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Two evolutionary units on the South American razor clam Ensis macha (Bivalvia: Pharidae): genetic and morphometric evidence
Abstract
The patterns of genetic and phenotypic diversity in marine life are the result of different geological and ecological processes. We analyzed the pattern of genetic and morphometric variation of the razor clam Ensis macha along its entire geographic distribution. This species is one of the most important shellfish resources of South America. To uncover the genetic variation across this species, we used sequences of the COI mitochondrial gene and of 856 nuclear orthologs. To describe morphological variation in the shape of the shell, we used elliptic Fourier analysis followed by multivariate statistics. Two main genetic lineages were found, designated as Northern and Southern clades. This genetic distinction is concordant with a biogeographic transition along the Pacific coast of Southern South America, which is also known for other taxa. Based on the genetic distance between the two lineages, each lineage can be considered an incipient species. Morphological approaches revealed similar results, though there was no strict concordance between the morphometric and the genetic results. Geological history and ecological processes could both be responsible for the variation across the range of E. macha. In particular, fragmentation and isolation between populations may have favored genetic diversification, while the environment may have molded the variation shell shape. Lastly, our results have important implications for fisheries management, to preserve biological diversity of the world’s southernmost razor clam species.
... Furthermore, the percentage of divergence detected with COI in M. donacium is lower in magnitude than the interspecific divergence reported for other molluscs such as species within the genus Ensis (E. macha, E. loboi, E. directus, E. terranovensis, E. silique, and E. magnus) which ranged from 3.2% to 6.5% (Márquez et al., 2020;Signorelli et al., 2022;Vierna et al., 2012Vierna et al., , 2014. The detected mito-nuclear discordance, and the degree of divergence of the COI haplogroups suggest that the haplogroups correspond to intraspecific level variation; there is a moderate mitochondrial divergence but there is no divergence at the nuclear markers 18S and 28S, evidencing that M. donacium is a single nuclear lineage. ...
... Further studies incorporating markers with higher mutation rate than 18S and 28S, such as SNPs, should be performed to assess the degree of population genetic structure among mitochondrial COI lineages of M. donacium, that could allow disentangling the origins of the detected mitonuclear discordance. However, based on the results and on patterns previously detected for other taxa, it is likely that the incongruent genetic structure of mitochondrial DNA and nuclear DNA of M. donacium is the result of isolation followed by secondary contact and admixture, as has been suggested for P. chilensis in the southeast Pacific (Haye & Muñoz-Herrera, 2013), and other taxa worldwide that fit the contraction-expansion demographic dynamics in the Pleistocene (e.g., Hiruta et al., 2017;Marko et al., 2010). Under this scenario, mitochondrial haplogroups of M. donacium would have evolved in separate glacial refuges (north and south), followed by post-glaciation secondary contact, without having achieved reproductive isolation, i.e., mitochondrial haplogroups could interbreed when in sympatry. ...
... Isolation followed by admixture is also consistent with the date of divergence of mitochondrial haplogroups and the estimated dates of population expansion of the mitochondrial haplogroups. These occurred during the Pliocene-Pleistocene epoch, which was characterized by glacial and interglacial events that could facilitate refugia for isolated populations followed by geographic expansion, as has been described for other marine species (Fernández Iriarte et al., 2020; González-Wevar et al., 2012;Haye & Muñoz-Herrera, 2013;Hiruta et al., 2017;Marko et al., 2010). The Pliocene-Pleistocene epoch was influenced by glaciations as one of the main geological processes in South America, with changes in coastal oceanography and climatic conditions (Fraser et al., 2012). ...
Mesodesma donacium is a surf clam endemic to the southeast Pacific coast, and it is an important resource species of the sandy beach artisanal fishery in Peru and Chile. Over time, the species has shown high variability in population dynamics (presence and abundance), which has been attributed to overfishing and environmental events. In this study, we assess the phylogeography of seven natural beds of M. donacium (17 to 42° S), to reveal the geographic distribution of the genetic diversity through the analysis of 278 sequences of the mitochondrial gene COI. Sequences of the nuclear genes 18S and 28S were used to evaluate the divergence of COI haplogroups. Two divergent parapatric mitochondrial haplogroups were found, which lacked divergence at nuclear markers (18S and 28S); this mito‐nuclear discordance allows inferring that there is no reproductive isolation of mitochondrial haplogroups. The North haplogroup is the only one present at the northernmost site, while only the South haplogroup was present in Cucao in the south. Between 28° and 32° S, coincident with a coastal biogeographic break at 30° S, both haplogroups are in sympatry. Haplogroups differed in their genetic structure, with the North haplogroup representing a single, highly diverse population and the South haplogroup with genetic differentiation and more restricted genetic diversity and gene flow. The divergence in mitochondrial haplogroups without nuclear divergence suggests a past scenario of geographic isolation in the northern and southern areas, without developing reproductive isolation, followed by secondary contact. Given the phylogeography, genetic information should be considered in restocking and management activities.
... The reported distribution range of Ensis macha goes from the San Matías Gulf (40°S) in the Atlantic Ocean to the northern coast of Peru (8°S) in the Pacific (Zaixso et al. 2015, Paredes et al. 2016, Márquez et al. 2017. However, a recent study based on genetic data (COI mitochondrial and 856 nuclear genes) revealed the presence of two clades along the Pacific coast of South America (Márquez et al. 2020). They were designated as northern and southern clades. ...
... The northern clade is mainly distributed in the Peruvian biogeographic province (a warm-temperate region), from Peru (8°S) to the Chilean coast at around 37°S, while the southern clade is distributed along the Magellan province (a cold-temperate region) from Chiloé (40°S) on the Pacific coast to northern Patagonia on the Atlantic coast (40°S) (Fig. 1, Table 1). Márquez et al. (2020) analysed the variation in external shell shape (outlines) using an elliptic Fourier analysis. They found that the two clades showed an overlapping morphospace, although there was a slight separation trend. ...
... They found that the two clades showed an overlapping morphospace, although there was a slight separation trend. The genetic distances reported by Márquez et al. (2020), plus new results based on landmark-based geometric morphometrics (GM), allowed the formal descriptions of a new species of Pharidae from the Pacific coast of South America. In order to maximize the separation between clades, 2D landmark-based GM was performed to analyse inner shell shape variation. ...
Summary: A new cryptic species of Ensis from the Pacific coast of South America based on geometric morphometrics is revealed. Ensis macha (Molina, 1782) is one of the most important shellfish resources in South America. It was historically reported from San Matías Gulf, Argentina in the Atlantic Ocean to the Peruvian coast in the Pacific. A recent study analysed the intraspecific variation of this species along its distribution range and the genetic results indicated the presence of
cryptic diversity. Two evolutionary clades were found: a southern clade (from cold-temperate waters) and a northern clade (from warm-temperate waters). New results based on geometric morphometrics supported the description of Ensis loboi n. sp. for the northern clade. The southern clade retains the name due to type locality of E. macha in Chiloé, Chile. The description of Ensis loboi n. sp. for the southeastern Pacific Ocean has important implications for future studies focused
on fisheries management and biogeographical radiation of the group.
... However, its distribution range is usually mentioned to the coasts of Peru (Osorio & Bahamondes 1970;Paredes et al. 2016;Valentich-Scott et al. 2020;Zaixso et al. 2015, among others). This range must be restricted after the genetic studies that revealed two genetic units (Márquez et al. 2020;Vierna Fernández 2014). The southern unit, distributed from Chiloe in the Pacific to San Antonio Oeste, in the Atlantic, must be attributed to Ensis macha and the northern unit, from Tubul, Chile to northern Peru to a new species, currently in process of description (Márquez et al. 2020). ...
... This range must be restricted after the genetic studies that revealed two genetic units (Márquez et al. 2020;Vierna Fernández 2014). The southern unit, distributed from Chiloe in the Pacific to San Antonio Oeste, in the Atlantic, must be attributed to Ensis macha and the northern unit, from Tubul, Chile to northern Peru to a new species, currently in process of description (Márquez et al. 2020). ...
In the present study, bivalves belonging to the superfamily Solenoidea that inhabit the Argentinean Sea are redescribed. The specimens studied in this work were collected by scuba diving in the Gulf of San José, Argentina. Additional specimens from different malacological collections were revised to update the geographical distribution of valid species. According to the literature, there exist two species for the "Argentinean" and "Magellan" biogeographical provinces. However, ten nominal taxa, with uncertain taxonomic status, have been mentioned for the study area. Field work, local collection survey and type material examination allow confirming two valid species: Solen (Ensisolen) tehuelchus Hanley (Solenidae) and Ensis macha (Molina) (Pharidae). A morphological comparison between S. tehuelchus and S. gaudichaudi Chenu and S. obliqua Spengler is provided as well type locality, repository and synonymy list. The type material of all related species are illustrated whenever possible. Establishing the valid names of these species is the first step towards more integrative studies including genetic and zoogeographical analyses.
... El estudio de genética del baunco, además, es interesante porque en otros estudios realizados en moluscos y crustáceos mediante secuencias de ADN mitocondrial se ha encontrado una zona de tensión o ruptura filogeográfica localizada en torno al paralelo 30ºS. Se trata de un área donde se produce un distanciamiento genético entre individuos de la misma especie localizados a ambos lados de la zona de tensión (Brante et al., 2012;Haye et al., 2019;Márquez et al., 2020;Zakas et al., 2009). Sin embargo, se desconoce si este fenómeno se produce también en los peces. ...
131 │ Genética poblacional del baunco Girella laevifrons, una especie de bajo nivel trófico candidata para la piscicultura marina sostenible en Latinoamérica, basada en el análisis de polimorfismos del ADN mitocondrial RESUMEN | Girella laevifrons (Kyphosidae) es una especie de pez herbívoro de potencial interés en la acuicultura de Perú. Para caracterizar la estructura genética de las poblaciones, se ha realizado un estudio de los polimorfismos de la región de control (RC) del genoma mitocondrial en 47 individuos de tres localidades que cubren toda el área de distribución de la especie. La diversidad haplotípica y nucleotídica observadas fueron muy altas, lo que sugiere que la especie se adaptará con facilidad a los cambios ambientales y a las condiciones de cría en cautividad. Se construyó una red filogenética mediante el método Median Joining, que indicó una ausencia de estructura filogeográfica. Estos resultados sugieren la existencia de una única población panmíctica a lo largo de toda el área de distribución de la especie. Palabras clave | variabilidad genética, filogegrafía, ADN Mitocondrial, estructura genética.
... Moreover, DNA Barcoding has been applied for the identification of Mollusca successfully (Jaksch et al. 2016;Sun et al. 2016;Juniar et al. 2021;Sari et al. 2021) and various other animal taxa, for example, using Cytochrome Oxidase Subunit I (COI) sequences applied in Pharidae bivalve (Márquez et al. 2020). In addition, DNA barcoding has successfully identified several variations of Clithon oualaniense (Gastropoda) from Madura (Juniar et al. 2021) and Donax incarnatus from Madura (Wijaya et al. 2023b). ...
Ambarwati R, Rahayu DA. 2024. Revealing species identity of edible razor clam Cultellus sp. (Bivalvia: Pharidae) from Madura Island, Indonesia. Biodiversitas 25: 1505-1513. Razor clams have an essential role as commercial commodities. One of the poorly-known edible razor clams from Madura, Indonesia, has not been identified as the species. This research aimed to identify the edible razor clam (Bivalvia: Pharidae) species from Madura Island, Indonesia. The samples of razor clams (Cultellus sp.) were collected from Bangkalan, Madura Island, Indonesia. Identification was conducted based on morphological and molecular characterization. The foot tissues of three individuals were processed for DNA isolation, electrophoresis, amplification, and sequencing to obtain the sequences of COI gene. The morphological characters of razor clam shells were analyzed descriptively and quantitatively. Data were collected from the COI gene sequences of razor clam Cultellus sp. and descriptively analyzed using bioinformatics software. The morphological identification revealed razor clams (Cultellus sp) from Bangkalan, Madura, Indonesia, Cultellus subellipticus. The nucleotide base composition sequences of C. subellipticus A, B & C consisted of Thiamine (T), Cytosine (C), Adenine (A), and Guanine (G) with a mean of 18.25, 12.92, 23.42, and 46.39%. Maximum Likelihood (ML) and Minimum Evolution (ME) phylogenetic analysis was also conducted using the Kimura 2 Parameter model to establish one major clade on C. subellipticus from the gene bank and a different group with Cultellus attenuatus and one out-group significantly different from the Ensis macha. This finding was strengthened by molecular identification results, which indicated the similarity with C. subellipticus from GenBank, with very high BOLD System data between 98.10-98.86%.
... El estudio de genética del baunco, además, es interesante porque en otros estudios realizados en moluscos y crustáceos mediante secuencias de ADN mitocondrial se ha encontrado una zona de tensión o ruptura filogeográfica localizada en torno al paralelo 30ºS. Se trata de un área donde se produce un distanciamiento genético entre individuos de la misma especie localizados a ambos lados de la zona de tensión (Brante et al., 2012;Haye et al., 2019;Márquez et al., 2020;Zakas et al., 2009). Sin embargo, se desconoce si este fenómeno se produce también en los peces. ...
Girella laevifrons (Kyphosidae) is a species of herbivorous fish of potential interest for aquaculture in Peru. To characterize the genetic structure of the populations, a study of the polymorphisms of the mitochondrial genome control region was carried out in 47 individuals from three localities that cover the entire distribution area of the species. The observed haplotypic and nucleotide diversity were very high, suggesting that the species will easily adapt to environmental changes and captive breeding conditions. A phylogenetic network was constructed using the median joining method, which indicated a lack of phylogeographic structure. These results suggest the existence of a single panmictic population throughout the entire range of the species.
Los manuscritos en extenso suponen memorias de los trabajos presentados en el XI FIRMA 2022 online y han
sido revisados por el comité editorial del libro. Las opiniones y manifestaciones científicas en los artículos, construcción gramatical, así como el estilo, particularmente en la forma de exposición de autores, referencias y usos de símbolos, se respetaron para su publicación y son responsabilidad de los
autores, quienes tienen también todo el derecho sobre ellos para su publicación por otras vías, incluyendo revistas científicas.
Tras un gran esfuerzo organizativo, en el XI Foro Iberoamericano de los Recursos Marinos y la Acuicultura, XI FIRMA 2021 online, se presentaron y discutieron temas de gran relevancia con exposiciones de más de 60 especialistas en el área de los recursos acuáticos y la acuicultura, con 7 conferencias magistrales y 12 sesiones de discusión. Esto
permitió alcanzar y sobrepasar las metas planteadas, llegando a los casi 3.500 participantes inscritos, repartidos por Iberoamérica y otras partes del mundo. La página web, del XI FIRMA, durante el evento fue visitada en más de 53.000 veces,
y sus principales usuarios (en total 8132) fueron de Ecuador (33%), Perú (13%), México (12%), Venezuela (9%), España (7%), Colombia (4,5%), USA (4%), Brasil (4%), Argentina (3%), Chile (2%) y <2% (Marruecos, Guatemala, Panamá, Italia, Cuba, Costa Rica, Alemania, Portugal y otros 29 países más), lo cual supone una visualización geográfica en casi 50 países, cubriendo toda América, Europa y gran parte de Asia y África.
En cuanto los trabajos científicos del evento, se publicaron más de 200 trabajos en formato de e-pósteres y videos, clasificados en 12 áreas del conocimiento, sobresaliendo las áreas de biodiversidad y conservación de los recursos (35), cultivo de peces y crustáceos
(50), biología, fisiología y ecología (28) y biotecnología y bioproductos (24).
En cuanto los trabajos científicos del evento, se publicaron más de 200 trabajos en formato de e-pósteres y videos, clasificados en 12 áreas del conocimiento, sobresaliendo las áreas de biodiversidad y conservación de los recursos (35), cultivo de peces y crustáceos (50), biología, fisiología y ecología (28) y biotecnología y bioproductos (24), de los cuales un selecto grupo de especialistas tuvieron la tarea de seleccionar los 3 mejores trabajos presentados y 3 menciones honoríficas.
De estos trabajos, unos XX son presentados in extenso a manera de proceeding en el presente libro del XI FIRMA 2022 online. En cuanto a la difusión de nuestras redes, tuvimos un alcance de unas 25.000 y 30.000 cuentas alcanzadas por nuestras publicaciones en Facebook e Instagram, respectivamente, manteniéndose activas cumpliendo con su objetivo informativo promocional.
De estos trabajos, unos XX son presentados in extenso a manera de proceeding en el presente libro del XI FIRMA 2022 online. En cuanto a la difusión de nuestras redes, tuvimos un alcance de unas 25.000 y 30.000 cuentas alcanzadas por nuestras publicaciones en Facebook e Instagram, respectivamente, manteniéndose activas cumpliendo con su objetivo informativo promocional.
The southern coastline of South America is a remarkable area to evaluate how Quaternary glacial processes impacted the demography of the near-shore marine biota. Here we present new phylogeographic analyses in the pulmonate Siphonaria lessonii across its distribution, from northern Chile in the Pacific to Uruguay in the Atlantic. Contrary to our expectations, populations from the southwestern Atlantic, an area that was less impacted by ice during glacial maxima, showed low genetic diversity and evidence of recent expansion, similar to the patterns recorded in this study across heavily ice-impacted areas in the Pacific Magellan margin. We propose that Atlantic and Pacific shallow marine hard-substrate benthic species were both affected during the Quaternary in South America, but by different processes. At higher latitudes of the southeast Pacific, ice-scouring drastically affected S. lessonii populations compared to non-glaciated areas along the Chile-Peru province where the species was resilient. In the southwest Atlantic, S. lessonii populations would have been dramatically impacted by the reduction of near-shore rocky habitat availability as a consequence of glacio-eustatic movements. The increase of gravelly and rocky shore substrates in the southwest Atlantic supports a hypothesis of glacial refugia from where the species recolonized lower latitudes across the Atlantic and Pacific margins. Our results suggest that current patterns of genetic diversity and structure in near-shore marine benthic species do not solely depend on the impact of Quaternary glacial ice expansions but also on the availability of suitable habitats and life-history traits, including developmental mode, bathymetry and the likelihood of dispersal by rafting.
Background: The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by
this technique.
Results: We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4–7.8%) while that of nuclear genes was low (0.06–0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these
results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.
Conclusions: Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.
Fluctuating asymmetry (FA) consists of random deviations from perfect symmetry, and it is a useful trait to monitor developmental stability and ecological stress. The principal goal in this work was to study shell shape FA in Mytilus platensis as a measure of stress of living in intertidal wild areas compared to subtidal cultured ones. Shell shape asymmetry was studied by geometric morphometrics using landmarks and semilandmarks from internal and external anatomical structures. We analyzed FA comparing shell shape from 452 individuals living at different habitats (intertidal rocky shores vs. subtidal longlines) in two Patagonian sites. We predict that mussels living in the intertidal present higher levels of morphological alterations (i.e., FA) than those from the subtidal, where the environmental stress is lower. We based the asymmetry analysis on the FA scores from Procrustes ANOVA; all effects of the model were statistically significant. The Procrustes FA scores differed significantly between habitats: intertidal populations presented higher FA scores than subtidal ones. As predicted, shell shape in Mytilus platensis is influenced by the habitat and these differences add evidence to the fact that FA is a suitable measure of developmental instability, indicating the inability of species to buffer stress in its developmental pathways.
Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single- or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novo assembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version.
Scorched mussels (Bivalvia: Mytilidae) are an important component of rocky shore assemblages around the world. The mussel beds of the mid-intertidal coasts of the south-western Atlantic are composed of two species of scorched mussels, which dominate the physiognomy and structure of the rocky shore communities. The present study investigates the variation in the shell-shape allometric trajectories of both species of mussels throughout their distributional range in the southwestern Atlantic coast, from latitude 34°S to 53°S. Shells of Brachidontes rodriguezii were collected at two Uruguayan localities and four Argentinean localities, while shells of Perumytilus purpuratus were collected at six Argentinean localities. Shell shapes of the specimens were studied by geometric morphometrics using landmark and semi-landmark methods. Different evolutionary histories and thermal regimes characterize these two species. Brachidontes rodriguezii seems to have a long history in the region and is present in a restricted area, the warm temperate region of the south-western Atlantic, while P. purpuratus seems to have a recent history and is present in a wide thermal range, involving the cold-temperate regions of the south-western Atlantic and south-eastern Pacific and the warm-temperate region of the south-eastern Pacific. Based on these considerations, we prompt the hypothesis that allometric trajectories of P. purpuratus shell shape is more variable and adapted to a specific habitat than B. rodriguezii. The impact of allometry was larger in P. purpuratus than in B. rodriguezii. Graphical evidence was gathered, showing that these two species differ in allometric growth forms and that the allometric shell morphology changes reflect environmental constraints and adaptation. While the intertidal mussel beds of the South American coasts are ecologically similar in appearance, we found that the allometric variation of the scorched mussels occurs in response to diverging evolutionary processes such as phenotypic plasticity in P. purpuratus and canalization in B. rodriguezii.
Novel sequencing technologies are rapidly expanding the size of datasets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic datasets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10-30X). Computational challenges for handling these large datasets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix.Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1,107 single copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and outgroups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close to distantly related taxa at high to low levels of coverage.Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic datasets from raw genome sequencing reads. Further, we found that with coverages above 5 - 10X, aTRAM was successful at assembling 80 - 90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic datasets for an extensive variety of applications, including phylogenomics.
The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python’s core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from
http://github.com/marekborowiec/AMAS/
under GNU General Public License.
Benthic organisms are among the most diverse and abundant in the marine
realm, and some species are a key factor in studies related to bioengineering.
However, their importance has not been well noted in biogeographic studies.
Macrofaunal assemblages associated with subtidal beds of the ribbed mussel
(Aulacomya atra) along South America were studied to assess the relationship
3 between their diversity patterns and the proposed biogeographic provinces in
the Southeastern Pacific and Southwestern Atlantic Oceans. Samples from
ribbed mussel beds were obtained from 10 sites distributed from the Peruvian
coast (17°S) to the Argentinean coast (41°S). The sampling included eight beds
in the Pacific and two in the Atlantic and the collections were carried out using
five 0.04 m2 quadrants per site. Faunal assemblages were assessed through clas-
sification analyses using binary and log-transformed abundance data. Variation
in the size and density of mussels, and in the species richness, abundance and
structure of their faunal assemblages were tested using a permutational multi-
variate analysis of variance. Faunal assemblages showed a north–south latitudi-
4 nal gradient along both the Pacific and Atlantic coasts. Binary and abundance
data showed a difference in the resulting clustering arrangement of Pacific sites
between 40°S and 44°S, indicating a pattern of continuity in the species distri-
bution associated with biological substrates. At a regional scale, the distribution
of species along the South American coast matched the general provincial pat-
5 tern shown by prior studies, which show two biogeographic
units on the Pacific coast separated by an intermediate (probably transitional)
zone and a single province on the Atlantic coast extending up to Northern
Argentina. Biological substrates such as ribbed mussel beds play an important
ecological role by making a similar habitat type available on a large scale for a
variety of invertebrate species. Despite such habitat homogeneity, however, the
associated fauna exhibit marked distribution breaks, suggesting strong con-
straints on dispersal. This therefore suggests that macrofaunal assemblages
could possibly be used as biogeographic indicators.
Background
Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of paired-end reads: aTRAM, automated Target Restricted Assembly Method. The aTRAM pipeline uses a reference sequence, BLAST, and an iterative approach to target and locally assemble the genes of interest.
Results
Our results demonstrate that aTRAM rapidly assembles genes across distantly related taxa. In comparative tests with a closely related taxon, aTRAM assembled the same sequence as reference-based and de novo approaches taking on average < 1 min per gene. As a test case with divergent sequences, we assembled >1,000 genes from six taxa ranging from 25 – 110 million years divergent from the reference taxon. The gene recovery was between 97 – 99% from each taxon.
Conclusions
aTRAM can quickly assemble genes across distantly-related taxa, obviating the need for draft genome assembly of all taxa of interest. Because aTRAM uses a targeted approach, loci can be assembled in minutes depending on the size of the target. Our results suggest that this software will be useful in rapidly assembling genes for phylogenomic projects covering a wide taxonomic range, as well as other applications. The software is freely available http://www.github.com/juliema/aTRAM.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-015-0515-2) contains supplementary material, which is available to authorized users.
ABSTRACT: Marine gastropods show pronounced plasticity in shell morphology in response to
local environmental risks such as predation and dislodgement by waves. Previous studies have
focused on juvenile and adult snails; however, adaptive plasticity might be expected to begin during
embryonic and early post-embryonic stages as a means of increasing survivorship when individuals
first become vulnerable. We tested the above hypothesis by measuring shell morphology
of encapsulated embryos and hatchlings of Acanthina monodon exposed to predator odor and
water turbulence. Subjects were assigned to 1 of 4 treatments: (1) predator odor + high water turbulence,
(2) no predator odor + high water turbulence, (3) predator odor + low water turbulence,
(4) no predator odor + low water turbulence (control). After approximately 1 mo, morphological
traits of the shell were measured using geometric morphometrics. Hatchlings, but not encapsulated
offspring, produced larger shells in the predator treatments. Encapsulated offspring and
hatchlings produced thicker shells in the predator treatments, irrespective of water turbulence,
whereas thinner shells were produced when high water turbulence acted alone. Even before
hatching, A. monodon can, thus, respond adaptively to potential mortality factors characterizing
the local external environment. Anticipating risk in this way should enhance survivorship from the
point of hatching through the vulnerable juvenile phase to adulthood.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Quantitative monthly samplings, in 2004, were carried out to estimate the density and biomass of Ensis macha (Molina 1782), from Morro Quemado area, Bay Independence, Pisco. The present study analyzes biometric relationships, growth parameters and somatic production using the ELEFAN I routine and the Crisp's method. During the year 2004 the rate of exploitation (E= 0.69 y⁻¹) was significantly bigger than the values of 2003 and the monthly landings (maximum of 335 t) and fishing effort (maximum of 848 trips) were twice increased. These changes induced in the same year a significant decrease of population mean density (D= 54.13 ind. m⁻²) and the halfway reduction of somatic production (P= 81.99 gAFDW m⁻² y⁻¹) and P/B rate (0.38 y⁻¹) values, regarding the values of the previous year. Also, a significant increment of total mortality rate (2.84 y⁻¹) and the fishing mortality rate (1.97 y⁻¹) were twice increased, regarding the previous year. It is assumed that the population of razor clams already was a overfishing commercial resource in the 2003 and that the increment of fishing pressure in the 2004, particularly during the second semester, intensified its overfishing resource condition.
The Quaternary of Tierra del Fuego is represented by glacial, glacio#uvial, glaciolacustrine, marine and aeolian deposits. Six drift units have been described, the oldest dating from the Late Pliocene: these are, starting from the oldest, the RmHo Grande, Sierra de los Frailes, Cabo VmHrgenes, Punta Delgada, Primera Angostura and Segunda Angostura Drifts. Neoglacial and `Little Ice Agea events are represented in cirques and higher mountain valleys. Marine deposits and raised beaches were formed during Middle Pleistocene, Late Pleistocene and Holocene interglacial stages. After the de"nitive ice-retreat (10 ka ago) vegetation changed from tundra and cold steppe to subantarctic forest environments. Marine deposits re#ect also colder conditions than the present ones. Aeolian processes prevailed in northern Tierra del Fuego, where semiarid conditions and the frequent westerlies favoured the retransportation of "ner
materials coming from pre-existing deposits. Before the opening of the Magellan Straits, earliest human colonization occurred in northern Tierra del Fuego ca. 11 ka BP, in tundra-like environmental conditions. Pedestrian hunters of camelids and foxes co-existed with Pleistocene fauna that became extinct during Late Glacial}Earliest Holocene times. The steppe area (inland and Atlantic coast) was successively occupied since then until recent times. On the other hand, the Beagle Channel coasts were occupied since 6 ka BP by
hunter}gatherer groups adapted to maritime littoral conditions. Finally, the easternmost area of the island was inhabited at least since 1.5 ka BP. The human settlements in these latter areas occurred under environmental conditions similar to the present ones, when the Fuegian forest was de"nitively established
A new Pliocene (3.4 Ma) mollusk fauna from Mejillones Peninsula, northern Chile is described and compared with the Pliocene La Cueva fauna of little constrained age from central Chile and some species from the Huenteguapi Sandstone overlying the Ranquil Formation on Arauco Peninsula, south central Chile. Preliminary correlation is based on faunal similarities. A total of 45 taxa were identified, of which Cyclocardia kieli sp. nov. is new to science. New combinations are Macron escalonia (Vermeij and DeVries, 1997), Austrofusus steinmanni (Möricke, 1896) and Leukoma antiqua (King, 1832). For several species, the oldest occurrences and range extensions are reported. Co-occurrence of warm water taxa, previously assigned to MIS 11, and typical Pliocene taxa on Mejillones cannot be confirmed. Pliocene and Pleistocene mollusk faunas from Mejillones are listed for comparison.
Phylogeography studies add insights into the geographic and evolutionary processes that underline the genetic divergence of populations. This work examines the geographic genetic structure of the Patagonian blennie, Eleginops maclovinus, a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters, using mitochondrial DNA cytochrome b sequences. We found 58 haplotypes in the analysis of 261 individual sequences of 833 base pairs in length. Among-population variance was very low (1.62%) and many haplotypes were shared between several populations across the species geographic range. Genetic differentiation was not consistent with a simple model of isolation by distance, possibly suggesting a lack of equilibrium between gene flow and local genetic drift. The analysis of mismatch distributions, neutrality tests, and the Bayesian Skyline Plot showed a pattern consistent with a recent population expansion event that may have taken place during the Middle Pleistocene.
Three biogeographic areas have been recognized along the Chilean coast, with biogeographic breaks located at 30 and 42 degrees S allowing us to test the concordance between biogeographic patterns and spatial patterns of genetic and morphological diversity in marine species. We examined the marine gastropod Acanthina monodon, whose range spans the 2 major biogeographic breaks detected in the South-Eastern Pacific (SEP) coast. This species exhibits high variability in the morphology of its shell and has a direct development cycle. Based on the analysis of mitochondrial sequences of 258 individuals from 9 locations in the 3 biogeographic areas, we found 3 clades with contrasting levels of genetic diversity and with spatial population genetic structure. A perfect match between biogeography and pylogeography was observed only at the 30 degrees S break. In contrast, we did not find a clear genetic break in concordance with the 42 degrees S phylogeographic break, although haplotype distribution suggested a second phylogeographic boundary located between 45 and 53 degrees S. Only one haplotype was observed in the most southerly location, which may be explained by the historical influence of glaciations. A break in shell morphology was evidenced only at around 40 to 46 degrees S, with a group characterized by thinner shells and longer spires compared to the northern group. Our results supported the concordance hypothesis and indicated that the influence of life cycle strategy, habitat discontinuity and historical processes may determine the phylogeographical and shell morphology spatial pattern of A. monodon. In contrast to previous studies, our genetic analysis showed the presence of a single Acanthina species along the SEP coast.
Ensis Schumacher, 1817 razor shells occur at both sides of the Atlantic and along the Pacific coasts of tropical west America, Peru, and Chile. Many of them are marketed in various regions. However, the absence of clear autapomorphies in the shell and the sympatric distributions of some species often prevent a correct identification of specimens. As a consequence, populations cannot be properly managed, and edible species are almost always mislabelled along the production chain. In this work, we studied whether the currently accepted Atlantic Ensis morphospecies are different evolutionary lineages, to clarify their taxonomic status and enable molecular identifications through DNA barcoding. For this, we studied 109 specimens sampled at 27 sites, which were identified as belonging to nine of those morphospecies. We analysed nucleotide variation at four nuclear (18S, 5.8S, ITS1, and ITS2) and two mitochondrial (COI and 16S) regions, although the 18S and 5.8S regions were not informative at the species level and were not further considered. The phylogenetic trees and networks obtained supported all morphospecies as separately evolving lineages. Phylogenetic trees recovered Ensis at each side of the Atlantic as reciprocally monophyletic. Remarkably, we confirm the co-occurrence of the morphologically similar E. minor (Chenu, 1843) and E. siliqua (Linné, 1758) along the NW Iberian coast, a fact that has been often overlooked. In South America, a relevant divergence between E. macha (Molina, 1792) individuals from Chile and Argentina was unveiled and suggests incipient speciation. We also confirm the occurrence of the North American species E. directus (Conrad, 1843) as far south as north-eastern Florida. Among the genomic regions analysed, we suggest COI as the most suitable DNA barcode for Atlantic Ensis. Our results will contribute to the conservation and management of Ensis populations and will enable reliable identifications of the edible species, even in the absence of the valves. The name Ensis coseli Vierna nom. nov. is proposed to replace E. minor Dall, 1899 non (Chenu, 1843).
Outlines of wings from 127 species of North American mosquitoes were digitized. Comparisons were made among several different methods of reducing the information in the resulting coordinates to a series of descriptors that could be used in multivariate analysis. Methods included Fourier analysis of both radii and tangent angle change functions. In addi- tion, the relatively new method of elliptic Fourier analysis was tried. Cluster and ordination analyses based on the various sets of descriptors summarized well the pattern of similarities and differences in wing shapes, but clusters of similar wings do not agree well with traditional taxonomic groupings. The use of elliptic Fourier descriptors appears to be especially promising for future work. (Fourier analysis; morphometrics; mosquitoes; image analysis; feature extrac- tion.)
The phylogeography of two sympatric Magellanic limpets of the genus Nacella was studied. The historical and contemporary processes underlying their intraspecific patterns in Argentina were inferred
using the mitochondrial cytochrome oxidase I gene. Results indicate different evolutionary histories in the two species. A
recent geographic and demographic expansion ~11,000 years ago, with absence of current genetic structuring, is proposed for
Nacella magellanica. In contrast, the phylogeographic pattern showed noticeable phylogenetic and geographic discontinuities in Nacella deaurata; slow continuous population size growth with current low levels of gene flow among its populations was also observed, indicating
demographic equilibrium. The beginning of divergence between these closely related limpets was estimated at about 270,000 years
ago with very little or none gene flow occurring after their splitting. These contrasting historic patterns could be related
to distinctive responses to climate changes associated with Pleistocene glaciations, as a result of differences in their ecological
traits.
For almost a century, a number of authors have analyzed the distribution patterns of the marine fauna and flora in the South American Pacific and particularly along the coast of Chile, with the purpose of determining the number of existing biogeographical units. Although the general, present day patterns are relatively well known, most studies have focused on distributional breaks and classification proposals rather than on the factors and dynamic processes that formed the identified spatial units. Even in the case of biogeographical classifications, published conclusions are based mainly on the analysis of one or few selected groups, exhibiting important differences in their criteria for selecting groups, the number of species involved, and their methodology. On the other hand, diverging conclusions among particular studies tend to obscure the more relevant, large-scale phenomenon of biota dynamics, one of the less known biogeographic aspects in Chile. Within that context, this paper presents a literature review on the marine biogeography of Chile and related subjects, with the following objectives: (a) to summarize the oceanographic, climatic and geomorphologic characteristics of the Chilean continental coast; (b) to discuss 27 biogeographic classifications published for the Chilean coast, analyzing both the procedures and criteria used by their authors, along with their main conclusions and agreements; (c) to assess the vicariant and dispersal processes associated with the displacement and modification of the regional biotas, regarding the available antecedentes on the prevailing conditions and main events during the Tertiary and Quaternary periods; and (d) to propose a scenario of biogeographic change based on historical determinants and their influence on the formation, character, and dynamics of biotas along the Chilean coast, emphasizing the identification and biogeographic nature of the main spatial units. From the preceding information, I propose a hypothesis of biogeographic classification for the level of biotas, not necessarily coincident with prior studies at lower levels such as flora or fauna. This classification identifies three major spatial units: a southern area which comprises an austral biota (Magellan Province), a northern area which comprises a warm-temperate biota (Peruvian Province), and a non transitional, Intermediate Area including mixed components of biota and exhibiting a poor biogeographic definition of both its character and hierarchical rank. I also discuss the different nature of two transitional zones located at the boundaries of the Intermediate Area, a southward induced transition and a northward contact transition, likely produced by the migration of biotas and glacial-tectonic events, respectively
Broad scale patterns of genetic structure in coastal communities are strongly affected by both ecological transitions and larval dispersal. Along the Chilean coast, we examined 2 species of co-distributed barnacles, Jehlius cirratus and Notochthamalus scabrosus, which span an ecological transition associated with a sharp increase in larval recruitment. A distinct break in haplotype frequencies in the mitochondrial cytochrome oxidase I (mtCOI) gene was detected in N. scabrosus, with only marginal genetic structure observed in J. cirratus, suggesting significant differences in either selective pressures or dispersal ability between the species. The nuclear gene elongation factor la was also analyzed in N. scabrosus, and similarly suggested limited gene flow. The sharp genetic transition is downstream of the described ecological transition, effectively mirroring a genetic cline described in a different barnacle species along the North American Pacific coast.
We report current genetic variation of popula-tions of the razor shell Ensis directus (Conrad 1843) (Mollusca: Bivalvia: Pharidae) in native (North American) and introduced (European) ranges using nuclear and mitochondrial sequence-based markers. We expected less variation within the introduced range, especially consid-ering the frequent mass mortality events observed in Eur-ope since the species was recorded for the first time in 1978. However, we found higher variation in Europe. The possible significance of temporal fluctuations of genetic variation, limited effect of random genetic drift, and multiple introductions are discussed. Interestingly, the multiple-introduction hypothesis contrasts with the gradual colonisation of European coastal waters but is supported by trained clustering analysis and by the intensity of transat-lantic shipping. Genetic and morphometric evidence strongly supports that examined individuals from a sup-posed E. directus population from Newfoundland (Canada) belong to a separate species. This new Ensis is formally described here and named E. terranovensis n.sp.
The tutorial explains how to develop a calibration model for spectroscopic data analysis by Principal Component Regression (PCR), PCR basically consists of Principal Component Analysis (PCA) followed by a Multiple Linear Regression (MLR) step. Different diagnostics must however be implemented to detect outliers, clustering tendency or nonlinearities in the data. The developed PCR model can further be optimized using UVE (uninformative variable elimination). The tutorial also explains how to handle replicates and how to perform different data preprocessings and/or pretreatments.
Since its first release in 2001 as mainly a software package for phylogenetic analysis, DAMBE has gained many new functions that may be classified into 6 categories: 1) sequence retrieval, editing, manipulation and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank and the new NeXML format for interoperabity, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony and maximum likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot as well as many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly and intuitive interface, and is freely available from http://dambe.bio.uottawa.ca.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
The macrobenthic community of the Straits of Magellan and the Beagle Channel was investigated
using a Reineck box corer at 22 stations during the Chilean “Cimar Fiordo 3” expedition in 1997. A
total of 173 taxa represented by 2188 individuals were identified and are reported for the investigated
area. Clear exponential relationships with depth were revealed by analysis of abundance, biomass, species
richness, and evenness. These patterns coincide with posited theories of pelagic-benthic coupling
and the source-sink hypothesis of colonisation-extinction dynamics. Polychaeta dominated macrobenthic
community abundance and biomass, 67% and 38% respectively, therefore consideration of biogeographic
affinities concentrated on this taxon. 13 species of polychaetes observed in the study area co-occur in
Antarctica suggesting biogeographic or evolutionary affinities between these adjacent regions.
The Mollusca are a large, diverse, and economically important group that ranges from slugs and snails through clams and oysters to octopus, squid, and cuttlefish. They are evolutionarily ancient and better known than most invertebrate groups because of their calcareous skeletons, which has led to their excellent preservation as fossils. This is a state-of-the-art summary of research into Molluscs and their evolution, including recent developments in phylogenetic analysis and molecular techniques. Since the last book on this topic was published in 1985, the vast amount of updated information found here should be on the bookshelf of every zoologist, evolutionary biologist, and taxonomist.
After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use, and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity.
Availability:
ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=apeFurther information may be found athttp://ape-package.ird.fr/.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
This new edition to the classic book by ggplot2 creator Hadley Wickham highlights compatibility with knitr and RStudio. ggplot2 is a data visualization package for R that helps users create data graphics, including those that are multi-layered, with ease. With ggplot2, it's easy to:
• produce handsome, publication-quality plots with automatic legends created from the plot specification
• superimpose multiple layers (points, lines, maps, tiles, box plots) from different data sources with automatically adjusted common scales
• add customizable smoothers that use powerful modeling capabilities of R, such as loess, linear models, generalized additive models, and robust regression
• save any ggplot2 plot (or part thereof) for later modification or reuse
• create custom themes that capture in-house or journal style requirements and that can easily be applied to multiple plots
• approach a graph from a visual perspective, thinking about how each component of the data is represented on the final plot
This book will be useful to everyone who has struggled with displaying data in an informative and attractive way. Some basic knowledge of R is necessary (e.g., importing data into R). ggplot2 is a mini-language specifically tailored for producing graphics, and you'll learn everything you need in the book. After reading this book you'll be able to produce graphics customized precisely for your problems, and you'll find it easy to get graphics out of your head and on to the screen or page. New to this edition:<
• Brings the book up-to-date with ggplot2 1.0, including major updates to the theme system
• New scales, stats and geoms added throughout
• Additional practice exercises
• A revised introduction that focuses on ggplot() instead of qplot()
• Updated chapters on data and modeling using tidyr, dplyr and broom
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.
2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.
3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.
4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
In the framework of univariate pairwise comparison procedures, Di Rienzo et al.[1] developed a hybrid technique joining a hierarchical clustering method with the principles of hypothesis testing. This paper presents an extension to the multivariate case. The new method gives an answer, on the bases of inferencial statistics, to the problem of determining the number of groups in hierarchical cluster analysis when there are replicates. Although, the method was developed as a test for the general hypothesis of equality of population centroids, it performs very well, considering size and power, as a pairwise comparison algorithm. Moreover it avoids the lack of transitivity of classical pairwise comparisons methods that yields to logical inconsistencies. The method is evaluated and compared, by Monte Carlo simulation, with a partitioning multivariate procedure proposed by Bozdogan and with a multiple comparison algorithm based on the Hotelling's T 2 statistic. An example of grouping provenances of a native South American tree is presented.
Crowding conditions in bivalve populations cause intraspecific competition processes, resulting in individual growth reduction. In aquaculture, density is usually maximized to obtain a greater commercial yield. Commercial farms provide an ideal scenario for studying the effect of density on mussel growth in suspended culture systems. In this study, different growth indicators for Mytilus galloprovincialis (growth rates, length and weight growth curves and size frequency distributions) were measured along a cultivation density gradient. Ropes cultured at different densities (220, 370, 500, 570, 700, 800 and 1150 ind/m) were hanged from a commercial raft and growth indicators were monitored monthly over the second phase of traditional culture in Galicia, from thinning-out to harvest (April to October 2008). A negative effect of density on individual growth was observed. Individuals cultured at lower densities presented higher growth rates and consequently reached greater weight and length values at the end of the experimental period than those cultured at higher densities. Differences in growth related to the cultivation density may suggest differences in intraspecific competition for limiting resources (space/food). Effects of density on growth started after 4 months of culture (August) when individuals reached sizes around 66 ± 1.3 mm. The increase in size of individuals in a population implies an increment of their food and space requirements, which in turn intensifies intraspecific competition. This fact should be considered in aquaculture management, since higher densities could be supported without effects on growth performance if cultured mussels are limited to a lower size.
Although commercial kits are available for automated DNA extraction, 'artisanal' protocols are not. In this study, we present a silica-based method that is sensitive, inexpensive and compliant with automation. The effectiveness of this protocol has now been tested on more than 5000 animal specimens with highly positive results. Ivanova). The present study seeks to overcome these constraints. Our study evaluated the effectiveness of several com- mercial glass fibre filtration (GF) plates, the core functional component in all silica-based DNA extraction kits. We worked only with 96-well plates that appeared structurally compatible with robotic systems. Specifically, we compared the performance of seven GF plates — two manufactured by BioLynx (B1, B2), three by PALL (P1-3) and two by Whatman (W1, W2). The B1 plate (no. F2008) was a 0.7- µ m glass fibre with 0.8 mL well; B2 (no. F2007) was a 1.0- µ m glass fibre with 0.8 mL well; P1 (no. 5051) was a 1.0- µ m glass fibre with 1 mL well; P2 (no. 5053) was a 3.0- µ m glass fibre media/0.2 µ m Bio-Inert membrane with 1 mL well; P3 (no. 5031) was a 1.0- µ m glass fibre media with 350 µ L well; W1 (no. 7505-0003) was a mini prep DNA binding plate with 0.8 mL well and W2 (no. 7700-7801) was a Unifilter plate with glass fibre media with 0.8 mL well. We began by identifying both buffer systems and protocols that enabled the use of these GF plates for manual DNA extraction. We then tested their performance under automation with a Biomek NX liquid-handling station (Beckman-Coulter) equipped with a filtration manifold. To provide a solid test of performance, we compared these results with those from a high performance commercial kit — the NucleoSpin96 (Machery-Nagel), hereafter termed the MN kit (Hajibabaei et al . 2005). Our performance comparisons employed DNA extracted from frozen tissues of six mammal species ( Glaucomys volans , Sorex fumeus , Clethrionomys gapperi , Blarina brevicauda,
The first edition of Geometric Morphometrics for Biologists has been the primary resource for teaching modern geometric methods of shape analysis to biologists who have a stronger background in biology than in multivariate statistics and matrix algebra. These geometric methods are appealing to biologists who approach the study of shape from a variety of perspectives, from clinical to evolutionary, because they incorporate the geometry of organisms throughout the data analysis. The second edition of this book retains the emphasis on accessible explanations, and the copious illustrations and examples of the first, updating the treatment of both theory and practice. The second edition represents the current state-of-the-art and adds new examples and summarizes recent literature, as well as provides an overview of new software and step-by-step guidance through details of carrying out the analyses. Contains updated coverage of methods, especially for sampling complex curves and 3D forms and a new chapter on applications of geometric morphometrics to forensics Offers a reorganization of chapters to streamline learning basic concepts Presents detailed instructions for conducting analyses with freely available, easy to use software Provides numerous illustrations, including graphical presentations of important theoretical concepts and demonstrations of alternative approaches to presenting results.
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