Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught in Tanzania

In recent years, a large number of individuals of the species Latimeria chalumnae, one of the living fossil coelacanths, have been landed off the coast of Tanzania. Although L. chalumnae specimens have also been landed at other localities in the western Indian Ocean, so far, viable populations of this species have been identified only at two localities, Comoros and South Africa. Therefore, the recent active catch off Tanzania suggests a new habitat for L. chalumnae. To examine the genetic background of the Tanzanian fish, we analyzed complete mtDNA sequences of two Tanzanian individuals (Kigombe-9 and Songo Mnara-1) collected from the north and south coasts of Tanzania. Using the recently reported criteria for six haplotypes established in a population genetic study for coelacanths living in the western Indian Ocean [Schartl, M., Hornung, U., Hissman, K., Schauer, J., Fricke, H., 2005. Relatedness among east African coelacanths. Nature 435, 901.], we characterized Songo Mnara-1 as haplotype 1 and Kigombe-9 as haplotype 5. We suggest that the Songo Mnara specimen is a member of the Comoran group, but was swept away by the South Equatorial current. The individual from Kigombe may be a member of an undiscovered population that exists near the boundary between Tanzania and Kenya. Further analysis using more than 19 individuals recently captured off the north coast of Tanzania will reveal whether a new population exists there. Our sequence data suggest additional variable sites in the mtDNA sequence that may define the population structure of coelacanths in the western Indian Ocean and also raise the possibility that the previously published Comoran coelacanth mtDNA sequence contains several critical errors including base changes and indels.     

An inventory of all known specimens of the coelacanth Latimeria chalumnae,with comments on trends in the catches

Synopsis A list is presented of all known specimens of the coelacanth Latimeria chalumnae based on a survey of the literature and of museum, aquarium and university holdings. Details are given of the date, place, time and depth of capture, the name and age of the fisherman, the length, weight and sex of the fish, the first literature record, the method of preservation and the present location of specimens, if known. A new number is assigned to each specimen. At least 172 coelacanths are known to have been caught since 1938. The first coelacanth was caught off South Africa but all properly documented, subsequent specimens have been caught off the islands of Grand Comoro and Anjouan in the Comoros. An appeal is made to the Comoran authorities for each specimen that is caught to be made available for scientific study. Museum authorities are also encouraged to allow their specimens to be X-rayed or dissected so that vital information can be obtained on fecundity, foetal nutrition and dietary preferences. It is essential for the coelacanth conservation effort that this inventory is maintained by the Coelacanth Conservation Council.     

Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa

Despite an on-going struggle to conserve the endangered black rhinoceros (Diceros bicornis) since the 1980s, huge capital investment and several genetic surveys, the level of genetic structure and connectivity among populations in southern Africa is not well understood. Here, we undertake a major population genetic study of black rhinoceros in the Zimbabwe Lowveld, an area inhabited by over half of that country’s original Zambezi descendants plus one large population sourced from the relict KwaZulu stock of South Africa. Using nuclear microsatellite and mitochondrial DNA data, we found much higher levels of genetic diversity in the indigenous Zimbabwean populations, where observed multilocus heterozygosity was 0.54 versus 0.40 in KwaZulu, and maternal haplotype diversity was 0.77 versus 0.03. We show, for the first time, that both gene pools can be differentiated from each other on the basis of nuclear markers. This, along with the discovery of recent gene flow between all Lowveld populations, suggests that Zimbabwean and South African gene pools were prehistorically connected.     

A newly recognized fossil coelacanth highlights the early morphological diversification of the clade

Previously considered an actinopterygian or an osteichthyan incertae sedis, the Devonian (Givetian-Frasnian) Holopterygius nudus is reinterpreted as a coelacanth. This genus is among the oldest coelacanths known from articulated remains, but its eel-like morphology marks a considerable departure from the conventional coelacanth body plan. A cladistic analysis places Holopterygius as the sister taxon of the Carboniferous (Serpukhovian) genus Allenypterus. Despite the specialized morphology of these genera, they occupy a surprisingly basal position in coelacanth phylogeny; only Diplocercides and Miguashaia are further removed from the crown. A morphometric analysis reveals that coelacanths were anatomically disparate early in their history. Conflicts between this result and those of previous studies challenge the adequacy of systematic character sets for describing historical patterns of morphological variety. Coelacanths have long had an iconic place in the study of vertebrate evolution for their apparent anatomical conservatism over geological time, but Holopterygius provides clear evidence for rapid morphological evolution early in the history of this clade.     

Extremely slow rate of evolution in the HOX cluster revealed by comparison between Tanzanian and Indonesian coelacanths

Coelacanths are known as "living fossils" because their morphology has changed very little from that in the fossil record. To elucidate why coelacanths have evolved so slowly is thus of primary importance in evolutionary biology. In the present study, we determined the entire sequence of the HOX cluster of the Tanzanian coelacanth (Latimeria chalumnae) and compared it with that of the Indonesian coelacanth (L. menadoensis), which was available in the literature. The most intriguing result was the extremely small genetic divergence between the two coelacanths. The synonymous divergence of the HOX coding region between the two coelacanths was estimated to be 0.07%, which is ~11-fold smaller than that of human-chimp. When we applied the estimated divergence time of the two coelacanths of 6 million years ago (MYA) and 30 MYA, which were proposed in independent mitochondrial DNA analyses, the synonymous substitution rate of the coelacanth HOX cluster was estimated to be ~11-fold and 56-fold smaller than that of human-chimp, respectively. Thus, the present study implies that the reduction of the nucleotide substitution rate in coelacanth HOX genes may account for the conservation of coelacanth morphology during evolution.     

The Second Recorded Living Coelacanth from North Sulawesi

A detailed account of the second coelacanth specimen known to have been captured in Indonesian waters is provided. The account is written in the official format of the Coelacanth Conservation Council's (CCC) inventory of known specimens of the living coelacanth Latimeria chalumnae, and the specimen is herein numbered CCC no. 175. Morphological measurements and fin ray counts are recorded. A comparison of these measurements and meristic data with those recorded for Comoran specimens of Latimeria chalumnae shows that the present specimen has a similar allometry to L. chalumnae. Ongoing genetic analyses should reveal the depth of divergence between the two known populations of living coelacanths and help determine if this specimen is conspecific with its Comoran counterparts.     

Invasion of rocky shores by a mytilid mussel reveals an abundant-centre distribution coupled with moderate increases in densities at its absolute range limits

Semimytilus patagonicus is an invasive mussel on the coast of southern Africa and has extended its range in recent years. We asked whether its distribution and abundance are consistent with the abundant-centre hypothesis (ACH). Marginal populations were located by monitoring 33 rocky shore sites in South Africa and southern Namibia in 2021. This revealed no changes to its distributional limits since 2020. At nine of these sites, population demography was measured to allow a comparison of their densities and size structure. Four were central populations on the west coast of South Africa (including the site where the species was first detected in 2009). Four were marginal populations in South Africa: two towards the cold range edge in the north and two towards the warm range edge to the south. The ninth population was in southern Namibia, representing a recent invasion event first detected in 2014. Across the species' South African range, the distribution of its abundance was generally consistent with the ACH, with the greatest abundance at its range centre and a gradual decrease towards the range edges. However, the ultimate marginal population at both its cold and warm range edges showed moderate upticks in abundance compared to the penultimate marginal populations. Additionally, marginal populations in South Africa typically included a greater proportion of large individuals. Recruitment intensity was greater in warm range edge populations than cold range edge populations. The size structure of the population in Namibia resembled those of central populations in South Africa. Moderate increases in densities at the absolute range limits suggest that the species is currently undergoing spread into regions associated with moderately optimal environmental conditions (ultimate range edge sites) after encountering regions associated with suboptimal environmental conditions (penultimate range edge sites).     

The demography of the coelacanth Latimeria chalumnae

Synopsis The very sparse data that are available on the abundance, population structure and biology of the coelacanth Latimeria chalumnae off Grand Comoro are summarised, and some simple numerical analyses are carried out to explore certain aspects of the population dynamics, particularly the age-profile of the population. The object has not been to provide estimates of key demographic parameters, such as mortality rates, but to propose various scenarios that are useful for comparison with real data as they become available. The analysis also makes it possible to reach some preliminary conclusions that are relevant to the management of the coelacanth population. For instance, it appears that the catch rate of coelacanths by artisanal fishermen may have a negligible effect on coelacanth survivorship, and it is more likely that population size and structure are determined by natural mortality rates and birth rates. It is suggested that predation is the main cause of natural mortality and that the main predators of coelacanths are likely to be large sharks. Interference with the traditional patterns of the Comoran artisanal fishery may threaten the coelacanth. Several important gaps in our knowledge of coelacanth demography are identified.     

Coelacanths: a human responsibility

The living coelacanth Latimeria chalumnae has a unique position in world biodiversity which raises important questions about conservation and ethics. Some relevant details of coelacanth biology are summarized, including those obtained by direct observation from submersibles. The importance of the coelacanth for evolutionary theory and palaeontology is shown to be paralleled in cultural, literary and artistic areas of human heritage. Threats to the Comoran coelacanths from artisanal fishing are described and conservation measures discussed in relation to local customs and economies as well as the promotion of tourism to spread a new awareness and concern for coelacanths worldwide.     

Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen

Despite its key location for population movements out of and back into Africa, Yemen has not yet been sampled on a regional level for an investigation of sub-Saharan, West Eurasian, and South Asian genetic contributions. In this study, we present mitochondrial DNA (mtDNA) data for regionally distinct Yemeni populations that reveal different distributions of mtDNA lineages. An extensive database of mtDNA sequences from North and East African, Middle Eastern and Indian populations was analyzed to provide a context for the regional Yemeni mtDNA datasets. The groups of western Yemen appear to be most closely related to Middle Eastern and North African populations, while the eastern Yemeni population from Hadramawt is most closely related to East Africa. Furthermore, haplotype matches with Africa are almost exclusively confined to West Eurasian R0a haplogroup in southwestern Yemen, although more sub-Saharan L-type matches appear in more northern Yemeni populations. In fact, Yemeni populations have the highest frequency of R0a haplotypes detected to date, thus Yemen or southern Arabia may be the site of the initial expansion of this haplogroup. Whereas two variants of the sub-Saharan haplogroup M1 were detected only in southwestern Yemen close to the Bab el-Mandeb Strait, different non-African M haplotypes were detected at low frequencies (approximately 2%) in western parts of the country and at a higher frequency (7.5%) in the Hadramawt. We conclude that the Yemeni gene pool is highly stratified both regionally and temporally and that it has received West Eurasian, Northeast African, and South Asian gene flow.     

Genetic diversity of <Emphasis Type="Italic">Bradysia difformis</Emphasis> (Sciaridae: Diptera) populations reflects movement of an invasive insect between forestry nurseries

The fungus gnat, Bradysia difformis (Sciaridae: Diptera) has recently been recorded for the first time from South Africa where it has been found in forestry nurseries. The presence of this insect in all the major forestry nurseries as the dominant and only sciarid species raises intriguing questions regarding its origin and population genetic structure. A 395 bp portion of the mitochondrial COI gene was analysed from B. difformis individuals collected from four nursery populations in South Africa and three nursery populations in Europe. Shared haplotypes between South African and European populations indicated a historical connection. South African populations showed high genetic diversity and low genetic differentiation. These patterns most likely reflect multiple and/or relatively large introductions of B. difformis into South Africa from its origin combined with subsequent and continued movement of plants between nurseries.     

Habitat and population size of the coelacanth Latimeria chalumnae at Grand Comoro

Synopsis In 1987 and 1989 coelacanths were observed for the first time in their natural habitat with the help of submersibles. Coelacanths were found between 150–253 m depth, their preferential depth seems to be around 200 m; the water temperature ranged between 16.5–22.8° C. During the day coelacanths aggregate in small non-aggressive groups in sheltered lava-caves. Caves might be a limiting factor for distribution. At night they leave the caves for hunting by drifting singly along the steep lava slopes. They migrate between different caves located within a large home range covering more than 8 km coastline. Coelacanths are site-attached, some for a period of at least 2 years. Our own observations and earlier catch records show that only the west coast of Grand Comoro is a suitable coelacanth habitat with more structural complexity and prey fish abundance than other coastlines of the island. From our survey we estimated a total coelacanth population off Grand Comoro to be 150–210 individuals; a saturated population would be 370–510 individuals. This small relict population seems to be stable. International protection of coelacanths against commercial interests is needed     

Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African–Australian biotic exchange

Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic diversity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic diversity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced samples to be most closely related to the southern‐most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an unsampled ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic diversity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes.     

Population genetics of Eldana saccharina Walker (Lepidoptera: Pyralidae) and the implications for management using biocontrol

The African sugarcane stalk borer, Eldona saccharina Walker (Lepidoptera: Pyralidae), is widely distributed throughout sub-Saharan Africa and is an important insect pest of maize and sugarcane. The insect shows significant variation in behaviour, host plant and natural enemy guild in different regions. Several attempts to redistribute the natural enemies of E. saccharina from West Africa to South Africa were unsuccessful. The significant behavioural, host plant and natural enemy variations as well as failures of biocontrol attempts evoked a hypothesis of genetic diversification. To evaluate this hypothesis a molecular analysis was conducted on geographically isolated populations of E. saccharina from East, North, South and West Africa, using the cytochrome c oxidase subunit I (COI) region of the mitochondrial genome. The results revealed that E. saccharina populations are separated into four major units corresponding to the West Africa, Rift Valley, South/East Africa and southern African populations. Mitochondrial DNA divergence among the four populations ranged from 1% to 4.98%. To examine the impact of the observed genetic variation on the fertility of inter-population crosses, a mating experiment was conducted between the Rift valley and South African population to produce an F1 generation, and these were backcrossed with the South African parent population. Fertility of eggs produced by the F1/parent population cross was significantly reduced when compared to fertility of the "true" South African line, and the F1/F1 cross. The contributions of the observed genetic differences and inter population incompatibility for the failure of previous biocontrol attempts are discussed and recommendations on future biocontrol practices are given.     

Invasion history of Lycium ferocissimum in Australia: The impact of admixture on genetic diversity and differentiation

Aim

We investigated the invasion history of Lycium ferocissimum, a spine-covered shrub native to South Africa that was introduced to Australia in the mid-1800s, and has since developed into a damaging invasive plant of undisturbed landscapes and pastures. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges.

Location

Samples were collected across South Africa (24 localities) and Australia (26 localities).

Methods

We used genotyping-by-sequencing (3117 SNPs across 381 individuals) to assess population genetic structuring in L. ferocissimum across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios.

Results

Clear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The L. ferocissimum plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with most of the genetic material from the Australian lineage originating from the Western Cape. Our analyses suggest that L. ferocissimum plants were originally introduced to South Australia, though it is unclear whether admixture occurred before or after its introduction to Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another.

Main Conclusions

Our results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of L. ferocissimum in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.     

Why coelacanths are not ‘living fossils’

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra‐specific molecular diversity does not imply low mutation rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra‐species levels of molecular diversity, inter‐species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ do not make sense from a tree‐thinking perspective. Editor's suggested further reading in BioEssays Tree thinking for all biology: the problem with reading phylogenies as ladders of progress Abstract     

Genetic analysis shows low levels of hybridization between African wildcats (Felis silvestris lybica) and domestic cats (F. s. catus) in South Africa

Hybridization between domestic and wild animals is a major concern for biodiversity conservation, and as habitats become increasingly fragmented, conserving biodiversity at all levels, including genetic, becomes increasingly important. Except for tropical forests and true deserts, African wildcats occur across the African continent; however, almost no work has been carried out to assess its genetic status and extent of hybridization with domestic cats. For example, in South Africa it has been argued that the long‐term viability of maintaining pure wildcat populations lies in large protected areas only, isolated from human populations. Two of the largest protected areas in Africa, the Kgalagadi Transfrontier and Kruger National Parks, as well as the size of South Africa and range of landscape uses, provide a model situation to assess how habitat fragmentation and heterogeneity influences the genetic purity of African wildcats. Using population genetic and home range data, we examined the genetic purity of African wildcats and their suspected hybrids across South Africa, including areas within and outside of protected areas. Overall, we found African wildcat populations to be genetically relatively pure, but instances of hybridization and a significant relationship between the genetic distinctiveness (purity) of wildcats and human population pressure were evident. The genetically purest African wildcats were found in the Kgalagadi Transfrontier Park, while samples from around Kruger National Park showed cause for concern, especially combined with the substantial human population density along the park's boundary. While African wildcat populations in South Africa generally appear to be genetically pure, with low levels of hybridization, our genetic data do suggest that protected areas may play an important role in maintaining genetic purity by reducing the likelihood of contact with domestic cats. We suggest that approaches such as corridors between protected areas are unlikely to remain effective for wildcat conservation, as the proximity to human settlements around these areas is projected to increase the wild/domestic animal interface. Thus, large, isolated protected areas will become increasingly important for wildcat conservation and efforts need to be made to prevent introduction of domestic cats into these areas.     

Reconstructing the introduction history of an invasive fish predator in South Africa

The Largemouth Bass (Micropterus salmoides) is a global invader with demonstrated ecological impacts on native fish communities. Introductions of fishes in freshwater ecosystems are often characterized as complex processes, yet an understanding of the nature of the introduction can inform management and conservation actions. Early in the twentieth century, two introductions of Largemouth Bass were made into South Africa for the establishment of a recreational fishery, and subsequent translocations have expanded their distribution to include much of southern Africa. In this study we quantified neutral genetic variation, modeled potential introduction scenarios, and identified potential source regions from within the native range. We documented limited levels of genetic diversity in nuclear microsatellite genotypes across populations (mean allelic richness = 1.80 and mean observed heterozygosity = 0.16) and observed low levels of genetic differentiation among four of the five focal populations (mean pairwise fixation index = 0.09), with a fifth population displaying greater levels of genetic divergence (mean pairwise fixation index = 0.27). A total of three cytochrome b haplotypes were recovered from South Africa samples and the single most common haplotype (93% of individuals) was identical to a haplotype from a population of Largemouth Bass in Maryland, USA. Using limited available stocking data along with outputs from Principal Component Analysis and approximate Bayesian evaluation of competing introduction scenarios we confirm the presence of multiple introductions. Despite evidence for multiple introductions, Largemouth Bass in South African water bodies harbor extremely low neutral genetic diversity, suggesting that even a very limited number of propagules can experience a high likelihood of success in invading nonnative waters.     

Testing for ecological and genetic Allee effects in the invasive shrub Senna didymobotrya (Fabaceae)

For an introduced plant species to become invasive, it must be able to reproduce even in initially small populations. We tested for Allee effects (reduced reproductive performance of individuals in small populations) in the nonclonal, buzz-pollinated shrub Senna didymobotrya in its invasive range in South Africa. The species is self-compatible, but we found that in its invasive range in South Africa it requires pollinators to set seed. Nearly all stigmas (90%) received pollen, but natural fruit set was very low (3-20%). Pollen receipt and fruit set were not significantly correlated with population size. We thus found no evidence for an ecological Allee effect arising from pollen limitation in small populations. Offspring seedling performance, measured in terms of stem volume and leaf area, was also not significantly correlated with the number of plants in the source population, indicating that genetic Allee effects, such as inbreeding depression, are either absent or of such a small magnitude that they would be unlikely to limit further spread of S. didymobotrya in South Africa.     

Silver coelacanths from Spain are not proofs of a Pre-scientific Discovery

In 1964 and 1965, two silver fish pendants depicting coelacanths and thought to be religious votive from Spanish churches were purchased on the art market in Spain, dated between the 17th and late 19th century, long before the discovery for science of the living coelacanth in 1938. It was speculated that they originated either from the Mediterranean, subtropical Atlantic, or subtropical Pacific (de Sylva 1966, Bruton 1985, Anonymous 1993, Greenwell 1994, Raynold & Mangiacopra 1995). Some authors believe that the silver fish pendants represent a new species of coelacanthiforms (Raynold & Mangiacopra 1995), others claimed the pendants to be only a wishful fantasy of scientists and not coelacanths at all (Thomson 1991). However, new studies revealed that the silver fish artefacts are indeed coelacanths but were in fact produced more recently with the Comorian coelacanth, Latimeria chalumnae, as a model.