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opennotspecifiedApr 2024View details →

FIGURE 8 in Morphological and genetic data challenge species and subspecies in the Lerista microtis group (Squamata: Scincidae)

FIGURE 8. Evolutionary relationships in Lerista lizards with focus on taxa in the L. microtis complex. (A) Results from a phylogenetic analysis based on 133,163 base pairs across 940 restriction site-associated nuclear DNA (ddRAD) loci. (B) Results from an analysis based on 1,143 base pairs from the cytochrome b mitochondrial marker. (C) Map depicting the sampling localities of specimens included in the genetic analyses. For clarity, a maximum of three samples per taxon outside of the L. microtis complex is shown in each tree; to provide a reference of intra-taxon divergences across Lerista, these samples were selected to include the most divergent individuals within each taxon. Nodal bootstrap support values> 70 are indicated with a black dot. Information on genetic samples are provided in Table A3, appendix.

Figure 6 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 6: Haplotype network of 11 haplotypes of Halymenia malaysiana and their distribution. Haplotype names are written beside the circles. Each cross in the lines between two haplotypes is a single mutation. The data were processed by PopART software.

Figure 4 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 4: Maximum likelihood phylogenetic tree inferred from the alignment of ITS1 sequences. Support values are shown as in Figure 3. The ribotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Alaria esculenta was used as an outgroup to root the tree. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site).

Figure 5 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 5: Distribution of haplotypes of Halymenia malaysiana in Sunda Shelf (Malaysia and Viet Nam) and the Philippines. 11 haplotypes (R1–R11) are defined by different colors. Sites 1–9 (S1–S9) were defined by Tan et al. (2018a). S10 is defined in this study. Dotted line represents the border of the Sunda Shelf. The data were processed by PopART software.

Figure 3 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 3: Maximum likelihood phylogenetic tree inferred from the alignment of the combined cox3 and tatC–tLeu sequences. Bootstrap values and Bayesian posterior probabilities>50% are shown, and "-" indicates a value <50%. The branch length is proportional to the sequence divergence indicated by the scale bar (substitutions per site). Refer to Uwai et al. (2006a) for explanation of the haplotype names and classification of the clades I to IV. The haplotypes detected in the Chinese samples in the present study are indicated with bold italicized fonts. Lessoniopsis littoralis was used as an outgroup to root the tree.

Figure 4 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 4: Halymenia malaysiana from Viet Nam (CDNT-H15) showing cystocarp development. (A) Auxiliary cell and ampullar filaments (white arrowheads). (B) Young cystocarp showing auxiliary cell and medullary filaments (black arrowheads). (C–E) Development of other young cystocarps showing a basal fusion cell, gonimoblast initial (black arrow) and gonimolobe enveloped by elongated ampullar filaments and secondary medullary filaments. (F) Mature cystocarp showing gonimoblast initial (gi, black arrow), basal fusion cell (fc), and gonimolobe (g). Scale bars = 20 µm; aux, auxiliary cell; g, gonimolobe; gi, gonimoblast initial; fc, fusion cell.

Figure 3 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 3: Halymenia malaysiana from Viet Nam showing habit and vegetative morphology. (A) Thallus in Van Phong Bay (VPKH-H2). (B) Herbarium voucher specimen CDNT-H15 collected at Nha Trang Bay. (C) Cross section through middle part of a young blade showing densely arranged cortical cells and sparse. loosely arranged, filamentous medullary cells of CDNT-H15. (D) Magnification of cortex layers from (C). (E) Anomalous refractive ganglionic cell (arrow) with 6 arms from CDNT-H15. Scale bars in (C–E) = 20 µm.

Figure 2 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 2: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of ITS1 sequences. The color areas in the pie charts are proportional to the ribotype frequency in the map. Small circles indicate undetected ribotypes. Each line connecting ribotypes represents one base mutation. The ribotypes detected in the Chinese samples in the present study are indicated in the ribotype network by the same colors as those in the map.

Figure 1 in Genetic diversity of Undaria pinnatifida populations from China and their genetic relationship with those from Įapan and Korea as revealed by mitochondrial and nuclear DNA sequences

Figure 1: Geographic distribution of haplotypes in natural and farmed populations of Undaria pinnatifida from China (A) and statistical parsimony network (B) of the combined cox3 and tatC–tLeu sequences. The color areas in the pie charts are proportional to the haplotype frequency in the map. Refer to Uwai et al. (2006a) and Table 3 for explanation of the haplotype names and classification of the clades I to IV, which are enclosed by boxes with lines of different patterns. Small circles indicate undetected haplotypes. Each line connecting haplotypes represents one base mutation. The haplotypes detected in the Chinese samples in the present study are indicated in the haplotype network with the same colors as those in the map.

Figure 2 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 2: Phylogeny of members of Halymenia inferred from maximum likelihood and Bayesian inference. Data set based on 1207 bp of partial rbcL. Bootstrap values and posterior probability of each method are shown at each node: (left) maximum likelihood/(right) Bayesian inference; *, full support (bootstrap value = 100%, posterior probability = 1.0); -, bootstrap value <50%. Numbers before countries are GenBank accession numbers. In bold face, samples collected in Viet Nam. See Supplementary Table S1 for more information on each taxon.

Figure 1 in New record of Halymenia malaysiana (Halymeniaceae, Rhodophyta) from Viet Nam, and its genetic diversity in the western Pacific

Figure 1: Map of Viet Nam coast and sampling sites (arrows). See Supplementary Table S1 for more information.

opennotspecifiedDec 2016View details →

Figure 2 in Seaweed reproductive biology: environmental and genetic controls

Figure 2: Synthetic overview of gamete formation, fusion and meiosis in Chlamydomonas with indications of the genes involved and their conservation in other algae (black, highly conserved; blue, somewhat conserved; red, not conserved).

opennotspecifiedDec 2016View details →

Figure 1 in Seaweed reproductive biology: environmental and genetic controls

Figure 1: Schematic representation of algal life cycles. Diploid and haploid stages are marked by white and black arrows, respectively. (A) Brown algal life cycle. Fucales are characterized by a diplontic life cycle. Meiosis in the reproductive tissue is immediately followed by gametogenesis and syngamy producing a diploid zygote. Most algae such as Dictyota, Scytosiphon and Laminaria exhibit a diplohaplontic life cycle where a haploid gametophyte alternates with a diploid sporophyte. Here following meiosis the resulting spore develops into a multicellular organism. Both haploid and diploid phases may be of identical morphology (isomorphic) (Dictyota), or the two phases may develop differently (heteromorphic) with either the gametophyte (Laminaria) or the sporophyte (Scytosiphon) being microscopic. Many unicellular algae (Chlamydomonas) are characterized by a haplontic life cycle where the formation of a zygote is immediately followed by a meiotic division. (B) Simplified diplohaplontic life cycle of Ectocarpus siliculosus. Meiosis (a) takes place in the sporophyte (diploid) to produce haploid spores. First cell division in germinating spores is asymmetric (b) and they grow into multicellular gametophytes. Gametophytes produce morphologically identical but physiologically differentiated male and female gametes (c), which fuse to form a zygote. After a symmetrical first cell division (d) the zygote grows into a diploid sporophyte. Alternatively, gametes that do not meet a partner of the opposite sex grow into diploid parthenosporophytes by means of parthenogenesis combined with endoreduplication (e) or into a haploid parthenosporophyte (f). The latter produces meiospores via a nonreductive apomeiotic event (g). (C) Life cycle of the red alga Chondrus showing three distinct stages: the gametophyte, the sporophyte and the carposporophyte, which develops parasitically on the gametophyte after fertilization. Loops connecting a generation with itself denote asexual reproduction mediated by vegetative reproduction (e.g. fragmentation, propagule formation) (Fucus, Dictyota), the formation of asexual spores (mitospores) (Dictyota, Ectocarpus, Laminaria), mitosis (Chlamydomonas) or parthenogenetic development of unfertilized (female) gametes (Scytosiphon, Laminaria, Ectocarpus). Figure adapted from Bogaert et al. (2013).

Figure 4 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 4: Four possible scenarios that explain colonization of the NW Atlantic from the NE Atlantic that attempt to reconcile data from this study and others that find no sexual reproduction in the NW Atlantic.

Figure 1 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 1: Collection localities of Porphyra umbilicalis populations in New Hampshire and Maine, USA. Pie charts show frequencies of genotypes in each population collection. The sum of genotype frequencies among all populations is also given.

Figure 2 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 2: Principal Components Analysis based on Nei's genetic distances among Porphyra umbilicalis genotypes. The genotypes as well as the individuals assayed with the genotype are given (DP =Dover Point, FS=Fort Stark, NL= Nubble Light, QH =Quoddy Head, RSP=Reid State Park, and W =Wiscasset).

Figure 3 in Genetic variation within and among asexual populations of Porphyra umbilicalis Kützing (Bangiales, Rhodophyta) in the Gulf of Maine, USA

Figure 3: Principal components analysis based on Nei's unbiased genetic distances among populations of Porphyra umbilicalis in the Gulf of Maine, USA.

opencc-by-4.0Nov 2024View details →

Recent genetic drift in the co-diversified gut bacterial symbionts of laboratory mice

Daniel D. Sprockett (1), Brian A. Dillard (1), Abigail A. Landers (2), Jon G. Sanders (1), Andrew H. Moeller (1,2)* 1 Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA 2 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA *To whom correspondence should be addressed: andrew.moeller@princeton.edu   Abstract: Laboratory mice (Mus musculus domesticus) harbor gut bacterial strains that are distinct from those of wild mice but whose evolutionary histories are unclear. Understanding the divergence of laboratory-mouse gut microbiota (LGM) from wild-mouse gut microbiota (WGM) is critical, because LGM and WGM have been previously shown to differentially affect mouse immune-cell proliferation, infection resistance, cancer progression, and ability to model drug outcomes for humans. Here, we show that laboratory mice have retained gut bacterial symbiont lineages that diversified in parallel (co-diversified) with rodent species for > 25 million years, but that LGM strains of these ancestral symbionts have experienced accelerated accumulation of genetic load during the past ~ 120 years of captivity. Compared to closely related WGM strains, co-diversified LGM strains displayed significantly faster genome-wide rates of fixation of nonsynonymous mutations, indicating elevated genetic drift, a difference that was absent in non-co-diversified symbiont clades. Competition experiments in germ-free mice further indicated that LGM strains within co-diversified clades displayed significantly reduced fitness in vivo compared to WGM relatives to an extent not observed within non-co-diversified clades. Thus, stochastic processes (e.g., bottlenecks), not natural selection in the laboratory, have been the predominant evolutionary forces underlying divergence of co-diversified symbiont strains between laboratory and wild house mice. Our results show that gut bacterial lineages conserved in diverse rodent species have acquired novel mutational burdens in laboratory mice, providing an evolutionary rationale for restoring laboratory mice with wild gut bacterial strain diversity.

opencc-by-4.0Nov 2024View details →

Genetic divergence in the natural regeneration of black poplar along the Vistula River in Poland

The dataset comprises nuclear microsatellite data (PCR products lengths) used in the paper "Genetic divergence in the natural regeneration of black poplar along the Vistula River in Poland". Abstract: Many years of land use transformation within river valleys have drastically changed these ecosystems. Black poplar is a tree species characteristic of riparian habitats. Unfortunately, due to specific environmental requirements, its populations have difficulties with natural regeneration. Here, we genotyped 623 black poplar individuals from four populations located along different sections of the Vistula River. This river, which is the largest in Poland, is characterized by the variable degrees of regulation and transformation of its natural environment. Each black poplar population consisted of a group of mature trees and a group of naturally regenerated trees. Our main goal was to assess the differences between the gene pools of mature trees and natural regenerations. The results showed that all populations were characterized by high and comparable values of the parameters of genetic diversity. Despite this, we distinguished 2-3 genetic clusters (depending on the method). The genetic differentiation among the natural regeneration groups was almost twice as high as that among the mature tree groups. The gene pools of most natural regenerations diverged from the gene pools of mature tree groups except for one population. This was also the only population where fully generative regeneration occurred, growing in the least transformed middle section of the river. Our research confirms the need to monitor seedlings and saplings along major rivers and to conduct molecular analyses to assess their gene pools. It can be assumed that due to the lack of suitable areas for seed germination, black poplar will reproduce mainly vegetatively, which may be a way to ensure the survival of the species. However, the adaptive potential of the youngest generations is unknown, especially in the face of progressive climate change. We conclude that to preserve black poplar genetic resources, ex situ protection in the form of local clone archives is necessary.