.44. 444444444 3 .2- 1i . u . n.4, - whflrflawfl i... .4 ”$34.4... J , «any, 14 .Zzfi. 1mg; .i can»? nunuur a 4.4.3333, 3&9. . .. L334. 5.. 3 5a :4 . 3.:7Lq..1. .fisiilira 444 I. 2...] L A . I :up I ,..15......V. THE” 1 \. 14.. L. \\ 534~;4,4 This is to certify that the thesis entitled MONARDA SECTION CHEIL YCTIS: PATTERNS OF SPECIATION AND ENDEMISM presented by JESSIE ANNE KEITH has been accepted towards fulfillment of the requirements for the MS. degree in Plant Biology/ EEBB WW WMajofififessor’s Signature /‘f 77247 2&0; Date MSU is an Affirmative Action/Equal Opportunity Institution —,—.-.- -.—-.—--n-o-o---0-.----o-a--.-.— ..-.—.-.-._._.-._.-._ _ LIBRARY Michigan State University PLACE IN RETURN BOX to remove this checkout from your record. To AVOID FINES return on or before date due. MAY BE RECALLED with earlier due date if requested. DATE DUE DATE DUE DATE DUE FE 0 {‘11sz 411244 6/01 cJCIFiC/Dateouepes-pJ 5 MONARDA SECTION CHEILYCTIS: PATTERNS OF SPECIATION AND ENDEMISM By Jessie Anne Keith A THESIS Submitted to Michigan State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Department of Plant Biology 2003 t '1 — —-*v .‘anfl; ,_ ..1 '4 pk) 'Y‘J ABSTRACT Monarda Section Cheilyctis: Patterns of Speciation and Endemism By Jessie Anne Keith Monarda Section Cheilyctis (Lamiaceae) includes six species. Five are narrow endemics, with four (M. viridissima, M. fruticulosa, M. maritima and M. stanfieldii) present in unique edaphic conditions in Texas and the fifth (M. humilis) occurring in arid regions of New Mexico. The sixth species, M. punctata, is widespread, occurring across much of the United States. Phylogenies based on two Adh loci, Adh type 1 (Ath) and Adh type 2 (Ath), were used to investigate patterns of speciation, species relationships and endemic status (neo- versus paleoendemic) of these Monarda species. It was hypothesized that narrow endemic species were neoendemics that had speciated as peripheral isolates of M. punctata. Both Adh] and A th phylogenies had three primary clades that depicted similar relationships between taxa. Monarda punctata was the most ubiquitous taxon across both phylogenies. Monardafruticulosa, M humilis, M. maritima and M viridissima sequences exhibited polyphyly and patterns consistent with lineage sorting across both Ath and Ath phylogenies. In both the Adhland Adh2 phylogeny sequences of M stanfieldii were sister to a large clade including all samples of the other five species. Phylogenetic results suggest that M. humilis, M fruticulosa, M. maritima and M. viridissima arose from their widespread congener, M punctata, and that M. stanfieldii is a sister taxon to the other five species. Likewise, it was concluded that M. fruticulosa, M. maritima and M. viridissima and M. humilis are most likely neoendemics while M stanfieldii is likely a paleoendemic species. FOR THE TWO MEN THAT INSPIRED ME TO PURSUE HIGHER EDUCATION MY FATHER, DR. JAMES HILTON KEITH AND MY GRANDFATHER, DR. ARCHIE JUSTICE MACALPIN iii I” ACKNOWLEDGMENTS I thank the following people for all of their support in helping me complete this work. Facultyt Alan Prather, Tao Sang, J effery Conner and Richard Triemer Fellow Graduate Students: Anna Monfils, Nathan Sammons, Kristine Kern, Jay Sobel, Orlando Alvarez-Feuntes, and Rachel Williams Post-doctoral Associates: Heather Hallen, Changbao Li and Eric Linton I also acknowledge the following institutions for providing funding for this research: The Herb Society of America ______________________________________ Research Grant M SU Plant Biology Department __________________________________ Paul Taylor Funding The MSU Graduate School __________________________________________ Travel Funding The MSU EEBB ___________________________________________________________ Research Grant TABLE OF CONTENTS LIST OF TABLES ______________________________________________________________________________________________________ v iii LIST OF FIGURES ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ix CHAPTER l-Introduction 1.1 Project Summary ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 1 1.2 Peripatric Speciation ........................................................................... 1 1.3 Neoendemism versus Paleoendemism ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 4 1.4 Overview of Taxa _______________________________________________________________________________ 5 1.5 Objectives.m,,_mmnmwmmm"Hmumm; ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 7 CHAPTER 2-Materials and Methods 2.1 Study System _______________________________________________________________________________________ 8 i.Taxonomic Classification of Monarda Section Cheilyctis. ............. 8_ ii. Morphology and Life History Traits _______________________________________________ 9 iii. Chromosome Numbers .................................................................. 12 vi. Physiography and Vegetation ________________________________________________________ 12 v. Edaphic Constraints ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, l 4 vi. Species Recognitionmmw“WWW._W,m._m__._ ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 15 2.2 Sampling ............................................................................................. 16 2.3 Marker Choice ..................................................................................... 19 2.4 DNA Extraction ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 21 2.5 Primers 21 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo CHAPTER 2—Materials and Methods continued 2.6 DNA Amplification ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 22 2.7 Cloning ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2 3 2.8 Adh Clone Isolation ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2 4 2.9 Restriction Digest Analysis of Adh _____________________________________________________ 2 S 2.10 Sequencing ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2 6 2.11 DNA Alignment __________________________________________________________________________________ 2 6 2.12 Identification of Putative Adh and nchS Loci ................................... 2 7 2.13 Outgroup Selection and Rooting ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2 7 2.14 Phylogenetic Analyses ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2 8 2.1 5 Phylogenetic Interpretation ................................................................. 3 1 CHAPTER 3—Resnlts 3.1 Identification of Putative Loci ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 33 3.2 Adht] ___________________________________________________________________________________________________ 38 3.3 .4th and Adht3 ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 4 2 3.4 .4th ___________________________________________________________________________________________________ 44 3.5 Adht3 ___________________________________________________________________________________________________ 4 9 3.6 Combined and Reduced Arflttl and AdhtZ __________________________________________ 51 3.7 nchS ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 53 CHAPTER 3—Discussion and Conclusions 4.1 General Overview of Results ______________________________________________________________ 55 4.2 Gene Trees and Species Trees ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 56 4.3 Gene Trees as Tools for Macroevolutionary Inference ,,,,,,,,,,,,,,,,,,,,,,, 57 vi CHAPTER 3-Discussion and Conclusions continued 4.4 Peripatric Speciation ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 58 4.5 Neoendemic and Paleoendemic Species ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 59 4.6 Lineage Sorting and Noncoalescence ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 61 4.7 Species Protection and Conservation __________________________________________________ 62 4.8 Prospects for Future Studies of Monarda Section Cheilyctis ,,,,,,,,,,,,, 64 4.9 Conclusions _________________________________________________________________________________________ 66 APPENDICES Aflil Sequence Alignment ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 6 8 Ath Sequence Alignment ____________________________________________ 81 Monarda Field Collection Data ______________________________________________________________________ 9 5 LITERATURE CITED 98 LIST OF TABLES CHAPTER l-Introduction Table 1. Species in the Genus Monarda .................................................. CHAPTER 2-Materials and Methods Table 2. Table 3. Table 4. Table 5. Table 6. Table 7. Table 8. Table 9. Taxonomic Ranks of Narrow Endemic Monarda ooooooooooooooooooo Morphology & Phenology of Monarda Section C heilyctism DNA collection for Adh DNA collection numbers for nchS ......................................... List of PCR Primers PCR Thermocycler Programs ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, . Maximum Likelihood Models ooooooooooooooooooooooooooooooooooooooooooooooooooo Phylogenetic Analyses Completed .......................................... . viii 5 17 18 22 23 29 30 LIST OF FIGURES CHAPTER l-Introduction Figure 1. Figure 2. Phylogenetic Model of Peripatric Speciation .......................... Geographic Distribution of Endemic Monarda ...................... CHAPTER 2-Materials and Methods Figure 3. Collection Locations for Endemic Monarda ,,,,,,,,,,,,,,,,,,,,,,,,,, Figure 4. Collection Locations for Monarda punctata ,,,,,,,,,,,,,,,,,,,,,,,,,,,, Figure 5. EcoRI Restriction Digest Patterns of Adh Homologs ,,,,,,,,,,,,, Figure 6. Base Frequencies in Adhl dataset ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Figure 7. Base Frequencies in Adh2 dataset ............................................. CHAPTER 3-Results Figure 8. Unrooted Phylogram of 99 Adh Ingroup Sequences .............. Figure 9. Unrooted Phylogram of Ingroup and Outgroup Sequences___ Figure 10. Strict Consensus of Ingroup and Outgroup Sequences ___________ Figure 11. Rooted Parsimony Tree of Adhl ............................................... Figure 12. Rooted Likelihood Tree of A0721 ............................................... Figure 13. Strict Consensus Tree of Adhl ................................................. Figure 14. Strict Consensus Tree of Ath and Ari/73 ................................. Figure 15. Rooted Parsimony Tree of Ath ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Figure 16. Rooted Likelihood Tree of Ath ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Figure 17. Strict Consensus Tree of Ath .................................................. Figure 18. Rooted Parsimony Tree of A dh3 ............................................... ix 3 7 18 19 31 32 35 39 40 41 43 47 48 50 CHAPTER 3—Results continued Figure 19. Combined and Reduced Adhl and Ari/22 Trees 52 Figure 20. Rooted Parsimony Tree of nchS ............................................. 54 INTRODUCTION 1.1 Project Summary Many historical events, geographic and genetic, have been used to explain potential modes of speciation. Allopatric and peripatric modes use geographic isolation of populations to explain species divergence. Under these modes of speciation, geographic isolation is expected to modify the genetic constitution of divided populations eventually resulting in their morphological, ecological and genetic separation. Phylogenetic studies of closely related species can be combined with geographic patterns of distribution to infer mode of speciation (Harrison 1991). This study utilizes a small cohesive group of North American mints (Lamiaceae) in the genus Monarda to test peripatric speciation using phylogenies generated from Adh loci. These taxa appear well suited for this purpose because the pattern of distribution found among its members conesponded to those expected for peripatric speciation. 1.2 Peripatric Speciation Speciation by peripheral isolation was first proposed by Mayr in 1942. Mayr believed that most species diverged in allopatry but that geographic isolation of small peripheral populations had the greatest potential for rapid speciation. He maintained that marginalized populations would be subjected to a higher degree of reduced geneflow and habitat dissimilarity resulting in founder effects (genetic drift in small populations), increased selection pressures and thus rapid speciation and morphological change (Mayr 1942, 1 976, 1982). Founder populations are expected to have only a fraction of the genetic composition found in parental populations (Mayr 1982). This genetic imbalance, when coupled with a change in the abiotic environment, has the potential to lead to heightened selection and ecological adaptation. This differs from the classic model of allopatric speciation where larger allopatric populations are expected to require longer periods of time to diverge phenotypically and genotypically due to larger more variable gene pools and more homogeneous habitats Harrison (1991) predicted that ancestral population structure between sister taxa could be discerned using patterns of geographic dispersion and molecular phylogenic data. He proposed a series of repeatable, testable patterns (geographic and phylogenetic) to model allopatric, peripatric and sympatric speciation. In the model of divergence of peripheral populations (peripatric speciation), he maintained that peripheral isolates would exist along the distribution margins of a more widespread sister taxon while appearing phylogenetically derived within a gene tree. Narrowly endemic Monarda are located along the geographic periphery of their widespread congener, M. punctata. This distribution pattern suggests that they may have speciated as peripheral isolates from M. punctata. Likewise, ITS and chNA provided little phylogenetic signal for these taxa which suggests they diversified recently (Prather et a1 2002, Monfils and Prather unpubl. data). Harrison’s phylogenetic model for peripheral isolation was used to test this hypothesis. In concordance with this model M. punctata was expected to appear in a more basal position of the phylogeny and paraphyletic to the endemic species. This pattern would indicate that M. punctata is an ‘ “1 NEH... ancestral species. For instance, in the hypothetical phylogenies below (Fig 1), M. pwrctatahasamorebasalpositioninflretree,andisparaphyletictoMfiuticulosaand M. virrHrZssima. Furthermore, M. fi'un'culosa and M. viridrlrsima are more closely related to geographically proximate M. punctata samples in the phylogeny. Figure 1: Geographic and hypothetical phylogenetic distributions given four samples of the widespread taxon M puncrara and two samples representing M viridissima and M fi'utr'culosa. 1.3. Neoendemism versus Paleoendemism Stebbins (1942 & 1942) defined two types of endemic species, paleoendemics and neoendemics. Paleoendemics were described as relict species whose once large distributions have been reduced to small disjunct populations that occur across a wide area (Mayer & Soltis 1994, Qian 2001). Due to their once widespread distribution, paleoendemics are expected to have highly heterozygous populations despite their small size (Macnair & Gardner 1993). In contrast, neoendemics are newer species that are expected to occur across very narrow range limits and are expected to have highly homozygous populations. The, criteria used to distinguish paleoendemics from neoendemics include geographic distribution, genetic variation and placement in the phylogeny. The majority of North America’s neoendemics are restricted to the southwest. This region is both a center for neoendemics in North America and the world (Qian, 2001). Narrow endemic Monarda taxa in Section Cheilyctr's are hypothesized to have speciated as peripheral isolates, therefore they are believed to be neoendemic species. Phylogentic patterns that would support their neoendemic status would be consistent with those mentioned for speciation by peripheral isolation. Neoendemics are expected to be derived within M. punctata and paleoendemics are expected to exist on more basal branches separate to M. punctata. 1.4 Overview of Tan The genus Monarda contains 19 species that are split into two subgenera, one of which is divided into two sections (Table 1). Section Cher'lyctis has five are narrow endemic species. Monardafiwiculosa, M. maritima, M stanfieldii and M viridissima are endemic to Texas, and M. humilrls', is endemic to New Mexico. Table 1: Species in Monarda (Turner, 1994, Prather et al.2002 and Prather and Keith 2003) with scientific and common names. Varieties and subspecies of Monarda punctata are included. Common names adapted from the National Plants Database. Species Common Names SUBGENUS CHEIL YCTIS SECTION ARISTA TAE M. citriodora Cerv. ex Lag Lemon Beebalm M. clincpodioides A. Gray Basil Beebalm M pectinata Nutt. Pony Beebalm SECTION CHEIL YCHS M. fruticulosa Epling Shrubby Beebalm M. humilis Prather & Keith Spreading Beebalm M. maritima (Cory) B.L. Turner Seaside Beebalm M. punctata L. Spotted Beebalm/Horsemint - var. arkansana (McClintock & Epling) Shinners Arkansas Spotted Beebalm - var. correllr’i B.L. Turner Correll’s Spotted Beebalm - var. coryi (McClintock & Epling) Cory Cory’s Spotted Beebalm - var. intermedia (McClintock & Epling) Waterfall Intermediate Spotted Beebalm - var. Iasiodonta Gray Spotted Beebalm - var. occidentalis (Epling) Palmer and Steyermar'k Western Spotted Beebalm - var. villicaulr’s (Pennell) Shinners Villous Spotted Beebalm - subw. punctata Epling Spotted Beebalm M. stanfieldii Small Stanfield’s Beebalm M viridissima Correll Green Beebalm SUBGENUS MONARDA M. didyma L. Scarlet Beebalm M brarburiana Beck Eastern Beebalm M clinopodia L. White Beebalm M. eplingiana Stand]. Epling’s Beebalm M. fistulosa L. Wild Beebalm or Bergamot M. lindher'meri Engelm. & A. Gray Lindheirner’s Beebalm M. media Willd. Purple Beebalm! Bergamot M. pringlei Femald Pringle’s Beebalm M russeliana Nutt. ex. Sims Redpurple Beebalm M flimlandrdosa Waterf. Wild Beebalm In contrast, M. punctata is widely distributed across the central and eastern United States, southeast Canada, and northeast Mexico (Fig.2). These species also appear to have distinct edaphic constraints in their distribution. No formal field studies have addressed interspecific hybridization between these species, but some field observations have been made. Monarda maritima is sympatric with M puncata (Turner 1994, Prather pers comm, Keith pers. obs), Turner indicated that it was found growing with other Monarda (unnamed taxa) and that no hybridization appeared to occur between them. Monarda virrkiissima is also sympatric with M. punctata populations (Turner 1994, Prather pers comm, Keith pets. Obs.). Turner found no evidence that these two taxa overlapped in distribution but Prather and Keith observed sympatric populations of M viridr’ssima and M punctata in Bastrop County Texas, although there was no evidence that they bloomed at the same time. Monardafi-utr’culosa and M. prmctata also grow together (Turner 1994, Prather pers comm., Keith pers. obs). However, Turner did not find evidence that populations were confluent while Prather and Keith found evidence of hybrid zones between them. Finally, M stanfieldii has not been found to intergrade with M punctata (Turner 1994, Prather pers comm., Keith pers. obs.). Turner indicated that M stanfieldr’i and M punctata do not intergrade, and Keith (pers. obs) found no evidence that M stanfieldir' populations in Blanca, Bumet and Llano counties were sympatric with M punctata. Lack of hybridization between these species suggests that they maintain unique gene-pools and helps substantiate their species designation. Figure 2: County distributions of Texas endemics, Monarda viridissima (v), M firdr'adosa (f), M marinara (m), M stanfleldii (s), and the New Mexico endemic, M Inmilis (h). (based on Turner (1994), Johnston and Correll (1979) and herbarium material from the University of New Mexico and New Mexico State University) 1.5 Objectives The purpose of this study was to test speciation by peripheral isolation and to determine the neo- and paleoendemic status of the six species in Monarda Section Cheib’ctrlr. It was hypothesized that the widespread taxon, M punctata, is the progenitor from which all narrow endemic species have derived. Narrow endemic Monarda taxa were also predicted to be neoendemic species. Geographic distributions and phylogenetic data were used to test this. The low copy nuclear gene, Adh, was used as the genetic marker for phylogenetic analyses. Maximum parsimony, maximum likelihood and Bayesian methods of inference were used to generate phylogenic trees. MATERIALS AND METHODS 2.1 Study System i. Taxonomic Classification of Monarda Section Cheilyctis. Three of the endemics have undergone conflicting taxonomic classifications (M fi-utr'culosa, M maritima and M stanfieldii). The taxonomic ranks of these species have been addressed in treatments by six primary authors (Table 2). Epling (1935), Epling and McClintock (1942) and Turner (1994) recognized M fi-uticulosa as a species due to its distinct morphology and apparent lack of hybridization with M punctata. Score (1967) reduced its rank to a variety because he believed that did intergrade with M punctata var. immaculata (a variety not recognized in this study). Similarly, both Cory (1936) and Scora (1967) classified M maritima as a variety of M punctata because they believed it shared characteristics with M fiwticulosa. In contrast, both Turner (1994) and Correll (1968) treated it as a species due to its distinct morphology, habitat and distribution. Monarda humilis was first described as a variety of M punctata (Torrey 1853) but was recently recognized as a species by Prather and Keith (2003). This taxon was elevated to specific status due to its distinct floral morphology and geographic distribution. Monarda stanfieldir‘ was first described by Small (1903) and was later accepted as a species by Turner ( 1994). Epling (1935) reduced it to a subspecies, and Cory (1936) and Scora (1967) treated it as a variety of M punctata. Jammie Monarda viridissima was described as a species by Correll (1968) because of its unique morphological characters and temporal reproductive isolation from M punctata. Correll observed little evidence of hybridization with M punctata in the field. Turner (1994) and Correll and Johnston (1979) maintained M viridissima at the species rank. Turner’s recent treatment of these Monarda was used for this study. He recognized the Texas endemics as species due to their distinct morphology, geographic distribution and apparent lack of gene introgression with M punctata. He did not include the New Mexican taxon (M humility) in his treatment. ii. Morphology and Life History Traits Several life history traits and morphological characters have been fundamental in distinguishing these species. Key differences between them include life cycle and phenology as well as floral and vegetative traits (Table 3). 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T . 3 Nucleotides Bases Fig 6: Histogram of the base frequencies (Average frequency/ 100) in the Arflrl dataset. These results are based on 1096 base sites. 31 Adh2 and Adh3 Base Frequencies Among Sites (1 120 sites) oouflouenbeig escrow Nucleotide Bases Fig 7: Histogram ofthe base frequencies (Average frequency/100) intheArflrZ andArflr3 datasets. These resultsarebasedon 1120 base sites. 32 as}; dawn h? RESULTS 3.1 Identification of Putative Loci Ninety-nine Adh sequences, approximately 1,200 basepairs in length were obtained fi'orn the six ingroup Monarda species. Two separate phylogenetic analyses were used to delineate potential loci. The fast phylogeny was generated by maximum parsimony and contained all 99 ingroup Monarda sequences. One hundred equally parsimonious trees were generated for this dataset, tree length was 1663, the consistency index (CI) was 0.518 and the retention index (R1) was 0.870. In an unrooted phylogram (Fig. 8), Acflrl and .4th were divided by 70 base changes and .4th and Add were divided by 20 base changes. This phylogeny was used to determine how and where ingroup sequences parsed, and allowed for better ingroup sequence selection for the second analysis. The second analysis contained 23 potential outgroup sequences (seven species) and nine ingroup sequences (five species) representing Ath , Adh2 and Adh3. The ingroup sequences were selected from several points across the each putative locus. Data were analyzed by maximum parsimony and two equally parsimonious trees were created with a length of 797, a CI of 0.649 and a R1 of 0.806. In an unrooted phylogram (Fig. 9), Acflrl and .4th were separated by 43 base changes and Adh2 and Adh3 were separated by 12 changes. A strict consensus tree was generated from the two most parsimonious trees (Fig. 10), and compared to the unrooted phylogram. Branch length disparity between the full Adh tree and outgroup tree was attributed to the increased sample number in the full Aflr tree and the inclusion of outgroup samples. Pycnanthemum samples appear to have a 33 fourth putative locus adjacent to Ath that is not found in Monarda, and no Pycnanthemum samples appear to branch within AflrZ. The Ath dataset was rooted with two M clinopodioides samples and P. muticum, P. Ioomisii and P. tenuifolium samples. The Adh2/Adh3 dataset was rooted with P. -muticum, P. Ioomisii, three M citriodora samples, and three P. tenuifolium samples. The ArflrZ dataset was rooted with two M citriodora and P. tenuifolium samples. 34 Locus MM ,1 70 20 \— Locus Adh3 Locus Adh2 — 5 changes Figure 8: An unrooted phylogram of ninety-nine Adh sequences representing all ingroup Monarda samples. The three putative loci, Adhl, Adh2 and Aflr3, are labeled. Seventy steps separate Acflrl and Adh2 and 20 steps separate Adh2 and Ad713. Several sequences branch between Adhl and Add but were found to fall in the Acfl12 dataset when .4th and Adh3 were separated and outgroup sequences were incorporated. 35 Locus Adh1 M. stanfleldli TX 2367 P. loomlall 66- P. tenulfollum 86-4 P. Ioomisli 66- P. mufleum 52-4 P. Muflollom 85-4 P. tenulfollum 97-3 M. viridissima TX 2 . ' M. punctata NJ 2189 12 M. punctataLA2305 M. frutlculosa 1920 M. eltrlodora 2419 I. cm 2375 M. citriodora 2375 Locus Adh2 —-—-10diaiges M. 11111in TX1920 M. citrlodora 2419 M. punctataNJ 2189 M. pmctata M0 2172 I. ellnopodloldea 2310 M. ellnopodloldea 2310 P. tenuifolium 55-4 P. tenuiican 975 P. mullcum 52-3 P. curvlpes 444 P. curvipes 446 P. virginianum M13 P. mutlcum 52-2 P. Ioornlall 66-1 P. vuginiaum Ml11 P. virg'nianum M17 P. tenultollum 80-8 M. punCtata SC 2401 Locus Adh3 Figure 9: Phylogeny of 23 outgroup sequences and nine ingroup sequences representing all three putative loci identified (Add, AflrZ and Acflr3). The branch dividing Acflil and AcflrZ has 43 changes and the branch dividing Act/12 and Adh3 has 12 changes. Taxon labels include species and DNA numbers. Samples in bold were chosen as outgroups for later analyses. 36 Strict Adh1 M. fruticulosa TX 1920 P—-—— M. punctala MO 2172 M. stanfieldii TX 2367 M.cllnopodloldea 2310 ——M.cllnopodloldea 2310 M. d’nopodioides 2310 P. Ioomlall 00-3 P. mutlcum 02-4 ___: P.100misiiSS-2 P. tenultollum 004 P. swipes 444 r—-__‘[: R W 44.3 P. muticum 52-3 _: P. muticum 52-3 P. viginianum Ml3 r— P. tenuifolium 554 I—— P. tenuitolium 97-5 Adh2 P. mutlcum 02-2 r— P. tenulfollum 004 P. Muflollllm 97-3 ____: M.dm2375 meltdown-2419 ___E: .- cltrlodora 24". I. citrlodm 2375 M. viridissima TX 2444 M. punctata NJ 2189 L—— MpuncldaLA2305 M. fruticulosaTX1920 Adh3 F——‘ M. pimctata SC 2401 M. punclala NJ 2189 P. tenulfollum 00-0 P. loomlall 00-1 P. virginianum 55-4 P. virghiamm 97a Figure 10: Strict consensus tree of 2 equally parsimonious trees representing 23 potential outgroup sequences and nine ingroup sequences from all three loci identified (Adhl , Adh2 and Adh3). The Pycnanthemum clade between Adhl and Adh2 represents a fourth putative locus that is unique to Pycnanthemum. Sequences that are in bold were chosen as outgroups. Taxon labels include species and DNA numbers. 37 3.2 Adhl The Adhl dataset had 35 ingroup sequences of all six species collected from 24 populations. Data were analyzed by maximum parsimony, parsimony bootstrap, maximum likelihood, the S-H test and Bayesian analyses. Thirty-seven most- parsirnonious trees were generated and each had a length of 480, a (C1) of 0.503 and a (RI) of 0.746. All uninformative characters were removed from the datasets before CI values were obtained. The S-H test was run on all 37 most parsimonious trees and one maximum likelihood tree (TrNef+G). The best maximum parsimony tree identified (Fig 11) had several topological differences relative to the TrNef+G tree (Fig. 12) including the placement of M stanfieldii, M maritima and M fi'uticulosa (2301 and 2317) samples. The parsimony strict consensus tree (Fig. 13) and Bayesian consensus tree shared the same topology, and bootstrap values and Bayesian node confidence values were applied to this phylogeny. The strict consensus tree had one major M punctata clade with M fiuticulosa, M humilis, M maritima and M viridissima sequences derived within it (Fig 13). The M punctata clade had a high Bayesian confidence value of 99 (NC99), but had bootstrap support less than 50 (BS-). Most of the M punctata samples were together in two smaller clades: One contained nine M punctata samples (2303, 2397, 2398, 2305, 2048, 2172, 2307 and 2396) and had strong support (BS81/N C100), while the second had four samples (193 7, 2048, and 2189) and higher support (99BS/100NC). Monardafi'uticulosa (2301 and 2317) and M maritima (2314, 2318 and 2319) samples shared two moderately well-supported clades (-BS/99NC and 59BS/100NC) within the larger M punctata clade. 38 I. punctah PI. 2303 in. punctm no 2172 4 “ in. puma n. 2301 n. punctat- PL 2303 . 4 ii: In. punctnta our asee Length. 480 16 re. w I I LA 2305 CI: 0.503 7 - 5 Iii. pence-ta m aces RI: 0.743 I 9 I II. punctata rm 2301 6 1 I. punetata TX 2300 5 MfruticulosaTX1920 2 MfiuticulosaTX1920 4 2 M. maritime TX 2314 3 M. maritime TX 2319 1° M. maritime TX 2318 M. fiuticulosa TX 2301 M.fiuticuosaTX2317 I. punetata AR 2000 M.maritimaTx 2318 M.viiidissimaTX2441 1” M. staifielleX2239 fl 1° M. stanfleldiiTX2369 1‘ Msmaeiduszzas I. prince-ta NJ 2100 3 I. pence-ta NJ 2100 I. punche- D! 1037 I. prince-ta m 2000 fl 10 M. viridiss'rna TX 2055 a. 5 l M. viridissima TX 2444 4 I. pallet-ta NI 2301 .9. 2| E a. par-cm em 2301 a 1‘ M. humilis NM 2176 ‘° M. viridissima TX 2441 21 3° n. punctata n: ma .7 1 M. stanfieldfi TX 2367 7 M. stmfieldil TX 2367 ,1 M. clincpodloidesTX2310 L—‘ M. clinopodioides TX 2310 19 r—g— P. lOOMSll ‘1 P. whom i P. tenuifolium —— Schemes Figure 11: The Adhl parsimony phylogram selected by the S-H test. Branches are labeled with steps. Taxon labels include species, state of origin and DNA number. The larger M punctata clade is labeled by the bar along the right margin. Tree length, CI and RI values are shown. 39 “Mon-Ma punchtaPL2303 HL—— Ionardapunctata I0 2172 I——-—M4marrla punctata PL 2307 Ji—‘E: Ion-m pence-ta Fl. 2303 . ummmmm L—-————Ionar0a pom-2300 ”—1 -—-- Menard- punctata Ill 2040 ‘ Ila-adaption”!!! 2301 Inca-mum [:— M. fl'uticulosa TX 1920 r M. frub'culosa TX 1920 __|———— M. fiuticulosa TX 2111 MmaritimaTX2318 —-—-— anilculosaTX2317 M. maitima TX 2318 — Monarch metat- 20001 __{-— M. maritime TX 2314 M. maitima TX 2319 m punctata 1031 Monarch parrot-ta 2100 _: We punctu- 2301 Menard. punctata 2307 ———-————— M. humilisNM21763 r M.viridissimaTX2444 J M. staifieldilTX2367 'M.siarneidiirx2367 WWW r—‘i MetanfleldliTX2239 MWITX2309 M.stanfleldiTX22$ __{ M.viritissimaTX2441 M.v'ridissimaTX2441 J M. clinopodbides 2310 L— M. clinopodioides 2310 r—~—-—— P. ioomisi 66-3 L- P. muticum 524 P. ionuiioium 86-4 —— 0.005 subsuuiionsisiia Figure 12: The Acflil likelihood phylogram using the TrNef+G model of substitution. Branches are labeled with values denoting substitutions per site. Taxon labels include species, state of origin and DNA number. 40 1001100 70/100 -/87 ‘ 74/1 00 MCI. pallet-t- PI. 2303 M. planet-ta OK 2300 M. poi-cm PI. 2397 ll. punchh no 2172 u. puma La 2305 L———— re. punctlta PI. 2303 499 name-mama r" re. pence-a NM 2307 1— M. punctu- TX 2300 ,— M. tiuflculosaTX 1920 L— M. fruticulosa TX 1920 97190 M. man'tima TX 2314 M. maritime TX 2319 M. maritima TX 2318 M. fluticulosa TX 2317 M. fruticulosa TX 2301 553/100 M. punctata an aoeo M. maitima TX 2318 70/100 100/100 M. viridissima TX 2441 M. stanfieldii TX 2239 l—I: M. stanfieldii TX 2369 M. stanfieldii TX 2239 u. punctata or: 1937 unmet-ta MI2040 npunceata M2100 99/100 I. panchr- NJ 2100 M. viridlssima TX 2055 M. viridissima TX 2444 I. puncture NI 2307 ifiCEu. puma m: 2307 M. humilis NM 2176 M. viiidisslma TX 2441 111N100 u. punchtl rx use ,— M. swoon 1x 236? l—M. stanfieidii TX 2367 J—M. clinopodioides 2310 l—M. clinopodioides 2310 J— P. Ioomlsi 66-3 L— P. muticum 52-4 P. tenuifolium 86-4 Figure 13: Strict consensus of 37 maximum parsimony trees from the full Adhl dataset. Taxon labels include species, state of origin and DNA number. Branches are labeled with bootstrap (left) and Bayesian node confidence values (right); only values above 50 are shown and values below 50 are labeled with dashes. The larger M punctata clade is labeled by the bar along the right margin. 41 This was the only narrow endemic species that was not within the M punctata clade. Two M stanfieldii clones (2367) appeared on the most basal branch sister to the M punctata clade and two additional M stanfieldii samples (2239 and 2369) were derived within the larger M punctata clade but with no support. Monarda viridissima was more widely dispersed in the phylogeny. Two samples (2055 and 2444) branched together with M punctata and two clones of the third sample (244]) were not supported in the larger M punctata clade. The single M humilis sample (2176) had good support (-BS/95 NC) being in a clade with two M punctata from New Mexico (2307). 3.3 .4th and Adh3 These data were analyzed by maximum parsimony, parsimony bootstrap and Bayesian analyses. The Adh2 and Adh3 dataset included 38 sequences and generated 6 most parsimonious trees with a length of 571 steps, a CI of 0.434 and R1 of 0.743. The parsimony and Bayesian consensus trees were identical and both parsimony bootstrap values and Bayesian node confidence values were applied to this tree (Fig. 14). Many sequences were replicated in both Adh2 and Adh3 trees. Outgroup sample, M citriodora had two sequences at the base of each putative locus (Fig. 14). The branch that delineated Adh2 and Adh3 had a high Bayesian node confidence value of 100 but no bootstrap support. Nearly all the samples in Adh3 were of geographically separate M punctata except for two M stanfieldii sequences (2369) in the clade with M citriodora (2419). Clades in Adh3 had several high Bayesian node confidence values but little to no bootstrap support. 42 Length: 786 CI: 0.0.434 RI: 0.743 56/100 100/100 84/100 73/92 86/100 —-1: H. punctata NJ 2100 M. punctata NJ 2100 -/87 61/91 458 -/100 100/100 JZMLC: M. punctata M1 2040 M. punctata TX 2300 M. punctata TX 2473 {—— N. 9006800. LA 2305 L—— M. punctata r1. ass-r M. humilis NM 2176 M. viridlsslma TX 2444 71/89 92/100 MfruticulosaTX2317 MfiuliculosaTX2301 1’11: 57/99 fl. pence-ta TX 2303 M. fiuticulosa 2420 100/100 M. pence-ta PI. 2300 l"— M. fl'UllCUkBa TX 1920 60/ 100 100/100 L— M.fiuticulosaTX1920 69/75 M. vindlsslma TX 2055 100/100 M. punctata MI 2040 M. punctata OK 2300 ——-—— M. maitima 2181 M. maritime 2181 ~— flpunctataflm 1001—1“): M. 310111301011 TX 2387 62/99 499.3 -/100 —/99.2 84/100 -/99.9 —i: M. cluiodora TX2419 M. citiiodora TX2375 M. puncture NJ 1040 ll. punches NJ 2100 M. 813111011111 TX 2367 100/1 4100 I. punctuta NJ 2109 I. punctata TX 2400 81/100 M. punctata TX 2307 r——-- M. punch“ TX 2303 51/999 L— 111. punctata so 2401 r—— ra. punctata TX 2300 L—-—- M. punctata rr. asae 4100 M. atmfieldii TX 2369 iS-S—LT. M summon TX 2369 ,-—— P. Ioomisii 66-1 M. cltriodora TX 2419 L— P. ionuiioium 86-8 P. muticum- 52-2 1“"" P. tenuitolium 55-4 L—— P.1onuiioium 97-3 Locus Adh2 Locus Adh3 Figure 14: Strict consensus of 6 maximum parsimony trees from the full .4er and Adh3 dataset. Taxon labels include species, state of origin and DNA number. Branches are labeled with bootstrap (left) and Bayesian node confidence values (right) and only values above 50 are shown. The Acflrl and Adh3 loci are labeled by the bar along the right margin. Tree length, CI and RI values are shown. 43 3.4 Adh2 As with Adhl, these data were analyzed by maximum parsimony, parsimony bootstrap, maximum likelihood, the S-H test and Bayesian analyses. The Adh2 dataset contained only 24 ingroup samples. This was due in part to the presence of Adh3 and difficulties in obtaining M maritima and M viridissima sequences for this locus. Many of the sequences that were selected for the Adh2 dataset fell within Adh3 because both duplicateS had the same restriction digest pattern and it was impossible to differentiate between them prior to sequencing. Likewise, I had much difficulty in obtaining Adh2 sequences from M maritima and M viridissima. Parsimony analysis of Adh2 data generated six trees with 446 steps, CI value of (0.588) and RI value (0.830) than the Adh2 and Adh3 combined tree. The topology of the best tree (Fig. 15) was identical to an additional tree generated by likelihood (Trn+I+G, Fig. 16) with the exception to its placement of M stanfieldii sequences relative to M citriodora. The parsimony strict consensus tree and the Bayesian tree shared the same tapology, and parsimony bootstrap values and Bayesian node confidence values were applied to its branches/nodes. This tree also contained one major clade of M punctata that had M fi-uticulosa, M humilis, M maritima and M viridissima sequences nested within it (Fig. 14), but the clade had poor Bayesian and bootstrap support (55BS/64NC). Like the Adhl tree, two clones of M stanfieldii (2367) were on a basal branch adjacent to the outgroup and were not derived within M punctata. 44 Most of the M punctata samples were together on one supported branch (74BS/89NC) that contained seven M punctata samples (2189, 2048, 2305, 2397, 2396 and 2473) with one M humilis (2176) and one M viridissima (2444) sample nested within. All three M fi'uticulosa samples were on one well-supported branch (68BS/93NC) with two M punctata samples. 45 M. punctata NJ 2100 4 M. punctata NJ 21139 M. planet-ta MI 2040 M. punctata LA 2300 M. punctata PI. 2307 9 7 5 M. punctata rx 2300 __‘[-7—— M. punctata TX 2473 M. humilis NM 2176 M. viridissima TX 2444 Length: 446 CI: 0.588 RI: 0.830 19 25 M. fruticulosa TX 2317 M. truticulosa TX 2301 M. punctata TX 2393 M. truticulosa TX 2420 19 M. punctata PI. 2300 ; I 12 [ M. truticulosa TX 1920 M. fruticulosa TX 1920 1 ‘ M. viridissima TX 2055 23 £111. punctata m 2048 1., '1 M. punctata OK 2300 16 M. maritima TX 2181 3 M. man'tlma TX 2181 ‘3 u. punctata an 2on 11 M. stanfieldii TX 2367 1i- M. stantieldii TX 2367 [no 31 9 . . 33 {—— M. citriodora TX 2419 L—L— M. citriodora TX 2375 J— P. tenuitoiium 554 I P. tenuitoiium 97-3 — 5 changes Figure 15: A phylogram of the full Acflrz tree. Taxon labels include species, state of origin, DNA number. Branches are labeled with base change values. The larger M punctata clade is labeled with a bar along the right margin. 46 r-- M. punctata NJ 2100 l“ u. punctata NJ ares ——-——— M. punctata M1 2040 ~—-——— M. punctata TX 2300 r“ —~—-—— M. pence-ta TX 2413 M. punctat- L0 2300 M. punctata PL 2307 M. humilis NM 2176 M. viridissima TX 2444 r———-—-—- M. fruticulosa TX 2317 M. tmticulosa TX 2301 M. punctata TX 2303 M. huticulosa TX 2420 M. punctata PL 2300 ___q M. fruticulosa TX 1920 —__[ M. fruticulosa 1x1920 M. viridlsslma TX 2055 M. punctata MI 2040 M. punctata OK 2300 r——— M. maritime TX 2181 M. maritima TX 2181 M. punch-ta All 2000 J—_ M. stanfieldii TX 2367 L— M. stanfieldii TX 2367 .___ M. citn'odora 2419 M. cttriodora 2375 ~-—-1 P. muticum 52-2 P. tenuifolium 55-4 ‘— P. tenuifotium 97-3 —--— 0.005 substitutions/site Figure 16: The A4012 likelihood phylogram using the Tm+I+G model of substitution. Branches are labeled with values denoting substitutions per site. Taxon labels include species, state of origin and DNA number. 47 M. punctata NJ 2100 ”’95 M. patient. NJ 2100 56/79 M. pmctata in 204s M. Metat- LA 2305 M. punctat- PI. 2307 100/100 95/100 r—— M. ptlim TX 2300 L—— M. punctat- TX 2473 I M. humilis NM 2176 M. viridissima TX 2444 M. fruticulosa TX 2317 M. fruticulosa TX 2301 M. pmetata TX 2303 M. initiculosa TX 2420 M. pretence PI. 2300 l——- M. truticulosa TX 1920 M. huticulosa TX 1920 88,78 M. viridissimaTX2055 100/100 M. punctat- M12040 55/- 861100 M. Metat- ON 2300 51/. M. maritime TX 2318 100/1 M. maritima TX 2318 1001100 I. W All 2000 100/100 J— M. stanfietdii TX 2367 l——— M. staniieidii TX 2367 74/89 96°00 88/100 55/100 55’“ 0 1001100 1001100 r—— M. citrlodoraTX2419 1— M. citnodora TX 2375 P. tenuitotium 55-4 P. tenuifotium 97-3 Figure 17: Strict consensus of the six most parsimonius trees of Adh2 with 20 ingroup sequences. Taxon labels include species, state of origin, and DNA number. Branches are labeled with bootstrap (left) and Bayesian node confidence values (right) and only values above 50 are shown. The larger M punctata clade is labeled by the bar along the right margin. 48 3.5 Adh3 This dataset contained eight M punctata samples and two M stanfieldii samples and was analyzed by parsimony analysis only. One maximum parsimony tree was generated and it had a length of 358, a CI of 0.676 and a R] of 0.408. Monarda stanfieldii samples were at the base of the tree with a M citriodora outgroup sequence. Monarda punctata samples were in two clades. One had M punctata samples only and the second included the M stanfieldii and M citriodora samples. 49 ~——-11-—~-— M. punctata 14.1 2139 9 7 -——— 12 M. punctat- NJ 2100 a 23 M. panama NJ 21119 11 22 M. punctata TX use 26 M. punctata TX 23111 ‘5 M. punctata 'nt 2393 8 ——1°——— M. punctata cc 2401 6 2‘ M. punctata u use 9 15 2° M. prince-ta rt. 2333 ———-—1-2—-—— M. stantieidii 2369 12 , 41 M. stantieldii 2369 7 I 3‘ M. citriodora 2419 23 P. ioomisii 66-1 1‘ P. tenuitoiium 86-8 10 changes Figure 18: Adh3 parsimony tree with 11 ingroup sequences. Branches are labeled with steps. Taxon labels include species, state of origin and DNA number. The M punctata clades are labeled by the bar along the right margin. 50 3.6 Combined and Reduced Adhl and Adh2 As with full Adhl and Adh2 datasets, these data were analyzed by maximum parsimony, parsimony bootstrap and Bayesian analyses. Adhl and Adh2 datasets were reduced so they shared the same samples (Fig 19). Eighteen trees were generated in the maximum parsimony analysis of the reduced Adhl dataset (length: 200, CI: 0.585, RI: 0.771). The parsimony strict consensus tree and the Bayesian tree shared the same tree topology (Fig. 15). Two trees were generated in the maximum parsimony analysis of the reduced Adh2 dataset (length: 275, CI: 0.618, RI: 0.835) and the parsimony strict consensus tree and Bayesian tree were also topologically the same. Both trees placed M stanfieldii (2367) sequences at the most basal branch of the tree. Monarda punctata was in two primary clades in both trees. Endemic species (M fi-uticulosa, M humilis, M maritima and M viridilrsima) showed a higher degree of variability regarding their placement in the trees, although each phylogeny had a clade that consistently contained the majority of the M fruticulosa sequences included in the study. 51 .8398 88 on gene 83.3 bee can 93.5 828, 3:02.38 32. 5.83m 85 £05 88888 .83 3.28. on. 3.8.88. .898. 28. o... 888 an as 3 8.28. a are ssosa .8 does 2:. 888288 as... as as: 333. 8 one: 88 8828.8 .o .11 18 5.888 .n Lil 88 x8 889% .2 8:09 88.0. rl 88888888 .2 - 718889 828.88 .2 8:8. Flaaméioese .2 885.388 : fiaiidlom 85¢ sees: .2 8: 85¢ 888:. .2 8:: 353-3.! 8. 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Due to the limited number of taxa in this dataset, no further analyses were run on these trees. 53 15 Pycnanthemum 22 M. viridissima TX 1908 M. punctata TX 1907 __ ‘ M. viridissima TX 1989-1 M. fruticulosa TX 1910 [ M. punctata NJ 19461 M. punctata NJ 1946-2 M. fruticulosa TX 1920-1 “ENGI— M. fruliculosa TX 1920-2 24 M. maritima TX 1977-1 I M. viridissima TX 1989-2 M. viridissima TX 1989-3 E M. punctataTX 1909-1 M. truficulosa TX 1920-3 M. frufiwlosa TX 1920-4 M. punctata Ml 1905-2 — M. punctataTX1909—2 M. fruficulosa TX 1920-5 - M. vin'dissimaTX 1908 ---5Ch80995 Figure 20: Full nchS sequence data representing ten different taxa. Taxon labels include genus/species, M. maritime TX 1977-2 Pycnanthemum 20 state of origin and DNA number. Locus l and 2 are listed along the right margin. 54 “Char. DISCUSSION 4.1 General Overview of Results The objectives of this project were to use the species in Monarda Section Cheilyctis to test whether speciation by peripheral isolation had occurred among the species of the section, and to determine whether the endemic species were paleo- or neoendemics. Data showed a high degree of Adh allelic variability within and between Monarda species. However, the phylogenetic results provided by Adh loci offered insight in answering these questions. In each dataset all of the methods employed, maximum parsimony, maximum likelihood, and Bayesian analyses consistently produced trees with similar topologies. Consistency in their phylogenetic results increased the chances that the best trees were found for interpretation. The Adhl phylogeny had the most complete representation of samples. All the endemic species were represented in the Adh2 phylogeny samples. Both phylogenies were used for interpretation. The Adh3 phylogeny had only M. punctata and M. stanfieldii samples. It is unknown whether this putative Adh locus is a pseudogene or functional duplicate, but its distinction fiom Adh2 suggests that there was enough variation in this duplicate to enable it to be distinguished as a separate type. Phylogenetic data of nchS were not complete enough to be included in the analysis, although Monarda to have two loci for the chloroplast-expressed nchS gene as opposed a single locus, as documented in other plant systems (Emshwiller and Doyle 1999). 55 4.2 Gene Trees and Species Trees There are limits that are inherent to the use of low copy nuclear genes for phylogenetic analysis. Phylogenies are hypotheses that can be useful tools for the inference of species relationships but there are caveats to those based on DNA markers. It is important to recognize that gene trees, particularly those based on nuclear genes, may not clearly reflect the same relationships as a true species tree (Doyle 1992, Schaal and Olsen 2000). Coding and noncoding gene regions can accrue genetic variation fi'om point mutations, insertions/deletions and meiotic recombination that can disseminate or be disseminated within and among populations independent of speciation events. Genetic changes such as these can convolute gene trees when species have not undergone complete lineage sorting. Homoplasy can also be a source of incongruence between gene trees and species trees (Doyle 1992). Because of these problems, it is prudent to obtain molecular phylogenies from at least two different genetic markers. In this study only Aflr sequences were used for analysis. Nonetheless, Adh has been widely used in phylogenetic studies (Sang 2002) and has gene regions that are highly conserved between distant organisms therefore greater confidence may be placed in its results. Additional complications can arise when using low copy nuclear genes for phylogenetic inference depending on whether gene homology is paralogous or orthologous. Orthologous homologs precede speciation and are followed by divergence of an ancestral sequence (Gogarten and Olendzenski 1999, Sang 2002). Therefore, orthologous sequences can be used for phylogenetic reconstruction of species. Paralogous homologs result from either a duplication or deletion event after that occurs after speciation. 56 __......__ _ ‘ .. {.1121 P ~. v ‘ —~‘v.q.-V" Paralogous sequences have been found to confound phylogenetic results, although some studies have shown them to be phylogenetically useful for both rooting purposes and to test comparative rates of divergence (Sang 2002). Ath and Adh2 are believed to be orthologous because they duplicated prior to the divergence of monocotyledonous and dicotyledonous plants (Sang pers. corn). These orthologs may be synonymous to Arflrl and Adh2 loci identified in this study, but this cannot be confirmed because much information about these genes is lacking. This conjecture was drawn from the fact that AcflzI and Adh2 sequences were found in all six species while Adh3 sequences were only found in M. punctata and M. stanfieldii. There is no evidence to suggest that A¢fl23 is orthologous. 4.3 Gene Trees as Tools for Mecroevolutionary Inference It is important to draw a clear distinction between population level research and studies like this where species-level gene trees are used to infer population level processes. Coalescent theory has supplied much of the theoretical foundation for predicted gene tree topologies given different demographic histories of the populations they represent (Maddison 1995, Avise 2000). In the absence of gene flow, inter-specific gene trees can depict shared evolutionary histories and allelic variation that may coalesce to a common ancestral gene (Harrison 1991). Population structure and genetic structure are key in understanding how gene trees can be used to infer speciation events. If discontinuity in population structure reflects historic barriers to geneflow then one might expect comparable phylogenetic discontinuity in the genetic variation of neutral genetic markers. 57 1‘.--' :. 23min! ‘w-n “..‘..-)..nmu This provides the underlying theory used by Harrison (1991) for his gene tree models of speciation. 4.4 Peripatric Speciation The hypothesis that narrow endemic Monarda taxa speciated as peripheral isolates of M. punctata had phylogenetic support for some species but not all. In addition to being the most morphologically variable and geographically widespread, M. punctata was the most ubiquitous taxon throughout both Adhl and Adh2 phylogenies. All narrow endemic species were derived within the large M. punctata clade with the exception of M. stanfieldii. This suggests that M. punctata is the progenitor of M. fi-uticulosa, M. hwnilts, M. maritima and M. viridissima and a sister taxon to M. stanfieldii. The Adh3 phylogeny included few samples, but was consistent with the result that M. stanfieldii is the sister group to M. punctata It was unexpected that M. punctata samples did not tend to exist on longer branches closer to outgroup samples. Factors that might explain why most M punctata appeared on shallow terminal tree branches include recent divergence of species resulting in shared ancestral polymorphisms, inter-specific gene introgression (Schaal et al. 1998, Templeton et al. 1995) or inadequate samplinglf allopatric species are sexually compatible and their populations expand resulting in a sympatric or parapatric distribution genetic distinction between them can be blurred (Macnair and Gardener 1998). In addition, shared ancestral polymorphisms that are maintained in sister species may also convolute gene tree results and can be misinterpreted as evidence for recent gene flow (Schaal and Olsen 2000). Based on what is known about the current geography, morphology, and life cycles of 58 these species these results are likely due to either low sampling or shared ancestral polymorphisms. Species are either geographically or temporily separated and they maintain unique morphological characteristics. It is likely that they speciated recently and rapidly, and it would have been prudent to include more M. punctata samples from Texas populations. In the Adhl parsimony trees, M. fi-uticulosa and M. maritima sequences were consistently on the same clades. Similarly, in the Adh2 parsimony trees all M. fi-uticulosa sequences shared the same clade, although the only M. maritima sample in the phylogeny existed in a different clade. Based on their placement in the Adhl phylogeny results suggest that M. fiwiculosa and M. maritima share more allelic variation with each other than any of the other narrow endemic species. This might suggest that there has been recent gene flow between these species, or that they diverged recently from a common ancestor. However, the results do not rule out the possibility that some of the endemics are sister taxa that derived independently from M. punctata. 4.5 Neoendemic and Peleoendemic Species Adh phylogenies provided useful information that could be used to infer the paleo- and neoendemic status of these species. Most M. stanfieldii (2367, 2369) samples were not derived within the larger M. punctata clade and had long branch lengths. This short-lived herbaceous perennial is thought to be completely geographically isolated from M punctata and inhabits a unique substrate (granitic sands) relative to the other narrow endemic species. Overall, the phylogenies provided strong evidence that M. stanfieldii is a paleoendemic S9 w 3'. C (.4 In both .4th and Adh2 parsimony trees, one clade consisted almost entirely of M. maritima and M. fruticulosa sequences as well as M. punctata samples from southeastern Arkansas (2060), southeastern Texas (2393) and northcentral Florida (23 89) to name a few. The close phylogenetic relationship between M. fi-uticulosa and M. maritima is not surprising considering they share a woody habit, perennial life cycle and they are the most geographically proximate of the narrow endemics. These results suggest these species are neoendemics, but also may indicate they may share a common ancestor. Monarda viridissima sequences are found in different positions across both phylogenies which suggests they have a high degree of allelic variability. Regardless, most sample sequences were on branches that were close to M. punctata samples, which suggests they are closely related. Their close genetic relationships were most apparent in the Adhl tree where M. viridissima sequences (2055 and 2444) clustered with M. punctata sequences. Geographic and phylogenetic data support that M. viridissima is a neoendemic species. Monarda humilis was not well represented in either dataset but some inferences can be made regarding its placement in the phylogenies. This species is the most geographically disjunct relative to the other southwestern narrow endemics, and like M. viridrlssima it was found within the larger M. punctata clade. Even though this species was represented by only one sample its apparently close genetic relationship suggests that it is also a neoendemic that speciated from M. punctata. 4.6 Lineage Sorting and Noncoalescence Several samples in the phylogeny appear to have allelic variation at given locus. In the Adhl tree, two M punctata (2307 and 2048) and one M maritima (2318) had alleles that consistently fell within the two separate clades. Likewise, two M viridissima sequences (2055, 2444) were within one clade, while the two remaining samples (2441) were in two separate locations in the phylogeny. Allelic variation in a phylogenetic marker leads to incongruence between gene trees and species trees. Such allelic variation may be caused by several phenomena such as lineage sorting, noncoalescence and gene flow between species. Lineage sorting refers to the fixation of different ancestral alleles for a given marker into a daughter species at speciation (Small and Wendel 2000). In cases of lineage sorting fixed alleles should be present throughout the species. If samples of a species from multiple populations had the same patterns of allelic variation in a phylogeny it may provide evidence for lineage sorting. In addition, shared ancestral polymorphisms caused by lineage sorting should be divided by many steps in a phylogeny, while newer alleles that have arisen afier speciation should have fewer steps dividing them. Lineage sorting is a more common problem in species that have diverged recently (Sang 2002). Noncoalescence refers to the introgression of alleles that are maintained as ancestral polymorphisms in a multi-gene family (Small and Wendel 2000). The events that lead to lineage sorting and noncoalescence both involve the maintenance of ancient allelic 61 polymorphisms and can produce phylogenetic results that show widely disparate taxa closely related on a gene tree. Introgression and hybridization both involve the transfer of genes from one species to another (Small and Wendel 2000). Introgression results in the permanent fixation of genes between species while species still maintain phenotypic distinction. In contrast, hybridization results in phenotypic intermediates and progeny with novel gene combinations which can either lead to a merging of species or create a platform for speciation. It is not certain which phenomena are the cause of allelic variation in the Adh phylogenies. Phylogenetic data alone is not sufficient to distinguish between lineage sorting, noncoalescence and gene flow between species. Further research is needed to determine this. 4.7 Species Protection and Conservation The Endangered Species Act does not use biological terms alone to define species. Instead species are defined based on the most up to date knowledge of the genetics, evolution and speciation of a given taxon. There are several considerations that may warrant species protection for some of the Monarda taxa used in this study. Monarda maritima has the most limited distribution of the Texas endemics. It is only known to exist within the Ingleside Terrace sand body that extends approximately 100 62 miles along the Texas coast. The fact that it is a coastal endemic indicates that it has likely suffered much habitat loss due to ranching and development associated with the oil industry. This plant is challenging to find in the field and has not been extensively collected, which suggests that it is not common in its range. All evidence indicates that this species is a good candidate for conservation. Monarda viridissima is limited to the Carrizo sands of the Blackland Prairies that extend in a discrete belt from northeastern to southwestern Texas. Populations have been found in only the central region of this belt. Monarda viridissima is not common in its range, but I was able to find it in moderate sized populations (>25 individuals). It is also noted as being rare in a list of southern U. S. endemics (Estill and Cruzan, 2001). Field observations suggested that it inhabits more established plant communities rather than newly disturbed sites, which concurs with its tendency to grow in established post-oak and pine-oak forests. Like M maritima, it may be in need of protection due to its limited range and propensity to exist in more established plant communities. Monardafi-uticulosa is the most abundant of the Texas endemic Monarda species. It occurs across the southern tip of the state in the coastal prairies and interior coastal plains. Within its range it can commonly be found in large populations that are often distributed along roadsides. Therefore, M fi-uticulosa is the least likely to be in immediate need of conservation, despite its narrow endemic status. 63 Monarda stanfieldii has a narrow range across the Central Texas Uplift. Like M viridzlssima, it only appears to grow in more established plant communities, and tends to prefer open woodlands (pers. obs.). This species was also difficult to find in the field, although one of the populations had a relatively good size (>50). Monarda stanfieldii is also likely to be in need of protection particularly because of its apparent paleoendemic status. It exists in more in established plant communities, its range is very small and it grows in very specific soils. 4.8 Prospects for Future Studies of Monarda Section Cheilyctis Several changes in our experimental design might have helped to better resolve phylogenetic relationships between these species. An increase in sampling, particularly of Texas M punctata, might have added useful information. Five varieties of M punctata were not included in this study. A more complete sampling of these taxa may have provided a better understanding of the origins of the Texas endemics. Additional samples could also better resolve patterns due to incomplete lineage sorting and noncoalescence. It would also would have been advantageous to include data fiom an additional low copy nuclear gene. Molecular phylogenies from distinct genetic markers can be used to compare and hopefirlly strengthen phylogenetic hypotheses, thus providing more tools for distinguishing gene trees and species trees (Schaal and Olsen 2000) A population-level study using Amplified Fragment Length Polymorphisms (AFLPs) for analysis may have resolved complicated reticulating patterns between these taxa. In several studies of Cichlid fishes, various genetic markers were used to determine the relationships between species, but all showed a high level of DNA polymorphisms among species (Klein et al. 1998, Moran and Kornfield 1995). Relationships between these Cichlids were not fully resolved until AF LPs were used for analysis (Albertson et al.1999). AF LPs are advantageous because thousands of genetic regions can be used to generate an organism’sgenetic profile, and no preexisting knowledge of its genome is required before use. Some individual relationships between species may also spur additional investigation regarding the history of these plants and their speciation. Manardafi-uticulosa and M maritima share more allelic variation with each other than any of the other endemics. This may suggest that there has been recent gene flow between them, or that they diverged recently from either a common ancestor. Our current knowledge of these species show that they do not overlap geographically or phenologically, which better supports the latter, although they exist is such close proximity that their geographic distributions may have overlapped recently. These species inhabit comparable substrates (homogenous beach sands), they are the most geographically proximate and they are both woody perennials. Geologic and physiographic history suggests that M maritima may have been separated from mainland species when the Ingleside Terrace was a barrier island. If M fi-uticulosa, or a shared M fi-uticulosa/M maritima ancestor had become isolated on the barrier-island this may have given it a window of time to diverge. Questions also arise regarding the speciation mechanism acting to maintain distinction between M punctata and M fiuticulosa. These are the only two species in the study that 65 grow in syrnpatry, bloom at the same time and are thought to have hybrid zones (pers. obs). They have been observed growing together along hilly sandy landscapes with M fi-uticulosa growing at the sandy hilltops, M punctata at the base of the hills, and possible hybrids along the cline between have been observed at one locality (Prather pers. comm). This distribution better fits a parapatric species distribution with disruptive selection acting to maintain genetic distinction between species. In a study by Leuth and Prather (unpubl.), soils were collected from some of these sites and reciprocal seed plantings of M punctata and M fiuticulosa were conducted. Results showed that M fi-uticulosa had better survivorship on its own soil than it did on M punctata soil. Other factors that may be involved include differences in water availability in high and low areas of the sandy soils or subsoil component, such as high salt content. 4.9 Conclusions Few studies have used phylogenies based on low copy nuclear genes to infer population- level processes (Schaal 2000) such as speciation by peripheral isolation. This research revealed a high degree of variation between alleles, loci and individuals in both Adhl and Adh2 datasets. Monarda punctata sequences were widely distributed across both phylogenies and M humilis, M fi-uticulosa, M maritima and M viridissima sequences derived within this larger M punctata clade. These results support the hypothesis that these narrow endemic Monarda speciated as peripheral isolates of M punctata. In contrast, phylogenies suggest that M stanfieldii speciated as sister to of M punctata. The data suggest that Monardafi-uticulosa, M humilis, M maritima and M viridissima are neoendemics while M stanfieldii is a paleoendemic. Likewise, the high degree of lineage sorting and noncoalescence in the dataset suggests that these species diverged recently and rapidly. 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