PHYLOGENETIC RELATIONSHIPS OF CAULERPA (CHLOROPHYTA) BASED ON COMPARATIVE CHLOROPLAST ULTRASTRUCTURE1,2

The ultrastructure of chloroplasts from 28 of the 73 species of Caulerpa Lamouroux (Chlorophyta, Caulerpales) has been studied to aid in interpreting phylogenetic relationships among the 12 recognized sections. Variations of systematic value include pyrenoid occurrence and fine structure, thylakoid architecture and amount of photosynthate storage. Comparisons of field and culture specimens indicate these characters are consistent. Chloroplast thylakoids are grouped into bands, with the distribution of bands differing among species. In the most common arrangement, bands are evenly distributed throughout the chloroplast. A few species show lateral displacement of bands whereas others have a majority of bands arranged at one end of the chloroplast. Starch is stored cither as one or two large grains (> 1 μm diam.) or numerous small grains (< 0.5 μm diam.). Electron-transparent regions are common in other species in which chloroplasts rarely store starch. Simple, embedded pyrenoids are present in several species of section Sedoideae. An opaque region occurs in chloroplasts of C. elongata which may represent an intermediate stage in the evolutionary loss of the pyrenoid. It is suggested that the chloroplast of Caulerpa evolved, from a large, complex, pyrenoid-containing organelle housing both photosynthetic and amylogenic functions, to a small, structurally simpler one, specialized for photosynthesis alone. A phylogeny of the 12 sections of Caulerpa is constructed, based on chloroplast evolution which agrees with an earlier morphology-based hypothesis on the origin and evolution of Caulerpa.     

A FORENSIC AND PHYLOGENETIC SURVEY OF CAULERPA SPECIES (CAULERPALES,CHLOROPHYTA) FROM THE FLORIDA COAST,LOCAL AQUARIUM SHOPS,AND E‐COMMERCE: ESTABLISHING A PROACTIVE BASELINE FOR EARLY DETECTION1

Baseline genotypes were established for 256 individuals of Caulerpa collected from 27 field locations in Florida (including the Keys), the Bahamas, US Virgin Islands, and Honduras, nearly doubling the number of available GenBank sequences. On the basis of sequences from the nuclear rDNA‐ITS 1+2 and the chloroplast tufA regions, the phylogeny of Caulerpa was reassessed and the presence of invasive strains was determined. Surveys in central Florida and southern California of >100 saltwater aquarium shops and 90 internet sites revealed that >50% sold Caulerpa. Of the 14 Caulerpa species encountered, Caulerpa racemosa was the most common, followed by Caulerpa sertularioides, Caulerpa prolifera, Caulerpa mexicana, and Caulerpa serrulata. None of the >180 field‐collected individuals (representing 13 species) was the invasive strain of Caulerpa taxifolia or C. racemosa. With one exception (a sample of C. racemosa from a shop in southern California belonged to the invasive Clade III strain), no invasive strains were found in saltwater aquarium stores in Florida or on any of the internet sites. Although these results are encouraging, we recommend a ban on the sale of all Caulerpa species (including “live rock”) because: morphological identification of Caulerpa species is unreliable (>12% misidentification rate) and invasive strains can only be identified by their aligned DNA sequences, and because the potential capacity for invasive behavior in other Caulerpa species is far from clear. The addition of the Florida region to the genetic data base for Caulerpa provides a valuable proactive resource for invasion biologists as well as researchers interested in the evolution and speciation of Caulerpa.     

Molecular Phylogeny and Barcoding of Caulerpa (Bryopsidales) Based on the tufA,rbcL, 18S rDNA and ITS rDNA Genes

The biodiversity assessment of different taxa of the genus Caulerpa is of interest from the context of morphological plasticity, invasive potential of some species and biotechnological and pharmacological applications. The present study investigated the identification and molecular phylogeny of different species of Caulerpa occurring along the Indian coast inferred from tufA, rbcL, 18S rDNA and ITS rDNA nucleotide sequences. Molecular data confirmed the identification of 10 distinct Caulerpa species: C. veravalensis, C. verticillata, C. racemosa, C. microphysa, C. taxifolia, C. sertularioides, C. scalpelliformis, C. serrulata, C. peltata and C. mexicana. All datasets significantly supported the sister relationship between C. veravalensis and C. racemosa var. cylindracea. It was also concluded from the results that the specimen identified previously as C. microphysa and C. lentillifera could not be considered as separate species. The molecular data revealed the presence of multiple lineages for C. racemosa which can be resolved into separate species. All four markers were used to ascertain their utility for DNA barcoding. The tufA gene proved a better marker with monophyletic association as the main criteria for identification at the species level. The results also support the use of 18S rDNA insertion sequences to delineate the Caulerpa species through character-based barcoding. The ITS rDNA (5.8S-ITS2) phylogenetic analysis also served as another supporting tool. Further, more sequences from additional Caulerpa specimens will need to be analysed in order to support the role of these two markers (ITS rDNA and 18S insertion sequence) in identification of Caulerpa species. The present study revealed the phylogeny of Caulerpa as complete as possible using the currently available data, which is the first comprehensive report illustrating the molecular phylogeny and barcoding of the genus Caulerpa from Indian waters.     

Taxonomic revision of the Agaraceae with a description of Neoagarum gen. nov. and reinstatement of Thalassiophyllum

We confirmed the monophyly of the Agaraceae based on phylogenetic analyses of six mitochondrial and six chloroplast gene sequences from Agarum, Costaria, Dictyoneurum, and Thalassiophyllum species, as well as representative species from other laminarialean families. However, the genus Agarum was paraphyletic, comprising two independent clades, A. clathratum/A. turneri and A. fimbriatum/A. oharaense. The latter clade was genetically most closely related to Dictyoneurum spp., and morphologically, the species shared a flattened stipe bearing fimbriae (potential secondary haptera) in the mid‐ to upper portion. The phylogenetic position of Thalassiophyllum differed between the two datasets: in the chloroplast gene phylogeny, Thalassiophyllum was included in the A. clathratum/A. turneri clade, but in the mitochondrial gene phylogeny, it formed an independent clade at the base of the Agaraceae, the same position it took in the phylogeny when the data from both genomes were combined despite a larger number of bp being contributed by the chloroplast gene sequences. Considering the remarkable morphological differences between Thalassiophyllum and other Agaraceae, and the molecular support, we conclude that Thalassiophyllum should be reinstated as an independent genus. Dictyoneurum reticulatum was morphologically distinguishable from D. californicum due to its midrib, but because of their close genetic relationship, further investigations are needed to clarify species‐level taxonomy. In summary, we propose the establishment of a new genus Neoagarum to accommodate A. fimbriatum and A. oharanese and the reinstatement of the genus Thalassiophyllum.     

Cryptic Speciation in the Genus Cryptoglena (Euglenaceae) Revealed by Nuclear and Plastid SSU and LSU rRNA Gene

The photosynthetic euglenoid genus Cryptoglena is differentiated from other euglenoid genera by having a longitudinal sulcus, one chloroplast, two large trough‐shaped paramylon plates positioned between the chloroplast and pellicle, and lack of metaboly. The genus contains only two species. To understand genetic diversity and taxonomy of Cryptoglena species, we analyzed molecular and morphological data from 25 strains. A combined data set of nuclear SSU and LSU and plastid SSU and LSU rRNA genes was analyzed using Bayesian, maximum likelihood, maximum parsimony, and distance (neighbor joining) methods. Although morphological data of all strains showed no significant species‐specific pattern, molecular data segregated the taxa into five clades, two of which represented previously known species: C. skujae and C. pigra, and three of which were designated as the new species, C. soropigra, C. similis, and C. longisulca. Each species had unique molecular signatures that could be found in the plastid SSU rRNA Helix P23_1 and LSU rRNA H2 domain. The genetic similarity of intraspecies based on nr SSU rDNA ranged from 97.8% to 100% and interspecies ranged from 95.3% to 98.9%. Therefore, we propose three new species based on specific molecular signatures and gene divergence of the nr SSU rDNA sequences.     

桃叶珊瑚属植物的叶绿体基因组结构特征及系统发育分析

为确定桃叶珊瑚属(Aucuba)植物叶绿体基因组的结构及其序列变异,揭示其属下种间亲缘关系,该研究对桃叶珊瑚(A. chinensis)、花叶青木(A. japonica var. variegata)等6种桃叶珊瑚属植物和丝缨花属植物黄杨叶丝缨花(Garrya buxifolia)进行二代测序,利用生物信息学软件对其叶绿体基因组序列进行组装和注释,并进行基本特征分析、序列比较以及系统发育分析。结果表明:(1)桃叶珊瑚属植物叶绿体基因组具典型的环状四分体结构,6条序列全长157 891～158 325 bp,均编码114个基因,包括80个蛋白质编码基因、30个tRNA基因和4个rRNA基因。(2)6种植物叶绿体基因组高频密码子数均为29个,偏好以A/U结尾,确定了这6条序列的最优密码子共100个,包含12个共有的最优密码子。(3)6条叶绿体基因组序列共检测到270条散在重复序列,133条串联重复序列以及412个SSR位点。(4)比较基因组学分析结果表明,该属植物叶绿体基因组序列高度保守。(5)从叶绿体基因组中筛选出10个高变片段。(6)系统发育分析结果显示支持桃叶珊瑚属为一个支持率较高的单系,与丝缨花属关系较近。该研究中的5种桃叶珊瑚属植物以及1种丝缨花属植物的叶绿体基因组均为首次测序组装,揭示了桃叶珊瑚属及其属下种间的系统发育关系,为桃叶珊瑚属植物的分类鉴定和系统发育提供了参考资料。     

DEFINING TAXON BOUNDARIES IN MEMBERS OF THE MORPHOLOGICALLY AND GENETICALLY PLASTIC GENES CAULERPA (CAULERPALES,CHLOROPHYTA)1

Numerous attempts to capture the morphological variability of the genus Caulerpa have resulted in an unstable classification of numerous varieties and formae. In the present study we attempted to test taxon boundaries by investigating morphological and genetic variation within and between seven taxa of Caulerpa, supposedly belonging to four species, sampled at different sites in a Philippine reef system. Using both field and culture observations, we described the relation between the variability of a set of morphological characters and ecological parameters, such as wave exposure, light intensity, and substrate type. Statistical analyses showed that the limits between two (out of three) ecads of the C. racemosa (Forsskål) J. Agardh complex were obscured by the presence of morphological plasticity. Other studied taxa of Caulerpa (i.e. C. cupressoides [Vahl] C. Agardh, C. serrulata [Forsskål] J. Agardh, and two formae of C. sertularioides [S. Gmelin] Howe) could be grouped based on morphology despite the presence of morphological plasticity. Our results indicated a strong association between light intensity and several quantitative morphological variables. Genetic diversity of these taxa was assessed by partial sequencing chloroplast rbcL and tufA genes and the ycf10‐chlB chloroplast spacer. In all phylogenetic analyses, C. serrulata, C. cupressoides, C. sertularioides, and the three ecads of C. racemosa emerged as distinct genetic units. Despite the presence of morphological plasticity and morphological convergence, a subset of morphological characters traditionally used in taxonomic delimitation still had sufficient discriminative power to recognize the terminal phylogenetic clades.     

红锥叶绿体基因组特征及系统发育分析

为确定红锥(Castanopsis hystrix)叶绿体基因组的结构组成情况,判定其在锥属中的进化位置及与同锥属叶绿体基因组的区别,为锥属物种鉴定、遗传多样性分析和资源保护提供相关依据。使用Illumina HiSeq 2500测序平台对红锥叶绿体基因组进行测序,通过生物信息学分析方法进行序列组装、注释和特征分析,并利用R、Python、MISA、CodonW和MEGA 6等生物信息学软件对其基因组结构和数目、密码子偏好性、序列重复、简单重复序列(simple sequence repeat,SSR)位点和系统发育进行分析。结果表明红锥叶绿体基因组大小为153754 bp,呈现四分体结构;共拥有130个基因,包含85个编码基因、37个tRNA基因和8个rRNA基因;通过密码子偏好性分析,平均有效密码子数为55.5,说明其密码子随机性强、偏好性低;通过SSR及长重复片段分析,检测到45个重复序列及111个SSR位点;与近缘种比较,发现其叶绿体基因组序列高度保守,尤其蛋白质编码序列相似度极高;此外,系统发育分析发现红锥与海南锥聚为一支,关系密切。本研究得到了红锥的叶绿体基因组基本情况与系统发育位置,为红锥的物种辨别、天然种群遗传多样性与功能基因组学提供前期研究铺垫。     

DNA SEQUENCE DATA DEMONSTRATE THE POLYPHYLY OF THE GENUS CYSTOSEIRA AND OTHER SARGASSACEAE GENERA (PHAEOPHYCEAE)1

Phylogenetic relationships in the Sargassaceae were explored using three DNA markers, and the monophyly of its genera was challenged. Nineteen out of 24 currently recognized genera were sampled, representing 63 species. The variable mt23S‐tRNA Val intergenic spacer could only be aligned within genera and could not be used to infer intergeneric relationships. The partial mt23S was also useful to delineate genera and was alignable at the family level but provided few informative characters. Analysis of mt23S DNA sequences together with chloroplast‐encoded psbA sequences resulted in a better resolved phylogeny. Hormophysa was the first genus to branch off within the Sargassaceae, followed by Myriodesma; then the three genera Caulocystis, Carpoglossum, and Scaberia in unresolved order; and then Acrocarpia. The other taxa studied here were divided over three major clades, but there was no branch support for the monophyly of two of these. The genera Bifurcaria, Cystoseira, Halidrys, and Sargassum appeared polyphyletic. The following taxonomic changes are proposed: a new genus Brassicophycus for Bifurcaria brassicaeformis (Kützing) E. S. Barton; reinstatement of the genus Sargassopsis for Sargassum decurrens (R. Brown ex Turner) C. Agardh; reinstatement of the genus Sirophysalis for Indo‐Pacific Cystoseira trinodis (Forsskål) C. Agardh; reinstatement of the genus Polycladia for the western Indian Ocean species Cystoseira indica (Thivy et Doshi) Mairh, Cystoseira myrica (S. G. Gmelin) C. Agardh, and Acystis heinii Schiffner; and reinstatement of the genus Stephanocystis for the North Pacific Cystoseira species and Halidrys dioica N. L. Gardner. The European Cystoseira species should be split into three genera, but no name changes are proposed yet, because diagnostic characters were found only for the clade including the type species. Some evolutionary trends could be discerned from the mt23S + psbA phylogeny.     

Molecular phylogeny and taxonomy of <Emphasis Type="Italic">Tanacetum</Emphasis> L. (Compositae,Anthemideae) inferred from nrDNA ITS and cpDNA <Emphasis Type="Italic">trn</Emphasis>H–<Emphasis Type="Italic">psb</Emphasis>A sequence variation

The genus Tanacetum L. consists of around 160 species of the Compositae-Anthemideae. It holds a crucial position for understanding the phylogeny of the tribe and its subtribal and generic classification. The present study focuses on the phylogenetic relationships of the species and aims at a discussion of the infrageneric classification and boundaries of the genus. Sequence information from a nuclear [nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS)] and a chloroplast marker [chloroplast DNA (cpDNA) trnH–psbA] was used to infer the phylogeny of Tanacetum and many representatives of closely related genera. Bayesian inference methods were used for the phylogenetic reconstructions based on a combined dataset including both sequence and indel information. Contrasting the high morphological diversity in the genus, sequence divergence among Tanacetum representatives included was found to be very low, leading to unresolved phylogenetic relationships within the genus. Nevertheless, the generic separation of Tanacetum from other members of subtribe Anthemidinae (i.e., Anthemis, Archanthemis, Cota, Nananthea, and Tripleurospermum) emerges, while other, presently accepted genera are found nested in Tanacetum (i.e., Gonospermum, Lugoa, and Xylanthemum). Finally, the phylogenetic independence of the SW European T. microphyllum from the rest of Tanacetum and the other genera of Anthemidinae is found to receive strong support and is also backed by its morphological uniqueness. The new genus Vogtia Oberpr. et Sonboli is described to accommodate Tanacetum microphyllum and the closely related species T. annuum. The sinking of Gonospermum, Lugoa, and Xylanthemum into a broadly circumscribed genus Tanacetum is proposed until more stable phylogenetic reconstructions based on more and more variable molecular markers are possible. Concerning the infrageneric classification of Tanacetum, the phylogeny does not support the separation of the white- and red-rayed species (the former genus Pyrethrum) from the discoid, disciform, or yellow-rayed ones (i.e., Tanacetum in the strict sense) at any infrageneric rank. The hypothesis by Tzvelev (1961) that the yellow-rayed representatives may have evolved from disciform ancestors receives little support.     

Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships

Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies have clarified the most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 82 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances were most likely to stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.     

Molecular Phylogenetics and Biogeography of the Caribbean-Centered <Emphasis Type="Italic">Croton</Emphasis> Subgenus <Emphasis Type="Italic">Moacroton</Emphasis> (Euphorbiaceae s.s.)

Initial molecular phylogenetic studies established the monophylly of the large genus Croton (Euphorbiaceae s.s.) and suggested that the group originated in the New World. A denser and more targeted sampling of Croton species points to a South American origin for the genus. The nuclear and chloroplast genomes indicate a different rooting for the phylogeny of Croton. Although we favor the rooting indicated by the chloroplast data our conclusions are also consistent with the topology inferred from the nuclear data. The satellite genera Cubacroton and Moacroton are embedded within Croton. These two genera are synonimized into Croton and a new subgenus, Croton subgenus Moacroton, is circumscribed to include them and their allied Croton species. Croton subgenus Moacroton is morphologically characterized by a primarily lepidote indumentum, bifid or simple styles, and pistillate flowers with sepals that are connate at the base. This newly circumscribed subgenus is found from North America to South America, and in contrast to the majority of Croton species most of its members are found in mesic habitats. The group is most diverse in the greater Caribbean basin. A molecular clock was calibrated to the phylogeny using the available Euphorbiaceae fossils. The timing and pattern of diversification of Croton is consistent with both the GAARlandia and Laurasian migration hypotheses. A single species, Croton poecilanthus from Puerto Rico, is placed incongruently by its nuclear and chloroplast genomes. The possibility of this species being of hybrid origin is discussed.      

Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate,Stephanosphaera pluvialis (Volvocales,Chlorophyceae), among Unicellular Algae

The genus Balticola comprises a group of unicellular green flagellate algae and is composed of four species formerly classified in the genus Haematococcus. Balticola is closely related to a colonial green flagellate, Stephanosphaera pluvialis. Although the phylogeny among these genera was previously investigated based on two nuclear gene sequences, the phylogenetic sister of S. pluvialis has yet to be determined. In the present study, the species diversity of Balticola and Stephanosphaera was investigated using 18S rRNA gene sequences, and phylogenetic analyses of combined nuclear and chloroplast gene sequences were performed to understand the evolutionary origin of coloniality in Stephanosphaera. The divergence times of four colonial volvocalean flagellates from their respective unicellular sisters were also estimated. Six Balticola genotypes and a single Stephanosphaera genotype were recognized, and one Balticola genotype was resolved as the sister of S. pluvialis, showing that Balticola is a nonmonophyletic genus. The divergence time of Stephanosphaera from its nearest Balticola relative was estimated to be 4–63 million years ago, and these genera represent the most recently diverged pair of unicellular and colonial flagellates among the Volvocales.     

Chloroplast genomic diversity in Bulbophyllum section Macrocaulia (Orchidaceae,Epidendroideae, Malaxideae): Insights into species divergence and adaptive evolution

Bulbophyllum is the largest genus in Orchidaceae with a pantropical distribution. Due to highly significant diversifications, it is considered to be one of the most taxonomically and phylogenetically complex taxa. The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus, and suitable molecular markers are necessary for species determination and phylogenetic analysis. A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study. Here, we sequenced the complete chloroplast genome of four Bulbophyllum species, including three species from section Macrocaulia. The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp. The chloroplast genomes included 113 unique genes encoding 79 proteins, 30 tRNAs and 4 rRNAs. Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents, and shared a number of indels, which mainly contribute to its monophyly. In addition, interspecific divergence level was also great. Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms. A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum. All of chloroplast genes in four Bulbophyllum species were under purifying selection, while 13 sites within six genes exhibited site-specific selection. A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood, Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum. Our findings provide valuable molecular markers to use in accurately identifying species, clarifying taxonomy, and resolving the phylogeny and evolution of the genus Bulbophyllum. The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.     

MOLECULAR PHYLOGENY OF THE UPRIGHT ERYTHROPELTIDALES (COMPSOPOGONOPHYCEAE,RHODOPHYTA): MULTIPLE CRYPTIC LINEAGES OF ERYTHROTRICHIA CARNEA1

The phylogeny of morphologically simple algae is problematic due to insufficient morphological characters to aid in distinguishing species and relationships. The problem is further compounded because multiple evolutionary lineages of morphologically similar species occur in most well‐sampled biogeographic locations; therefore, location cannot be used as a proxy for species. The phylogeny of the upright members of the Erythropeltidales is partially clarified by combining molecular data, unialgal culture observations, and worldwide sampling. Our results show that there are several well‐supported lineages within the Erythropeltidales with only two morphologically recognizable taxa at present. The first is the genus Porphyrostromium, with a well‐developed basal crust, which includes two Erythrotrichia species (Porphyrostromium ligulatum comb. nov. and Porphyrostromium pulvinatum comb. nov.). The second is the branched species Erythrotrichia welwitschii (Rupr.) Batters. There are also six strongly supported Erythrotrichia carnea–like lineages. While not completely satisfactory, we propose that one lineage (lineage 2) with samples close to the type locality be designated as E. carnea with a specific isolate as an epitype. The lack of morphology to differentiate the other lineages leads to a taxonomy based solely on gene sequencing and molecular phylogeny, with rbcL sequences differentiating the lineages proposed. We hold off on proposing more species and genera until more data and samples can be gathered.     

Phylogeny of firs (genus <Emphasis Type="Italic">Abies</Emphasis>, Pinaceae) based on multilocus nuclear markers (AFLP)

To study the phylogenetic relationships, evolutionary history, and molecular systematics of firs (genus Abies), the phylogenetic reconstruction, based on nuclear multilocus markers—amplified fragment length polymorphism (AFLP)—was conducted. Using seven combinations of selective primers, 84 samples of 39 taxa were genotyped for 553 polymorphic AFLP loci. A comparison with our earlier chloroplast and mitochondrial phylogenies of the genus (in 2014) shows that the nuclear phylogeny generally is more congruent to the chloroplast tree. Most of the clades resolved by the chloroplast phylogeny were supported also in the AFLP tree. Employing the nuclear DNA-based tree, we revealed the presence of new groups and the differences in the topology of several clades. AFLP confirmed the monophyly of Asian species of section Balsamea and their sister position in relation to the American group of species of this section. As shown by the tree of chloroplast DNA, Asian species of section Balsamea do not form a monophyletic group, but belong to the clade comprising the majority of Asian species. Phylogenetically mitochondrial DNA data to a large extent are not congruent to the nuclear and chloroplast DNA trees, and are more in line with geographical distribution of species. Conflicts between nuclear and cytoplasmic phylogeny were analyzed. Taking them into account, we consider the hypothesis of a hybrid origin of particular groups of firs, including ancient hybridization in section Balsamea. A comparison of molecular data with traditional taxonomy of the genus is discussed.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.