Creationism in Crisis - How Changing the Environment Affects Evolution - Naturally

Lake Victoria cichlids

The Nile perch is a menace to endemic cichlids

Pictured on the left is the Nile perch, a voracious predator introduced into Lake Victoria by humans to satisfy meat demands in the 1950s. On the right, several species of endemic cichlids that were markedly affected are shown. The populations of some of these species declined so much that their genomic structure remained significantly altered even after　their numbers climbed back up.

Nile Perch Invasion Triggered Genetic Bottlenecks in Lake Victoria's Endemic Cichlids The introduction of the Nile perch to Africa’s largest lake impacted the genomic structure of multiple local species | Tokyo Tech News | Tokyo Institute of Technology

The East African cichlids are an embarrassment to creationists because they are one of the best examples of rapid speciation over a known geological age from an initial founder population of one species.

Between 17,000 and 16,000 years ago, towards the end of the last Ice Age, there was a surge of icebergs and glacial meltwater into the North Atlantic which altered ocean currents and changed the weather pattern over the African and Asian monsoon areas, which experienced a resulting mega-drought. Analysis of sediments show that this caused Lake Victoria, Lake Albert and Lake Tana to dry up and disappear.

A similar event 14,000 - 15,000 years ago caused Lake Victoria to dry up again and a subsequent lowering of water levels 5,000 years ago left a small satellite lake, Lake Nabugabo, isolated. From this we know how long ago each lake received its founding population of cichlids from their feeder rivers. In the case of Lake Victoria, this was between 14,000 and 15,000 years ago. We also know that the micro-lake, Lake Nabugabo, has been isolated for just 5,000 years. By contrast, nearby Lake Tanganyika is tens of millions of years old and has remained filled for all that time. See AfricaPaleo - FOCUS 1: Lake levels and evolution.

So, we know exactly the maximum time for which these cichlids have been diversifying.

Tell me all about the East African cichlids and how they have radiated into many different species in the East African lakes from an initial founder population. East African cichlids are a fascinating example of adaptive radiation, a process where a single ancestral species rapidly diversifies into many new species to exploit a variety of ecological niches. This phenomenon is particularly pronounced in the East African Great Lakes—Lake Victoria, Lake Malawi, and Lake Tanganyika. Here's a detailed look at the cichlids and their incredible diversification:

Introduction to East African Cichlids

Cichlids are a family of freshwater fish, known for their diversity and vibrant colors. They are native to tropical and subtropical waters, with a significant concentration in East Africa. These lakes are home to more than 1,500 species of cichlids, many of which are endemic to specific lakes or regions.

Mechanisms of Diversification

1. Geographic Isolation: The formation and changes in the East African Rift Valley led to the creation of isolated lakes and waterways. This geographical isolation allowed different populations of cichlids to evolve independently.
2. Ecological Niches: The lakes provide a variety of habitats, including rocky shores, sandy bottoms, and open water, each offering different resources and challenges. This diversity in habitats has driven cichlids to adapt to specific niches.
3. Sexual Selection: Sexual selection, particularly female choice, plays a crucial role in the diversification of cichlids. Female cichlids often prefer males with specific color patterns or behaviors, leading to the rapid emergence of distinct species.
4. Phenotypic Plasticity: Cichlids exhibit high levels of phenotypic plasticity, meaning they can rapidly adjust their morphology and behavior to new environments. This flexibility facilitates quick adaptation and speciation.

Adaptive Radiation in the Major Lakes

1. Lake Victoria: Despite its relatively young age (about 15,000 years), Lake Victoria is home to over 500 species of cichlids. These species have evolved to exploit different food sources such as algae, insects, and other fish. The lake's turbulent history, including periods of drying out and refilling, has contributed to the rapid and diverse radiation of cichlids.
2. Lake Malawi: Lake Malawi hosts around 1,000 cichlid species, making it one of the most species-rich lakes in the world. These cichlids are known for their specialized feeding strategies, including algae scraping, insect hunting, and scale-eating. The clear waters of Lake Malawi allow for vivid coloration, which is a significant factor in mate selection and thus drives speciation.
3. Lake Tanganyika: The oldest and deepest of the three lakes, Lake Tanganyika has around 250 cichlid species. The cichlids here are highly diverse, with a range of body shapes and sizes adapted to different ecological roles, from sand-dwelling species to those that inhabit rocky crevices.

Examples of Adaptation

1. Trophic Specialization: Cichlids have evolved various mouth shapes and digestive systems to specialize in different types of food. For example, some have developed elongated snouts to extract invertebrates from crevices, while others have strong jaws for crushing shells.
2. Coloration and Mate Selection: Different species exhibit distinct coloration patterns that are used in mate selection. This has led to reproductive isolation and the formation of new species. In Lake Victoria, for instance, slight variations in water clarity can lead to changes in perceived color and thus influence mating preferences.
3. Behavioral Adaptations: Cichlids exhibit diverse behaviors, from complex breeding rituals to parental care strategies. These behaviors help them exploit different ecological niches and reduce competition.

Conservation Concerns

The remarkable diversity of East African cichlids is under threat from various factors:

• Habitat Destruction: Pollution, deforestation, and agricultural runoff degrade the lakes' environments.
• Invasive Species: Non-native species, such as the Nile perch in Lake Victoria, have caused significant declines in cichlid populations.
• Overfishing: Unsustainable fishing practices threaten many cichlid species, particularly those targeted for the aquarium trade.

Conclusion

East African cichlids are a prime example of how environmental factors, ecological opportunities, and evolutionary processes interact to produce a stunning array of biodiversity. Their rapid and extensive radiation into myriad species highlights the dynamic nature of evolution and the importance of preserving these unique ecosystems.

And, to add to creationist's embarrassment, a group of researchers from the Tokyo Institute of Technology have shown how the introduction of the predatory Nile perch, Lates niloticus has been a major environmental change which has pushed populations of Lake Victoria cichlids into a narrow bottleneck which has left markers in the species genome, showing how intense environmental selectors can shape evolution.

The team's research has just been published, open access, in the Oxford Academic journal, Molecular Biology And Evolution. They also explain their research in a Tokyo Institute of Technology news release:

Nile Perch Invasion Triggered Genetic Bottlenecks in Lake Victoria's Endemic Cichlids

The introduction of the Nile perch to Africa’s largest lake impacted the genomic structure of multiple local species

Newfound evidence reveals that the upsurge of the exotic Nile perch in Lake Victoria had long-lasting effects on the genetic diversity of various local cichlid species, report scientists from Tokyo Tech. Through large-scale comparative genomic analyses, the researchers found concrete proof in the collective genome of multiple species that this artificially introduced perch decimated many local fish populations, causing a 'bottleneck effect.'

The careless introduction of exotic species by humans into ecosystems can lead to truly catastrophic results, as has been proven time and time again. One tragic example is the introduction of the Nile perch, a large freshwater fish found in waterbodies in Africa, into Africa's largest lake—Lake Victoria.

Brought to Lake Victoria in the 1950s to meet commercial demand for its meat, the Nile perch devastated native populations of fish known as haplochromine cichlids. By the 1990s, experts estimated that more than 200 species of endemic cichlids had been driven to extinction by this fierce predator. Interestingly, the remaining species could also have been deeply affected by the severe population loss caused by the Nile perch, since such events tend to reduce the genetic diversity of surviving groups. However, how much the genetic structure of cichlids was affected by the introduction of the Nile perch remains unclear.

Against this backdrop, a research team from Tokyo Institute of Technology (Tokyo Tech), The Graduate University for Advanced Studies, SOKENDAI in Japan and Tanzania Fisheries Research Institute in Tanzania decided to shed some light on the issue. In their latest study, which was published in Molecular Biology and Evolution, the researchers conducted large-scale comparative genomics analyses on multiple species of cichlids endemic to Lake Victoria, which provided detailed insights into the effects of the invasive Nile perch since its introduction to this environment. The team included Associate Professor Masato Nikaido and doctoral student Minami Imamoto from Tokyo Tech.

Through a genomic analysis that included 137 haplochromine species, the researchers discovered that four species from the Mwanza Gulf (located in the southern part of the lake) experienced what is known as a 'bottleneck event.' In simple terms, the population of these species was reduced so much that the genetic diversity within the population had significantly decreased.

Further investigation by the researchers painted the Nile perch as the culprit for the observed changes in the genetic structure of these four species.

"The timing of the bottleneck, which began during the 1970s-1980s and ended by the 1990s-2000s, corresponded to the historical records of these endemic haplochromines' disappearance and later resurgence. This is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s.

Associate Professor Masato Nikaido, Corresponding author
Department of Life Science and Technology
School of Life Science and Technology
Tokyo Institute of Technology, Tokyo, Japan

Out of the four species, the researchers noted that the egg-eating cichlids Haplochromis sp. 'matumbi hunter' and Haplochromis microdon had experienced particularly severe bottleneck effects. For matumbi hunter, this effect was so pronounced that its genome had diverged significantly even from those of closely related species.

Our findings support the previously existing hypothesis that carnivorous fishes, including egg-eaters, should have experienced a stronger bottleneck. This study presents, for the first time, the impacts of the Nile perch upsurge on the genetic structure of Lake Victoria haplochromines

Associate Professor Masato Nikaido.

Worth noting, the loss of genetic diversity due to short-term bottleneck effects can seriously hamper a species' fitness and adaptability in the long-term. Thus, taken together, these newfound insights tell a cautionary tale of just how bad the introduction of exotic species can be, even for species that survive extinction.

Researchers identified species that suffered severe damage due to the introduction of Nile perch, providing new insights into conservational biology. Genetic evaluations can offer practical solutions for protecting local fauna, such as discovering species needing urgent protection and establishing no-fishing zones. Notably, some cichlid species, previously thought extinct, are gradually being rediscovered. Furthermore, developing conservational strategies based on comparative genomics may facilitate the resurgence of the ecosystem.

Technical detail is in the team's open access paper in Molecular Biology And Evolution:

Abstract
Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines” disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. “matumbi hunter,” a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

Introduction
Invasion of exotic species generally influences the ecomorphologies and demography of endemic species (Salo et al. 2007; Pyšek et al. 2020). The expansion of invaders could be the primary cause of endemic species” population loss, resulting in a drastic change in the population structure and genetic diversity of endemic species (Wang et al. 2005; Fukuda et al. 2016; Burne et al. 2017; Colautti et al. 2017.1).

Lake Victoria in East Africa suffered a severe environmental upheaval caused by the rapid upsurge of Nile perch (Lates niloticus). Nile perch is a large carnivorous fish introduced to Lake Victoria in the 1950s to meet rising commercial demand as a table fish (Fryer 1960; Hauser et al. 1998; Pringle 2005.1). The primary constituent of the lake's fish fauna is haplochromine cichlids, which experienced explosive adaptive radiation within only 15,000 years, generating 700 endemic species comprising 13 trophic groups (Seehausen 1996; McGee et al. 2020.1; Meier et al. 2023; Ngoepe et al. 2023.1). Nile perch expanded their niches in a few decades, and in the 1980s, their catches reached the maximum recorded (Kaufman 1992; Pringle 2005.1). Meanwhile, haplochromine catches were the worst in that period, and researchers were aware of the loss of their species diversity (Kaufman 1992; Natugonza et al. 2021). Consequently, in the 1990s, more than 200 endemic haplochromines were thought to be extinct after the upsurge of Nile perch, and the population size of each trophic group has also substantially declined (Ribbink 1987; Ogutu-Ohwayo 1990; Kaufman 1992; Witte, Goldschmidt, Wanink, et al. 1992.1; Seehausen 1996; Natugonza et al. 2021). Although a few decades later, population size has been recovered in some haplochromines (Witte et al. 2007.1; Kishe-Machumu et al. 2015; Natugonza et al. 2021), the magnitude of population loss in each species and the associated impacts on genetic structure remain to be elucidated.

Haplochromis sp. “matumbi hunter” (here referred to as matumbi hunter), a haplochromine species found in the Mwanza Gulf belonging to the piscivorous group “paedophage,” has been assumed to have experienced a population bottleneck (Figs. 1a and b). As more than half of the 500 haplochromines in Lake Victoria are not formally described and named (Turner et al. 2001; Witte et al. 2007.1), matumbi hunter is also a taxonomically undescribed species newly reported by Seehausen (1996). Paedophage is a piscivorous trophic group that eats eggs and fries by stealing them from mouthbrooding cichlids (Greenwood 1959). Along with having typical anatomical features for paedophages, matumbi hunter shows peculiar phenotypes not seen in either other paedophages or rock-dwelling cichlids, such as a slender and gray body (supplementary fig. S1a, Supplementary Material online). Field investigations from the late 1990s to early 2000s suggested a small population size of matumbi hunter, coincided with the era of haplochromine disappearance after the Nile perch invasion (field observation in 2005 by M.A.; Seehausen 1996). Interestingly, while most endemic haplochromines are composed of a mixture of different alleles of V1R2 (olfactory receptor genes), matumbi hunter was fixed to an allele that was exclusively observed for them, implying their poor genetic diversity (Nikaido et al. 2014). Notably, piscivores, including paedophages, were considered the major victims of the Nile perch invasion because their trophic level and feeding substrates (haplochromine cichlids) coincided with Nile perch, resulting in more significant ecomorphological changes than the other trophic groups (Witte, Goldschmidt, Goudswaard et al. 1992.2; Seehausen 1996; McGee et al. 2015.1).

Fig. 1. Sampling information and localities of 7 haplochromine cichlids endemic to Lake Victoria and A. stappersii as an outgroup. These species were included for genetic statistics comparison. a) Pictures of the 8 species. Colored triangles for paedophages and circles for others next to species names correspond to sampling locations on the map. Paedophages, Haplochromis sp. “matumbi hunter,” and H. microdon was shaded by a yellow box. A photo of A. stappersii was retrieved from Meier, Marques et al. (2017.2). b) Sampling localities of all samples in a). The area marked by a red square in the bottom left map represents the location of Mwanza Gulf, Lake Victoria, and the map of the enlarged Mwanza Gulf is shown on the right. The number of samples per species obtained in each sampling locality is shown next to markers colored by species, corresponding to the labels in a). Samples without locality information are noted as unknown.

This study attempts to understand the evolutionary history of paedophages after the introduction of exotic predators. We first examined the genetic structure of 97 haplochromines endemic to Lake Victoria. We demonstrated that although paedophages share a certain proportion of genetic ancestry, matumbi hunter has a distinct and unique genetic structure. Population genetics statistics and estimated demography in the last few hundred years provided convincing evidence of recent short-term bottleneck events in four species, including the matumbi hunter and the other paedophage Haplochromis microdon. The bottleneck period in the four species corresponded to the ages of the mass extinction of haplochromines. We captured the most intensive bottleneck in matumbi hunter, as they showed nearly half of the nucleotide diversity (π) compared to others and 99.97% loss of effective population size (N_e) after the bottleneck (decreased from N_e ≈ 292,785 to N_e ≈ 90 in 10 generations). Together, the phylogenetic analyses and estimated speciation times confirmed that the matumbi hunter is an ingroup of the paedophage clade. Their distinct genetic structure was caused by their strong bottleneck after the Nile perch expansion.

Minami Imamoto, Haruna Nakamura, Mitsuto Aibara, Ryo Hatashima, Ismael A Kimirei, Benedicto B Kashindye, Takehiko Itoh, Masato Nikaido
Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria Molecular Biology and Evolution 41(6), June 2024, msae093, https://doi.org/10.1093/molbev/msae093

Copyright: © 2024 The authors/ Society for Molecular Biology and Evolution.
Published by Oxford University Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Unsurprisingly, given what we know of how evolution works, the introduction of a new predator changed the dynamic of environmental selectors in favour of some allele which enabled the carriers to avoid being predated or to protect their offspring against predation, so these increased in the species gene pool. Why creationists find this hard to understand is either a reflection on their poor education, poor thinking ability or willful ignorance, or possibly all three.

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