PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10
Abstract
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
... They were performed in PAUP*4.0b8 (Swofford, 1998) and MrBayes version 3.1.2 (Huelsenbeck and Ronquist, 2001) programs. ...
... A heuristic ML search (again with 100 replications of stepwise addition and TBR branch swapping) was implemented in the PAUP*4.0b8 (Swofford, 1998) software package. Other Clupeiformes sequences retrieved from the GenBank were included in the ingroup: S. aurita (AF472584), Engraulis encrasicolus (AY923823), Sardinops sagax (AF472586), Sardinops caeruleus (AF472585). ...
In the Southwestern Atlantic Ocean, several described species of Clupeiformes overlap their geographical distribution in the coastal areas from Rio Grande do Sul (Southern Brazil) to Bahía Blanca (Argentina) and the Río de la Plata estuary. Larvae and juveniles of the SW Atlantic menhaden Brevoortia aurea are very difficult to discriminate from those of other clupeids belonging to the genera Platanichthys and Ramnogaster inhabiting the same environments. Here we implemented phylogenetic analyses based on mitochondrial cytochrome b sequences and morphometric and osteological studies to achieve unambiguous species recognition in different ontogenetic stages of six endemic species of Clupeiformes from the Southwestern Atlantic Ocean. All phylogenetic analyses based on the cytochrome b gene yielded a robust support to the existence of highly structured and monophyletic groups conforming clupeiforms taxa. These monophyletic entities were consistent with major groups accessed through the first two principal components (PCs) from morphometric variation among taxa. Both approaches resulted in accurated and complementary tools for the individual assignment in clades and groups within Clupeiformes during different ontogenetic stages in their life cycle. The detection of species-specific spawning and nursery areas through accurated methodological approaches of identification constitute a prerequisite for a sustainable management in pelagic fisheries.
... All analyses were performed with the PAUP* software package, version 4.0a (build 169) (Swofford 2002). For the ...
The “Diahot Tooth” is an isolated postcanine tooth of a large herbivorous mammal, discovered in the Diahot region of northern New Caledonia in 1875. Most authors have identified it as an upper premolar of a rhinocerotid, but an alternative proposal is that it belongs to a diprotodontoid marsupial that has been named Zygomaturus diahotensis. Either possibility raises biogeographical difficulties, because New Caledonia has been isolated from other major landmasses for 80 million years, and neither rhinocerotids nor diprodotontoids appear to be good candidates for such a long-distance overwater dispersal event. Here, we present a novel interpretation of the affinities and origin of the Diahot Tooth, based on qualitative study of its preserved morphology and quantitative phylogenetic analyses that include both rhinocerotids and diprotodontoids.
We show that the Diahot Tooth most closely resembles the first deciduous premolar of Western Eurasian Miocene teleoceratine rhinocerotid Brachypotherium brachypus, with the few discrepancies relating to traits that are known to be variable in B. brachypus. Our phylogenetic analyses also support this relationship. The preservation of the Diahot Tooth closely resembles that of B. brachypus teeth from the “Faluns Sea” of the Loire basin, and we propose that the New Caledonian specimen originated there and was taken to New Caledonia by a European colonist during the mid-19th century, where it was lost, rediscovered, and incorrectly assumed to be autochthonous.
... The character-taxon matrix was analysed in PAUP v.4.0a169 [64] by conducting a heuristic search (10.000 replicates using fast stepwise addition) with tree bisection and reconnection branch swapping to search for trees. Parsimony was set as the optimality criterion and all branch lengths of less than zero were set to collapse. ...
Among terrestrial tetrapods, the origin of herbivory marked a key evolutionary event that allowed for the evolution of modern terrestrial ecosystems. A 100 Ma gap separates the oldest terrestrial tetrapods and the first undisputed herbivorous tetrapods. While four clades of early tetrapod herbivores are undisputed amniotes, the phylogenetic position of Diadectomorpha with respect to Amniota has long been controversial. Given that the origin of herbivory coincides with the oldest amniotes, and obligate herbivory is unknown within amphibians, this suggests that a key adaptation necessary to evolve obligate herbivory is unique to amniotes. Historically, phylogenetic analyses have found Diadectomorpha as the sister-group to amniotes, but recent analyses recover Diadectomorpha as sister-group to Synapsida, within Amniota. We tested whether diadectomorphs are amniotes by updating the most recent character–taxon matrix. Specifically, we added new characters from the lower jaw and added diadectomorph taxa, resulting in a dataset of 341 characters and 61 operational taxonomic units. We updated the description of five diadectomorph jaws using microcomputed tomography data. Our majority-rule consensus places Diadectomorpha as sister-group to Synapsida; other methods do not recover this relationship. We revise diadectomorph taxonomy, erecting a new species from the early Permian Bromacker locality, Germany, and a new genus to accommodate ‘Diadectes’ sanmiguelensis.
... Uncorrected pairwise distances (UPDs) of the fragment 12S (≈857 bp) and 16S rRNA genes (AR-BR, ≈585 bp) between the new species and the remaining species of the Hyloscirtus larinopygion group were calculated in PAUP* (Swofford 2002). To minimize missing data, we excluded short 12S rRNA sequences of the new species KU 202731 (≈400 bp) and H. staufferorum (Duellman and Coloma, 1993) QCZA 45967 (≈499 bp) from the UPDs calculations. ...
We present the description of a novel treefrog species inhabiting the Andean streams in southeastern Ecuador that has been erroneously identified as Hyloscirtus lindae for four decades. The new species is closely related to H. tapichalaca and is part of the southern clade of the H. larinopygion group, which comprises five species confined to the southeastern Andes of Ecuador to the northeastern Andes of Peru. It is diagnosed from its close relatives by a unique combination of characteristics, including hypertrophied forelimbs in males, a pronounced, curved, and protruding spine-shaped prepollex, a substantial supracloacal flap, supratympanic fold, digital discs colored in shades of orange-red or bright-red, and the concealed surfaces of limbs displaying a bluish-gray hue and dorsal spicules in males. We briefly explore the implications of this discovery for the evolution of arm morphology in the H. larinopygion group. Our findings underscore the continued importance of periodically reviewing historical specimens, leading to unexpected discoveries; once again confirming the importance of natural history museums and their custodian biological collections.
... Maximum likelihood (ML) phylogenetic trees were constructed with RAxML (Stamatakis 2014) after identifying the best-fitting nucleotide evolution model with ModelTest-NG (Darriba et al. 2020). The shortest maximum parsimony (MP) tree was identified by conducting a heuristic search and 100 random additions of sequences (RAS) with PAUP 4.0b10 (Swofford 2003). Statistical support for ML and MP tree nodes was obtained with 100 bootstrap replicates, saved in Newick format, and edited using TreeGraph 2 (Stöver and Müller 2010), collapsing nodes for the minimum 50% consensus rule. ...
Ophiostoma haidanensis is described as a new species of the Ophiostoma piceae complex isolated from yellow-cedar (Callitropsis nootkatensis (D. Don) Oerst. ex D.P. Little) sapwood in the Haida Gwaii island archipelago and the North Coast of British Columbia, Canada. The fungus is characterized by the production of a typical sporothrix-like asexual morph but is distinguished morphologically from other members of the O. piceae species complex by its large, multiseptate primary conidia. Phylogenetic analysis of DNA sequences from the nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and the β-tubulin (BTUB) and translation elongation factor 1-α (TEF1) genes supports the inclusion of O. haidensis as a distinct member within the O. piceae complex. To our knowledge, this is the first report of a blue stain fungus infecting yellow-cedar, an ecologically, culturally, and economically important conifer naturally distributed along the coastal forests of the Pacific Northwest in North America.
... Crenuchus spilurus was used to root the phylogenetic tree. The analysis was performed under the GTR þ I þ G substitution model estimated in MrModeltest 2.2 (Nylander, 2004) together with PAUP Ã (Swofford, 1998) under the Akaike information criterion (AIC). Two runs of 10 million generations each and four Markov Monte Carlo (MCMC) chains were performed, with 25% burn-in and parameters sampled every 1000 generations. ...
Characidium represents the most widely distributed and species-rich fish genus within the family Crenuchidae in the Neotropical region, with numerous species described over the last decade. Despite this taxonomic progress, the understanding of species boundaries and population variation within the genus remains limited. In response, an integrative study was undertaken, utilizing both morphological and molecular data from neotropical freshwater ecoregions with rivers that drain the Brazilian northeastern. The primary objective of this investigation was to elucidate taxonomic delimitations and, where relevant, propose new species hypotheses. Our results propose the existence of 15 operational taxonomic units (OTUs) as species hypotheses. Among these, 10 were identified as valid species, four represented morphotypes that hold the potential of constituting new species, and one OTU was determined as a new species, corroborated by all proposed delimitation methods. Our results demonstrated discrepancies between morphological and molecular data, highlighting the challenges in defining taxonomic boundaries within Characidium. Moreover, our findings provided insights into the intricate diversification history of Characidium species, applied to the species that occur in northeastern Brazilian drainages. We proposed that historical events, such as river connections and barriers, have played a significant role in shaping the current distribution patterns of the genus.
... Maximum parsimony (MP) bootstrap analyses were performed with PAUP v. 4.0a169 (Swofford 2002), with 1 000 bootstrap replicates using five rounds of heuristic search replicates with random addition of sequences and subsequent TBR branch swapping (MULTREES option in effect, steepest descent option not in effect, COLLAPSE command set to MINBRLEN, each replicate limited to 1 million rearrangements) during each bootstrap replicate. All molecular characters were unordered and given equal weight; analyses were performed with gaps treated as missing data; the COLLAPSE command was set to minbrlen. ...
Pestalotioid fungi were isolated in pure culture from symptomatic plants of Callistemon laevis, C. viminalis, Luma apiculata (marketed as "Myrtus luma"), Myrtus communis sub-sp. tarentina, and M. communis var. microphylla (M. communis 'Microphylla'), showing twig canker, dieback and defoliation. The isolates were identified to species by ITS, tef1 and tub2 sequences, which revealed the presence of six species of Neopestalotiopsis (N. camelliae-oleiferae, N. hispanica, N. iberica, N. rosae, N. rosicola, and N. zakeelii) and one species of Pestalotiopsis (P. biciliata). While most species were isolated only once or twice, the majority of isolates belonged to N. rosae (13) and N. hispanica (8). Pathoge-nicity was investigated by pathogenicity tests on all hosts, which confirmed the patho-genicity of all Neopestalotiopsis species on at least some of the hosts tested, while P. bi-ciliata did not cause any disease symptoms. Neopestalotiopsis hispanica and N. rosae caused symptoms in all hosts of the present study, while the other Neopestalotiopsis species tested showed no symptoms on Luma apiculata.
... The matrix includes 20 taxa and 30 characters (see SOM, Supplementary Online Material available at http://app.pan. pl/SOM/app69-Zhang_etal_SOM.pdf) and was performed with PAUP 4.0b10 (Swofford 1993) under the heuristic search option. All characters are treated as unordered and are equally weighted. ...
... To further evaluate the identity of Rhodomonas strains included in the phylogenetic analyses, divergence estimates for all pairwise comparisons (including Rhinomonas reticulata and Pyrenomonas helgolandii) were made using PAUP* (Swofford 2003). A total of 1,610 base pairs of the SSU rDNA gene were included. ...
Rhodomonas (Cryptophyceae) and species assigned to this genus have undergone numerous taxonomic revisions. This also applies to R. marina studied here as it was originally assigned as a species of Cryptomonas and later considered a variation of R. baltica, the type species. Despite being described more than 130 years ago, R. marina still lacks a comprehensive characterization. Light and electron microscopy were employed to delineate a strain from western Greenland. The living cells were 18 μm long and 9 μm wide, elliptical in shape with a pointed to rounded posterior and truncated anterior in lateral view. Two sub-equal flagella emerged from a vestibulum, where also a furrow extended. In transmission electron microscopy, the furrow was associated with a tubular gullet and the pyrenoid embedded in a deeply lobed chloroplast. The chloroplast contained DNA in perforations and was surrounded by starch grains. A tubular nucleomorph was enclosed within the pyrenoid matrix. In scanning electron microscopy, the inner periplast consisted of rectangular plates with rounded edges and posteriorly these were replaced by a sheet-like structure. The water-soluble pigment was Crypto-Phycoerythrin type I (Cr-PE 545). A phylogenetic inference based on SSU rDNA confirmed the identity of strain S18 as a species of Rhodomonas as it clustered with congeners but also Rhinomonas, Storeatula, and Pyrenomonas. These genera formed a monophyletic clade separated from a diverse assemblage of other cryptophyte genera. To further explore the phylogeny of R. marina a concatenated phylogenetic analysis based on the SSU rDNA-ITS1-5.8S rDNA-ITS2- LSU rDNA region was performed but included only closely related species. The secondary structure of nuclear internal transcribed spacer 2 was predicted and compared to similar structures in related species. Using morphological and molecular signatures as diagnostic features the description of R. marina was emended.
... Ambiguous regions were excluded from the analyses and gaps were treated as missing data. The phylogeny website tool "ALTER" (Glez-Peña et al. 2010) was used to convert the alignment fasta file to Phylip format for RAxML analysis and AliView and PAUP 4.0 b 10 were used to convert the alignment fasta file to a Nexus file for Bayesian analysis (Swofford 2003). ...
Ganoderma is a large and diverse genus containing fungi that cause white rot to infect a number of plant families. This study describes G. phyllanthicola and G. suae as new species from Southwest China, based on morphological and molecular evidence. Ganoderma phyllanthicola is characterized by dark brown to purplish black pileus surface with dense concentric furrows, pale yellow margin, irregular pileipellis cells, small pores (5–7 per mm) and ellipsoid to sub-globose basidiospores (8.5–10.0 × 6.0–7.5 µm). Ganoderma suae is characterized by reddish brown to oxblood red pileus surface and lead gray to greyish-white pore surface, heterogeneous context, wavy margin and almond-shaped to narrow ellipsoid basidiospores (8.0–10.5 × 5.0–7.0 μm). The phylogeny of Ganoderma is reconstructed with multi-gene sequences: the internal transcribed spacer region (ITS), the large subunit (nrLSU), translation elongation factor 1-α gene (TEF-1α) and the second subunit of RNA polymerase II (RPB2). The results show that G. suae and G. phyllanthicola formed two distinct line-ages within Ganoderma. Descriptions, illustrations and phylogenetic analyses results of the two new species are presented.
... Sequences were aligned using MAFFT (Multiple Alignment using Fast Fourier Transform) algorithm (Katoh and Toh 2008), as implemented in Geneious and the final alignment was checked with Geneious and Mesquite v. 3.04 (Maddison and Maddison 2015). Sequence divergences (uncorrected p-distances) of 18S among genera were calculated using PAUP*4.0b 10 (Swofford 2002). ...
... The new sequences were aligned with MAFFT 7.490 (Katoh & Standley, 2013) to ITS and Cox1 sequences from type or authentic strains of ingroup and outgroup species retrieved from Gen-Bank. For each DNA barcode sequence, a neighbour-joining (NJ) tree was constructed using the Kimura-2-parameter model (Kimura, 1980) with 1000 bootstrap replicates in PAUP 4.0b10 (Swofford, 2003). The resulting trees were used to determine relationships among barcode sequences based on sequence similarities, rather than for phylogenetic reconstruction. ...
Pythium sensu stricto (s.s.) and Globisporangium species are important components of the soil microbial community and exhibit diverse lifestyles, including mycoparasitism. However, a comprehensive understanding of the species diversity of these mycoparasites in the West Azarbaijan province of Iran is lacking. In this study, a total of 114 mycoparasitic Pythium s.s. and Globisporangium isolates were obtained from agricultural soils collected from six regions in the province. Through DNA barcoding, all Globisporangium isolates were identified as G. nunn, while the barcode markers were insufficient to accurately resolve species boundaries in Pythium s.s. By combining morphological and multilocus sequence data, five species within the genus Pythium s.s. were identified: P. salmasense sp. nov., a potentially new species, and three known species, P. acanthicum, P. ornamentatum, and P. periplocum. Pythium ornamentatum was the most common species and found in all regions studied, followed by G. nunn and P. acanthicum, which were both isolated from four regions. While the isolates of G. nunn showed no mycoparasitic activity against Sclerotinia sclerotiorum, all Pythium s.s. species were capable of infecting the hyphae of this pathogen. The existence of mycoparasitic species is promising for biological control of soil‐borne fungal pathogens in the province. The widespread occurrence of P. ornamentatum, G. nunn, and P. acanthicum may suggest their adaptation to local soil and environmental conditions, indicating their potentially superior effectiveness in controlling plant diseases across different regions if used as biocontrol agents.
... To account for the possibility that any discordance in our trees is due to hybridisation (given the possibility for historic migration between islands) or incomplete lineage sorting (ILS), we applied the species tree reconstruction method SVDQuartets (Chifman and Kubatko, 2014) implemented in PAUP* v.4.0a (Swofford, 2003). Analysis was run on a NEXUS formatted alignment (with no restrictions on ambiguity codes), using exhaustive sampling (38,528 quartets) and with 100 bootstrap replicates. ...
... 33 As an outgroup, a sequence of the closely related Candida haemulonii was used. Phylogenetic analysis utilised both the neighbor-joining (NJ) and Bayesian inference (BI) techniques, conducted through MEGA X 34 , PAUP 35 , and MrBayes (ver. 3) 36 . ...
Candida auris is an emerging fungal pathogen associated with multi-drug resistance rates and widespread outbreaks in hospitals and health care units worldwide. Sequencing studies have revealed that different clonal lineages of the fungus seem to be prevalent among distinct geographical sites. The first case of C. auris in Northern Greece was reported in Thessaloniki in October 2022, almost two years after the first isolation in Greece (Athens 2019). The Mycology Laboratory of the Medical School of Aristotle University of Thessaloniki stands as the reference laboratory for fungal diseases in Northern Greece and a meticulous search for the yeast, in plenty of suspicious samples, has been run since 2019 in the Lab as well as a retrospective analysis of all its yeasts’ collection, back to 2008, with negative results for the presence of C. auris. Here, are presented the findings concerning the outbreak and surveillance of C. auris in Northern Greece, mainly the region of Thessaloniki and the broader area of Macedonia, from October 2022 until August 2023. The isolates from Northern Greece continue to fall in Clade I and present with an almost equal and stable sensitivity profile until now.
... Garzapelta muelleri (Reyes et al., 2024). The dataset was constructed in PAUP* 4.0 (Swofford, 2003) and exported as a NEXUS (Maddison et al., 1997) file. ...
Recent collecting of fossil vertebrates in the Chinle Formation at Petrified Forest National Park (PEFO) and reinvestigation of historic collections resulted in the recognition of a new aetosaurian taxon, Kryphioparma caerula. Although distinctive, K. caerula was initially described from several fragmentary paramedian osteoderms from PEFO and the nearby Placerias Quarry, however the anatomy of the lateral osteoderms remained unknown. Here, we refer an isolated lateral osteoderm from the Placerias Quarry to K. caerula based on an ornamentation composed of large elliptical-to-rounded pits on the dorsal surface that are randomly arranged, a prominent anterior bar, a strongly obtuse angle between two partially preserved flanges, an elongate lateral eminence (spine) with a strongly embayed posterior margin, and sharp anterior ridge. This combination of anatomical features of the isolated lateral osteo-derm is clearly aetosaurian and differs in significant ways from the other known aeto-saurian taxa from the site. A parsimony analysis recovers K. caerula nested within the inclusive clade Typothoracinae. This lateral osteoderm demonstrates that K. caerula was a spinose aetosaur, a bauplan observed in both typothoracine and desmatosuchin aetosaurians. Thus, further highlighting observed convergence between these groups and indicating a need for a reevaluation of lateral osteoderm characters used for phy-logenetic analyses.
... were also included in the analysis to complete the first evolutionary lineage as recognized by Friesen & al. (2006). Parsimony analysis was performed with PAUP* v.4.0b10 (Swofford, 2002) using heuristic searches with tree bisection-reconnection (TBR) branch swapping and 100 random addition sequence replicates without tree limit. Bootstrap support (BS; Felsenstein, 1985) was estimated with 1000 bootstrap replicates, each with 100 random addition sequence searches. ...
The present study aims to reveal phylogenetic and phylogeographical patterns of the Eurasian species of Allium subg. Amerallium, covering 75% of the species in the Mediterranean region and East Asia, as well as 12 North American species representing most sections of the monophyletic American part of the subgenus. We sampled 38 species of A. subg. Amerallium out of a total of 52 species from the Old World. A molecular phylogeny of A. subg. Amerallium was constructed based on predominantly non-coding sequences from two nuclear ribosomal RNA regions (ITS, ETS), and four chloroplast (cp) regions (trnL-trnF, atpB-rbcL, rpl32-trnL, rps16 intron). Most clades are well supported in the analyses of the combined nuclear and chloroplast data. However, analyses of single chloroplast fragments produced different topologies, which can be explained by differences in the variability of the chloroplast regions studied. Analysis of all cpDNA fragments combined produced a similar topology compared to the tree based on nuclear data. Most sections in the Eurasian part of A. subg. Amerallium are monophyletic. Only the position of A. chamaemoly (monotypic A. sect. Chamaeprason) nested in A. sect. Molium makes the latter paraphyletic. Different positions of A. chamaemoly within nuclear and plastid trees indicate an ancient hybridogenic origin. Monophyly of the American species of A. subg. Amerallium suggests an origin from extinct North Asian taxa. Currently, only one species from this ancient group, A. kingdonii, still exists in the eastern Himalayas.
... Each Bayesian analysis comprised two independent runs of 2,000,000 generations from a random starting tree with one cold chain and three hot chains, and sampled the cold chain every 100 generations. Maximum Parsimony (MP) was constructed by PAUP* v.4.0b10 (Swofford, 2002) with 1000 bootstrap replicates using heuristic search. For the MSC method, recent studies have suggested that this method can yield a more accurate phylogenetic backbone when using plastid datasets (Gonçalves et al., 2019). ...
Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, investigations into the relationship between hybridization events and fern diversity are notably lacking. Lecanopteris s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within Lecanopteris through the integration of phylo-biogeography reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size in Lecanopteris, attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional 'pumila' and 'crustacea' groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the 'pumila' and 'darnaedii' groups; (5) L. luzonensis is the maternal parent of L. 'Yellow Tip', with L. pumila suggested as a possible paternal parent; (6) L. 'Tatsuta' is a hybrid between L. luzonensis and L. crustacea; (7) Lecanopteris first diverged during the Neogene and then during the middle Miocene climatic optimum in Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of Lecanopteris have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of Lecanopteris.
... The sequence alignments were analysed with Bayesian inference (BI) using MrBayes 3.1.2 (Ronquist & Huelsenbeck, 2003) with maximum likelihood (ML) using PAUP* 4.0a169 (Swofford, 2003). The BI analysis for each gene was initiated with a random starting tree and was run with four chains for 1.0 × 10 6 generations. ...
Using results of the phylogenetic analysis of rRNA gene sequences and morphological data of Anguinoidea, a narrow definition for the genus Ditylenchus Filipjev, 1936 is proposed and discussed. Two new genera, Ditylenchoides gen. n. with type species, Ditylenchoides destructor (Thorne, 1945) gen. n., com. n. and other fourteen species and genus Paraditylenchus gen. n. containing the type species, Paraditylenchus gallaeformans (Oliveira et al., 2013) gen. n., com. n. are erected. Adults of the genus Ditylenchoides gen. n. differs from those of Ditylenchus in body length, number of incisures in lateral field, tail terminus shape and types of plant symptoms induced. Paraditylenchus gen. n. differs from Ditylenchus in body length, post-vulval uterine sac length and bursa length. Ditylenchus drepanocercus Goodey, 1953 is transferred to the genus Zeatylenchus Zhao et al., 2013 as Zeatylenchus drepanocercus (Goodey, 1953) comb. n. New diagnoses for the genera Ditylenchus and Zeatylenchus are also proposed. Phylogenetic results indicate independent origins of the ability to induce gall formation and tissue swelling in plants within representatives of the superfamily Anguinoidea.
... We carried out parsimony and Bayesian phylogenetic analyses. We used PAUP 4.0 (Swofford, 2017) for the parsimony analysis, with Petrolacosaurus kansensis selected as outgroup, all characters treated as ordered, and completing a heuristic maximum parsimony analysis, with random-addition sequences (1000 replicates), tree bisection and reconnections, and a maximum of 1000 trees. Strict and majority rule consensus (MCR) trees (50%) were then produced. ...
... The phylogenetic analysis was carried out with PAUP 4.0a 169 (Swofford 2002). A heuristic search retained four most parsimonious trees (length ¼ 644; Consistency Index ¼ 0.4658; Homoplasy Index ¼ 0.6025; Retention Index ¼ 0.7509) and resolved A. australis as a member of Archaeomenidae at Node D. Other cladograms (Fig. 11) for major clades include: Node L, Varasichthyidae as a sister group of crown teleosts; Node E, Pholidophoridae; Node G, Ankylophoridae as a sister clade; Node C, Prohalecites as sister to other Teleostei. ...
The discovery of an exceptionally preserved specimen of the Mesozoic teleost fish Aphnelepis australis from the upper Kimmeridgian (Upper Jurassic) Talbragar Fossil Fish Bed in New South Wales, together with historic confusion over its phylogenetic affinities, has prompted a detailed reassessment of the taxon. The new specimen of A. australis is skeletally complete and exhibits the dorsal fin with long principal dorsal fin rays and characteristic squamation comprising heavy rhombic scales anterior to insertions of the dorsal fin and anal fin, and much lighter and thinner weakly crenulate scales on the posterior half of the body. A cladistic analysis resolves A. australis as a member of Archaeomenidae, along with Archaeomene tenuis, Wadeichthys oxyops, Oreochima ellioti, Gurvanichthys mongoliensis, Zaxilepis quinglongensis, and Aphnelepis australis.
... For a technical hierarchical illustration of the ITS1 variation, we used an MP (maximum parsimony) algorithm implemented in PAUP 4.0 (Swofford, 2003). Heteroplasmic positions with double peaks were IUPAC-coded. ...
Ancient lakes are hotspots of species diversity, posing challenges and opportunities for exploration of the dynamics of endemic diversification. Lake Baikal in Siberia, the oldest lake in the world, hosts a particularly rich crustacean fauna, including the largest known species flock of harpacticoid copepods with some 70 species. Here, we focused on exploring the diversity and evolution within a single nominal species, Harpacticella inopinata Sars, 1908, using molecular markers (mitochondrial COI, nuclear ITS1 and 28S rRNA) and a set of qualitative and quantitative morphological traits. Five major mitochondrial lineages were recognized, with model‐corrected COI distances of 0.20–0.37. A concordant pattern was seen in the nuclear data set, and qualitative morphological traits also distinguish a part of the lineages. All this suggests the presence of several hitherto unrecognized cryptic taxa within the baikalian H. inopinata, with long independent histories. The abundances, distributions and inferred demographic histories were different among taxa. Two taxa, H. inopinata CE and H. inopinata CW, were widespread on the eastern and western coasts, respectively, and were largely allopatric. Patterns in mitochondrial variation, that is, shallow star‐like haplotype networks, suggest these taxa have spread through the lake relatively recently. Three other taxa, H. inopinata RE, RW and RW2, instead were rare and had more localized distributions on either coast, but showed deeper intraspecies genealogies, suggesting older regional presence. The rare taxa were often found in sympatry with the others and occasionally introgressed by mtDNA from the common ones. The mitochondrial divergence between and within the H. inopinata lineages is still unexpectedly deep, suggesting an unusually high molecular rate. The recognition of true systematic diversity in the evaluation and management of ecosystems is important in hotspots, as it is everywhere else, while the translation of the diversity into a formal taxonomy remains a challenge.
... The DNA sequences were edited and assembled using the Phylogenetic analyses of the sequence data were performed using the maximum parsimony (MP) in PAUP version 4.0b10 (Swofford, 2003). For MP analysis, all characters were equally weighted, gaps were treated as missing, and character states were treated as unordered. ...
In the present study, specimens kept in Fungarium of Van Yüzüncü Yıl University-Türkiye (VANF) were evaluated based on morphological and molecular characters, and identified as Dissingia confusa as a new record from Eastern Türkiye. Ascocarp, hymenium, stipe, ascospores, ascus and paraphyses were considered as diagnostic morphological characters and the nucleotide sequences of the large subunit (LSU) ribosomal DNA and the translation elongation factor 1-alpha (TEF1-α) were referred as molecular data. A phylogenetic analysis was performed with Maximum parsimony and Bayesian inference methods. The DNA sequences of 15 (7 for TEF1-α) Dissingia and 27 (14 for TEF1-α) Helvella specimens downloaded from the GenBank database were included in the analysis to estimate phylogeny between the two close genera. Morphological evaluations and genetic evidences confirmed that Dissingia is phylogenetically separated from Helvella at genus level and helped to identify the studied specimens as D. confusa as a new record in Türkiye. Detailed description, colour images of fresh and dried ascomata, along with photographs of microscopic characters and the obtained phylogenetic trees are given.
... To evaluate statistical congruence amongst the loci RPB2 and TEF1, the partition homogeneity test (PHT) was performed in PAUP*4.0b10 (Swofford 2002) with 1000 replicates. The aligned sequences were combined in BioEdit and analyzed with Bayesian inference (BI) and maximum likelihood (ML) methods to determine the phylogenetic position of the specimens. ...
Trichoderma clavaticapitatum sp. nov. is described and illustrated based on specimen collected from alpine Hengduan Mountains, Yunnan Province, China. The fungus is characterized by simple, clavate stromata with a capitate fertile part, flask-shaped, subglobose to oblong perithecia, and cylindrical asci containing 16 part-ascospores. Morphological characteristics and analyses of combined RPB2 and TEF1 DNA sequences support its placement in Trichoderma. Differences between the novel species and its close relatives are compared in detail. Additionally, Hypocreopsis rhododendri, a rare fungus, is reported for the first time from the country.
... As in Hershkovitz (2024a), I performed MP, ML, and MP bootstrap (1000 replicates) analyses for the separate and combined data sets using PAUP version 4 (Swofford, 2003). The ML analysis used the general time-reversible substitution model with gamma among-site rate variation correction and all parameters estimated using an MP tree. ...
Reanalysis of Mutisioideae nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) rpl32-trnL spacer sequences demonstrates that the monotypic genus Macrachaenium Hook.f. pertains to Mutisioideae (Asteraceae) tribe Mutisieae, in which it was classified formerly, and not Nassauvieae, in which it is classified currently. The analysis also highlights persistent uncertainty regarding the relations of the genus Spinoliva G.Sancho, Luebert & Katinas.
... The sequences of Scopuloides allantoidea C.C. Chen & Sheng H. Wu (2021: 432) and S. rimosa (Cooke) Jülich (1982: 422) obtained from GenBank were used as outgroups to root trees following Zhao et al. (2023). Maximum parsimony analysis was performed in PAUP* version 4.0b10 (Swofford 2002) with the same parameters described by Song et al. (2016) All characters were equally weighted, and gaps were treated as missing data. Trees were inferred using the heuristic search option with tree bisection and reconnection (TBR) branch swapping and 1000 random sequence additions, maxtrees were set to 5000, branches of zero length were collapsed, and all parsimonious trees were saved. ...
A new poroid wood-inhabiting fungus in the Polyporales, Luteoporia tenuissima, from southwest China, is described based on morphological and molecular evidence. Luteoporia tenuissima is characterized by annual, resupinate basidiomata with lemon chrome pores when fresh, becoming cinnamon buff when dry, tissues becoming purple in KOH, a monomitic hyphal system, generative hyphae thick-walled and bearing clamp connections, and ellipsoid, smooth basidiospores measuring 2.9–3.8 × 1.9–2.4 µm. The phylogenetic analysis based on ITS + nLSU rDNA sequences shows that the new species belongs to Luteoporia, forming a monophyletic lineage with strong support, clustering with L. albomarginata and L. citriniporia. Both morphological characteristics and molecular phylogeny confirm the placement of the new species within the genus Luteoporia. A full description, illustration, phylogeny of the new species, and comparisons with morphologically similar or phylogenetically related species are provided. In addition, an identification key is provided for the currently known Luteoporia species.
... The data set was concatenated including all mtDNA and nuclear fragments and partitioned by fragment and codon position. Appropriate models of nucleotide substitution for Bayesian analyses were identified using the program MrModeltest v2.2 (Nylander, 2004), run in PAUP Ã v4.0b10 (Swofford, 2002). The best-fit models were selected using the Akaike information criterion (AIC). ...
... Utilizing SequenceMatrix v1.7.8, we connected the aligned mitochondrial genes to form a single, unified mitochondrial dataset (Vaidya et al. 2011). In order to detect any phylogenetic discrepancies between distinct mitochondrial genes, an initial partition homogeneity test was performed using PAUP v 4.0b10 (Swofford 2002) according to previous studies (Xiang et al. 2013). PartitionFinder 2.1.1 was utilized to pinpoint the most suitable models of partitioning and evolutionary processes for the merged mitochondrial dataset (Lanfear et al. 2017). ...
Rhizopus microsporus Tiegh. 1875 is widely used in a variety of industries, such as brewing, wine making, baking, and medicine production, as it has the capability to break down proteins and generate surface-active agents. To date, the mitochondrial genome features of early evolved fungi from the Rhizopus genus have not been extensively studied. Our research obtained a full mitochondrial genome of R. microsporus species, which was 43,837 bp in size and had a GC content of 24.93%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 7 intronic ORFs, 24 tRNAs, and 2 rRNA genes. Through the use of the BI phylogenetic inference method, we were able to create phylogenetic trees for 25 early differentiation fungi which strongly supported the major clades; this indicated that R. microsporus is most closely related to Rhizopus oryzae.
... Second, we inferred a species-level phylogeny using a coalescent model in the program SVDquartets (Chifman & Kubatko, 2014), as implemented by PAUP v.4.0a166 (Swofford, 2002). Analyses were performed using the MS30 dataset, with all individuals grouped by taxa and omitting the mat-forming outgroup. ...
The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation.
Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification.
Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species.
Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
... Primary collection data for voucher specimens are deposited in the EMEC public database at https://essigdb.berkeley.edu/. The DNA sequences used include those previously used in the revision of Nurus (Will and Monteith 2018) Models of nucleotide evolution were chosen for each partition and base position for the coding sequences with the aid of mrModelTest (Nylander 2004) and PAUP* (Swofford 2002). Using the hierarchical likelihood ratio test and Akaike information criterion (Akaike 1973), the chosen models applied were GTR+I+Γ for 28S, CAD2 position 3, and COI position 3; GTR for CAD2 positions 1-2; and HKY+I+Γ for COI positions 1-2. ...
The genus Nuridius Sloane is revised and expanded to 10 species including its type species Nuridius fortis Sloane, 1890, three newly described species: Nuridius frickei sp. nov., type locality Peases Lookout, Eungella National Park, QLD, Nuridius pluto sp. nov., type locality Jimna State Forest, QLD, and Nuridius darlingtoni sp. nov., type locality Bulburin National Park, QLD, and six species previously included in Nurus Motschulsky that are here combined in Nuridius: Nuridius curtus (Chaudoir, 1865), Nuridius grandis Sloane, 1910, Nuridius nox (Darlington, 1961), Nuridius medius (Darlington, 1961), Nuridius rex (Darlington, 1961), and Nuridius niger
(Chaudoir, 1878). Pachymelas Tschitschérine, 1902 is considered a junior synonym of Nuridius. Bayesian analyses of a combined matrix and partitioned matrices of partial sequences from three loci (28S, COI and CAD) found support for Nuridius as a clade separate from Nurus. The comparative study of morphological features allows for recognition of the 10 species and an identification key is provided. Images of habitus and key external features, along with the aedeagus of each species are provided. All species distributions are mapped, and biogeographical implications discussed. Short notes are given on burrow-making and egg deposition into formed, two-part soil capsules by species of both Nurus and Nuridius. Conservation issues are briefly discussed
Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources.
Pseudips Cognato, 2000 species are distributed in the western mountains of China and in western North America where
they feed and complete their life cycle under the bark of spruce and pine trees (Pinaceae: Picea and Pinus spp.). The phylogenetic
relationships of the three previously recognized species are as follows: Pseudips orientalis (Wood and Yin, 1986)
is sister to a monophyletic group consisting of Pseudips concinnus (Mannerheim, 1852) and Pseudips mexicanus (Hopkins,
1905). Morphological variation has been observed among some populations which has challenged species boundaries. We
conducted a review of morphological characters and reconstructed a DNA-based phylogeny of individuals from multiple,
widely disjunct locations to test the limits of the three species. A mostly resolved DNA-based phylogeny demonstrated
reciprocal monophyly for Canadian/US and Mexican populations, no overlap of inter- and intraspecific pairwise COI DNA
sequence differences, and corroborated diagnostic morphological characters. In addition, >10% COI DNA sequence difference
as well as diagnostic morphological characters were observed between P. orientalis individuals from Tibet and Qinghai,
China. As a result, Pseudips radiatae (Hopkins, 1915), status restored is resurrected from synonymy with P. mexicanus
and Pseudips yak Cognato and Smith, new species is described. Potential prehistoric environmental scenarios contributing
to Pseudips speciation are discussed.
We provide the first conclusive evidence that at least one leech species ( Chtonobdella sp . from Madagascar) can jump. For each jump, the leech coils back before taking off. Visually, this appears somewhat like a backbending cobra or a spring being pulled back to maximize potential energy.
Abstract in Malagasy is available with online material.
Rhytismatales M.E. Barr ex Minter (Leotiomycetes, Ascomycota) is an order mostly consists of plant-associated ascomycetes with a global distribution. Among host plant taxa in diverse relationships, Rhododendron L. is one of the most preferred host genera of Rhytismatales. Rhododendron is the largest genus of Ericaceae Juss. and presents a high species diversity in southwestern China. In this study, the species diversity of Rhytismatales on twigs of Rhododendron spp. is investigated based on over 100 specimens recently collected in China. These were examined morphologically and by multi-gene phylogenetic analyses based on molecular sequence data from the internal transcribed spacer (ITS) region, the large subunit of the ribosomal RNA gene (nrLSU) and the mitochondrial small subunit (mtSSU rDNA). Eight monophyletic groups with strong support and distinct morphological characteristics are proposed as new genera, namely Lophodermiopsis, Neotryblidiopsis, Occultimyces, Rhodohypoderma, Septofusella, Septomyces, Shuqunia, and Yingrenia. Thirty-three new species are recognized, and three new combinations are proposed. Apparently, twigs of Rhododendron spp. have been repeatedly colonized during evolution by members of Rhytismatales and most of these species specifically develop their ascomata on this substrate. Radiation on this substrate occurred relatively recently leading to species diversity within genera. Information on all 54 species of Rhytismatales on twigs of Rhododendron spp. are combined in a complete revision of this group of fungi based on morphological characteristics and phylogenetic analyses. Keys to genera and species of Rhytismatales on twigs of Rhododendron spp. worldwide are provided. The results of the molecular phylogenetic analysis indicate that a natural classification of Rhytismatales on genus level cannot be defined based on few morphological characteristics, but a combination of many morphological characteristics together with information derived from molecular sequence data, the host relationship, as well as the organ infected are necessary. Keywords-36 new taxa-Host organ specificity-Phylogeny-Taxonomy INTRODUCTION The order Rhytismatales M.E. Barr ex Minter belongs to Leotiomycetes (Ascomycota) and
Colletotrichum species cause the anthracnose disease that affects a wide variety of fruit, vegetable, and ornamental hosts. During the summer of 2018–2019, infected leaves of Ficus benjamina var. variegata with typical anthracnose symptoms were collected from several greenhouses in Miyandoab (West Azarbaijan Province) and Maraghe (East Azarbaijan Province) counties, Iran, with an incidence of 10 to 21%. The fungus was isolated and identified as Colletotrichum orchidearum, based on morphological features and multi-gene sequence analyses (ITS‒rDNA, GAPDH, CHS-1, HIS3, ACT and TUB2 genes). Pathogenicity assays were conducted on two-year-old potted plants with conidial suspensions under greenhouse conditions. Typical anthracnose symptoms including fungal conidiomata were developed on the inoculated leaves, while control plants remained symptomless. Re-isolation and re-identification of the inoculated fungi confirmed Koch’s postulates. This study provides the first evidence of C. orchidearum causing anthracnose disease on Ficus benjamina var. variegata in Iran and the world.
The molecular phylogeny of Kazakhstan’s Fritillaria karelinii (Fisch. ex D. Don) Baker was reconstructed and analyzed to confirm its genetic identification and phylogenetic position. The BLAST results were matched at a high rate of 98%, and (nrITS and rbcL) formed a single clade in the phylogenetic analysis. The studied plant belongs to the branch of the subgenus Fritillaria Tourn. ex L., which is consistent with the literature. This confirmed a clear genetic identification and taxonomic position of the studied plant. Despite some sequence differences between the Kazakhstani and Chinese species (C1, C3, C5) found in the nrITS region, no specific sequence existed for the other markers (rbcL and trnH-psbA). The outcomes of the antioxidant activity of F. karelinii fractions were prepared by extraction with 70% ethanol and separation into several fractions using the partition procedure with chloroform, ethyl acetate, n-butanol, and water. Among these, the ethyl acetate fraction most significantly affected the activity in the FC, DPPH, and FRAP assays.
The genus Tarzetta is distributed mainly in temperate forests and establishes ectomycorrhizal associations with angiosperms and gymnosperms. Studies on this genus are scarce in México. A visual, morphological, and molecular (ITS-LSU) description of T. americupularis, T. cupressicola, T. davidii, T. durangensis, T. mesophila, T. mexicana, T. miquihuanensis, T. poblana, T. pseudobronca, T. texcocana, and T. victoriana was carried out in this work, associated with Abies, Quercus, and Pinus. The results of SEM showed an ornamented ascospores formation by Mexican Taxa; furthermore, the results showed that T. catinus and T. cupularis are only distributed in Europe and are not associated with any American host.
Flax (Linum usitatissimum L.), as the earliest oil and fiber crop, is a model plant for genetic inferences of plant domestication processes involving multiple domestication events. However, a puzzle has emerged from several genetic studies, as dehiscent cultivated flax is genetically more related to its progenitor pale flax (L. bienne Mill.), and winter cultivated flax is well mixed with oil or fiber cultivated flax, while capsular dehiscence and winter hardiness are the major characteristics of pale flax. For this, a comparative analysis was conducted with 16 Linum samples representing pale flax and four domestication groups of cultivated flax (oil, fiber, winter, and dehiscent) using 454 pyrosequencing, Sanger resequencing and microsatellite data. It was found that the genomic sampling of genetic variants from the three applied methods yielded similar genetic information on pale flax and four groups of cultivated flax. The revealed genetic relationships did not show significant departures from the previous findings, but instead supported an early, independent domestication of a primitive flax lineage for oil use, followed by a subsequent flax domestication process with multiple domestication events for capsular dehiscence, oil, fiber and winter hardiness. Domestication on capsular dehiscence occurred earlier than domestication on winter hardiness. Domestication on winter hardiness was more complicated than domestication on capsular dehiscence.
The presence of Dromornithidae in the Australian Cenozoic fossil record was first reported in 1872, yet although eight species and hundreds of specimens are known, key information on their morphology remains elusive. This is especially so for their skulls, which contributes to a lack of resolution regarding their relationships within Galloanserae. The skull of the Pleistocene dromornithid, Genyornis newtoni, was initially described in 1913. Additional fossils of this species have since been discovered and understanding of avian skull osteology, arthrology, and myological correlates has greatly advanced. Here we present a complete redescription of the skull of Genyornis newtoni, updating knowledge on its morphology, soft-tissue correlates, and palaeobiology. We explore the diversity within Dromornithidae and make comprehensive comparisons to fossil and extant galloanserans. Furthermore, we expand on the homologies of skull muscles, especially regarding the jaw adductors and address the conflicting and unstable placement of dromornithids within Galloanserae. Findings support generic distinction of Genyornis newtoni, and do not support the close association of Dromornithidae and Gastornithidae. We thus recommend removal of the dromornithids from the Gastornithiformes. Considering character polarities, the results of our phylogenetic analyses, and palaeogeography, our findings instead support the alternative hypotheses, of dromornithids within, or close to, the Suborder Anhimae with Anseriformes.
Sound management of coastal resources is based on science-based decisions. Bottlenose dolphins are found around Puerto Rico; however, limited information exists on the ecology, behavior, sex ratio, distribution patterns, and population structure presenting, challenges in managing the bottlenose dolphin as defined in the Marine Mammal Protection Act of 1972. We sequenced the mitochondrial control region (mtDNA-CR) of 27 live and 11 stranded dolphins from Puerto Rico, five stranded dolphins from Guadeloupe and included sequences from the North Atlantic and the Pacific Ocean. Our genetic data from the new samples indicates the presence of distinct genetic lineages (inshore—represented by coastal individuals) and worldwide-distributed form (represented by both coastal and offshore individuals) in Puerto Rico. DNA divergence between inshore/coastal and offshore haplotypes ranged from 4.34 to 6.58%. All haplotypes from Puerto Rico have been previously reported from the Caribbean and North Atlantic. Genetic analysis yielded a complex population structure without a clear geographic signal; an expected result from a highly mobile marine mammal. A clade consisting exclusively of coastal dolphins of the Caribbean and the western North Atlantic was recovered. Offshore haplotypes from the eastern and western North Atlantic were generally clustered with offshore haplotypes of the Caribbean. Coastal and offshore haplotypes from the Pacific differed from those from the Atlantic. When we partitioned the data by form (coastal vs. offshore) and ocean (Atlantic vs. Pacific), we detected significant population differentiation (FST = 0.4089), indicating limited gene flow between forms and across oceans.
Background
Wood-rotting fungi as an important group within the Basidiomycota are known for their ecological role in the forest ecosystem in terms of decaying living and dead trees and recycling nutrients in forest ecosystems. Many new species were revealed in the last five years. In the present study, during an ongoing study on Scytinostroma, a new species of Scytinostroma was found from China. It is described and illustrated on the basis of the morphological and phylogenetic evidence.
New information
Scytinostroma bambusinum sp. nov. is described as a new species, based on morphological and molecular evidence. It is characterised by annual, resupinate and broadly ellipsoid basidiomata with white to cream hymenophore, a dimitic hyphal structure with generative hyphae bearing simple septa, the presence of cystidioles and amyloid basidiospores measuring 5.5–7 × 4–5.3 µm. Phylogeny, based on molecular data of ITS and nLSU sequences, shows that the new species forms an independent lineage and is different in morphology from the existing species of Scytinostroma.
Despite the high biological and ecological diversity of the South China Sea, limited research has been conducted on the deep‐sea species diversity of caridean shrimps. Based on the collections from three scientific expeditions conducted in the South China Sea, 31 caridean species, belonging to nine families, were reported, including the identification of two species not previously documented in this region, namely Janicella spinicauda (A. Milne‐Edwards, 1883) and Systellaspis curvispina Crosnier, 1988. In addition to morphological features, the COI and 16S gene sequences of these species were analyzed to assess their evolutionary relationships within each family. Phylogenetic analyses, with highest species coverage to date, indicated that similarity in morphological characteristics does not always lead to closer phylogenetic relationships and some defining characteristics for specific taxa are not always synapomorphies but may be the result of convergent evolution. Our results establish reliable evolutionary relationships within specific taxa and highlight the necessity for further taxonomic revisions within these taxa.
Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in four species, including two paedophages, which began during the 1970s–1980s, and population size rebounded during the 1990s-2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines’ disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the four species that likely experienced bottleneck, Haplochromis sp. ‘matumbi hunter,’ a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the five paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.
Octopuses are an important fishery resource in the Ryukyu Archipelago, Japan, and Octopus cyanea is an important fishery resource in this region. Although a gradual downward trend in catches of O. cyanea in the Ryukyu Archipelago has been reported, no study has focused on the connectivity and genetic structure, which are important parameters for conservation strategies. We used partial sequences of mitochondrial COI and MIG‐seq, which can efficiently obtain single nucleotide polymorphism (SNPs) to evaluate genetic diversity and patterns of gene flow among three populations of O. cyanea in the Ryukyu Archipelago. We combined population genetic analyses with biophysical approaches to understand larval dispersal patterns and the regional connectivity. Although there was a tendency for the Yaeyama population to become isolated from the Okinawa‐jima populations, high genetic diversity was maintained overall, indicating frequent genetic exchange between populations. Population genetic analyses combined with larval dispersal simulations revealed that the contemporary migration of O. cyanea is asymmetric patterns among the three populations, suggesting that western coast of Okinawa‐jima Island functions as a source population among the three populations we examined. The potential implications of this study on the conservation management of O. cyanea were discussed, namely that future population assessment approaches are needed to include western coast of Okinawa‐jima populations. In addition, this study indicates that at least two different management units should be considered. This study is the first population genetic study of O. cyanea in the Ryukyu Archipelago and provides fundamental information on the genetic population structure of this species in this region.
An eco‐monitoring programme to assess faunal biodiversity in the main rivers of the northern Iberian Peninsula (Spain) reveals the first occurrence of the marbled crayfish Procambarus virginalis (Decapoda: Cambaridae) in Iberian inland waters. Iberian specimens have been identified by combining morphological and genetic traits. We discuss the most plausible pathways and introduction vectors, its potential invasiveness and subsequent impacts on host localities. Our preliminary results raise concern about the potential threat of P. virginalis to native fauna and ecosystem dynamics, as P. virginalis was found in an area of great cultural and ecological importance with relevant populations of endangered species. Due to the invasive history of the marbled crayfish, eradication of these individuals is urgent. This study confirms the importance of early warning systems for exotic species, keeping the population, forest guards and field technicians informed about potential invasive species to execute a rapid and effective response.
Premise
Shared geographical patterns of population genetic variation among related species is a powerful means to identify the historical events that drive diversification. The Sphagnum capillifolium complex is a group of closely related peat mosses within the Sphagnum subgenus Acutifolia and contains several circumboreal species whose ranges encompass both glaciated and unglaciated regions across the northern hemisphere. In this paper, we (1) inferred the phylogeny of subg. Acutifolia and (2) investigated patterns of population structure and genetic diversity among five circumboreal species within the S. capillifolium complex.
Methods
We generated RAD sequencing data from most species of the subg. Acutifolia and samples from across the distribution ranges of circumboreal species within the S. capillifolium complex.
Results
We resolved at least 14 phylogenetic clusters within the S. capillifolium complex. Five circumboreal species show some common patterns: One population system comprises plants in eastern North America and Europe, and another comprises plants in the Pacific Northwest or around the Beringian and Arctic regions. Alaska appears to be a hotspot for genetic admixture, genetic diversity, and sometimes endemic subclades.
Conclusions
Our results support the hypothesis that populations of five circumboreal species within the S. capillifolium complex survived in multiple refugia during the last glacial maximum. Long‐distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium could have contributed to current geographic patterns. These results indicate the important role of historical events in shaping the complex population structure of plants with broad distribution ranges.
With populations of land snails of very small size like Vertiginidae, questions have arisen as to whether populations of relatively distant islands in archipelagos are really isolated from each other. Apart from other flight agencies, airborne transport of loose specimens is not improbable in stormy weather conditions. Currently, mechanisms of wind-borne transport of sand particles over short and long distances have been intensively studied. The results are available in the literature on sediments, allowing the calculation of probable flight distances for particles in suspension.
For living snails of the Aegean species Truncatel-lina rothi, an average fall velocity of 2.6–2.7 m s⁻¹ has been determined in experiments under laboratory conditions. Applying these results, Truncatellina living on an island at 100 m altitude and close to the coast could be transported up to several kilometers in heavy storms, which are not uncommon in the Aegean archipelago (Greece). This would imply that many of the Aegean islands are not effectively isolated for minute snail species, and that genetic interchange between island populations is probably frequent.
A new statistical method for estimating divergence dates of species from DNA sequence data by a molecular clock approach is developed. This method takes into account effectively the information contained in a set of DNA sequence data. The molecular clock of mitochondrial DNA (mtDNA) was calibrated by setting the date of divergence between primates and ungulates at the Cretaceous-Tertiary boundary (65 million years ago), when the extinction of dinosaurs occurred. A generalized leastsquares method was applied in fitting a model to mtDNA sequence data, and the clock gave dates of 92.311.7, 13.31.5, 10.91.2, 3.70.6, and 2.70.6 million years ago (where the second of each pair of numbers is the standard deviation) for the separation of mouse, gibbon, orangutan, gorilla, and chimpanzee, respectively, from the line leading to humans. Although there is some uncertainty in the clock, this dating may pose a problem for the widely believed hypothesis that the bipedal creatureAustralopithecus afarensis, which lived some 3.7 million years ago at Laetoli in Tanzania and at Hadar in Ethiopia, was ancestral to man and evolved after the human-ape splitting. Another likelier possibility is that mtDNA was transferred through hybridization between a proto-human and a protochimpanzee after the former had developed bipedalism.
Viewed from a geological perspective, present-day animal and plant communities in many parts of the world have a remarkably short history. The environmental revolution at the end of the Pleistocene, a mere 10 000 years ago, triggered major shifts in the ranges of species and hence composition of communities. Present-day communities in the boreal and temperate zones assembled at this time by combining species that survived the northern environment of the Last Cold Stage with those returning from more temperate refugia. Increasing evidence suggests that the well-studied European southern and eastern refugia for thermophilous animal and plant taxa were supplemented by cryptic refugia in northern Europe during the Late Pleistocene. These northern refugia would have been in areas of sheltered topography that provided suitable stable microclimates, and could partially explain the ‘nonanalogue’ mammalian assemblages of the Late Pleistocene. They also have implications for phylogeography and speciation.
Indirect methods using genetic markers are the primary measure of gene flow levels among interbreeding populations. Results from studies employing these methods are often ambiguous and open to multiple interpretation. This is primarily due to low resolution of molecular markers and low precision of model-based estimates. Studies of paternity, kinship and phylogeography generate the most reliable results. Future studies should employ more powerful analytical methods, analyse loci independently, and attempt to distinguish confounding contributions of vicariance to isolation-by-distance studies. Moreover, direct assessment of movement remains the most valid approach to many key issues in population biology.
Although several decades of study have revealed the ubiquity of variation of evolutionary rates among sites, reliable methods for studying rate variation were not developed until very recently. Early methods fit theoretical distributions to the numbers of changes at sites inferred by parsimony and substantially underestimate the rate variation. Recent analyses show that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies.
We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.
Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimate intraspecific phylogenies in two ways: (1) rooting the phylogeny and (2) resolving ambiguities in a cladogram. This information will allow one to reduce the number of alternative phylogenies and incorporate the uncertainties involved in reconstructing intraspecific phylogenies into subsequent analyses that depend heavily on the topology of the tree.
Using two sets of nucleotide sequences of the human and simian T-cell leukemia/lymphoma virus type I (HTLV-I/STLV-I), one consisting of 522 bp of the env gene from 70 viral strains and the other a 140-bp segment from the pol gene of 52 viral strains, I estimated cladograms based on a statistical parsimony procedure that was developed specifically to estimate within-species gene trees. An extension of a nesting procedure is offered for sequence data that forms nested clades used in hypothesis testing. The nested clades were used to test three hypotheses relating to transmission of HTLV/STLV sequences: (1) Have cross-species transmissions occurred and, if so, how many? (2) In what direction have they occurred? (3) What are the geographic relationships of these transmission events? The analyses support a range of 11-16 cross-species transmissions throughout the history of these sequences. Additionally, outgroup weights were assigned to haplotypes using arguments from coalescence theory to infer directionality of transmission events. Conclusions on geographic origins of transmission events and particular viral strains are inconclusive due to small samples and inadequate sampling design. Finally, this approach is compared directly to results obtained from a traditional maximum parsimony approach and found to be superior at establishing relationships and identifying instances of transmission.
Mitochondrial DNA, inherited predominantly through the female line, has been exceptionally useful for reconstructing phylogenies (Avise, in Molecular markers, natural history and evolution. New York: Chapman and Hall (1994)). However, at the lowest taxonomic level, if there are polymorphisms within species the lineages of mitochondria need not correspond to the lineages of the species (Avise, in Phil. Trans. R. Soc. Lond. B 312, 325-342 (1986)). We find that a classic organism in ecological genetics, Cepaea nemoralis, has the most extreme intraspecific variation and polymorphism so far recorded, and that at least one other pulmonate land mollusc also has very high levels of mitochondrial diversity. Making the simplest assumptions, the data suggest times of divergence as long ago as 20 million years between haplotypes now coexisting within a single population. There are four overlapping explanations of the diversity: (i) that mitochondrial evolution in pulmonates is exceptionally fast; (ii) that the morphs have differentiated in isolated 'refuges' and then come together; (iii) that natural selection has acted to preserve the variation; and (iv) that the population structure of pulmonates favours the persistence of ancient haplotypes. We argue for the importance of the last explanation.
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
Keywords:cladogram estimation;gene genealogy;phylogeography;population genetics;software
Phylogenetic reconstruction--the method by which biologists examine the relationship between living and extinct organisms in an effort to identify evolutionary pathways--has seen radical changes in the last ten years. But as rapid advances in mathematical, molecular, developmental, and cladistic techniques have greatly improved reconstruction efforts, they have also sparked controversy, especially with regard to the assumptions and data underlying the cladistic method. This book brings together contributions from a wide range of practitioners in order to find common ground. By examining numerous models from a variety of fields, the book serves as a guide to the latest methods of classification and phylogeny reconstruction and provides insights into the relative merits that each approach has to offer. In particular, developmental studies emerge as a significant factor in cladogram construction. Splendidly written and wide-ranging in scope, Models in Phylogeny Reconstruction will be welcomed by students and researchers in systematic and evolutionary biology.
A new coalescent is introduced to study the genealogy of a sample from the infinite-alleles model of population genetics. This coalescent also records the age ordering of alleles in the sample. The distribution of this process is found explicitly for the Moran model, and is shown to be robust for a wide class of reproductive schemes.
Properties of the ages themselves and the relationship between ages and class sizes then follow readily.
The possibility that a high rate of selectively neutral mutation can account for both genetic polymorphism and gene substitution in evolution is investigated theoretically. A species divided into partially isolated local populations is considered, and relations found between the local population size, the number of populations, the migration and mutation rates, and the degree of polymorphism within and between populations. It is shown that if selectively neutral mutation rates are high enough (perhaps 10-6 per generation per cistron) to account for observed rates of evolution, then either the total population size of a species, now or in the geologically recent past, must be small (⩽106), or hybrids between local populations will be heterozygous at almost all loci.
Fossil land snail shells constitute a valuable source of paleoenvironmental information for the Quaternary. They can be dated by a variety of methods, including radiocarbon, amino acid racemization and epimerization, and perhaps also and ESR. The vast majority of paleoenvironmental studies based on land snail shells have examined the faunal composition of fossil assemblages, from which a variety of paleoenvironmental characteristics such as biome, temperature, and moisture conditions have been reconstructed. Still, there are a number of problems involved in using this approach and these are discussed. Shell morphology has occasionally been used to reconstruct such factors as rainfall and temperature. Stable isotope studies on Quaternary land snails include: analysis of δ18O values of organic matter in the shells, to reconstruct C4 plant distributions from which rainfall amounts can be inferred, and analysis of δ18O values of shell carbonate, from which trends in the oxygen isotope composition of rainfall can be reconstructed. Stable carbon isotopes of shell carbonate have also been studied but their interpretation is not clear. Amino acid epimerization analysis ( ratios) of land snail shells has been used for estimation of paleotemperatures. Some potential uses of land snail shells for paleoenvironmental reconstruction include the study of stable isotopes of H and N, periodic growth lines, and deposits of pedogenic carbonates on the shells.
When a population splits in two and the resulting populations evolve independently, genetic divergence may occur due to mutation and genetic drift. This paper considers the influence these factors have on the genetic composition of two samples drawn from the respective populations at some time after the split. Analytical formulas and numerical examples are given of (i) the probability distribution and moments of the allele frequencies, (ii) the number of alleles in common between the samples, and (iii) the probability that the samples are monomorphic.
Studies of population structure were undertaken at six sites in the Tenby (South Wales) colony of the Mediterranean coastal land snail Theba pisana (Müller). Over four years, the density of adult (two-year-old) snails was estimated as ranging from 39 to 202 m-
2 during the summer active season; half-grown juvenile (one-year-old) density was estimated during the same time of year as between 13 and 436 m-
2; no estimates were made of the density of younger snails. Significant aggregation was shown for both adults and juveniles. Estimates of variance of dispersal over 100 days (0489 to 1601 m2) suggest that T. pisana is rather sedentary when compared with the few other snail species for which comparable information is available. Combining the data on density and dispersal with an estimate of variance of family size, yields estimates of effective neighbourhood size ranging from 115 to 4130. These results are compared with data for other organisms, especially other species of land snail.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Helicid snails are suitable organisms for research addressing both ecological and evolutionary questions. They are easy to collect and mark, and because of their limited power of dispersal and their generally patchy distribution, snails exhibit extensive demographic and genetic population structure even on a microgeographic scale (Baur 1993). As one major group of land snails, several species of the family Helicidae are adapted to grassland ecosystems. Small land snails of the sub-family Helicellinae especially prefer habitats of dry open grassland with sparse vegetation. In Germany, habitat of this type is generated and maintained mainly by agricultural use, especially sheep grazing and viticulture. In the course of structural changes in agriculture during the last decades, sheep grazing has nearly vanished, and former grasslands and vineyards have either turned into intensively used monocultures or have been abandoned. This has led to a substantial loss of habitat due to natural succession and has resulted in progressive fragmentation and isolation (Henle & Kaule 1991). Thus, several snail species are endangered in Germany (Jungbluth 1986, Bogon 1990, Körnig 1992). We therefore focussed our research on two Helicellinae snails, Trochoidea geyeri (SOOS, 1926) and Candidula unifasciata (POIRET, 1801). Both species are rare today in Germany and are considered to be extinct in several states (Bundesländer). In the present case study, we analyse the population structure of T. geyeri and C. unifasciata in different grassland ecosystems: firstly, in the agricultural landscape near Halle (Bliss et al. this volume: 161–168), and secondly, in an abandoned vineyard complex on a limestone hill in the upper Kinzig valley (Hesse, Germany) with characteristic dry grassland on calciferous soil.
Population structure was estimated in a continuous population of a small land snail (Trochoidea geyeri). Mark-recapture experiments and randomly amplified polymorphic DNA analyses indicate that the population structure can be described by the isolation by distance model of Wright (1946). Estimates of density and dispersal suggest a neighbourhood size of 70-208 individuals on an area of 13-21 m(2). A principal component analysis of the randomly amplified polymorphic DNA data reveals clinal variation of genetic composition across the population, as predicted by the neighbourhood concept. An analysis of molecular variance indicates substantial genetic structuring. Comparisons of the genetic distances, expressed as euclidean distances among individuals, versus the geographic distance between sampling sites yield a highly significant positive correlation (Mantel test: r = 0.567, p < 0.0001). The revealed pattern of populational subdivision on a microgeographic scale seems to be one of the principal processes generating and maintaining genetic diversity within populations of small land gastropods.
The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.
The n-coalescent is a continuous-time Markov chain on a finite set of states, which describes the family relationships among a sample of n members drawn from a large haploid population. Its transition probabilities can be calculated from a factorization of the chain into two independent components, a pure death process and a discrete-time jump chain. For a deeper study, it is useful to construct a more complicated Markov process in which n-coalescents for all values of n are embedded in a natural way.
The application of principles from coalescence theory to genealogical relationships within species can provide insights into the process of diversification and the influence of biogeography on distributional patterns. There are several features that make some organisms more suitable for detailed studies of historical processes; in particular, limited dispersal, which serves to conserve the patterns of genetic variation that developed during colonization. We describe the potential benefits of studies that integrate analyses of genetic variation with information from the fossil pollen record and present recent examples of the application of quantitative methods of phylogeographic analysis.
Spectacular progress has been made recently in the study of evolution at the molecular level, primarily due to new biochemical techniques such as gene cloning and DNA sequencing. In this book, the author summarizes new developments and seeks to unify studies of evolutionary histories of organisms and the mechanisms of evolution into a single science - molecular evolutionary genetics.
A population of constant size is subjected to mutation, such that each mutant is of a new allelic type. For the particular population model studied in this paper, the age of an allele, whose present frequency is known, is a random variable with distribution independent of the frequencies of other alleles. As a consequence of reversibility of the population process, the age of an allele, from the past to the present, has the same distribution as its time to extinction, from the present into the future. This verifies, and re-interprets, certain diffusion approximations found by Kimura and Ohta [Genetics75, 199–212 (1973)] and Maruyama [Genet. Res. Cambridge23, 137–143 (1974)].
The n0 coalescent of Kingman (1982a, b) describes the family relationships among a sample of n0 individuals drawn from a panmictic species. It is a stochastic process resulting from n0 − 1 independent random events (coalescences) at each of which n (2 ≤ n ≤ n0) ancestral lineages of a sample are descended from n − 1 distinct ancestors for the first time. Here a similar genealogical process is studied for a species consisting of two populations with migration between them. The main interest is with the probability density of the time length between two successive coalescences and the spatial distribution of n − 1 ancestral lineages over two populations when n to n − 1 coalescence takes place. These are formulated based on a non-linear birth and death process with killing, and are used to derive several explicit formulae in selectively neutral population genetics models. To confirm and supplement the analytical results, a simulation method is proposed based on the underlying bivariate Markov chain. This method provides a general way for solving the present problem even when an analytical approach appears very difficult. It becomes clear that the effects of the present population structure are most conspicuous on 2 to 1 coalescence, with lesser extents on n to n − 1 (3 ≤ n) coalescence.This implies that in a more general model of population structure, the number of populations and the way in which a sample is drawn are important factors which determine the n0 coalescent.
The widespread use of restriction endonucleases and DNA sequencing provides a wealth of data on the genetic structure of natural populations. From such data, detailed phylogenies can be constructed and qualitatively different kinds of mutational and substitutional processes can be studied. A neutral model can be constructed to describe the frequencies of sequence haplotypes according to the haplotypes from which they arose and the types of substitution that distinguish them. One feature of such a model is that it examines the ancestors of various sequences. Deleterious selection against a character has a distinct effect on descendant sequences. Individuals containing many deleterious characters leave few or no descendants because these individuals are quickly eliminated by selection. Hence, such a model lends itself to the study of deleterious selection. It is possible to determine if selection is required by searching for any set of mutation rates that can explain an observed set of data. Simulations of artificial populations without selection suggest that this method seldom indicates selection when none is present. Furthermore, recent recombination events between the sequences do not induce false indications of deleterious selection. The method may, however, require relatively large simple sizes in order to accurately reflect the true nature of populations. The method is often very conservative and may not indicate selection when it is, in fact, present.
The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment
of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order
to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are
varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific
gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather
than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced
gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new
program, CLUSTAL W which is freely available.
The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the root of an intraspecific gene tree and the relative ages of the haplotypes. By using a recursive equation, exact root probabilities can be calculated for small cladograms and sample sizes. These exact probabilities indicate that root probabilities are not very sensitive to the parameter theta, which is four times the mutation rate times the inbreeding effective size. The exact probabilities also indicate that root probabilities are not very sensitive to the absolute numbers of each haplotype (allele) class, only their relative proportions. The exact method, unfortunately, is not feasible for implementation with larger data sets with present algorithms and computers. However, the exact results suggested a simple heuristic for determining outgroup weights; that is, finding the haplotype that is the oldest in the sample and that can serve as an outgroup for the remainder of the haplotype tree. Computer simulations revealed that these outgroup weights are strongly correlated with actual age and are much better indicators of haplotype age than is the haplotype frequency, another commonly used indicator of relative age.
We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.
A number of methods have already been described for the isolation of genomic DNA. Some methods of DNA isolation, for example CsCl-gradients, require large amounts of tissue, and are not suitable for the isolation of DNA from small tissue samples. Protocols that yield DNA in quality from small amounts of tissue frequently involve detergents (cetyltrimethylammonium bromide, SDS) or enzyme treatment (e.g. proteinases) in specialized buffer systems, whose preparation is often time consuming and expensive. We therefore developed a rapid method of DNA isolation using commercial biological laundry detergent concentrate (Persil Mega Perls( and Frosch( ) as detergent/buffer-system. Tissue (500 mg) was ground with sea sand in a 1.7 ml Eppendorf tube containing one spatula point of washing powder (40 mg) dissolved in 1.5 ml deionized water. The tissue/laundry detergent-mixture was then incubated overnight at 37C, and half of the resulting homogenate (750 ml) was extracted once with phenol-chloroform-isoamylalcohol (25:24:1), followed by RNAse treatment for 1 h at 37C (0.2 mg/ml), and one extraction with chloroform-isoamylalcohol. The DNA was precipitated overnight at -20C by adding 0.1 vol 3 M sodium acetate and 2 vol ice-cold 98% ethanol and centrifugated for 15 min
Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species' geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.
A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/.
Coalescent theory represents the most significant progress in theoretical population genetics in the past two decades of this century. It is now widely recognized as a cornerstone for rigorous statistical analyses of molecular data from populations. In the future, challenges from the rapidly expanding body of molecular data will continue to inject fresh blood into the development of coalescent theory. As the 21st century looms, we review recent progress in coalescent theory and discuss some prospects for future developments, particularly with regard to human population genetics.
The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.
Keywords:cladistic nested analysis;historical processes;phylogeography;population genetics;software
Mollusks are an extraordinarily diverse group of animals with an estimated 200,000 species, second only to the phylum Arthropoda. We conducted a comparative analysis of complete mitochondrial ribosomal large subunit sequences (LSU) of a chiton, two bivalves, six gastropods, and a cephalopod. In addition, we determined secondary structure models for each of them. Comparative analyses of nucleotide variation revealed substantial length variation among the taxa, with stylommatophoran gastropods possessing the shortest lengths. Phylogenetic analyses of the nucleotide sequence data supported the monophyly of Albinaria, Euhadra herklotsi + Cepaea nemoralis, Stylommatophora, Cerithioidea, and when only transversions are included, the Bivalvia. The phylogenetic limits of the mitochondrial LSU rRNA gene within mollusks appear to be up to 400 million years, although this estimate will have to be tested further with additional taxa. Our most novel finding was the discovery of phylogenetic signal in the secondary structure of rRNA of mollusks. The absence of entire stem/loop structures in Domains II, III, and V can be viewed as three shared derived characters uniting the stylommatophoran gastropods. The absence of the aforementioned stem/loop structure explains much of the observed length variation of the mitochondrial LSU rRNA found within mollusks. The distribution of these unique secondary structure characters within mollusks should be examined.
Global climate has fluctuated greatly during the past three million years, leading to the recent major ice ages. An inescapable consequence for most living organisms is great changes in their distribution, which are expressed differently in boreal, temperate and tropical zones. Such range changes can be expected to have genetic consequences, and the advent of DNA technology provides most suitable markers to examine these. Several good data sets are now available, which provide tests of expectations, insights into species colonization and unexpected genetic subdivision and mixture of species. The genetic structure of human populations may be viewed in the same context. The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help our understanding of how organisms were so affected.
Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena.
Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and earlier methods for doing so are underutilized. We review models that address the crucial distinction between the gene divergence, the parameter that is typically recovered in molecular phylogeographic studies, and the population divergence, which is in most cases the parameter of interest and will almost always postdate the gene divergence. Assuming that population sizes of ancestral species are distributed similarly to those of extant species, we show that phylogeographic studies in vertebrates suggest that divergence of alleles in ancestral species can comprise from less than 10% to over 50% of the total divergence between sister species, suggesting that the problem of ancestral polymorphism in dating population divergence can be substantial. The variance in the number of substitutions (among loci for a given species or among species for a given gene) resulting from the stochastic nature of DNA change is generally smaller than the variance due to substitutions along allelic lines whose coalescence times vary due to genetic drift in the ancestral population. Whereas the former variance can be reduced by further DNA sequencing at a single locus, the latter cannot. Contrary to phylogeographic intuition, dating population divergence times when allelic lines have achieved reciprocal monophyly is in some ways more challenging than when allelic lines have not achieved monophyly, because in the former case critical data on ancestral population size provided by residual ancestral polymorphism is lost. In the former case differences in coalescence time between species pairs can in principle be explained entirely by differences in ancestral population size without resorting to explanations involving differences in divergence time. Furthermore, the confidence limits on population divergence times are severely underestimated when those for number of substitutions per site in the DNA sequences examined are used as a proxy. This uncertainty highlights the importance of multilocus data in estimating population divergence times; multilocus data can in principle distinguish differences in coalescence time (T) resulting from differences in population divergence time and differences in T due to differences in ancestral population sizes and will reduce the confidence limits on the estimates. We analyze the contribution of ancestral population size (theta) to T and the effect of uncertainty in theta on estimates of population divergence (tau) for single loci under reciprocal monophyly using a simple Bayesian extension of Takahata and Satta's and Yang's recent coalescent methods. The confidence limits on tau decrease when the range over which ancestral population size theta is assumed to be distributed decreases and when tau increases; they generally exclude zero when tau/(4Ne) > 1. We also apply a maximum-likelihood method to several single and multilocus data sets. With multilocus data, the criterion for excluding tau = 0 is roughly that l tau/(4Ne) > 1, where l is the number of loci. Our analyses corroborate recent suggestions that increasing the number of loci is critical to decreasing the uncertainty in estimates of population divergence time.
Intraspecific phylogeographic methods provide a means of examining the history of genetic exchange among populations. As part of a study of the history of Helix aspersa in the Western Mediterranean, we performed a phylogenetic analysis based on partial sequences of the mitochondrial large ribosomal subunit (16S) gene. Our samples include 31 H. a. aspersa populations from North Africa previously investigated for anatomical and biochemical characters. To clarify subspecific relationships, three individuals of the subspecies H. a. maxima were also studied. The molecular phylogeny inferred agrees largely with previous results, in splitting H. a. aspersa haplotypes into an eastern and a western group. H. a. maxima haplotypes form a third lineage arising before the H. a. aspersa groups. Divergence times estimated between the lineages suggest that dispersal during Pleistocene glaciation and vicariance events due to Pliocene geological changes in the western Mediterranean may both have played a significant part in the establishment of the present range of H. aspersa.
A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-population n-island model and a source-sink population model. Our estimation method as coded in migrate is tested against genetree; both programs deliver a very similar likelihood surface. The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.
In an effort to link quantitative morphometric information with molecular data on the population level, we have analysed 19 populations of the conchologically variable land snail Candidula unifasciata from across the species range for variation in quantitative shell traits and at the mitochondrial 16S ribosomal (r)DNA locus. In genetic analysis, including 21 additional populations, we observed two fundamental haplotype clades with an average pairwise sequence divergence of 0.209 +/- 0.009 between clades compared to 0.017 +/- 0.012 within clades, suggesting the presence of two different evolutionary lineages. Integrating additional shell material from the Senckenberg Malacological Collection, a highly significant discriminant analysis on the morphological shell traits with fundamental haplotype clades as grouping variable suggested that the less frequent haplotype corresponds to the described subspecies C. u. rugosiuscula, which we propose to regard as a distinct species. Both taxa were highly subdivided genetically (FST = 0.648 and 0.777 P < 0.001). This was contrasted by the partition of morphological variance, where only 29.6% and 21.9% of the variance were distributed among populations, respectively. In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets. Partial least square analysis of environmental factors against shell trait variables in C. u. unifasciata revealed significant correlations between environmental factors and certain quantitative shell traits, whose potential adaptational values are discussed.