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It has long been recognized that the process of preserving biological specimens results in alterations of body shape, though detailed studies examining the degree to which morphological changes occur throughout the preservation process are lacking. We utilize geometric morphometric analyses, an increasingly common tool for examining shape variation...
Context in source publication
Context 1
... sizes changed among preservation time periods for all species except P. carbonaria, indicating body changes over preservation time relative to field specimens (Table 4). Negative slopes among time periods indicated consistent shrinkage between landmarks among cyprinids and poeciliids relative to field specimens (S2 Table). ...
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Citations
... In this study, specimens from different regions were preserved with non-uniform methods due to field conditions, resulting damages for several morphological parameters in several populations, especially morphometrics, which may not be ideal to be compare to each other between populations. Preservation using ethanol on fish specimens can significantly alter fish morphology, especially eye size and body size including body depth in less than a year (Sotola et al., 2019). Several species in the javanicus group were identified as O. javanicus due to high morphological similarity between members of the group, namely O. hubbsi in 1981 and Oryzias huagiangensis in 1996. ...
Members of the Adrianichthyidae family share typical distributions, as does the javanicus group, which inhabits western parts of Southeast Asia. Javanicus group members, specifically Oryzias javanicus and Oryzias hubbsi, is the only Adrianichthyidae species that can be spotted in Sundaland Indonesia. Morphological identification and the species distribution mapping of Oryzias specimens from Sundaland in this study were interpreted using ecoregional and dendogram tree approach. Specimens were collected from 11 areas representing five ecoregions in Sundaland Indonesia. Specimens were collected from islands of Java, Sumatra, Belitung and Kalimantan. Six individuals from each population of Oryzias were sampled for morphological identification. Specimens collected from estuaries were morphologically identified as O. javanicus and specimens from freshwater identified as O. hubbsi. Distribution of O. hubbsi from Salatiga is the first record from Central East Java (CEJ) ecoregion, which was previously only distributed in Southern Sumatra-Western Java (SWJ) ecoregion. Morphology of O. hubbsi from Sundaland Indonesia has mean of Standard Length (SL) 1.56 cm, Total Length (TL) 1.94 cm, Anal rays (A) 16, Pectoral rays (P) 8, and Dorsal rays (D) 6. Meanwhile, morphology of O. javanicus from Sundaland has mean of SL 2.07 cm, TL 2.56 cm, A 22, P 11, and D 6.
... Body arching is a source of non-biological deformation that biases comparative settings, especially those encompassing morphometrics approaches (e.g., Clarke & Friedman, 2018), because it leads to underestimating standard measurements of fish size (i.e., body length). Although it can often be easily solved by applying basic mathematical corrections (e.g., Pan et al., 2019), the problem is strongly accentuated when applying more powerful multidimensional methods of shape analysis such as geometric morphometrics, requiring a non-trivial solution (Fruciano et al., 2020;Sotola et al., 2019). ...
Postmortem body curvature introduces error in fish morphometric data. Compared to living fish, the causes of such body curvature in fossils may be due to additive taphonomic processes that have been widely studied. However, a protocol that helps to correct its effect upon morphometric data remains unexplored. Here, we test two different mathematical approaches (multivariate regression and the so-called ‘unbending functions’) available to tackle fish geometric morphometric data in two exceptionally preserved gonorynchiformes fossil fishes, Rubiesichthys gregalis and Gordichthys conquensis , from the Las Hoyas deposits (Early Cretaceous, Spain). Although both methods successfully correct body curvature ( i.e ., removing misleading geometric variation), our results show that traditional approaches applied in living fishes might not be appropriate to fossil ones, because of the additional anatomical alterations. Namely, the best result for 2D fossil fishes is achieved by correcting the arching of the specimens (mathematically “unbending” them). Ultimately, the effect of body curvature on morphometric data is largely taxon independent and morphological diversity mitigates its effect, but size is an important factor to take into account (because larger individuals tend to be less curved).
... The utilization of collection fishes may present some bias depending on the analytical purpose, due to problems related to dehydration and weight lost. Despite this wellknown problem, the ideally recommended utilization of fresh fish (Sotola et al. 2019), in many cases is unfeasible. In addition, macroscopical and ecomorphological analyses in long-time preserved fish had been widely done worldwide, even studying sensible structures, such as digestive tracts (Marinsek et al. 2017) and epibranchial organs (Cohen et al. 2020), which indicates that our results were not compromised by preservation. ...
Ecomorphological studies have been developed in the most diverse coastal environments worldwide, playing a key role in the comprehension of the relationship between ecological niche and morphology. Such approach has been useful to better understand the coexistence of fishes with similar body shape by the biological implications that ecomorphological indices have in the feeding habits differentiating species niche. Engraulidae is a fish family that play primary roles in pelagic trophic webs, and many of its representatives are typically by-catch components that have not received fair attention in trophic ecology studies. This study aimed to evaluate the ecomorphological relationships of five engraulids on a Brazilian tropical sandy beach. Eleven ecomorphological features related to diet and locomotion from juveniles of Anchoa januaria (Steindachner, 1879), Anchoa tricolor (Spix & Agassiz, 1829), Anchovia clupeoides (Swainson, 1839), Anchoviella lepidentostole (Fowler, 1911) and Lycengraulis grossidens (Spix & Agassiz, 1829) were calculated and employed in cluster and principal component analysis. The differences in the species ecomorphological indices evidence niche divergence among them, with morphologically close species presenting distinct feeding preferences, and those with common feeding preferences showing distinct morphology despite their phylogenetically proximity. Our results contribute to a better understanding of trophic web structures and coexistence strategies developed by morphologically close species to avoid competition in coastal environments.
... Fish specimens are typically fixed in a 10% formalin solution prior to long-term storage in 70% ethanol (Sidlauskas and Konstantinidis 2022). Formalin is inexpensive and effective at preserving soft tissues, including external characteristics and organs that are important for morphological and life history studies (Watson and Werb 2013;Holmes et al. 2016;Sotola et al. 2019;Vaz et al. 2022), but it forms DNA-DNA and DNA-protein cross-linkages and promotes DNA fragmentation and base modification (Simmons 1999;Hykin et al. 2015). These effects can inhibit the success of Sanger sequencing, the traditional technology used for DNA bar coding and sequencing of targeted loci, which relies upon DNA with low fragmentation and high integrity (Chase et al. 1998;Bucklin and Allen 2004;Campos and Gilbert 2012;Hykin et al. 2015). ...
Objective
Recent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and short‐read sequencing methods offer opportunities to analyze highly fragmented DNA from formalin‐fixed specimens so long as enough DNA of sufficient quality is recovered.
Methods
We compared two protocols developed to extract DNA from formalin‐fixed tissues using specimens of three freshwater fishes: the Southern Brook Lamprey Ichthyomyzon gagei , Slimy Sculpin Cottus cognatus , and Brown Trout Salmo trutta . Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey).
Result
Likelihood models generally did not detect DNA quantity differences between extraction protocols nor tissue types; however, 6.0–8.7× more DNA was recovered from Slimy Sculpin caudal fins than from muscle tissue. Extraction protocol had mixed effects on DNA purity; the wash protocol outperformed the no‐wash protocol for Slimy Sculpin and Brown Trout, but the reverse was true for the lamprey. Purer DNA was recovered from the caudal fins; however, fragment lengths were generally greater from muscle tissue for both ray‐finned species.
Conclusion
Our results suggest that the best tissue for sampling may depend on the quality metric considered most important for a study's objectives and that omitting time‐consuming tissue wash steps can yield DNA of quantity and quality comparable to DNA from more complex methods. Regardless of species, the DNA extracted from most samples using both protocols met quantity and quality thresholds that are likely to result in short‐read sequencing success. These results provide optimism for unlocking the wealth of genetic information in natural history collections for use in fisheries management and conservation genomics.
... Good and high-quality preservation results require proper handling during the preservation process, such as tools used, maintain cleanliness of materials, and use fresh fish. There are many different types of fish preservation processes, such as salting, drying, impregnating, fermenting, and refrigerating the fish [16]- [19]. Indonesian fishermen perform a traditional process of drying fish using direct sunlight. ...
The abundance of fish catches in Indonesia is excellent potential. Still, if the abundant results cannot be adequately managed and are just wasted, it will eventually lead to bad things. This problem was also found in Seraya Village, Karangasem, Bali, where large fish yields and the fish processing process were still constrained by weather and environmental conditions causing the expected results to not be achieved. To overcome this, a photovoltaic (PV) system-based fish dryer was developed that can assist the fish drying process. Utilization of this system is also supported by good solar energy potential. The system can generate 402.78 Wh of electrical energy per day, covering 104.89% of the electrical energy demand of the fish dryer. The results of statistical tests using the Mann-Whitney test for fish weight and unpaired t-test for fish moisture content showed no significant results (p>0.05). This value states that there is no difference in the results of drying fish with the PV system and the traditional method. From this, we can conclude that fish drying using a solar power system works similarly to conventional fish drying methods.
... Ideally, morphological data (e.g., total length [TL]) should be collected from fresh specimens as preservation methods of any kind will alter body shape and size (e.g., Sotola et al., 2019). In our study, formalin fixation and alcohol preservation would have resulted in shrinkage in lengths (e.g., Shields and Carlson, 1996;Kristoffersen and Salvanes, 1998). ...
Fourhorn sculpin (Myoxocephalus quadricornis) is ubiquitous in Canadian Arctic waters with a more common marine and brackish form and a rarer freshwater form. There is a paucity of information available for the freshwater form from Canadian waters. In the summer of 2003, we serendipitously collected 28 of the freshwater form of fourhorn sculpin from Lake Tuborg, Ellesmere Island, Nunavut. The fish ranged in size from 62 mm to 171 mm total length and age from 1 to 12 years with females growing faster and to a larger theoretical maximum total length than males. The sculpin preyed mainly upon the crustacean, Mysis segerstralei, but were also opportunistic feeders (e.g., Arctic charr (Salvelinus alpinus) eggs) and cannibalistic. Although our sample of fourhorn sculpin is small, the data from these fish represent the only information from a fully freshwater form population of the species from Canadian waters. We also present an updated list of the known Canadian lacustrine and riverine populations of fourhorn sculpin.
... Preservation method (i.e., frozen or liquid fixation) can have an impact on the body morphology of fishes as noted by Leslie and Moore (1986), Sotola et al. (2019), and Fruciano et al. (2020. Fruciano et al. (2020 is of most interest here as they estimated the effects of preservation (fresh, frozen, formalin, and alcohol) on downstream statistical analysis and found only minor, but statistically significant, effects, even when mixing samples preserved differently. ...
Objective
Here we determine how traditional morphometrics (TM) compares with geometric morphometrics (GM) in discriminating among morphologies of four forms of ciscoes of the Coregonus artedi complex collected from Lake Huron.
Methods
One of the forms comprised two groups of the same deepwater cisco separated by capture depth, whereas the other three forms were shallow‐water ciscoes.
Result
Our three groups of shallow‐water ciscoes were better separated (3% vs. 19% overlap) in principle component analysis (PCA) with TM data than with GM data incorporating semilandmarks (evenly spaced nonhomologous landmarks used to bridge between widely separated homologous landmarks). Our two deepwater cisco groups, comprising a putatively single form collected from different depths, separated more in PCAs with GM data (33% overlap) than in PCAs with TM data (66% overlap), an anomaly caused by greater decompression of the swim bladder and deformation of the body wall in the group captured at greater depths. Separation of the two deepwater cisco groups captured at different depths was not affected by the removal of semilandmarks. Assignment of forms using canonical variate analysis accurately assigned 86% of individuals using TM data, 98% of individuals using GM data incorporating semilandmarks, and 100% of individuals using GM data without semilandmarks. However, we considered assignments from the same form of deepwater cisco into separate groups as misassignments resulting from different capture depths, which reduced the accuracy of assignments with GM data incorporating semilandmarks to 66%.
Conclusion
Our study implies that TM will continue to have an important role in morphological discrimination within Coregonus and other fishes similarly shaped.
... As preservation continued, size declines persisted such that by the end of the study (465 weeks after euthanasia), SVL had declined by 3.35% and SL by 2.0% on average (Table 4; Fig. 2; Supporting Information, Table S2). A recent study of fish specimens found that fish also continue to shrink in ethanol over a short period of 8 weeks (Sotola et al., 2019), a finding both corroborated and expanded upon by our present study. In our study, SVL and spine length (characters that include a substantial cartilaginous component and are not independent of each other) both appeared to shrink during fixation and preservation, emphasizing the importance for such long-term scrutiny across multiple characters. ...
Preservation of museum specimens depends on chemical fixation and preservation, processes that might distort the original material. Relatively few studies have examined the effects of preservation in potentially susceptible soft-bodied taxa, such as herpetofauna, and those that have rarely extend over more than a few months. We collected six common morphological measurements from the same set of radiographed specimens of the Neotropical lizard Anolis sagrei over nearly 10 years to investigate whether morphometric changes result from fixation in formalin and/or subsequent long-term preservation in ethanol. Snout–vent length declined by 3.5% on average over 10 years, starting almost immediately with fixation and continuing to decline during fluid preservation, eventually levelling off at 40 weeks and beyond. The mostly ossified component of snout–vent length, spine length, declined by 2% on average, but the decline did not begin until fluid preservation commenced and continued throughout the duration of the study. Other characters showed significant decline over the course of the study. Our findings suggest caution when combining fresh and preserved specimens or specimens of different preservation ages, because a decline in snout–vent length but not in other allometrically proportional characters will introduce error when correcting characters for body size in preserved animals.
... Special attention was paid to specific characteristics of the specimens (length and diagnostic features from original descriptions) to confirm their type status. Recent length measurements are commonly less than those given in original descriptions due to some shrinkage of the body that commonly occurs during ethanol preservation (Sotola et al. 2019). ...
Zoological collections remain the main archive of animal biodiversity on Earth, and are of major importance especially in times of large-scale biodiversity decline. The most vital part of these collections are the type specimens, which represent the original and unique reference for respective species. A full digitisation of the entire Natural History Museum Vienna collections is currently ongoing. In the meanwhile, annotated lists of groups of types based on a thorough study of all aspects of historical museum specimens considering the Extended Specimen approach are an essential resource for researchers to perform taxonomic revisions, phylogenetic studies, barcoding, and conservation management. As the first example for the Fish Collection, we provide a catalogue of type specimens of actinopterygian species described by Maximilian Holly and deposited in the Natural History Museum of Vienna. All together, the presented catalogue includes 141 specimens in 128 lots (catalogue numbers) of 41 species-group taxa (species and subspecies). We present data on nomenclatural status of the specimens to clarify type localities and dates, review taxonomic histories for all taxa and their validity or synonymisations, a full bibliography of the original descriptions and related literature, and illustrations for especially poorly known taxa. The holotype of one invertebrate species in Asteroidea is also included as a single species described by Holly in echinoderms; Polychaeta will follow in Part 2 of the catalogue. We aim to provide a comprehensive taxonomic guide to Holly’s types highlighting the importance of research on type specimens for clarifying existing taxonomic problems and importance for species conservation.
... Another important factor is the sample storage and preparation process that involves condition treatment liquid containing formalin and alcohol, which can affect the results. Sotola et al. reported on the effect of formalin and ethanol on morphology, where significant changes in body shape among fresh and formalin-fixed specimens were observed [40]. Moreover, changes in body shape continue to occur after subsequent ethanol preservation. ...
Glyphosate contamination in fresh water is a major problem in agricultural countries. It affects many vital organs in freshwater organisms that are important in the food chain. Hence, the effects of glyphosate on living organism organs are of particular interest. However, several existing techniques for evaluating the effect of glyphosate on aquatic organisms require stained tissue. To study organ tissue with minimal processing, alternative technique is demanded. Here, we investigated the used of optical coherence tomography (OCT) as an alternative tool for ex vivo evaluation of the effect of glyphosate on organ tissues of aquatic organisms, i.e., hybrid catfish (Clarias gariepinus × Clarias macrocephalus). The targeted samples were organ tissues from the brain, gill, and liver of hybrid catfish after glyphosate exposion at concentration of 10 mg L⁻¹ for 24 hours. The alteration was then verified by histology, and immunohistochemistry. The study found that all three techniques provide correlated results. We observed that OCT clearly showed damage to the brain and gill tissues of glyphosate-exposed hybrid catfish. However, the alteration in liver tissue was observable but not clear for this low concentration of exposure. The results from histology and immunohistochemistry confirmed the effect of glyphosate on brain, gill, and liver tissues of hybrid catfish. The results suggest that all three techniques could be used to examine the effects of glyphosate exposure in hybrid catfish. However, the choice of a suitable technique depends upon the purpose of the study.
