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opencc-zeroAug 2020View details →

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, while the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous studies were taxonomically limited. We greatly improve the phylogenetic underpinning for Diapensiaceae with the most inclusive taxonomic sampling thus far, employing both nuclear and plastid gene sequence data for at least one sample per species in the family. Our estimates indicate that genera of Diapensiaceae variously diverged in the Eocene, Oligocene, and early to mid-Miocene. Biogeographic analysis suggests that the probable ancestor of the Diapensiaceae crown clade originated in the Nearctic, with vicariance events contributing to the current distribution of the disjunct taxa. Ecological niche, when considered in a phylogenetic context, clustered based on biogeographic realm. In general, greater ecological overlap was found at younger nodes and greater niche divergence was found among distantly related species. Diversification in Diapensiaceae appears to have been shaped by both large-scale biogeographic factors, such as vicariance, and divergence in ecological niche among closely related species.

opencc-by-4.0Sep 2020View details →

Data collection for Tsuji et al., 2020, Microbial ecology of phototrophs in Boreal Shield lakes, Chapter 3: Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes (PhD thesis)

This data collection includes supplementary or raw data files related to Chapter 3 of the PhD thesis of Jackson M. Tsuji, "Biogeography and activity of chlorophototrophs in the ferruginous water columns of Boreal Shield lakes" (in "Microbial ecology of phototrophs in Boreal Shield lakes"). Specifically, the following files are included: <ul> <li>ASV_table_non_rarefied_counts.tsv.gz -- non-rarefied ASV table containing 16S rRNA gene amplicon data presented in this study as raw counts. Beyond the index column and sample columns, two additional columns, "Consensus.Lineage" and "Sequence" are included in the table. These columns include the taxonomic classification of the ASV (according to Silva) and the ASV sequence, respectively.</li> <li>ASV_table_non_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>ASV_table_rarefied_counts.tsv.gz -- same as "ASV_table_non_rarefied_counts.tsv.gz", except that data is rarefied to 12,000 sequences per sample. Five samples were dropped due to having <12,000 sequences.</li> <li>ASV_table_rarefied_percent.tsv.gz -- same as above, but the data are normalized within each sample and expressed as percentages (i.e., sum to 100%).</li> <li>MAG_abundances_to_unassembled_reads.tsv.gz -- table like an ASV table showing the relative abundances (expressed as percentages) of metagenome-assembled genomes within metagenomes. Aside from the index column and sample columns, additional columns are included to provide the taxonomic classification of the MAGs (based on the Genome Taxonomy Database) and the CheckM statistics of the MAGs. Relative abundances of MAGs in a metagenome are calculated as the number of mapped reads to the MAGs from the given metagenome divided by the total number of unassembled metagenome reads for that metagenome (times 100%).</li> <li>MAG_abundances_to_assembled_reads.tsv.gz -- same as above, except that relative abundances are divided by the total number of unassembled metagenome reads for that metagenome that mapped to that metagenome's assembled contigs.</li> <li>core_sample_metadata.tsv -- table of core physico-chemical and geographic metadata for the samples in this study (used to build biplots presented in the chapter). Note that "nd" means "no data available", and any measurements below detection limits have been set to 0. A limited number of values were inferred from other sampling time points -- these are noted in the table for TDFe measurements, and in addition, the light attenuation coefficient for Lake 373 in Sept. 2017 was inferred from the Sept. 2016 coefficient due to no light data being available for Sept. 2017 samples.</li> <li>metadata_descriptions.tsv -- descriptions of all metadata columns in the above file.</li> </ul>

opencc-zeroMay 2020View details →

Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian‐ eastern North American Nyssa (Nyssaceae)

Nyssa (Nyssaceae, Cornales) represents a classical example of the well‐known eastern Asian‐eastern North American floristic disjunction. The genus consists of three species in eastern Asia, four species in eastern North America, and one species in Central America. Species of the genus are ecologically important trees in eastern North American and eastern Asian forests. The distribution of living species and a rich fossil record of the genus make it an excellent model for understanding the origin and evolution of the eastern Asian‐eastern North American floristic disjunction. However, despite the small number of species, relationships within the genus have remained unclear and have not been elucidated using a molecular approach. Here we integrate data from 48 nuclear genes, fossils, morphology, and ecological niche to resolve species relationships, elucidate its biogeographic history, and investigate the evolution of morphology and ecological niches, with the goal toward a better understanding of the well‐known EA‐ENA floristic disjunction. Results showed the Central American (CAM) N. talamancana was sister to the remaining species, which were divided among three, rapidly diversified subclades. Estimated divergence times and biogeographic history suggested Nyssa had an ancestral range in Eurasia and western North America in the late Paleocene. The rapid diversification occurred in the early Eocene, followed by multiple dispersals between and within the Erasian and North American continents. The genus experienced two major episodes of extinction in the early Oligocene and end of Neogene, respectively. The Central American N. talamancana represents a relic lineage of the boreotropical flora in the Paleocene/Eocene boundary that once diversified in western North America. The results supported the importance of both the North Atlantic land bridge and the Bering land bridge (BLB) for the Paleogene dispersals of Nyssa and the BLB for the Neogene dispersals and the role of Central America as refugia of the Paleogene flora. The total‐evidence based dated phylogeny suggested that the pattern of macroevolution of Nyssa coincided with paleoclimatic changes. We found a number of evolutionary changes in morphology (including wood anatomy and leaf traits) and ecological niches (precipitation and temperature) between the EA‐ENA disjunct, supporting ecological selection driving trait evolutions following geographic isolation. We also demonstrated challenges in phylogenomic studies of lineages with rapid diversification histories. The concatenation of gene data can lead to inference of strongly supported relationships incongruent with the species tree. However, conflicts in gene genealogies did not seem to impose a strong effect on divergence time dating in our case. Furthermore, we demonstrated that rapid diversification events may not be recovered in divergence time dating analysis using BEAST if critical fossil constraints of the relevant nodes are not available. Our study provides an example of complex bi‐directional exchanges of plants between Eurasia and North America in the Paleogene but "out of Asia" migrations in the Neogene to explain the present disjunct distribution of Nyssa in EA and ENA.

opencc-zeroDec 2012View details →

Data from: Biogeography of scorpions in the Pseudouroctonus minimus complex (Vaejovidae) from south-western North America: implications of ecological specialization for pre-Quaternary diversification

Aim: The aim of this study was to assess the impact of pre-Quaternary tectonics and orogeny relative to that of Pleistocene climate change on diversification within the Pseudouroctonus minimus complex, a group of vaejovid scorpions with stenotopic habitat requirements. Location: South-western North America (United States and Mexico). Methods: Multilocus sequence data (1899 base pairs from two mitochondrial and two nuclear genes) were generated from 65 samples of scorpions in the minimus complex. Phylogeographical structure within the minimus complex was explored using model-based phylogenetic methods and a general mixed Yule coalescent model to identify independent geographical clusters. A time-calibrated multilocus species tree was reconstructed using a multispecies coalescent approach. Ancestral areas were estimated at divergence events across the tree using a probabilistic Bayesian approach. Results: Extensive geographical structure was evident within two well-supported clades. These clades probably diverged over 25 million years ago (Ma), based on estimated mean divergence dates, followed by 14 divergences in the Miocene (25–5 Ma) and 4 divergences in the Pliocene and Pleistocene (< 5 Ma). The ancestral origin of the minimus complex was reconstructed to be across California and the Mexican Highlands. The Chihuahuan Desert was colonized twice from the Mexican Highlands, and one dispersal event occurred from the Mexican Highlands back to California. Main conclusions: Spatial and temporal patterns of evolution in the minimus complex support predictions that stenotopy promoted pre-Quaternary diversification. Miocene and Pliocene geomorphology, perhaps in concert with climate change, induced allopatric divergence across the heterogeneous landscape of south-western North America. Stenotopic scorpions such as the minimus complex provide a model for exploring correlations between Earth history and biological diversification.

opencc-zeroDec 2016View details →

Data from: Ecology, biofacies, biogeography and systematics of micromorphic lingulate brachiopods from the Ordovician (Darriwilian–Sandbian) of south-central China

Ordovician (Darriwilian to Sandbian) micromorphic linguliform lingulate brachiopods are described from the Guniutan Formation at the Fenxiang section in Hubei province, and the Maocaopu and Cili sections in Hunan province of south-central China, situated on the Yangtze Platform. A total of 7560 specimens from 155 limestone samples (within the interval of Lenodus variabilis – Pygodus anserinus biozones) are assigned to 22 species, representing a low taxonomic diversity and low abundance fauna. The fauna is dominated by the Acrotretoidea, mainly species of the Torynelasmatidae, with Torynelasma the most abundant (more than 40% of total number of specimens), along with the Eoconulidae and Eoconulus (18% of total) representing the second most common forms. Species of the Ephippelasmatidae are also common (16% of total) diverse, and include representatives of Myotreta and Numericoma, as well as Ephippelasma, whereas species of the Scaphelasmatidae are somewhat less common (13% of total). All three investigated sections represent outer shelf environments, but the Maocaopu section is situated in a relatively deeper position, in proximity of the south-eastern outer margin of the Upper Yangtze Platform, close to its boundary with the Jiangnan Slope. A quantitative analysis of the relative abundance data was carried out in order to investigate the biofacies distribution of the micromorphic brachiopod communities across the Yangtze Platform, something that has not been attempted before with Palaeozoic linguliforms. Six lingulate microbrachiopod communities could be recognized in the sections. The major biofacies shift, which occurred in the Cili section in the upper part of the Microzarkodina ozarkodella Zone, at the time of the onset and initial rise of the Mid Darriwilian Carbon Isotope Excursion (MDICE) suggests that these biofacies may have been depth controlled.

FIGURE 10 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 10. Simulium (M.) nr. selwynense, Makira (Santa Cristobal). Penultimate/early lastinstar larva. a, left lateral view. b, pharate pupal gill. c, hypostomal teeth. d, mandible teeth, sensillum, and serrations. e, dorsal view of head, probably female. f, hypostoma and postgenal cleft. g, anal sclerite and circlet of hooks.

FIGURE 5a–c in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 5a–c. Simulium (M.) nr. selwynense, Santa Isobel. Lastinstar larvae. a, left lateral views, female upper, male lower. b, dorsal view of female larva head. c, dorsal view of male larva head.

FIGURE 7 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 7. Simulium (G.) rhopaloides n. sp. Guadalcanal. Early last instar larva, Holotype. a, left lateral view. b, pharate pupal gill. c, hypostomal teeth. d, mandible teeth, sensillum, and serrations. e, dorsal view of head. f, hypostoma and postgenal cleft. g, anal sclerite and circlet of hooks.

FIGURE 4 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 4. Simulium (M.) nr. selwynense, Rendova, New Georgia Islands. Lastinstar larva. a, left lateral view. b, pharate pupal gill. c, hypostomal teeth. d, mandible teeth, sensillum, and serrations. e, dorsal view of head. f, hypostoma and postgenal cleft. g, anal sclerite and circlet of hooks.

FIGURE 1 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 1. Bougainville (PNG) and the Solomon Islands. The 200m bathymetric contour is indicated. Numbers and letters associated with islands are number of recognised species and subgenus (M = Morops, G = Gomphostilbia).

FIGURE 5 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 5. Simulium (M.) nr. selwynense, Santa Isobel. Lastinstar larvae. d, pharate pupal gill. e, hypostomal teeth. f, anal sclerite and circlet of hooks. g, hypostoma and postgenal cleft. h, mandible teeth, sensillum, and serrations.

FIGURE 9a–c in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 9a–c. Simulium (M.) nr. pohaense, Malaita. Last instar larva. a, left lateral view, male. b, dorsal view, female larva head. c, dorsal view, male larva head.

FIGURE 3 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 3. Simulium (G.) noroense, New Georgia, New Georgia Islands. Penultimate instar larva. a, left lateral view. b, pharate pupal gill. c, hypostomal teeth. d, mandible teeth, sensillum, and serration. e, dorsal view of head. f, hypostoma and postgenal cleft. g, anal sclerite and circlet of hooks.

FIGURE 2 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 2. Simulium (G.) noroense, Kolumbangara, New Georgia Islands. Penultimate instar larva. a, left lateral view. b, pharate pupal gill. c, hypostomal teeth. d, mandible teeth, sensillum, and serration. e, dorsal view of head. f, hypostoma and postgenal cleft. g, anal sclerite and circlet of hooks.

FIGURE 11 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 11. Localities of new Simuliidae material from the Solomon Islands. a, Stream near Ringgi, Kolumbangara, New Georgia Islands. b, Upper Sakumbare River, New Georgia, New Georgia Islands. c, Upper Toropi River, Rendova, New Georgia Islands (J. Polhemus in background). d, Garana River (3 km inland), Santa Isabel. e, Charovuga River, Guadalcanal. f, Aluta River, cascade, Malaita (R. Englund in background). g, Puepue River, Makira.

FIGURE 8 in Simuliidae (Diptera) of the Solomon Islands: new records and species, ecology, and biogeography

FIGURE 8. Simulium (G.) hiroshii, Malaita. Female adult. a, left lateral view. b, frontal view of head. Specimen in alcohol.