Phylogeographic patterns, genetic affinities and morphological differentiation between Epipactis helleborine and related lineages in a Mediterranean glacial refugium

Background and Aims

In the Mediterranean basin, the Italian peninsula has been suggested to be one of the most important glacial refugia for temperate tree species. The orchid genus Epipactis is widely represented in the Italian peninsula by widespread species and several endemic, localized taxa, including selfing and outcrossing taxa. Here the phylogenetic and phylogeographic relationships in a group of closely related taxa in Epipactis are investigated with the aim of understanding the role of this refugial area for cladogenesis and speciation in herbaceous species, such as terrestrial orchids.

Methods

Ribosomal DNA (rDNA) was employed to assess phylogenetic relationships, and plastid sequence variation in the rbcL–accD spacer was used to reveal phylogeographic patterns among plastid haplotypes using a parsimony network.

Key Results

Low genetic variation and shared ribotypes were detected in rDNA, whereas high levels of sequence variation and a strong phylogeographic structure were found in the examined plastid region. The parsimony plastid haplotype network identified two main haplotype groups, one including E. atrorubens/microphylla/muelleri/leptochila and the other including all accessions of E. helleborine and several localized and endemic taxa, with a combination of widespread and rare haplotypes detected across the Italian peninsula. A greater genetic divergence separated the Italian and other European accessions of E. helleborine.

Conclusions

Phylogenetic and phylogeographic patterns support a working hypothesis in which the Italian peninsula has only recently been colonized by Epipactis, probably during the most recent phase of the Quaternary age and, nevertheless, it acted as a remarkable centre of diversification for this orchid lineage. Changes in pollination strategy and recurrent shifts in mating system (from allogamy to autogamy) could have represented the mechanism promoting this rapid diversification and the observed high taxonomic complexity detected in the E. helleborine species complex.     

Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution

Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA-trnH intergenic spacer, petB-petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concerns A. vulneraria and A. lemanniana, whose placement in the parsimony analysis of the ITS data appears to be due to a strong long-branch effect. Analysis of the secondary structure of the ITS1 spacer showed a strong bias towards transitions in A. vulneraria and A. lemanniana, many of which were also characteristic of certain outgroup taxa. This may contribute to the conflicting placement of this clade in the MP tree for the ITS data. Additional conflicts between the plastid and ITS trees were more taxonomically focused. These differences may reflect the occurrence of reticulate evolution between closely related species, including a possible hybrid origin for A. hystrix. The patterns of incongruence between the plastid and the ITS data seem to correlate with taxon ranks. All of our phylogenetic analyses supported the monophyly of Anthyllis (incl. Hymenocarpos). Although they are often taxonomically associated with Anthyllis, the genera Dorycnopsis and Tripodion are shown here to be more closely related to other genera of Loteae. We infer up to six major clades in Anthyllis that are morphologically well-characterized, and which could be recognized as sections. Four of these agree with various morphology-based classifications, while the other two are novel. We reconstruct the evolution of several morphological characteristics found only in Anthyllis or tribe Loteae. Some of these characters support major clades, while others show evidence of homoplasy within Anthyllis.     

Ecological differentiation and cladogenesis of Baldellia (L.) Parl. (Alismataceae)

The Iberian Peninsula is home to a large number of endemic species that often show strong genetic subdivisions which indicate possible isolation of populations in the past. Numerous phylogeographic and phylogenetic studies on Iberian flora and fauna have revealed this territory to be the origin of genetic differentiation during the Pleistocene Ice Age. To better understand the influence of Plio-Pleistocene climatic oscillations on the cladogenesis and population structuring of refugial taxa restricted to freshwaters of the Iberian Peninsula, we studied the evolutionary history of the small European genus Baldellia, both from a phylogenetic/phylogeographic perspective and regarding its ecological characteristics. Molecular analyses were based on four plastid regions and nuclear ITS2 ribosomal spacer from individuals belonging to geographically isolated Baldellia populations, while the relationships between climate and Baldellia species distribution was investigated by redundancy analysis applied to the climatic data with the occurrence of Baldellia species as external variables. The absence of a clear phylogenetic signal most likely reflects a common and recent cladogenesis for Baldellia. In contrast, the more rapidly evolving plastid sequences indicate a recent phylogeographic history of refugial repartition and ecological segregation probably occurring during the last glaciation, a scenario well supported by marked differences in species?? ecological preferences and climate analysis.     

Molecular phylogenetics of Hypoxidaceae--evidence from plastid DNA data and inferences on morphology and biogeography

Phylogenetic relationships of the monocot family Hypoxidaceae (Asparagales), which occurs mainly in the Southern Hemisphere, were reconstructed using four plastid DNA regions (rbcL, trnL intron, trnL-F intergenic spacer, and trnS-G intergenic spacer) for 56 ingroup taxa including all currently accepted genera and seven species of the closely related families Asteliaceae, Blandfordiaceae, and Lanariaceae. Data were analyzed by applying parsimony, maximum likelihood and Bayesian methods. The intergenic spacer trnS-G--only rarely used in monocot research--contributed a substantial number of potentially parsimony informative characters. Hypoxidaceae consist of three well-supported major clades, but their interrelationships remain unresolved. Our data indicate that in the Pauridia clade one long-distance dispersal event occurred from southern Africa to Australia. Long-distance dispersal scenarios may also be likely for the current distribution of Hypoxis, which occurs on four continents. In the Curculigo clade, the present distribution of Curculigo s.s. on four continents could support a Gondwanan origin, but the level of divergence is too low for this hypothesis to be likely. The main clades correspond well with some floral characters, habit and palynological data, whereas chromosomal data exhibit plasticity and probably result from polyploidization and subsequent dysploidy and/or aneuploidy. Evolutionary flexibility is also suggested by the number of reported pollination syndromes: melittophily, myophily, sapromyophily, and cantharophily. Based on our phylogenetic results, we suggest cautious nomenclatural reorganization to generate monophyly at the generic level.     

Molecular taxonomy in the dark: evolutionary history, phylogeography, and diversity of cave crayfish in the subgenus Aviticambarus, genus Cambarus

Freshwater crayfish species in the subgenus Aviticambarus (Cambaridae: Cambarus) are restricted to caves along the Cumberland Plateau, the Sequatchie Valley, and the Highland Rim which extend along the Tennessee River in southcentral Tennessee and northern Alabama. Historically, three stygobitic species, Cambarus jonesi, Cambarus hamulatus, and Cambarus veitchorum, comprise this subgenus. We examine species' boundaries and phylogeographic structure of this imperiled Southern Appalachian assemblage to shed light on patterns of cave colonization. We also provide estimates of genetic diversity for conservation status assessment. Using geologic evidence, phylogeographic analyses, and sequence data from five gene regions (two nuclear: Histone H3 and GAPDH and three mitochondrial: 12S, 16S, and CO1 totaling almost 2700 base pairs), we identify two well-supported cryptic species in addition to the three currently recognized taxa. Four of these taxa exhibit low levels of genetic variation both currently and historically, which may indicate local extirpation events associated with geological and river basin changes. Our results also support other recent findings that pre-Pleistocene paleodrainages may best explain the current patterns of aquatic faunal biodiversity in the Southern Appalachians.     

High intra-individual sequence variation in the nuclear rDNA LSU-5S intergenic spacer in the Sargassaceae (Fucales, Phaeophyceae)

Of four species of Sargassaceae, representing the genera Carpophyllum, Cystoseira, Landsburgia, and Sargassum, the intergenic spacer of the ribosomal cistron was amplified using a forward primer annealing at the 3′-end of the large subunit (LSU) of the ribosomal cistron and a reverse primer annealing at the 5S rRNA gene. The PCR products were cloned and the DNA sequences of multiple clones were determined. Almost each clone showed a unique DNA sequence. Intra-individual variation of this LSU-5S intergenic spacer was extremely high and was characterized by great length variation and a high number of short tandem repeats. Sequences were unalignable and therefore it was concluded that the LSU-5S intergenic spacer is unsuitable for phylogenetic and phylogeographic studies of sargassacean taxa.     

Phylogenetic analysis of Asplenium subgenus Ceterach (Pteridophyta: Aspleniaceae) based on plastid and nuclear ribosomal ITS DNA sequences

Phylogenetic relationships among 20 taxa of the fern genus Asplenium subgenus Ceterach (Filicopsida, represented by 73 accessions) were investigated using DNA sequence data from the nuclear ribosomal internal transcribed spacers (ITS nDNA) and plastid trnL-F intergenic spacer. In addition, a single sample per taxon was used in an analysis of the plastid rbcL gene. Chromosome counts were determined for all the samples, and these demonstrated a range from diploid to octoploid. Analyses of the DNA sequence data indicated that Asplenium subgenus Ceterach is polyphyletic, implicating homoplasy in the characters previously used to circumscribe this taxon. Plastid trnL-F and rbcL analyses resulted in identical tree topologies. The trees produced from the separate plastid and nuclear matrices agree in (1) the recognition of identical groups of accessions corresponding to A. dalhousiae, A. ceterach, A. aureum, A. cordatum, A. phillipsianum, and A. haughtonii; (2) the division of A. subg. Ceterach into two subclades, a Eurasian-Macaronesian and a strictly African alliance; (3) the position of A. dalhousiae as a member of the former subclade; (4) the lack of genetic variation in A. cordatum despite its morphological variability; and (5) the clustering of each autopolyploid with their diploid ancestor. However, the plastid and nuclear trees differ in their placement of A. haughtonii and A. dalhousiae, which might be due to different evolutionary histories of nuclear and plastid genomes, and is possibly an indication of ancient hybridization. The analyses confirm the existence of several strictly African taxa. Asplenium phillipsianum and A. cordatum each form species complexes of diploid and autopolyploid taxa, from which a third, morphologically intermediate, allotetraploid species has originated. Asplenium haughtonii is a distinct endemic species from Saint Helena. The maternally inherited plastid sequences support the hypothesis that A. aureum is an ancestor of A. lolegnamense and of A. octoploideum. Because gene conversion did not eliminate divergent ITS alleles in the allopolyploids, their reticulate ancestry could be demonstrated. Biparentally inherited nrITS sequences support the allopolyploid status of A. aureum, A. lolegnamense, and A. punjabense, indicating they share the ancestral A. javorkeanum genome.     

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS‐trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.     

A phylogenetic hypothesis for the Aizoaceae (Caryophyllales) based on four plastid DNA regions

The Aizoaceae is the largest family of leaf succulent plants, and most of its species are endemic to southern Africa. To evaluate subfamilial, generic, and tribal relationships, we produced two plastid DNA data sets for 91 species of Aizoaceae and four outgroups: rps16 intron and the trnL-F gene region (both the trnL intron and the trnL-F intergenic spacer). In addition, we generated two further plastid data sets for 56 taxa restricted to members of the Ruschioideae using the atpB-rbcL and the psbA-trnH intergenic spacers. In the combined tree of the rps16 intron and trnL-F gene region, three of the currently recognized subfamilies (Sesuvioideae, Mesembryanthemoideae, and Ruschioideae) are each strongly supported monophyletic groups. The subfamily Tetragonioideae is polyphyletic, with Tribulocarpus as sister to the Sesuvioideae and Tetragonia embedded in the Aizooideae. Our study showed that the group consisting of the Sesuvioideae, Aizooideae, and Tetragonioideae does not form a monophyletic entity. Therefore, it cannot be recognized as a separate family in order to accommodate the frequently used concept of the Mesembryanthemaceae or "Mesembryanthema," in which the subfamilies Mesembryanthemoideae and Ruschioideae are included. We also found that several genera within the Mesembryanthemoideae (Mesembryanthemum, Phyllobolus) are not monophyletic. Within the Ruschioideae, our study retrieved four major clades. However, even in the combined analysis of all four plastid gene regions, relationships within the largest of these four clades remain unresolved. The few nucleotide substitutions that exist among taxa of this clade point to a rapid and recent diversification within the arid winter rainfall area of southern Africa. We propose a revised classification for the Aizoaceae.     

Phylogeny and phylogeography of Arenaria section Pseudomoehringia

Phylogeographic and evolutionary studies are necessary to establish solid taxonomic treatments and to implement effective conservation programs. Unfortunately, a well‐argued and well‐founded taxonomic framework is still lacking for some Mediterranean taxa. This is the case of Arenaria section Pseudomoehringia, a group that currently comprises three species endemic to the Iberian Peninsula (A. funiculata, A. suffruticosa, and A. tejedensis) and A. glochidisperma, which is restricted to the Rif mountains, North Africa. However, the taxonomic boundaries and phylogenetic relationships among these species are still uncertain. To explore the evolutionary history and phylogeographic patterns within this section, analyses based on nuclear (amplified fragment length polymorphism and internal transcribed spacer) and plastid DNA markers (psbA‐3’ trnK‐matK and rps16) were performed. Our study has confirmed the monophyly of the section, in which two species are clearly identified (A. funiculata and A. glochidisperma) and an additional species complex (“A. suffruticosa + A. tejedensis complex”) is also supported as a monophyletic clade. The phylogeographic results point toward a dispersal event of a common ancestor of the group from the Iberian Peninsula, giving rise to A. glochidisperma in North Africa. Moreover, A. funiculata and A. glochidisperma are identified as closely related species edaphically differentiated across the Strait of Gibraltar. Our study indicates low levels of a recent gene flow among populations of the “A. suffruticosa + A. tejedensis complex,” which are genetically highly structured and suggest an isolation by distance pattern, probably due to a combination of ecological and geographic barriers. Furthermore, the taxonomic and conservation status of taxa included in Arenaria section Pseudomoehringia has been reviewed.     

Phylogenetic relationships in Pleurothallidinae (Orchidaceae): combined evidence from nuclear and plastid DNA sequences

To evaluate the monophyly of subtribe Pleurothallidinae (Epidendreae: Orchidaceae) and the component genera and to reveal evolutionary relationships and trends, we sequenced the nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2) and 5.8S gene for 185 taxa. In addition, to improve the overall assessments along the spine of the topology, we added plastid sequences from matK, the trnL intron, and the trnL-F intergenic spacer for a representative subset of those taxa in the ITS study. All results were highly congruent, and so we then combined the sequence data from all three data sets in a separate analysis of 58 representative taxa. There is strong support in most analyses for the monophyly of Pleurothallidinae and in some for inclusion of Dilomilis and Neocognauxia of Laeliinae. Although most genera in the nine clades identified in the analyses are monophyletic, all data sets are highly congruent in revealing the polyphyly of Pleurothallis and its constitutent subgenera as presently understood. The high degree of homoplasy in morphological characters, especially floral characters, limits their usefulness in phylogenetic reconstruction of the subtribe.     

毛茛叶报春高分化的谱系地理结构

毛茛叶报春（Primula ranunculoides Chen）是我国特有的珍稀濒危花卉,其野生种质资源已十分稀少。为了揭示其谱系地理结构,本文对11个居群114个个体的叶绿体trnL-F和trnS-G基因片段进行了测序分析。结果共检测到10个单倍型,除YJPA和YJPB两居群共享一个单倍型（H9）外,其余各居群均仅有一个特有单倍型,居群内不存在单倍型多样性。毛茛叶报春具高分化的谱系地理结构,居群间的总平均遗传距离达0.015,单倍型间的平均突变次数高达31.2步,两者均显著高于同属的近缘种。其种子散布能力弱、生境片断化和地理隔离明显及两年生的生活史可能是导致其高分化谱系地理结构产生的主要原因。Samova、Structure以及TCS分析均支持将毛茛叶报春11个居群的遗传结构分为6组,它们与地形（山脉）关系密切对应,彼此间分化明显,因此建议不同山体的居群应视为不同的保护单元进行遗传管理。     

Molecular Systematic Study of <Emphasis Type="Italic">Chrysosplenium</Emphasis> Series <Emphasis Type="Italic">Pilosa</Emphasis> (Saxifragaceae) in Korea

To address systematic issues pertaining to series Pilosa of Korean Chrysosplenium, the phylogenetic relationships of the 35 accessions of Korean Chrysosplenium taxa were examined using the DNA sequence data obtained from the nuclear ribosomal internal transcribed spacer (ITS) regions and the psbK-I gene of the plastid genome. The results from both ITS and psbK-I sequence data indicated that Chrysosplenium flaviflorum formed a well-supported clade that merits species status of the taxon. The ITS phylogenetic trees detected two distinct lineages in Chrysosplenium pilosum var. fulvum. Geographically, one lineage was widely distributed throughout the country whereas the other was confined to Gyeonggi and Gangwon provinces. The plants sampled from Jeju Island, which have been recognized as C. pilosum var. sphaerospermum [C. hallaisanense] exhibited no DNA sequence feature segregating them from C. pilosum var. fulvum [C. barbatum] distributed in the mainland area of Korea. The plastid DNA sequence data was not fully in concordance with the nuclear ribosomal ITS data and the current taxa delimitation. These results suggest incomplete lineage sorting or that plastid genome capture may have occurred during the evolution of some taxa examined in the present study.     

Phylogenetics and biogeography of the neotropical fern genera Jamesonia and Eriosorus (Pteridaceae)

Jamesonia and Eriosorus are two traditionally recognized fern genera in the Neotropics that together form a monophyletic group. Molecular phylogenetic analyses for this study suggest, however, that neither genus is itself monophyletic and that several independent lineages with the jamesonia morphotype have each undergone a fairly recent radiation in páramo ecosystems. A robust phylogeny was generated based on sequence data of the nuclear external transcribed spacer (ETS) of 18S-26S rDNA, the plastid gene rps4 and the intergenic spacer rps4-trnS. Several conclusions can be made concerning the evolutionary history and biogeographic patterns of the Jamesonia-Eriosorus complex: (1) "jamesonia" is polyphyletic, making "eriosorus" paraphyletic; (2) all analyses recover three major clades in the Andes; (3) two well-supported clades can be recognized, corresponding to the northern vs. central Andes; and (4) the sister taxon of the Andean radiation is the Brazilian taxon Eriosorus myriophyllus. Jamesonia is a potential example of a recent adaptive radiation because the group is characterized as being morphologically and ecologically diverse and its habitat is of recent origin.     

The colonization history of Juniperus brevifolia (Cupressaceae) in the Azores Islands

Background

A central aim of island biogeography is to understand the colonization history of insular species using current distributions, fossil records and genetic diversity. Here, we analyze five plastid DNA regions of the endangered Juniperus brevifolia, which is endemic to the Azores archipelago.

Methodology/Principal Findings

The phylogeny of the section Juniperus and the phylogeographic analyses of J. brevifolia based on the coalescence theory of allele (plastid) diversity suggest that: (1) a single introduction event likely occurred from Europe; (2) genetic diversification and inter-island dispersal postdated the emergence of the oldest island (Santa Maria, 8.12 Ma); (3) the genetic differentiation found in populations on the islands with higher age and smaller distance to the continent is significantly higher than that on the younger, more remote ones; (4) the high number of haplotypes observed (16), and the widespread distribution of the most frequent and ancestral ones across the archipelago, are indicating early diversification, demographic expansion, and recurrent dispersal. In contrast, restriction of six of the seven derived haplotypes to single islands is construed as reflecting significant isolation time prior to colonization.

Conclusions/Significance

Our phylogeographic reconstruction points to the sequence of island emergence as the key factor to explain the distribution of plastid DNA variation. The reproductive traits of this juniper species (anemophily, ornithochory, multi-seeded cones), together with its broad ecological range, appear to be largely responsible for recurrent inter-island colonization of ancestral haplotypes. In contrast, certain delay in colonization of new haplotypes may reflect intraspecific habitat competition on islands where this juniper was already present.     

The discovery and phylogenetic implications of a novel 41 bp plastid DNA deletion in wild potatoes

Insertions and deletions (indels) are common in intergenic spacer regions of plastid DNA and can provide important phylogenetic characters for closely related species. For example, a 241-bp plastid DNA deletion in the trnV-UAC/ndhC intergenic spacer region has been shown to have major phylogenetic importance in determining the origin of the cultivated potato. As part of a phylogenetic study of the wild potato Solanum series Piurana group we screened 199 accessions of 38 wild potato species in nine of the 19 tuber-bearing (Solanum section Petota) series that have not been examined before for indels in the trnV-UAC/ndhC intergenic spacer region. A novel 41 bp deletion (but no 241 bp deletion) was discovered for 30 accessions of three species: S. chiquidenum (5 of 10 accessions), S. chomatophilum (19 of 28), and S. jalcae (6 of 6). Accessions with and without this deletion are found throughout much of the north-south range of all three species in northern and central Peru, but not east of the Marañón River. Multivariate morphological analyses of these 44 accessions showed no morphological associations to the deletion. The results suggest extensive interspecific gene flow among these three species, or a common evolutionary history among species that have never been suggested to be interrelated.     

Contributions to a molecular phylogeny and systematics of Anemone and related genera (Ranunculaceae-Anemoninae)

Plastid atpB/rbcL intergenic spacer sequences were obtained from 21 selected taxa and one hybrid of Anemoninae (Anemone, Pulsatilla, Hepatica) and compared with Ficaria (Ranunculinae) as an outgroup. From the resulting matrix (1226 bp) a single most parsimonious tree was obtained (Fig. 1 ). The branching of this tree is confirmed by many informative indels and appears largely congruent with past plastid restriction analyses. Several new taxa are added. The monophyly of the Anemoninae and their early split into two major clades is supported: clade I with the chromosome base number x = 8, clade Ⅱ with the reduced x = 7. Clade Ⅰ is made up of the basal Pulsatilla and the Rivularis + Vitifolia groups. The Multifida group links to the crown groups Coronaria, Blanda and Nemorosa. Clade Ⅱ consists of the basal Dichotoma group, followed by Hepatica, and finally by the N. Hemisphere Narcissiflora and the S. Hemisphere Antucensis groups as sisters. The problems of the Anemoninae ancestry, phylogenetic differentiation, and recent attempts for systematic classification are critically discussed. In view of the still incomplete sampling of DNA data, aconservative and informal approach to classification problems is recommended.     

Cryptic diversity in a widespread North American songbird: phylogeography of the Brown Creeper (Certhia americana)

The identification of species via morphological characteristics has traditionally left cryptic species undescribed in taxa under selection for morphological conservation (or a lack of selection for morphological change). Treecreepers (Genus: Certhia) have a conserved morphological appearance, making it difficult to ascertain relationships in the genus based on morphology alone. Recent genetic and song structure studies of Eurasian Treecreepers identified cryptic species within Old World Certhia that were previously undescribed using morphological characteristics. Here, we use mtDNA to investigate cryptic diversity and patterns of diversification in the Brown Creeper (Certhia americana), the single described Certhia species in the Americas. Phylogenetic analyses identified six well-supported geographically-structured clades; the basal divergence separates a northern and a southern lineage in the Brown Creeper, likely cryptic species previously characterized as many subspecies. Sympatry is prevalent between clades in western North America, where possible contact zones warrant further investigation. Allopatry appears to be the primary driver of deep phylogeographic structure within the Brown Creeper; however, within clade diversity is highly correlated with the life history traits of the populations that comprise the geographically structured phylogroups.     

Origin of the disjunct tetraploid Cardamine amporitana (Brassicaceae) assessed with nuclear and chloroplast DNA sequence data

Seventy-four nucleotide sequences from the ITS regions of nuclear ribosomal DNA and 76 from the trnL-trnF spacer of chloroplast DNA were used to address the origin of tetraploid Cardamine amporitana, the conspecifity of central Italian and northeastern Spanish populations, and the possible cause for such geographic disjunction. Because of the complex lineage relationships in Cardamine, the sampling included 22 taxa. In the results, both data sets are highly congruent in supporting a close relationship of C. amporitana to the widespread Eurasian C. amara. Low genetic variability in northeastern Spanish populations of C. amporitana suggests long-distance dispersal from central Italy. The interior position of the single northeastern Spanish haplotype in a statistical parsimony network of trnL-trnF haplotypes however does not support this scenario and invokes other plausible phylogeographic explanations. The disappearance of geographically intermediate populations and genetic impoverishment by migration and isolation, both probably associated with Quaternary climatic oscillations, appears as an alternative hypothesis to explain the phylogeographic pattern. A recent hybridization event is reported between C. amporitana and a diploid from the C. pratensis group in central Italy on the basis of additive polymorphisms in ITS for all the 22 distinguishing nucleotides.