence. We advocate that tests encompassing additional data, e.g., traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.

Notes

As described in Methods, the data archived here were produced from functions in R package DDD.

Instead of calling the DDD functions mentioned above directly, the first author developed and used a utility R package for the project, called "DDvTDtools", that calls DDD functions and manages their input and output in a standard way. The package is available on GitHub (https://github.com/TheoPannetier/DDvTDtools), and can be cloned from there or installed from within R (remotes::install_github("TheoPannetier/DDvTDtools")). For instructions on how to run the simulations and obtain the maximum likelihood parameter estimates, I refer to the README.md file of this package.

Simulated trees are stored in files with the pattern simXX-PARA.RData, where XX is the model name (DD or TD) and PARA a four-digit code specifying parameter values (see ReadMe.txt for more details)

The results of the maximum likelihood procedure are stored in data frames, in files with the pattern simXX_optimYY_PARA_INITK.rds, where YY is the name of the model fitted to a tree (DD or TD, can be the same or different as XX), and INITK specifies initial parameter values (see ReadMe.txt for more details)

Data for empirical phylogenies follow the same naming pattern; simulated trees are stored in files with pattern simXX_FAMILY_FROM.RData, and the results of maximum likelihood are stored in files with pattern FAMILY_simXX_optimYY_FROM.rds, where FAMILY is the name of a family of birds or mammals, and FROM specifies which values the trees were simulated with (see ReadMe.txt for more details).

Funding provided by: Nederlandse Organisatie voor Wetenschappelijk Onderzoek
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100003246
Award Number:

Funding provided by: Faculty of Natural Sciences, University of Stirling*
Crossref Funder Registry ID:
Award Number:

Funding provided by: Faculty of Natural Sciences, University of Stirling
Crossref Funder Registry ID:

Files

ReadMe.txt

Files (700.1 MB)

Name Size Download all
md5:8b2ad302f0f4c2eeddbfce19fd605520
38.0 kB Download
md5:69de3f8118f44dc29e67ac9280bf2418
38.1 kB Download
md5:ecab37981df68654ae5f77ac4d7577bf
39.6 kB Download
md5:be8de9e7e87b29821fe5327368e7a601
44.8 kB Download
md5:7b694a76de11c1c902211b33d280606f
39.7 kB Download
md5:c212d79d74409b7d04bc8aee5c58c854
44.7 kB Download
md5:e4f4ca7b9ea532edfc781d5ff442fa49
36.8 kB Download
md5:44a7fafb22065d55dde740cd3ec11e4b
35.7 kB Download
md5:50eae9cea84e9a9c3d4f28e0c26c56a1
39.3 kB Download
md5:4c8f452c9e696aaa43298a64b1df8f19
44.4 kB Download
md5:0c42bb71dbe2d50cca88e241ec18a6bb
38.9 kB Download
md5:05e279d7abaebbc1c3e127a74970695c
43.5 kB Download
md5:2431fbdf65b38e8e97945c6821c3e0e1
378 Bytes Download
md5:332693f82e3888ff7904c7329585e147
7.1 kB Download
md5:1853007ecff20d8aed73ad348dabfa9d
1.4 kB Download
md5:6817105a3bd83c989f66af590615010a
1.4 kB Download
md5:6265b5c3987c2d740ce23651c059df3d
959 Bytes Download
md5:6073f39a78cbaa0f17e987c388ee93d3
37.0 kB Download
md5:c13e1422dd7b48056004b06abf562660
36.6 kB Download
md5:5f2dfb3f48855209895b757b35158e21
38.9 kB Download
md5:6565e398552861522d26587ec10011ac
43.9 kB Download
md5:21cd841d99b72cece6d0b9f6b6537eb7
38.7 kB Download
md5:385ec52330239427896fb11a13809140
43.8 kB Download
md5:6d38e2ab4c92cb4cd1c1ad82ba2a4694
38.2 kB Download
md5:5643e93e2cbc086c4beb451038f0a8dd
38.3 kB Download
md5:f521f059d844e50e9614e440cf85f3f2
39.8 kB Download
md5:be2b7226ce36747846209ff3e79a3097
44.8 kB Download
md5:b1c456102961001355a1ae525a7d194e
39.8 kB Download
md5:85ee9b8e6d49d974bf439dc135a47b02
44.6 kB Download
md5:e471e8906eb3daf12ecf5ad5cc63c627
2.5 kB Download
md5:c19b40d02fe1254419c652245c5c166e
2.4 kB Download
md5:9e28e0bbfc132a30d98199c5579e7747
1.6 kB Download
md5:4b0f3ad9d3c58fdd8a9d6f82844d5873
2.6 kB Download
md5:62248ad531251d713339528f602e1acd
4.8 kB Download
md5:41b7512cfcc0e65a37a2473c4d44bde4
3.1 kB Download
md5:9da4890afc4e7d9f646d095b087c5ef4
4.8 kB Download
md5:8848e1bee4873e5172358b4a1d6d628c
4.6 kB Download
md5:c2d5159c03379ad786d87ccbcaa2ead0
2.9 kB Download
md5:436ad10900dc5fb21fe60711af3cfdc5
36.3 kB Download
md5:d843e76fd62712bdf0b896b9b43c1344
35.3 kB Download
md5:a0aa02c552f0de8ba166cefe587637c7
38.4 kB Download
md5:af88db22a623ee1a54ebd58ea8f7cdb6
43.7 kB Download
md5:d08d84790cd5a674882b1466d5e8e81f
36.5 kB Download
md5:7d149cc1066760be2c98f5bb20904331
43.2 kB Download
md5:df592714d5b330b42e0fa12a87130843
7.1 kB Preview Download
md5:848e25b87cca4f866537dbb43de9b8f6
791.5 kB Download
md5:26920506968388dbf71f9314b11b15e6
1.1 MB Download
md5:4b590c793b4a60e0307c318bd7d3f570
1.2 MB Download
md5:597898a383817e781628e353d6fb81ce
1.4 MB Download
md5:57cc0294bb5da867b514018d16691c9a
1.1 MB Download
md5:081895154a4cf06ec721b86e3834ef88
2.4 MB Download
md5:c65a4479e08dc44380c029e585eeda1f
3.2 MB Download
md5:c1ba70807bf2e2a56e41be21a0e7c13e
4.2 MB Download
md5:30a941c949fc89b63a9f4c93621a6b9f
1.1 MB Download
md5:1b447d9415868d4b5adfb0e3bfaa2360
2.3 MB Download
md5:e2bbeb783cbada8fe8cf08d4cb1aaa8a
3.4 MB Download
md5:c0bfa3e41e56cc2603641bff1af6026e
6.8 MB Download
md5:7492d0205672c9d5ab4f3c96e8853988
5.1 MB Download
md5:13d47be889d9e12c9231f7d730cb2bc8
9.8 MB Download
md5:967bcc97c4bfe6974ef1040a9f196afc
7.7 MB Download
md5:78e9a78be127f030abbb4df0cd3fd9d0
13.6 MB Download
md5:75fe7e2c110d0a67b6bc91c6922d37a0
1.1 MB Download
md5:58dcbf628ebd1ee94ba7ca46ae9c2183
4.1 MB Download
md5:f4670860e7a6b302831f5ac76ef19fec
6.6 MB Download
md5:2936aac7834a4ae9ec76b0af13871c16
11.5 MB Download
md5:20491fc1d3c31230ea983b597436c08c
1.1 MB Download
md5:2ce82bf4032844668a7c15a746a85c62
11.5 MB Download
md5:1071a265c17317e4a4977721f8193cca
22.4 MB Download
md5:87ffdc567da56eb4d9bba58f1a67a8ba
41.6 MB Download
md5:473728cf0d4c2ad432a7e20a079c384f
6.0 MB Download
md5:3a953a7539e5a2fde88e1a8f2361eb63
7.1 MB Download
md5:7c562fd5a41018afeea735f1702ff00e
3.1 MB Download
md5:74e46c88b5105a1842526759d7d74987
44.6 kB Download
md5:db81d7709307862cf7c507cc551fd789
45.8 kB Download
md5:9054880f19743e26b3d2447a305687df
41.5 kB Download
md5:09b8f1cb9cf3eb53ae93dfa691ae2345
45.7 kB Download
md5:64428e06f8c9a35201b2375f0b96d040
41.4 kB Download
md5:6f45c078832e94e6dd8948f4e621c674
44.8 kB Download
md5:a5336118c67005342628f53356904d9e
42.2 kB Download
md5:a9b75c97270e57ef36346835f0f96324
44.7 kB Download
md5:e849a0a19952fd4bb7c60ee44db79c17
40.9 kB Download
md5:0e3393daa80f62b6b4ab6aa0e59a18f7
45.2 kB Download
md5:c90b7fb47389e4e5cd3b77c30cca2ebd
41.2 kB Download
md5:eafca4b966e6f5ed0c022af31d41842b
44.7 kB Download
md5:ff00ddbbb014f3c0aac9397fedbff40a
43.5 kB Download
md5:3f1435900abe0814eff56325426c7410
40.7 kB Download
md5:9af09ed36addf46882a069dd5bc17c35
44.3 kB Download
md5:21cd375bf312c7cc5f2626d1f802afe5
40.5 kB Download
md5:248aba0724d003f5d4ddb9b5d63d263b
44.6 kB Download
md5:b963340c6ef6803d812cad8818fb4745
44.8 kB Download
md5:4e88c4ecaa1562fe453fa6ac1d572292
40.9 kB Download
md5:abe7b93464feaf674b912514e618b4d4
45.1 kB Download
md5:d18464686b497b1d13c3dd7de8c10d9e
44.5 kB Download
md5:521c2ba67e76d0e507b6727270a216ec
46.0 kB Download
md5:1c8758a1114b1fdb2a8c1d575086e7a1
38.6 kB Download
md5:ceb278aeb14a14ddbd136ef03e312278
43.5 kB Download
md5:c55a46b01b3688fa350d8d8f9e2086bc
38.6 kB Download
md5:b415df2b05954fb19d45a08ebe46674d
44.3 kB Download
md5:151b501ffd4804118de2224d65f1d36d
45.0 kB Download
md5:7408373011baa63daaad2b8601888b1c
42.8 kB Download
md5:5550f7e7b1eb44caa3bdfff5958d379f
44.8 kB Download
md5:9880deb9c120374c91a9df72e284b399
45.6 kB Download
md5:5189e959b36dfcfbfd99c832db8eb5b5
41.4 kB Download
md5:13ffdd1131945e1b69fd5ca0ee79b0a6
45.5 kB Download
md5:fef3e15b8e9ec7310fbf5eb38fce3835
41.2 kB Download
md5:a2b13775e907dd103b7a47f6073f7737
44.7 kB Download
md5:cd1f1a9e66e93286119003780eccad53
42.8 kB Download
md5:6ef8d613383858864b92c7a973010e13
44.8 kB Download
md5:b8bf884ee1b9b2b507be9248b750621e
40.9 kB Download
md5:140b146c910e3aae341417da84005bac
45.2 kB Download
md5:6fb0ef28d22d9d87ef1d855fc8071bff
41.2 kB Download
md5:4fba700c09ade60744f28f3655794145
44.5 kB Download
md5:f35c48491efca5de6fd02bfcef91920d
43.3 kB Download
md5:d743e01b2d25d9dc22b2733398c70054
41.1 kB Download
md5:11179e488af92763db045b2dc93ac3b3
44.4 kB Download
md5:370c4e423ce32586165351057fe6b742
40.7 kB Download
md5:a0d7ef6d4467838b6b5c57e0f7c623ca
44.7 kB Download
md5:f85f691c14a8fe4e712a1bbc33419f7b
44.9 kB Download
md5:157d06b9ac00745662f9d3503f5671a2
41.0 kB Download
md5:ac766ee22b6b54a63cdc6c1c79923613
45.2 kB Download
md5:297227f4ba28f711c0f83f6ad3a6362a
44.3 kB Download
md5:c04dc1b1ea66eb70bbddd4c1ba455a63
45.7 kB Download
md5:699cbbffa9a3324f18a9e48e13713b20
38.0 kB Download
md5:3e30f27ac9692aec4609123cd88e2a99
44.3 kB Download
md5:d333dab45f7b97ac151a552bf356a083
38.0 kB Download
md5:0669997071eb0e3542e4820205cdac5f
44.4 kB Download
md5:eee19628b44879f655f1d1c48d409609
45.0 kB Download
md5:8ce83a761433df466f88764dbebc2d20
47.3 kB Download
md5:b9d1c9f56debb25fd9071474c5e79118
7.6 MB Download
md5:88e3251e51d1e4fc6c55b56859eb3899
979.4 kB Download
md5:42416cd6f62f5e1552382580bb257a7d
760.0 kB Download
md5:9993ff5dee4613ab572bf8e02e73f359
1.2 MB Download
md5:f18318d27ef44af8a8c18798e6cd2471
1.3 MB Download
md5:7ff732b7edb21bf8a3519de7d2d77a69
1.4 MB Download
md5:2f738a9561bd949e90656f34022708b2
1.2 MB Download
md5:ea5f4cf0cba9bf36064cbe3ccd3809b1
2.9 MB Download
md5:4f98fede1c5a65d45b2417a3db73ed07
4.2 MB Download
md5:05f71df4b755a3c7815bcee3d254c675
5.6 MB Download
md5:754933a139c971fb8c4b30b18b3c52c1
1.2 MB Download
md5:72d3322ad1ce6b5fe8da782dd24c9915
2.4 MB Download
md5:d4ce916ecd81b4bd48cb20eb97a7ea96
4.1 MB Download
md5:bb24866dad5606b49f6ca580f08b8e77
7.8 MB Download
md5:6c5232ab31daf361d15e3aef08af0225
7.0 MB Download
md5:d06dcd548b8298fd6f46d8f743d3f36c
12.9 MB Download
md5:023244fde1c265fc685cd897f4138c02
11.8 MB Download
md5:a5d518ea3f3c469b909de3dee31e0e31
19.8 MB Download
md5:25a2cb83ab423d5fc5fc043514a5f93e
3.0 MB Download
md5:1b32b2367b6d3c4ef4b3f957c5604bba
7.8 MB Download
md5:397b6eed99806d9a533d548dfb115b19
14.3 MB Download
md5:1e7ab44e6b64d6bf0027e91861a152d4
29.6 MB Download
md5:4702c8e0fcbc1eeb6017403336a7bb38
3.0 MB Download
md5:a7d47b90ddba9b7f6908cbb3a29a704f
29.5 MB Download
md5:314cb0966b1fb0c27cce703f0186f3f3
70.5 MB Download
md5:df1a3f6dd14883064d34d1bf7f4007c4
199.6 MB Download
md5:a3d53e9940b7976908935e2440f232db
7.6 MB Download
md5:b30c2463626efda2fc7090ff31113a38
6.3 MB Download
md5:732790eb8bf4ef02da4d933c42d06ea9
9.4 MB Download
md5:d62cbd8ccf8bb91a0736d3f6c730e42c
8.4 MB Download
md5:30b096680b57ff92094886ecaeb8aebf
5.1 MB Download
md5:96ff43e0002835b130be7131ab42d4f2
4.4 MB Download
md5:7eec1142e01a3b9028ab815fe46e3235
45.6 kB Download
md5:c9b467ff82739c63bd65fd79821bdf9e
46.4 kB Download
md5:e5d064fcca094f43ad75ada398dd722e
38.4 kB Download
md5:e793ba563f7f4722a76904f8cd9dd2fb
46.2 kB Download
md5:48bd0989941854522908e8ce43aacf8a
28.4 kB Download
md5:805ed062a18b538b0aa3dba3a98f37d5
44.8 kB Download
md5:5f5ad8ac789223c31dac52b5347cea71
46.1 kB Download
md5:9c641c55e0788767786ec6a40a7f1ddc
46.8 kB Download
md5:b85d6f1485561fe8869cfb680d1d2c24
30.9 kB Download
md5:e43893022252a64939ba6f98ad585aa7
46.8 kB Download
md5:2d1bbb3f81a9a47a432785e44046ece3
32.4 kB Download
md5:a819f6560ad7605fb145f250bae33b50
45.6 kB Download
md5:fba1a3ff48ce5272a6657bab608a2f98
48.9 kB Download
md5:89b26fcec62f7478817606c50e91fcd9
46.7 kB Download
md5:a2e0b892fcb4445ceccabc8def64289e
46.7 kB Download
md5:e6e52d30b263e09384c223c559082c92
29.8 kB Download
md5:8f5bc2bc8ea6153c4a32e49d3bfed218
47.0 kB Download
md5:e3f57aa249295cf95cb3c4651b0c9c3a
47.0 kB Download
md5:8a415560ea3ece8939c5ed74f4806927
30.8 kB Download
md5:1aac182932784a0169848e941ea4f0ab
47.1 kB Download
md5:3d0bc725850d80b204e75f56927bfbf9
46.0 kB Download
md5:93172bbfc0540d3f7d815885c774c31f
47.1 kB Download
md5:7e56f411c3a5ee3c63927260a213aab8
43.9 kB Download
md5:3a26b4a447019a04032c0a634cb0263c
46.8 kB Download
md5:763fefe27d903c15733cd512132e7ce1
44.2 kB Download
md5:2acc3c12d10ddf12979758105812e2b5
46.8 kB Download
md5:491883f3b79e5e9cd9d90ed80524510a
47.0 kB Download
md5:ae84f651cd3f1b55f59f17d0409654aa
48.2 kB Download
md5:2005d8e200aa183004b4735d4a775713
45.8 kB Download
md5:d5a55829ffa21588c05cc42d8d4c1907
46.2 kB Download
md5:4739111f0976cfd00ac69a3ed4dbc101
38.4 kB Download
md5:c5e19a7637017259763f9ed0085f13de
46.0 kB Download
md5:dcf10a250061727f365dd3bce41da12f
40.7 kB Download
md5:9663e25d84f5d1861b19738c9141709c
44.8 kB Download
md5:37480c9218027b8cb5796bfdc8feb81c
46.3 kB Download
md5:63d0a9f0a125e7537ee99f4d94c554f6
46.7 kB Download
md5:0f0db8d6e6049ba3b32b084e0692c6b7
30.8 kB Download
md5:7d3023821f8b37d0173dc30c4d9b8bea
46.7 kB Download
md5:fffb116a92941f1d05d722f0b33198cd
32.4 kB Download
md5:3707951dfceffb6306b50d3f94db7828
45.4 kB Download
md5:c75094415f507c809bc6dc5d4504c4ed
48.3 kB Download
md5:b58befb59bd38b1788f058456bce57d2
46.6 kB Download
md5:9650aa58fe060fa6ff696a0199b45680
46.7 kB Download
md5:96ed077c537678265d9207b4ae0edb27
29.9 kB Download
md5:663f4a81b25c0e2611f965965b3b3c4f
47.3 kB Download
md5:fb10cd31d89d3d53d051a0f2b11ba4d5
46.8 kB Download
md5:ef029456ab30b2385d3bb5db4a6ba340
30.7 kB Download
md5:63cdf4e3b6e3fc91a2afaf5fca6a6232
47.1 kB Download
md5:da531a2dd1f08e63f1114c68b8e4b92b
46.0 kB Download
md5:3ec9ca0e0bf5610ac65cf76856d9af78
46.9 kB Download
md5:f99edd2803856d1daba2a5a307e2c14a
42.8 kB Download
md5:ef2d25caad549667daa9726db4850165
47.3 kB Download
md5:2d3f75aff60d6ddac2915213a7e287e8
43.2 kB Download
md5:6b8ddc277e93c99259279b1fefb8a6d4
46.7 kB Download
md5:27a05ec52db17d4e231515c594c40219
46.7 kB Download
md5:be811f287c3ddbe7157df1d3912ef209
44.8 kB Download
md5:66672fc5b5754be2ff526c86cbeb4495
8.8 MB Download
md5:59670e21fe2e0fc83eabc48625210626
9.4 MB Download
md5:9d9496fedcd7931d3abb2f8fabb75981
1.2 MB Download
md5:abedcbef714218449bb4e858df73bc6b
922.7 kB Download
md5:31917e60089c0a5acd96772e6b1bd44a
419 Bytes Download

Additional details