Large Species Research Articles

Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak.

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z starting from z = 1 and color coding z in m/z spectra. CHARDA combines the analysis of ion signal decay rates in the time-domain data (transients) in Fourier transform (FT) MS with the interrogation of mass defects (fractional mass) of biopolymers. Being applied to individual isotopic peaks in a complex protein tandem (MS/MS) data set, CHARDA aids peptide mass spectra interpretation by facilitating charge-state deconvolution of large ionic species in crowded regions, estimating z even in the absence of an isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust, and consistent with conventional FTMS and FTMS/MS data acquisition procedures. An effective charge-state resolution Rz ≥ 6 is obtained with the potential for further improvements.

Small-scale low-tropic ocean farming and coastal rural landscapes: Why the logistics of seaweed matter? Insights from Ireland for collaborative planning

Kelps are part of large brown macroalgae species with a fundamental role in temperate to subpolar coastal marine ecosystems and their cultivation has been expanding as part of several efforts and countries' policies. This study explores the relevance of post-harvesting logistics planning involving marine operations of emerging seaweed-based supply chains including kelp species. In the Irish context, we explore the potential of collaboration among low-tropic ocean farming sectors regarding shared space and infrastructure in rural and remote landscapes. Based on empirical data and a novel methodological approach, a multi-method analysis was performed involving geographic information systems, mathematical modelling and qualitative content analysis. The results indicate large potential production and collaboration capacity if current licensed areas and existing infrastructure were integrated with kelp cultivation for further processing and distribution in 40 local supply hubs and 14 optimal locations for shared processing facilities. Moreover, the different transportation scenarios considered indicate that costs and greenhouse gas emissions could be minimised by reducing moisture content locally and with increased payload. Further linkages reveal uncertainties in the uses of alternative methods of preservation such as ensiling and a lack of attention to non-market values. For future valorisation in diverse commercial and non-commercial applications, seaweed farming and collaborative processing opportunities still need to be incorporated into societal discourses and futures envisioned by rural coastal communities, including the engagement of young generations in such transformation pathways.

Development of a new kappa-carrageenan hydrogel system to study benthic diatom vertical movements.

Benthic diatom vertical movement has been investigated mainly through indirect measurements based on chlorophyll a fluorescence and spectral reflectance signals. The presence of sediment hinders direct imaging and grazers activity renders the work under controlled conditions very difficult. This study provides a tool to study diatoms movement in a 3D hydrogel matrix. Synthetic and natural hydrogels were tested to find the best 3D transparent scaffold where diatoms could grow and freely move in all directions. Polyamidoamines (PAAm) hydrogels were no-cytocompatible and hyaluronic acid (HA) only allowed diatoms to survive for 2-days. Natural hydrogels made of gelatin/Na-alginate, Na-alginate and kappa-carrageenan (KC) were cytocompatible, with KC showing the best properties for diatom growth and movement on a long term (up to 2 months). Comparing Nitzschia spathulata, Gyrosigma limosum and Navicula phyllepta growth in liquid media vs in KC gels, we found that diatoms reached a significantly higher final biomass in the hydrogel condition. Hydrogels were also useful to isolate large size diatom species e.g., Nitzschia elongata, that did not survive in suspension. Finally, we showed three ways to study diatom species-specific movement in KC hydrogels: 1) controlled species mix; 2) natural diatom assemblages with grazers; and 3) natural diatom assemblages without grazers. With our system, single diatoms could be imaged, identified, and counted. In addition, different stimuli, e.g., light intensity and light composition can be applied and their effects on movement and physiology studied without being masked by sediment or impaired by meiofauna.

Sexual Selection And Species Recognition Promote Complex Male Courtship Displays In Ungulates

Abstract Identifying the evolutionary drivers of sexual signal complexity is a key challenge in the study of animal communication. Among mammals, male bovids and cervids often perform elaborate gestural displays during courtship, consisting of ritualized movements of various parts of the body but the causes underlying interspecific variation in complexity of such displays remain poorly understood. Here we apply the comparative method to investigate which factors may have either promoted or constrained gestural repertoire size. We found that sexual selection was a strong predictor of gestural display complexity in male bovids and cervids. Repertoire size was positively correlated with breeding group size, an indicator of the intensity of sexual selection on males. Moreover, repertoires were larger in species adopting non-territorial and lek breeding mating systems than in species adopting resource-defence territoriality, a finding that can be explained by more emphasis on direct benefits than indirect benefits in resource-defence systems, where male mating success may also be less skewed due to difficulty in monopolising mates. The results also indicate that gestural repertoire size was positively correlated with the number of closely-related species occurring in sympatry. This is consistent with display complexity being selected to facilitate species recognition during courtship and thereby avoid interspecific hybridization. At the same time, repertoire size was negatively associated with male body mass, possibly due to the energetic and mechanical constraints imposed on movements in very large species. By contrast, we found no evidence that the habitat drives selection for complex gestural courtship displays.

Connecting Habitats: Modelling Landscape Connectivity for Large Mammals in Omo-Shasha-Oluwa Forest Reserves, South-West Nigeria

Abstract Preserving landscape connectivity in the Omo-Shasha-Oluwa Forest Reserves is crucial due to human-induced fragmentation, shrinking habitats, and disrupted migration routes for wildlife. From 2014 to 2016, we conducted surveys to gather large mammal presence data, mapping their distribution using the MaxEnt algorithm. Employing Circuitscape software and circuit theory concepts, we predicted connectivity patterns for six large mammal species. Our results consistently showed robust predictive performance, with Area Under the Curve (AUC) values exceeding 0.75 for species distribution models. Notably, we identified suitable habitat patches for seven key species, spanning 1760 km2 for C. civetta, 1515 km2 for T. Scriptus, 729 km2 for L. cyclotis, 1693 km2 for P. porcus, 1350 km2 for C. mona, 1406 km2 for P. maxwellii, and 1379 km2 for C. torquatus. Our analysis highlighted distance to human settlements as the most significant predictor for habitat models concerning T. Scriptus, C. civetta, P. maxwellii, C. torquatus, P. porcus, and C. mona, whereas land use type emerged as a critical factor for L. cyclotis. Furthermore, examination of maximum current flow patterns revealed varying degrees of connectivity among habitat patches, indicating potential bottlenecks to species movement, particularly across major rivers and in areas affected by human activities. These findings offer crucial insights for conservation efforts, guiding strategies to preserve wildlife metapopulation dynamics in the Omo-Shasha-Oluwa Forest Reserves landscape

The effect of miniaturization on the evolution of sexual size dimorphism in geckos.

The evolution of miniaturization can result in dramatic alterations of morphology, physiology and behavior; however the effects of miniaturization on sexual dimorphism remain largely unknown. Here we investigate how miniaturization influences patterns of sexual size dimorphism (SSD) in geckos. Measuring 1,875 individuals from 131 species, we character-ized patterns of SSD relative to body size across two families. We found that miniaturized species were more female-biased than non-miniaturized species. Additionally, one family which contained many miniaturized species (Sphaerodactylidae) displayed allometric pat- terns in SSD with body size, where larger species were male-biased and smaller species were more female-biased. Smaller species in this lineage also produced proportionally larger eggs. By contrast, another family containing few miniaturized species (Phyllodactylidae) displayed a more isometric trend. Together, these observations are consistent with the hypothesis that selection for increased reproductive success in small species of Sphaerodactylidae results in female-biased SSD in these taxa, which in turn drives the positive SSD allometry observed in this lineage. Thus, selection for increased miniaturization in the clade may be offset by selection on maintaining a female size in smaller taxa that ensures reproductive success.

Yak genome database: a multi-omics analysis platform

BackgroundThe yak (Bos grunniens) is a large ruminant species that lives in high-altitude regions and exhibits excellent adaptation to the plateau environments. To further understand the genetic characteristics and adaptive mechanisms of yak, we have developed a multi-omics database of yak including genome, transcriptome, proteome, and DNA methylation data.DescriptionThe Yak Genome Database (http://yakgenomics.com/) integrates the research results of genome, transcriptome, proteome, and DNA methylation, and provides an integrated platform for researchers to share and exchange omics data. The database contains 26,518 genes, 62 transcriptomes, 144,309 proteome spectra, and 22,478 methylation sites of yak. The genome module provides access to yak genome sequences, gene annotations and variant information. The transcriptome module offers transcriptome data from various tissues of yak and cattle strains at different developmental stages. The proteome module presents protein profiles from diverse yak organs. Additionally, the DNA methylation module shows the DNA methylation information at each base of the whole genome. Functions of data downloading and browsing, functional gene exploration, and experimental practice were available for the database.ConclusionThis comprehensive database provides a valuable resource for further investigations on development, molecular mechanisms underlying high-altitude adaptation, and molecular breeding of yak.

Comparing local ecological knowledge with camera trap data to study mammal occurrence in anthropogenic landscapes of the Garden Route Biosphere Reserve

AbstractAccurate information on wildlife occurrence in anthropogenic landscapes is essential to develop effective conservation measures. Monitoring multiple mammal species in heterogeneous landscapes can be challenging because of the diversity of land‐uses and species behaviors. Therefore, different monitoring methods are better adapted to different contexts. We compared data obtained from camera traps with data gathered through an online survey to document the presence of mammal species in mosaic landscapes of the Garden Route Biosphere Reserve in South Africa. The survey detected the same 15 species as the camera traps as well as the additional common duiker. Both methods effectively detected most large mammal species, whereas results were less consistent for smaller species and carnivores. Combining the two methods enabled us to produce more robust estimates of species absence and confirm species presence reported by survey respondents. In less disturbed areas, respondents with good ecological knowledge were effective at monitoring mammal species, while extending the spatial coverage of the study. Bearing in mind the limitations of each method, camera traps and an online survey could complement each other if combined. Together, they can provide a more comprehensive understanding of mammal communities in anthropogenic landscapes, increasing both spatial coverage and the number of species sightings.

Surface functionalization of nickel foam with two-dimensional conjugated MOFs Fe3(hexaiminotriphenylene)2 for highly efficient oxygen evolution reaction

The design of high-efficient, low-cost, and stable electrocatalysts for oxygen evolution reaction (OER) is highly demanding for energy conversion applications. Metal-organic frameworks (MOFs), with large surface area and flexible molecular species, can supply atom-dispersed metal active coordination sites (M−NX, M−SX, M−OX) for OER and have been regarded as potential catalysts for practical applications. However, it is still challenging to use MOFs as OER catalysts directly due to their low conductivity and poor stability. Herein, we successfully synthesized a 2D c-MOF of Fe3(HITP)2 (HITP = 2,3,6,7,10,11-hexaiminotriphenylene) on the surface of nickel foam (NF) by using a layer-by-layer self-assembly strategy. The Fe3(HITP)2/NF-x electrode (x = 5, 10, 15, 20 is the number of cycles) exhibited impressive OER catalytic activity in alkaline electrolyte (1 M KOH), which is superior or comparable to most of the transition metal-based materials reported. Typically, Fe3(HITP)2/NF-15 were able to fully expose the Fe-N4 catalytic sites with an overpotential of 224 mV at a current density of 10 mA·cm−2 and a Tafel slope of 45.4 mV·dec-1. This was mainly attributed to the higher ECSA value, better kinetic process, and fast charge transfer ability of Fe3(HITP)2/NF. In addition, the current density of Fe3(HITP)2/NF-15 remained at 97.3 % of the initial current density after 24 h i-t stability test, showing excellent catalytic stability. This work provided a novel design strategy for the direct application of MOFs to OER applications.

Flow similarity model predicts allometric size dependence, curvature, and covariation of 285 North American tree species

AbstractScaling patterns in plants have long interested biologists, particularly whether different species share similar patterns of growth, and whether differences in growth trajectories depend on plant size. Using 8,794,737 measurements for 285 species from the U.S. Forest Inventory and Analysis database, we test several predictions emerging from a recently published “flow similarity” model for plant growth and allometry. We show that the model's predicted curvature for intraspecific relationships between height, dbh, and biomass is found in 88.1% of examined cases, and empirical slopes fall as predicted between the elastic similarity and flow similarity predictions in 71.1% of cases. We also find a strong size dependence in observed intraspecific allometric exponents, with large species, particularly gymnosperms, converging near the expectation for elastic similarity and the central tendency among small species approaching the expectations for flow similarity in most cases. Our results support the idea that differences in growth patterns across plant species depend on plant size and their attendant hydraulic and/or biomechanical demands and helps to delineate the bounds of the theoretical morphospace in which they occur.

Antitumor effects of polydopamine coated hydroxyapatite nanoparticles and its mechanism: Mitochondria-targeted ROS and calcium channels

Nano hydroxyapatite (nHA) has been acknowledged for its inhibition efficiency on tumor cells and its excellent biocompatibility for normal tissue and cells. However, the low inhibitory efficiency of tumor cells and the ambiguous inhibitory mechanism limited its further application. In this work, four kinds of nHA with different sizes was prepared, and the one with the highest inhibition efficiency on 4T1 cells was screened as a substrate for developing the nanoparticles coated with polydopamine (PDA) coating, which was named nHA-PDA. Both in vivo and in vitro experiments were employed, and the results showed significantly higher inhibitory activity against 4T1 cells and 4T1-bared tumors by nHA-PDA. Further investigation revealed that the oxidative stress induced by PDA results in a large Reactive Oxygen Species (ROS) accumulation, thus triggering the mitochondria-dependent apoptosis pathway ROS-JNK/MAPK and inducing the cascade reaction of inhibiting the anti-apoptosis protein-Bcl-2 expression and activating the expression of the critical genes in apoptosis signaling pathway (caspase 3 and caspase 9). Besides, the significant increase of intracellular [Ca2+] may also be an essential reason for the damage of mitochondria, eventually leading to apoptosis.

Exploring the spatial variation of mercury in the Gulf of St. Lawrence using northern gannets as fish samplers

Mercury (Hg) is a ubiquitous and pervasive environmental contaminant with detrimental effects on wildlife, which originates from both natural and anthropogenic sources. Its distribution within ecosystems is influenced by various biogeochemical processes, making it crucial to elucidate the factors driving this variability. To explore these factors, we employed an innovative method to use northern gannets (Morus bassanus) as biological samplers of regurgitated fish in the Gulf of St. Lawrence. We assessed fish total Hg (THg) concentrations in relation to their geographical catch location as well as to pertinent biotic and anthropogenic factors. In small fish species, trophic position, calculated from compound-specific stable nitrogen isotopes in amino acids, emerged as the most influential predictor of THg concentrations. For large fish species, THg concentrations were best explained by δ13C, indicating higher concentrations in inshore habitats. No anthropogenic factors, such as pollution, shipping traffic, or coastal development, were significantly related to THg concentrations in fish. Moreover, previously published THg data in mussels sampled nearby were positively linked with THg concentrations in gannet prey, suggesting consistent mercury distribution across trophic levels in the Gulf of St. Lawrence. Our findings point to habitat-dependent variability in THg concentrations across multiple trophic levels. Our study could have many potential uses in the future, including the identification of vulnerability hotspots for fish populations and their predators, or assessing risk factors for seabirds themselves by using biologically relevant prey.

Shifting mammal communities and declining species richness along an elevational gradient on Mount Kenya.

Conservation areas encompassing elevation gradients are biodiversity hotspots because they contain a wide range of habitat types in a relatively small space. Studies of biodiversity patterns along elevation gradients, mostly on small mammal or bird species, have documented a peak in diversity at mid elevations. Here, we report on a field study of medium and large mammals to examine the impact of elevation, habitat type, and gross primary productivity on community structure. Species richness was observed using a camera trap transect with 219 sites situated across different habitat types from 2329 to 4657 m above the sea level on the western slope of Mt Kenya, the second highest mountain in Africa. We found that the lowest elevation natural habitats had the highest species richness and relative abundance and that both metrics decreased steadily as elevation increased, paralleling changes in gross primary productivity, and supporting the energy richness hypothesis. We found no evidence for the mid-domain effect on species diversity. The lowest elevation degraded Agro-Forestry lands adjacent to the National Park had high activity of domestic animals and reduced diversity and abundance of native species. The biggest difference in community structure was between protected and unprotected areas, followed by more subtle stepwise differences between habitats at different elevations. Large carnivore species remained relatively consistent but dominant herbivore species shifted along the elevation gradient. There was some habitat specialization and turnover in species, such that the elevation gradient predicts a high diversity of species, demonstrating the high conservation return for protecting mountain ecosystems for biodiversity conservation.

Seed‐dispersal mode and habitat connectivity underpin variation in carbon stocking between Brazilian biomes

Abstract In tropical forests, about 60%–80% of woody plant species depend on animal–plant interactions for dispersal. The dependence on animal species for dispersal makes this interaction very fragile in the face of anthropogenic changes in land use. Disrupting seed‐dispersal processes, principally zoochoric dispersal, could significantly alter the long‐term carbon storage potential of tropical forests. An important question is how landscape structure changes tree carbon stocks in different types of tropical vegetation and how variation is mediated by the dispersal mode of animal (zoochoric) or abiotic (non‐zoochoric) seeds. We focused on tree plots at 126 sites in Brazil spanning four types of forest and savanna vegetation, and calculated carbon stored in zoochoric, non‐zoochoric, and large frugivore‐dispersed species. Our results showed that carbon stocks in zoochoric species and non‐zoochoric species differ significantly among vegetation types, with rainforests having higher stocks in zoochoric species and deciduous seasonally dry tropical forests having higher values in non‐zoochoric species. A greater area of native vegetation promotes higher proportions of carbon stocks dispersed by large frugivore species, whereas a higher mean shape index reduces this proportion. Synthesis. This study highlights that seed‐dispersal type underpins the variation in carbon stocks between vegetation types and that the maintenance of habitat of large dispersers and connectivity are key for retaining carbon stocks in zoochoric species, particularly in rainforest and cerrado sensu stricto.

Morphological and molecular data combined reveal inter- and intraspecific cranial shape variations in bats of Artibeus Leach, 1821 (Chiroptera: Phyllostomidae)

Abstract Since morphological traits may overlap among species within a complex, the integration of morphological and mitochondrial data could provide crucial insights for distinguishing species, as observed in fruit-eating bats of the genus Artibeus. Therefore, the application of geometric morphometric (GM) techniques could yield more refined and robust analyses of inter- and intraspecific variations. In this study, we generated two datasets: one with molecular delimitation data based on the barcode region (COI) and the other with cranial size and shape data using GM methods. Our aims were to investigate variations between large and small species within the genus Artibeus, as well as to explore potential factors influencing such variations. The results from species delimitation revealed molecular operational taxonomic units (MOTUs) supporting the morphological identification. Analyses using GM techniques demonstrated significant inter- and intraspecific variations in cranial size and shape among Artibeus species. The combined outcomes suggest the absence of a significant phylogenetic signal influencing skull variation. This scenario indicates that potential historical ecological factors may have directly influenced the cranial morphology of these species, acting as significant selection forces in geographical space and generating intraspecific variations in Artibeus planirostris.

The effects of fire on large‐ and medium‐sized mammal communities: what do we know? A review

Abstract Large‐ and medium‐sized mammals play a unique role in ecosystem dynamics. They can change the physical and biotic landscape by altering the flow of resources among trophic levels, thereby affecting ecosystem functioning. Although the effects of fire on some ungulates have been well studied, data gaps exist for many species, including canids, felids, mustelids and ursids among others. To address this knowledge gap, we conducted a literature review to synthesize what is known about large and medium mammal responses to fire, including communities, species richness and species interactions in connection with fire. Twenty‐seven large and medium mammal species were studied. Fifty percent of the studies examined ungulates, far exceeding studies of other trophic levels. Eighty‐six percent were conducted on large mammals with significantly fewer studies on medium‐sized mammals. Only four studies examined multiple species responses to fire. Results indicated that fire had a largely positive effect on large‐ and medium‐sized mammals. However, considerable heterogeneity exists within and among taxa. Most fire research has been conducted on focal species rather than on biodiversity, and a large data gap exists on the interactions within or among large‐ and medium‐sized mammals. Forest management focus is changing from fire suppression to reinstating natural fire regimes. Effectiveness monitoring programmes will be needed to test the efficacy of restoration strategies in mammalian communities.

Depth Range Extension for the Misty Grouper Hyporthodus mystacinus Documented via Deep-Sea Landers throughout the Greater Caribbean

Misty Groupers (Hyporthodus mystacinus) are one of the largest and most geographically widespread grouper species and one of the few grouper species known to occur at depths greater than 200 m. However, aspects of their basic biology, behavior, and ecology remain poorly understood, leaving significant gaps in our ability to evaluate their functional role throughout the vertical water column, as well as our understanding of their conservation needs in a changing ocean. Through in-situ video observation obtained using deep-sea landers in both The Bahamas and Cayman Islands over multiple years, we documented Misty Grouper occurrence up to 470 m depth in the mesopelagic zone. These observations provide a new depth range extension for the species and illuminate the potential importance of deep-water habitats for large grouper species in the wider Caribbean.

Insights from 20 years of mammal population research in Indonesia

Abstract Mammal populations are declining in biodiverse tropical regions. Global analyses have identified Indonesia as a hotspot of vertebrate decline, although relatively few data are available to substantiate these claims. We reviewed research articles published during 2000–2020 on 104 medium-sized to large terrestrial mammal species found in Indonesia to help inform conservation management and future research. We identified 308 peer-reviewed studies published in English or Bahasa Indonesia, with an increase in publication rate (articles published per year) over time. Studies of species distributions dominated the literature, followed by publications on abundance, species diversity and combinations of these topics. Most publications concerned single-species studies conducted at a single location and a single point in time. We identify four key issues that should be addressed by future research and conservation efforts: (1) disproportionate focus on a small number of species; (2) geographical bias towards west Indonesia (Sumatra, Kalimantan and Java–Bali), with few published studies from central (Sulawesi, Nusa Tenggara and Maluku) and east (Papua) Indonesia; (3) limitations to survey design, sampling effort and data analysis; and (4) lack of long-term wildlife population studies. We also note challenges local researchers face in publishing their studies in international journals because of language barriers and costs. Greater use of existing biodiversity data and continued capacity building for local researchers, particularly those in central and east Indonesia, are critical to effectively guide future wildlife monitoring and improve the conservation status of Indonesian mammals.

Resource partitioning in hammerhead shark species out-migrating from coastal ecosystems in the Gulf of California

Juveniles of large hammerhead shark species occupy coastal nurseries before migrating offshore to reproduce. In the central Gulf of California, artisanal elasmobranch fisheries have reported catches of juvenile scalloped Sphyrna lewini and smooth S. zygaena hammerhead sharks, but their local foraging habits are yet to be fully understood. In this study, the trophic niches of both hammerhead species as well as of sympatric Pacific sharpnose sharks Rhizoprionodon longurio were investigated using stable isotope values (δ13C, δ34S and δ15N) and fatty acid compositions in whole blood and muscle tissues. Despite interspecific similarities among trophic niches, smooth hammerheads were characterized by lower δ13C, higher δ34S and greater proportion of docosahexaenoic acid (DHA) in both tissues, suggesting they were already partly relying on offshore pelagic resources. For scalloped hammerheads, muscle reflected coastal dietary resources, while offshore trophic markers were detected in blood integrating prey signal over shorter time periods, indicating their more recent initiation of ontogenetic migration. Multidimensional niche calculation revealed low overlap between hammerhead shark trophic niches, implying that potential fine-scale differences in habitat use could reduce competition between these morphologically and ecologically similar species. In the meantime, the isotopic niches of juvenile scalloped and smooth hammerheads were smaller than that of Pacific sharpnose sharks, suggesting they could be more specialized consumers. Overall, the identification of foraging grounds for juvenile hammerhead sharks calls for a future characterization of their residency time in coastal ecosystems to further understand their interactions with fishing pressure in the Gulf of California.

A deep search for large complex organic species toward IRAS16293-2422 B at 3 mm with ALMA

Complex organic molecules (COMs) have been detected ubiquitously in protostellar systems. However, at shorter wavelengths ($ sim 0.8$\,mm), it is generally more difficult to detect larger molecules than at longer wavelengths sim 3$\,mm) because of the increase in millimeter dust opacity, line confusion, and unfavorable partition function. We aim to search for large molecules (more than eight atoms) in the Atacama Large Millimeter/submillimeter Array (ALMA) Band 3 spectrum of IRAS 16293-2422 B. In particular, the goal is to quantify the usability of ALMA Band 3 for molecular line surveys in comparison to similar studies at shorter wavelengths. We used deep ALMA Band 3 observations of IRAS 16293-2422 B to search for more than 70 molecules and identified as many lines as possible in the spectrum. The spectral settings were set to specifically target three-carbon species such as i- and n-propanol and glycerol, the next step after glycolaldehyde and ethylene glycol in the hydrogenation of CO. We then derived the column densities and excitation temperatures of the detected species and compared the ratios with respect to methanol between Band 3 ($ sim 3$\,mm) and Band 7 sim 1$\,mm, Protostellar Interferometric Line Survey) observations of this source to examine the effect of the dust optical depth. We identified lines of 31 molecules including many oxygen-bearing COMs such as CH$_3$OH, CH$_2$OHCHO, CH$_3$CH$_2$OH, and c-C$_2$H$_4$O and a few nitrogen- and sulfur-bearing ones such as HOCH$_2$CN and CH$_3$SH. The largest detected molecules are gGg-(CH$_2$OH)$_2$ and CH$_3$COCH$_3$. We did not detect glycerol or i- and n-propanol, but we do provide upper limits for them which are in line with previous laboratory and observational studies. The line density in Band 3 is only $ sim 2.5$ times lower in frequency space than in Band 7. From the detected lines in Band 3 at a $ level sim 25-30<!PCT!>$ of them could not be identified indicating the need for more laboratory data of rotational spectra. We find similar column densities and column density ratios of COMs (within a factor $ sim 2$) between Band 3 and Band 7. The effect of the dust optical depth for IRAS 16293-2422 B at an off-source location on column densities and column density ratios is minimal. Moreover, for warm protostars, long wavelength spectra ($ sim 3$\,mm) are not only crowded and complex, but they also take significantly longer integration times than shorter wavelength observations sim 0.8$\,mm) to reach the same sensitivity limit. The 3\,mm search has not yet resulted in the detection of larger and more complex molecules in warm sources. A full deep ALMA Band $2-3$ (i.e. sim 3-4$\,mm wavelengths) survey is needed to assess whether low frequency data have the potential to reveal more complex molecules in warm sources.