Category 1: The organization of genetic alleles

In item 4, the AC identified in the quantitative stage was that sister chromatids are considered as separate chromosomes. According to the students’ understanding, a duplicated chromosome refers to the presence of two chromosomes. During the interview stage, new alternative conceptions were identified, including the notion that Aa genotypes indicate the presence of the A allele on one sister chromatid and the a allele on the other sister chromatid, without requiring crossingover. In this scenario, when students observed a duplicated chromosome with an A allele on both sister chromatids and its corresponding counterpart with a a allele on both chromatids, as depicted in the diagrams of letters B and D (figure 4), some students mistakenly believed that the genotype was duplicated. They described the genotype as AAaa for this gene locus instead of Aa:

E4 (Item 4, figure 4): I believe it's the letter A [...]. In [letter] B and [letter] D they put the AA alleles on the same chromosome, as if the information was duplicated like that [...] the chromosomes with the two strands and on those two strands the alleles are the same, AA, and there's another strand with aa, that doesn't make much sense to me.

Another AC found in this category was that Aa genotypes indicate that dominant and recessive alleles cannot coexist on the same chromosome. Because of this, dominant alleles A, B, and D should be on the same chromosome and recessive alleles a, b, and d on the other, as shown in the diagram - letter B (figure 4):

E8 (Item 4, figure 4): [...] I believe that one of the chromosomes contains these dominant alleles while the other would contain these recessive alleles.

Elementary genetic concepts are commonly introduced in classes about Mendel’s Laws, where the concept of genetic alleles is typically discussed. Nonetheless, teachers do not always teach this term in greater detail beyond conceptualization, such as the proper arrangement of alleles on chromosomes (^{GUERRA; TAVARES; VILAS-BOAS, 2022}). One example is the utilization of Punnett's square, in which students arrange the alleles on a chart to display the genotype of the gametes of the parents and offspring. However, the precise positioning of these alleles within the homologous chromosomes, as well as the intricate mechanisms involved in the process of meiosis, are occasionally overlooked. Therefore, students may develop a tendency towards mechanistic thinking, lacking the ability to establish connections among pertinent concepts such as genotype, gene locus, sister chromatids, homologous chromosomes, DNA replication, and alleles.

In an analysis of diagrams of meiosis completed by undergraduates in Biological Sciences, ^{Guerra, Tavares, and Vilas-Boas (2020)} identified AC with respect to heterozygosity and alleles. The students depicted cells containing dominant and recessive alleles that were arranged on a single chromosome, without any instances of permutation. The reasoning in this study is akin to that of the students because, in both instances, the researchers failed to consider the fundamental concept that DNA replication results in the formation of identical sister chromatids. Additionally, it is important to note that the allelic forms are situated at the same gene locus in the homologous chromosomes, rather than on the sister chromatids.

In addition to a lack of knowledge of gene alleles between homologues, students may experience conceptual difficulties due to the fact that the language of genetics is characterized by extensive terminology and brings together abstract concepts that are sometimes used interchangeably, such as genes, alleles, and loci. One example is the common usage of the term gene to refer to a specific genetic allele, such as the gene associated with Duchenne muscular dystrophy. Furthermore, if the student is familiar with the concept of allele, they may not have fully grasped the representation of genetics at the molecular and microscopic levels through diagrams and symbols.

Category 2: The structure of chromosomes

Regarding the relationship between chromosomes and sister chromatids, some interviewees believe that ‘true’ chromosomes consist of two chromatids, whereas unreplicated chromosomes are merely chromatids, and thus should not be considered individual chromosomes:

E9 (Item 8, figure 5): It would only be [letter] C, right?

Source: Adapted from ^{Kalas et al. (2013}).

Figure 6 Item 12 of the adapted MCI 

Entrevistadora: Do you think there are how many chromosomes here [in letter B]? E9: There won't be any, there will be chromatids.

This idea that chromosomes will always be made up of sister chromatids during cell division was discovered to be shared by 18% of seniors in the quantitative stage and is consistent with the study by ^{Dikmenli (2010)}, which was carried out with 124 Turkish undergraduates. According to the author, this concept had not been previously reported in the literature. Afterwards, the same conception was found among 25% of a sample of 193 Canadian university students (^{KALAS et al., 2013}).

Guerra, Tavares, and Vilas-Boas (2022) note that it is commonly assumed in biology teaching that chromosomes must always be composed of sister chromatids. This occurs because chromosomes are typically defined in terms of highly compressed structures, specifically the duplicated metaphase chromosomes that can be seen using an optical microscope. It is thus important to emphasize to students that both duplicated and nonduplicated forms of chromosome representation are equally valid. However, the correct representation depends on the specific moment in the cell cycle when the cell is located.

Additionally, some of the subjects of the interviews were unable to distinguish between the terms chromosomes and sister chromatids. Approximately 30% of first-year students or seniors commonly believe that each chromatid in a pictorial representation is considered a distinct chromosome:

E3 (Item 8, figure 5): For this question, I’d choose both letter A and letter B, as, in letter A, for example, there are eight chromosomes, even though they’re homologous, four of them are duplicates. In option B, the chromosomes are not duplicated. It is a haploid cell, but there are still eight chromosomes. In letters C and D, they got a total of 16 chromosomes.

E4 (Item 8, figure 5): I’d go with marking [letters] A and B, keeping in mind what is a chromosome. A chromosome is basically the ribbon, a ribbon-like thing. So, like, if there are eight chromosomes, you just gotta check out which [cells] have eight ribbons, and these are in [letters] A and B.

In the findings of ^{Kalas et al. (2013}), the developers of the ICM, the distinction between the two concepts was identified as one of the main difficulties encountered by the respondents. According to a study conducted by Infante-Malachias et al. in 2010, freshmen and senior students enrolled in the biology course at the University of São Paulo (USP) showed difficulty distinguishing between homologous chromosomes and sister chromatids when asked to draw or identify them. Many university students identified the separate chromatids by dividing the short and long chromosome arms. This approach resulted in a break within each chromatid and the formation of V-shaped figures. Moreover, ^{Dikmenli (2010)} discovered through drawings and interviews that around 30% of undergraduate biology students believed that homologous chromosomes and sister chromatids had identical meanings.

There is a need to emphasize the difference between the two concepts in classes on the subject because, although they are still terms dealt with in basic education, alternative conceptions persist in higher education. Differentiating between the two concepts may be challenging due to the varying visual representations of chromosomes that students encounter when studying Genetics and Cytology. These representations can include the shape of a ‘X’ or other forms, as shown in item 5 (figure 5). Because of the similarity in spelling and phonetics, which adds up to the lexical density of genetics, it is also possible to understand why these concepts are confusing.

A common source of confusion among students pertains to the notion that the composition of chromosomes shows variability depending on the ploidy level of the cell. This alternative conception aligns with the results obtained from the quantitative phase of this investigation, which were supported by 71% of seniors and 60% of freshmen:

E3 (Item 4, figure 4): So, at this one, my first move would be to rule out alternative C, because I reckon that’s a haploid cell, and it's claiming that the plant is diploid.

Interviewer: Why do you reckon it's haploid?

E3: Considering that just one little stick is there, I assume it's just one chromosome being depicted, you know? Because it's not duplicated. [...] I reckon that [letters] B and D represent the diploid chromosomes, from a diploid cell.

Likewise, ^{Guerra, Tavares, and Vilas-Boas (2022}) found that undergraduates understand that n refers to cells with single chromosomes and 2n to those with duplicated chromosomes. With the same reasoning, Finnish university students associate the state of the chromosomes - replicated or not - with the concepts of diploidy and haploidy, respectively, even after lectures on the subject (M^{URTONEN; NOKKALA; SÖDERVIK, 2018}). Similar AC have been documented in older literature (^{KINDFIELD, 1994}), indicating that these conceptions persist among students from various cultural backgrounds and educational levels.

In this study, three potential factors were examined that could potentially influence the development and longevity of alternative conceptions regarding ploidy and chromosome structure. One idea held by some students is that DNA replication increases the cell's ploidy, as stated by student E4:

E4 (Item 6): It's because if I'm thinking about replication, which is going to give rise to two daughter cells, a cell that is 2n would have to be, temporarily, 4n, the mother cell, so that the two daughters, each, are 2n.

Therefore, prior to DNA replication, the student identifies a haploid cell with a single chromosome. After replication, the student notices a diploid cell with duplicated chromosomes. The second reason for confusion lies in the distinction between chromatids and homologous chromosomes. In a diploid cell, the presence of sister chromatids, rather than homologous chromosomes, is what defines its characteristics. AC may have a connection to the origins of certain words. For instance, the term diploid is derived from the Greek word diplòos, which means double. Similarly, the term haploid is derived from the Greek word haplo, which means single. This association between the terms diploid and haploid and the concepts of double and single chromosomes, respectively, may be influenced by these etymological origins.

In relation to the categorization of chromosomes based on the location of the centromere, there exists a perspective among certain students positing that telocentric chromosomes are incomplete, implying the absence of certain segments:

E9 (Item 8, figure 5): [...] there [student points to letter D] they [the chromosomes] are incomplete, right? Some of them.

This conception indicates a limited understanding of the various types of chromosomes. The students may be primarily acquainted with the typical depiction of metacentric chromosomes. In a study conducted by Rodríguez Gil, Fradkin, and CastañedaSortibrán (2019), it was observed that students at a university in Mexico did not include telocentric and acrocentric chromosomes in their drawings, even though they were specifically instructed to do so. The explanation for this result is provided by the authors, who highlight that metacentric chromosomes are frequently observed and studied. These chromosomes are immobilized during the metaphase of mitosis and exhibit a classical ‘X’ shape. Additionally, the metacentric human chromosomes are the largest and most visible, which accounts for their widespread representation.

Finally, a dissociation was identified between the representation of duplicated chromosomes and the underlying molecular process, DNA replication:

E6 (Item 5, figure 5): The chromosome is not duplicated, it only has its two sister chromatids.

E9 (Item 5, figure 5): That one I think would be the letter A, two sister chromatids [...]. To me, it does not represent a replication process.

There is a disconnection between two interconnected fields of biology, namely Molecular Biology and Genetics. This result was also observed in the quantitative stage among approximately 50% of the students, providing confirmation for the initially formulated hypothesis. ^{Guerra, Tavares, and Vilas-Boas (2022}) have reported challenges in visualizing microscopic structures, such as chromosomes, and establishing their connection to the underlying molecular processes. ^{Lewis, Leach, and Wood-Robinson (2000}) highlight a significant challenge faced by students regarding the inherent connection between fundamental genetic structures, such as the physical relationship between genes, DNA, and chromosomes. This challenge is made worse by the unclear use of terminology when subjects are taught in separate parts and when the connection between ideas is not highlighted. According to ^{Chu and Reid (2012)}, one obstacle to learning Genetics is the requirement to navigate various levels of biological organization, including molecular, microscopic, symbolic, and phenotypic levels. Reasoning about concepts and processes that occur at multiple levels simultaneously can potentially lead to mental overload for students.

Category 3: The process of DNA replication

Item 6: In a eukaryotic cell, DNA replication results in an increase in: (a) amount of DNA in that cell. (b) number of chromosomes in that cell. (c) number of DNA molecules in that cell. (d) ploidy of that cell (e.g., from 2n to 4n). (^{KALAS et al., 2013}).

The hypothesis formulated in the quantitative step, regarding the relationship between DNA replication and cell division, is that students do not remember or are unaware of the process by which sister chromatids are formed. In this qualitative step, a new alternative conception was identified, which suggests that DNA replication results in the formation of a new chromosome:

E2 (Item 6): [DNA replication] increases the number of molecules and the number of chromosomes. The number of DNA molecules, because they’re going to take one as a template to form the other, so, the number of DNA molecules will double. I think it’s going to do that with all the material, right? I think the number of chromosomes will double as well.

The alternative conception mentioned above may arise from the use of different mathematical terms that are used interchangeably in the field of Genetics. For instance, DNA replication is often referred to as chromosome duplication, which can cause confusion among students. This ambiguity in terminology may lead students to believe that DNA replication always leads to an increase in the number of chromosomes. Additionally, students may mistakenly think that DNA replication is a necessary process for the mother cell to accurately distribute its genetic material to the daughter cells. The conception mentioned was also discovered by ^{Kalas et al. (2013}) in a study involving 40% of the students who were involved in the development of the ICM at the University of British Columbia. It is noteworthy that some students may lack awareness of the phase that occurs before mitosis and meiosis, along with its characteristics, significance, and molecular and microscopic implications.

Category 4: The products of meiosis

In terms of meiotic products, some students contend that gametes are like mitotic cells in that they contain the same genetic material as the mother cell. This idea aligns with the data that was interpreted during the quantitative step among approximately 50% of all students:

E3 (Item 12, figure 6): I think I would only mark letter A in this one [...]. In letter B and letter D, I think we’re missing chromosomes. They’re representing some of the chromosomes of the mother cell, but since it said that it went through regular meiosis, I’m thinking that it might be lacking one chromosome or something. The letter A is one of the representations of the potential daughter cells.

The confusion between mitosis and meiosis was identified by Gil, Fradkin e CastañedaSortibrán (2018). These researchers observed that Mexican university students created similar diagrams of meiosis II and mitosis in their cell division illustrations. In a study conducted by ^{Etobro and Banjoko (2017)}, a multiple-choice genetics exam was used to evaluate 120 Nigerian educators. The results showed that 84% of the participants correctly understood that meiosis in a mother cell leads to the formation of identical daughter cells. This conception can be attributed to the similarity between the two division processes and the idea, often disseminated during teaching and information sources, that mitosis is equivalent to meiosis II. This association has the potential to cause confusion among students regarding the outcomes of the two processes, potentially leading them to mistakenly believe that gametes resemble post-mitotic cells.

One potential approach to enhance comprehension of the meiosis process is to employ a variety of teaching strategies, moving away from relying solely on a single method, such as the traditional approach that emphasizes knowledge transmission and memorization. Implementing a plural methodological proposal is important in education, as students possess diverse cognitive, motivational, and emotional backgrounds. These differences may lead to individual preferences regarding teaching styles (^{LABURÚ; ARRUDA; NARDI, 2003}).

There are several proposals in the scientific literature for additional ways of teaching meiosis. Two examples include the combine and recombine with dominoes approach (^{GUIMARÃES et al., 2008}) and the Meiosis on paper method (^{VILAS-BOAS; TAVARES, 2022}). These approaches utilize low-cost and easily prepared models to visually represent each stage of the meiotic process, including the representation of different alleles. These activities provide students with an opportunity to explore the connection between meiosis and Mendel’s Laws, sexual reproduction, genetic variability, and fundamental genetic concepts like genotype, homologous chromosomes, sister chromatids, and ploidy.