DOI: 10.5061/dryad.9kd51c5xg
title: Data for: A phylogenomic investigation of species diversity, morphology, and biogeography in <em>Neptunia</em> Lour. (Fabaceae: Caesalpinioideae: Mimoseae)

description: Neptunia Lour. (Fabaceae) is a pantropical genus of 22 species and is the
 sole genus of Mimoseae with fully aquatic species, N. oleracea and N.
 plena. The aquatic species are pantropically distributed, while the 20
 terrestrial species are confined within continents separated by oceanic
 barriers. Due to species having broad distributions, polyploidy, and
 cryptic morphology, Neptunia species delimitations remain uncertain and
 have not been comprehensively sampled in previous phylogenetic studies. To
 that end, we tested species delimitations in Neptunia by sampling multiple
 accessions of all species and infraspecific taxa and determined
 relationships through phylogenomics, identified the ancestral states of
 habitat and taxonomically defining characters, and estimated the
 historical biogeography of the group to determine the hypothetical
 ancestral area. A target-capture approach was applied with the
 Angiosperms353 bait-set to sequence 353 orthologous nuclear loci for
 phylogenetic inference of 94 ingroup and 11 outgroup individuals.
 Time-calibrations and comparative methods were employed to reconstruct the
 chronogram and estimate ancestral states. Analyses of the filtered nuclear
 loci recovered a monophyletic Neptunia and provided insight into species
 delimitations in closely related diploid and polyploid species. We
 recognize N. windleriana and N. heliophila as synonyms based on
 phylogenetic reconstructions and morphology, reducing the number of
 species to 20. A newly described species, N. proxima, was polyphyletic.
 Single-seeded Neptunia species formed a clade, but other taxonomically
 important traits lacked phylogenetic signal. The aquatic N. oleracea was
 sister to the clade of the aquatic N. plena and the terrestrial species
 from the Americas, and ancestral character estimation analyses inferred
 two separate transitions into aquatic habitats. This transition into
 aquatic environments and being polyploid likely promoted the widespread
 distributions of the two aquatic Neptunia species. The early
 diversification of Neptunia was widespread in Asia, North America, or
 South America, and a rapid radiation occurred in Australia. Our results
 support recent taxonomic circumscriptions and provide the first fully
 sampled and well-resolved molecular phylogeny of Neptunia.
description: # Data for Becklund & Schenk 2025. A phylogenomic investigation of
 species diversity, morphology, and biogeography in Neptunia Lour.
 (Fabaceae: Caesalpinioideae: Mimoseae). *Systematic Botany* 50(4). ##
 Description of the data and file structure Alignments are in Fasta or
 Nexus formats. ### Neptunia.Phylogeny.Alignments.zip \--contains 196
 supercontig alignments that were reconstructed from sequencing data from
 target capture with Angiosperms353 bait set (Johnson et al. 2019). The
 number corresponds to the targeted gene from Angiosperms353. If the file
 was modified with Phylter (e.g., tips were dropped due to noise) the file
 contains the suffix phylter.aligned.fasta. Otherwise, the files contain
 the suffix supercontig.aligned.fasta. All files are supercontigs (exon and
 intron region reconstructed with HybPiper [Johnson et al. 2016]). The
 alignments here were used to reconstruct the Astral species tree. Methods
 are described in the manuscript. ### Neptunia_14_lociBeast.nex \--is the
 alignment of 14 loci used in the BEAST analyses. The loci included
 (numbers corresponding to Angiosperms353 supercontig loci that were also
 used in species tree dataset) are: 4796, 5335, 5339, 5398, 5404, 5454,
 5634, 5933, 6098, 6258, 6450, 6462, 6488, 7013 ## Alignment Tip Names
 Information The final names of the samples were updated from the original
 names if they were identified incorrectly from the herbarium sheet
 information. Some alignments may not have been updated; here are the
 original tip names from sequencing and updated taxonomy displayed in trees
 and GenBank data. Tab-delimited list. Names_in_Alignment:
 Final_Names_in_Species_Tree\_ Acaciella_angustissima_LEB61: Acaciella
 angustissima LEB61 (Texas, USA) Albizia_julibrissin_LEB67: Albizia
 julibrissin LEB67 (Ohio, USA) Calliandra_eriophylla_LEB73: Calliandra
 eriophylla LEB73 (Arizona, USA) Desmanthus_velutinus_LEB58: Desmanthus
 velutinus LEB58 (Texas, USA) Desmanthus_virgatus_LEB48: Desmanthus
 virgatus LEB48 (Texas, USA) Lemurodendron_capuronii_EJMK435: Lemurodendron
 capuronii EJMK435 (Madagascar) Neptunia_amplexicaulis_ARB13356: N.
 amplexicaulis ARB13356 (Queensland, AUS)
 Neptunia_amplexicaulis_f_richmondii_B3044: N. amplexicaulis f richmondii
 B3044 (Queensland, AUS) Neptunia_amplexicaulis_F5856: N. amplexicaulis
 F5856 (Queensland, AUS) Neptunia_dimorphantha_BMW5175: N. dimorphantha
 BMW5175 (Queensland, AUS) Neptunia_scutata_DLL2661: N. scutata DLL2661
 (Northern Territory, AUS) Neptunia_dimorphantha_DWR63K: N. dimorphantha
 DWR63K (Western Australia, AUS) Neptunia_monosperma_LEB68: N. monosperma
 LEB68 (Queensland, AUS) Neptunia_gracilis_ARB2633: N. gracilis ARB2633
 (Queensland, AUS) Neptunia_gracilis_DHQ7689A: N. gracilis DHQ7689A
 (Queensland, AUS) Neptunia_gracilis_LJD722: N. gracilis LJD722
 (Queensland, AUS) Neptunia_gracilis_ML4160: N. gracilis ML4160
 (Queensland, AUS) Neptunia_gracilis_var_glandulosa_BW722: N. gracilis var
 glandulosa BW722 (Northern Territory, AUS)
 Neptunia_gracilis_var_glandulosa_GMW4977: N. gracilis var glandulosa
 GMW4977 (Northern Territory, AUS) Neptunia_gracilis_var_glandulosa_ME3201:
 N. gracilis var glandulosa ME3201 (Northern Territory, AUS)
 Neptunia_heliophila_IR11469: N. heliophila IR11469 (Queensland, AUS)
 Neptunia_heliophila_JRH2177: N. heliophila JRH2177 (New South Wales, AUS)
 Neptunia_heliophila_JRM2305: N. heliophila JRM2305 (Northern Territory,
 AUS) Neptunia_hispida_GL2941: N. hispida GL2941 (Northern Territory, AUS)
 Neptunia_hispida_ML7779: N. hispida ML7779 (Northern Territory, AUS)
 Neptunia_insignis_ARB18740: N. insignis ARB18740 (Queensland, AUS)
 Neptunia_insignis_IGC2139: N. insignis IGC2139 (Queensland, AUS)
 Neptunia_javanica_OEW20: N. javanica OEW20 (Myanmar)
 Neptunia_javanica_PES34: N. javanica PES34 (Indonesia)
 Neptunia_javanica_RP5491: N. javanica RP5491 (Thailand)
 Neptunia_longipila_SvL5099: N. longipila SvL5099 (Western Australia, AUS)
 Neptunia_lutea_DJR4801: N. lutea DJR4801 (Texas, USA)
 Neptunia_lutea_DL2381: N. lutea DL2381 (Texas, USA)
 Neptunia_lutea_FRW2706: N. lutea FRW2706 (Texas, USA)
 Neptunia_lutea_LEB62: N. lutea LEB62 (Texas, USA) Neptunia_lutea_RK39772:
 N. lutea RK39772 (Alabama, USA) Neptunia_major_ARB24919: N. major ARB24919
 (Queensland, AUS) Neptunia_major_BMS414: N. major BMS414 (Northern
 Territory, AUS) Neptunia_major_HD8836: N. major HD8836 (Western Australia,
 AUS) Neptunia_monosperma_AF363: N. monosperma AF363 (Queensland, AUS)
 Neptunia_monosperma_DLL1068: N. monosperma DLL1068 (Northern Territory,
 AUS) Neptunia_monosperma_DLL2008: N. monosperma DLL2008 (Northern
 Territory, AUS) Neptunia_oleracea_BR95: N. oleracea BR95 (Mexico)
 Neptunia_oleracea_CR6650: N. oleracea CR6650 (Madagascar)
 Neptunia_oleracea_JPE1580: N. oleracea JPE1580 (Benin)
 Neptunia_oleracea_JWN413: N. oleracea JWN413 (Sri Lanka)
 Neptunia_oleracea_KS36: N. oleracea KS36 (Thailand)
 Neptunia_oleracea_LA2519: N. oleracea LA2519 (Costa Rica)
 Neptunia_oleracea_LF2315: N. oleracea LF2315 (Kenya)
 Neptunia_oleracea_MR10494: N. oleracea MRY10494 (Peru)
 Neptunia_oleracea_PAS3810: N. oleracea PAS3810 (Botswana)
 Neptunia_oleracea_RKG592: N. oleracea RKG592 (Zimbabwe)
 Neptunia_paucijuga_CRM3954: N. paucijuga CRM3954 (Northern Territory, AUS)
 Neptunia_paucijuga_NJC662: N. paucijuga NJC662 (Northern Territory, AUS)
 Neptunia_plena_ARN4253: N. plena ARN4253 (Mexico) Neptunia_plena_DB6673:
 N. plena DB6673 (Puerto Rico) Neptunia_plena_GEC9600: N. plena GEC9600
 (Costa Rica) Neptunia_plena_GGH60910: N. plena GGH60910 (Brazil)
 Neptunia_plena_GRP27727: N. plena GRP27727 (Jamaica)
 Neptunia_plena_ILW512: N. plena ILW512 (Ecuador) Neptunia_plena_JVWM198:
 N. plena JVWM198 (Queensland, AUS) Neptunia_plena_JW3786: N. plena JW3786
 (Northern Territory, AUS) Neptunia_plena_LEB52: N. plena LEB52 (Texas,
 USA) Neptunia_plena_LOsn: N. plena LOsn (Queensland, AUS)
 Neptunia_plena_MJJJ3980: N. plena MJJJ3980 (Guyana) Neptunia_plena_PSB277:
 N. plena PSB277 (Ecuador) Neptunia_plena_RDW12337: N. plena RDW12337
 (Malaysia) Neptunia_plena_REJV35: N. plena REJV35 (Venezuela)
 Neptunia_plena_RG06173: N. plena RG06173 (Venezuela)
 Neptunia_plena_TRVD921100: N. plena TRVD921100 (Mexico)
 Neptunia_proxima_KRM17070: N. proxima KRM17070 (Queensland, AUS)
 Neptunia_proxima_KRM18188: N. proxima KRM18188 (Queensland, AUS)
 Neptunia_pubescens_ANE4276: N. pubescens ANE4276 (Mississippi, USA)
 Neptunia_pubescens_EPK41174: N. pubescens EPK41174 (Florida, USA)
 Neptunia_pubescens_G8073: N. pubescens G8073 (Florida, USA)
 Neptunia_pubescens_GS2411: N. pubescens GS2411 (Uruguay)
 Neptunia_pubescens_JdJJ4081: N. pubescens JdJJ4081 (Dominican Republic)
 Neptunia_pubescens_JH941: N. pubescens JH941 (Peru)
 Neptunia_pubescens_JJS2627: N. pubescens JJS2627 (Florida, USA)
 Neptunia_pubescens_JJS2678: N. pubescens JJS2678 (Florida, USA)
 Neptunia_pubescens_LEB46: N. pubescens LEB46 (Texas, USA)
 Neptunia_pubescens_LEB53: N. pubescens LEB53 (Texas, USA)
 Neptunia_pubescens_LEB54: N. pubescens LEB54 (Texas, USA)
 Neptunia_pubescens_LEB65: N. pubescens LEB65 (Texas, USA)
 Neptunia_pubescens_LEB66: N. pubescens LEB66 (Texas, USA)
 Neptunia_pubescens_OA1743: N. pubescens OA1743 (Argentina)
 Neptunia_pubescens_var_microcarpa_LEB57: N. pubescens var microcarpa LEB57
 (Texas, USA) Neptunia_pubescens_var_microcarpa_R38840: N. pubescens var
 microcarpa R38840 (Mexico) Neptunia_scutata_JE2995: N. scutata JE2995
 (Northern Territory, AUS) Neptunia_scutata_PRF421: N. scutata PRF421
 (Western Australia, AUS) Neptunia_scutata_RWP4866: N. scutata RWP4866
 (Western Australia, AUS) Neptunia_tactilis_JRC6043: N. tactilis JRC6043
 (Queensland, AUS) Neptunia_tactilis_JRM2168: N. tactilis JRM2168 (Northern
 Territory, AUS) Neptunia_triquetra_LGJvdM3867: N. triquetra LGJvdM3867
 (India) Neptunia_valida_ARAPR1079: N. valida APR1079 (Western Australia,
 AUS) Neptunia_valida_RWP3309: N. valida RWP3309 (Western Australia, AUS)
 Neptunia_windleriana_RMH19075: N. windleriana RMH19075 (Brazil)
 Neptunia_xanthonema_AVS3332: N. xanthomena AVS3332 (Queensland, AUS)
 Neptunia_xanthonema_RWP2931: N. xanthomena RWP2931 (South Australia, AUS)
 Prosopidastrum_mexicanum_RM17061: Prosopidastrum mexicanum RM17061
 (Mexico) Prosopis_glandulosa_LEB49: Prosopis glandulosa LEB49 (Texas, USA)
 Parkinsonia_aculeata_LEB56: Parkinsonia aculeata LEB56 (Texas, USA)
 Dichrostachys_cinerea_ERR7618736: Dichrostachys cinerea ERR7618736
 Mimosa_aculeaticarpa_LEB55: Mimosa aculeaticarpa LEB55 (Texas, USA)
 Neptunia_dimorphantha_DLL1912: N. dimorphantha DLL1912 (Northern
 Territory, AUS) ## References Johnson, M. G., E. M. Gardner, Y. Liu, R.
 Medina, B. Goffinet, A. J. Shaw, N. J. C. Zerega, and N. J. Wickett. 2016.
 HybPiper: Extracting coding sequence and introns for phylogenetics from
 high-throughput sequencing reads using target enrichment. *Applications in
 Plant Sciences* 4: apps.1600016. Johnson, M. G., L. Pokorny, S. Dodsworth,
 L. R. Botigué, R. S. Cowan, A. Devault, W. L. Eiserhardt, et al. 2019. A
 universal probe set for targeted sequencing of 353 nuclear genes from any
 flowering plant designed using k-medoids clustering. *Systematic Biology*
 68: 594–606.