257 research outputs found
Trans-species polymorphism, HLA-disease associations and the evolution of the MHC
No full textCurrently, the paradigm is that Major Histocompatibility Complex (MHC) polymorphism is maintained by balancing selection on the immune genes. However, other evolutionary forces besides selection also play a role in the population genetics of this multigene family. van Oosterhout proposed a new theory of MHC evolution called Associative Balancing Complex (ABC) evolution1. This theory incorporates the effects of the evolutionary forces in the entire MHC region (peri-MHC), and it proposes that recessive deleterious mutations can accumulate in the peri-MHC in a process similar to Muller’s ratchet2. These mutations are not easily purged because epistasis and high gene diversity in the MHC reduce the efficacy of natural selection. Because natural selection is less efficient, it could also make the MHC prone to the onslaught of genomic parasites such as retroviruses and transposable elements (TEs). The accumulated genetic load has important consequences for the evolution of this immune gene family, and it can reinforce linkage disequilibria and help to maintain the MHC polymorphism. ABC evolution offers new insights into some of the most puzzling aspects of the MHC, including the occurrence of identical MHC sequences in diverged species (i.e. trans-species polymorphism). It may also explain why the large numbers of disease-associated mutations are not removed by natural selection, and why the genes that protect vertebrates against infectious diseases are associated to such a wide variety of genetic disorders
Astiotrema turneri Bray, Oosterhout, Blais & Cable, 2006, n. sp.
No full text<i>Astiotrema turneri</i> n. sp. <p>(Figs 1–3)</p> <p> <b>Type­host:</b> <i>Pseudotropheus</i> [= <i>Metriaclima</i>, <i>Maylandia</i>] <i>zebra</i> (Boulenger 1899), Perciformes, Cichlidae, zebra mbuna.</p> <p> <b>Other hosts:</b> <i>Pseudotropheus emmiltos</i> (Stauffer <i>et al.</i> 1997), Perciformes, Cichlidae; <i>Labeotropheus trewavasae</i> (Fryer 1956) Perciformes, Cichlidae, scrapermouth mbuna; <i>Melanochromis vermivorus</i> Trewavas, 1935, Perciformes, Cichlidae, purple mbuna.</p> <p> <b>Site:</b> Intestine.</p> <p> <b>Type­locality:</b> Thumbi West Island (14°01'22.83"S 34°49'16.63"E), Monkey Bay, Southern Malawi (03/09/05).</p> <p> <b>Other localities:</b> Domwe Island (13°58'05.43"S 34°49'04.01"E) (06/09/05; 16/09/05) and Zimbawe Rock (13°57'40.73"S 34°48'08.88"E) (10/09/05), Monkey Bay, southern Lake Malawi; Mpanga Rocks (10°25'49.65"S 34°16'44.64"E) (19/09/05), Luwino Reef (10°26'17.41"S 34°17'00.16"E) (19/9/05) and Chirwa Island (10°27'48.94"S 34°16'35.77"E) (19/9/05), Chilumba, northern Lake Malawi; all Malawi.</p> <p> <b>Prevalence:</b> <i>P. zebra</i> at Thumbi West – 3/24 (12.5%), at Zimbawee Rock 1/27 (3.7%), at Domwe Island – 1/61 (1.6%), at Mpanga Rocks – 2/16 (12.5%), at Luwino Reef 0/17 (0%), at Chirwa 0/12 (0%); <i>L. trewavasae</i> at Domwe Island – 1/6 (16.7%); <i>M. vermivorus</i> at Thumbi West – 1/6 (16.7%), at Domwe Island – 1/42 (2.4%); <i>P. emmiltos</i> at Mpanga Rocks – 3/18 (16.6%), at Luwino Reef – 5/17 (29.4%).</p> <p> <b>Intensity:</b> 1–2.</p> <p> <b>Deposition of specimens:</b> holotype BMNH 2006.6.6.1, paratypes BMNH 2006.6.6.2–12. Coll: JC, CvO & JB.</p> <p> <b>Etymology:</b> The species is named after Prof. George F. Turner, University of Hull, who has devoted much of his career to the study of adaptive radiation and explosive speciation in Lake Malawi cichlids, and who introduced us to the field sites used in the current study.</p> <p> <b>Description:</b> Based on 11 ovigerous specimens, some flattened at fixation. Measurements and ratios in Table 1. Body oval, tapering at both ends, widest in midhindbody, bright orange in life (Figs 1, 2). Tegument spinous to posterior extremity, spines sparser in hindbody. Oral sucker subglobular, subterminal. Prepharynx short or apparently absent, often restricted to posterior cavity of oral sucker. Pharynx oval. Oesophagus long narrow, rectilinear. Intestinal bifurcation in posterior forebody. Caeca fairly long, reaching to varying level of post­testicular region. Testes two, oval to indented, oblique to virtually symmetrical, separated by uterus, in anterior half of hindbody. Post­testicular distance generally long. Cirrus­sac elongate claviform, not reaching into hindbody. Seminal vesicle unipartite, narrower distally with surrounding gland­cells. Pars prostatica thick­walled vesicular proximally, narrower distally, surrounded by gland­cells, merges into short, indistinct ejaculatory duct (Fig. 3). Genital atrium small. Genital pore median or slightly submedian, immediately anterior to ventral sucker. Ovary rounded, entire or indented. Mehlis’ gland postero­median to ovary. Canalicular seminal receptacle large, distinct, posterior to ovary. Laurer’s canal opens dorsally at level of Mehlis’ gland. Uterus fills most of body posterior to ovary, reaching extracaecally in fully gravid specimens, passes between testes, between anterior testis and ovary, and to genital atrium. Eggs numerous, tanned, relatively elongate. Metraterm of similar length to cirrus­sac with a narrow sheath of gland­cells. Vitellarium follicular, in lateral fields from level of oesophagus, pharynx, intestinal bifurcation or occasionally posterior part of ventral sucker, to posterior testis or just into post­testicular region. Excretory system not detected. Pore terminal.</p>Published as part of <i>Bray, Rodney A., Oosterhout, Cock Van, Blais, Jonatan & Cable, Joanne, 2006, Astiotrema turneri n. sp. (Digenea: Plagiorchiidae) from cichlid fishes (Cichlidae: Perciformes) of Lake Malawi, southeastern Africa, pp. 43-58 in Zootaxa 1319</i> on pages 45-46, DOI: <a href="http://zenodo.org/record/273567">10.5281/zenodo.273567</a>
The behaviours and spatial distributions of captive sand tiger sharks (Carcharius taurus) in a marine aquarium
No full textThis study was conducted between January 2003 and November 2004 to determine the effects of season (mating and non-mating), feeding regime and time period on voluntary swimming speeds, spatial distribution and behaviours of sand tiger sharks (Carcharias taurus) at the Blue Planet Aquarium, England. Each shark was observed for periods of 15 minutes and every 15 seconds the position of a focal shark and its behaviour were recorded. In total over 200 hours of observations were made.In previous years, mating behaviours had been observed in this aquarium from January through to May (hereafter “the mating season”). Males increased swimming speed significantly and the females decreasing speed during the mating season. Spatial distribution in the tank was significantly different between mating - and non-mating seasons, with males spending more time in the areas commonly frequented by females during the mating season. The nearest neighbour and give-way occurrences, measures which may reflect the dominance hierarchy between sharks, were not influenced by mating season. C. taurus individuals who frequently gave-way at encounters were significantly more likely to avoid encounters at distance. During the mating season, pre-copulatory behaviours were also recorded. Numbers of displayed mating behaviours differed significantly between individuals. Furthermore, there was a significant positive correlation between swimming speeds and mating behaviours, male sharks with the fastest swimming speed displayed the most mating behaviours.To determine feeding regime effects, data were recorded on both feeding and non-feeding days. Swimming speed was not found to significantly change between feeding and non-feeding days. Likewise, there was no effect on give-way occurrences between feeding and non-feeding days. Spatial distribution was however effected, and on feeding days the sharks spent more time in and around the sections where they were fed.Time of day was divided in to six periods with varying lighting conditions and different diver and visitor presence/absence. Time period affected all variables recorded, and swimming speeds were significantly faster during the night time periods. Spatial distribution differed between the day and night time periods, and the sharks are particularly active at night (i.e. they spent a higher proportion of time patrolling and less time resting at night). Throughout the day time periods there were no detectable changes in shark swimming speed, spatial distribution and behaviours between, and the analysis suggests that presence of divers and visitors has no detectable effects on these sharks
The behaviours and spatial distributions of captive sand tiger sharks (Carcharius taurus) in a marine aquarium
No full textThis study was conducted between January 2003 and November 2004 to determine the effects of season (mating and non-mating), feeding regime and time period on voluntary swimming speeds, spatial distribution and behaviours of sand tiger sharks (Carcharias taurus) at the Blue Planet Aquarium, England. Each shark was observed for periods of 15 minutes and every 15 seconds the position of a focal shark and its behaviour were recorded. In total over 200 hours of observations were made.In previous years, mating behaviours had been observed in this aquarium from January through to May (hereafter “the mating season”). Males increased swimming speed significantly and the females decreasing speed during the mating season. Spatial distribution in the tank was significantly different between mating - and non-mating seasons, with males spending more time in the areas commonly frequented by females during the mating season. The nearest neighbour and give-way occurrences, measures which may reflect the dominance hierarchy between sharks, were not influenced by mating season. C. taurus individuals who frequently gave-way at encounters were significantly more likely to avoid encounters at distance. During the mating season, pre-copulatory behaviours were also recorded. Numbers of displayed mating behaviours differed significantly between individuals. Furthermore, there was a significant positive correlation between swimming speeds and mating behaviours, male sharks with the fastest swimming speed displayed the most mating behaviours.To determine feeding regime effects, data were recorded on both feeding and non-feeding days. Swimming speed was not found to significantly change between feeding and non-feeding days. Likewise, there was no effect on give-way occurrences between feeding and non-feeding days. Spatial distribution was however effected, and on feeding days the sharks spent more time in and around the sections where they were fed.Time of day was divided in to six periods with varying lighting conditions and different diver and visitor presence/absence. Time period affected all variables recorded, and swimming speeds were significantly faster during the night time periods. Spatial distribution differed between the day and night time periods, and the sharks are particularly active at night (i.e. they spent a higher proportion of time patrolling and less time resting at night). Throughout the day time periods there were no detectable changes in shark swimming speed, spatial distribution and behaviours between, and the analysis suggests that presence of divers and visitors has no detectable effects on these sharks
Genetic load: Genomic estimates and applications in non-model animals
No full textGenetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This ‘genetic load’ has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components — the realized load (or expressed load) and the masked load (or inbreeding load) — can improve our understanding of the population genetics of deleterious mutations
Genetic factors affecting establishment during invasions : the introduction of the topmouth gudgeon (Pseudorasbora parva) and the rainbow trout (Oncorhynchus mykiss) in Europe
No full textThe study of biological invasions is a major research topic, both because of the ecological and economical damage caused by invasive species and also as a great natural experiment to study evolutionary responses of non-native populations to their new environment, and the factors influencing invasions. Introduced species often evolve rapidly, despite the assumed loss of genetic variation associated with bottlenecks during the invasion process. In order examine the processes and mechanisms affecting the outcome invasions I studied two non-native fish species, the topmouth gudgeon (Pseudorasbora parva) is an Asian cyprinid that is found in most European countries as a result of accidental introductions. Rainbow trout (Oncorhynchus mykiss) has been introduced from the United States for aquaculture and angling, however, despite numerous introductions, it has only been able to establish in few European waters. I used mitochondrial DNA and microsatellite markers to understand the invasion history of these species and the factors that influence their establishment success/failure. Part of the cytochrome b gene was analysed in European and native Asian P. parva populations and microsatellite markers were used to investigate the source populations of the species. The analyses elucidated the colonisation pattern of P. parva in Europe and supported the hypothesis that the species spread through long-distance and stepping-stone methods and originate from admixed source populations. In O. mykiss, part of the d-loop region of the mitochondrial genome was analysed to compare the phylogeographic structure of native US and introduced European populations to examine the spread of the species outside its native range, as well as to find out whether the resistant Hofer strain is the source population of the European rainbow trout populations. I found that European populations are likely to originate from various sources, mainly from California. The Hofer strain is likely to have contributed to some of the wild European populations. Assessing the role of these processes is fundamental in understanding invasive species and finding suitable management practices to control them. From an evolutionary point of view, I was able to detect some of the processes that are important during invasions, in these studies particularly the role of multiple introductions and introduction from genetically admixed source populations
Population genetics of the cichlid, Cynotilapia afra (Günther 1894), in its native and introduced ranges in Lake Malawi
No full textSpecies introductions can provide unplanned and occasionally replicated experiments that can be studied to understand fundamental ecological and evolutionary processes associated with range expansions in the natural world. The cichlid species flock of Lake Malawi consists of an estimated 451-800 species and is a textbook example of explosive speciation that has been studied as a model system of evolution in the past three decades. In addition, fish are of major socio-economic importance to Malawian people, and they form an important source (circa 70%) of animal protein in their diet. Furthermore, fisheries activity employs 3% of the country's population and contributes to 4% of the country's Gross Domestic Product (GDP).This thesis studies a well documented, human mediated introduction of a rocky-shore, plankton-feeding cichlid fish Cynotilapia afra into Lake Malawi National Park. This introduction has important evolutionary and ecological consequences on the native populations of Pseudotropheus zebra, and here I investigate its population genetic impacts using contemporary molecular genetic tools and analyses. Three hypotheses were tested:1. Introduction events are usually associated with a small founder population size, and the resulting genetic bottleneck is expected to reduce genetic variation of C. afra in the introduced range.2. The invasive scenario during the introduction followed a stepping stone pattern, or alternatively, it occurred as several independent introductions of C. afra in Lake Malawi National Park.3. Introgressive hybridisation between C. afra and P. zebra may have facilitated the introduction of the invading C. afra population and restored its depleted genetic variation associated with the founder event. Furthermore, the gene pool of C. afra has more non-native genetic material as compared to P. zebra. Samples were collected from six native and four introduced populations of C. afra, as well as three native populations of P. zebra. The latter species is from a different genus, although laboratory experiments indicate that both species hybridise in laboratory conditions. Sequence variation in the mitochondrial DNA (mtDNA) control region was analysed using 15 individuals per sample population and 60 individuals per sample population were genotyped at six microsatellite loci. These data were analysed to test the three hypotheses and identify potential source populations, infer introduction patterns (stepping stone or independent), and deduct whether introgressive hybridisation may have facilitated the founder event and subsequent establishment of C. afra in the invasive range in Lake Malawi Natural Park. The three data chapters in this thesis discuss the findings of the mtDNA sequence study (Chapter 2) and the microsatellite study (Chapter 3). In Chapter 4, I analyse the microsatellite data in further detail and consider the role of introgression by using Bayesian analysis tools.The mtDNA study presented in Chapter 2 reveals that C. afra and P. zebra mtDNA sequences show high levels of lineage sorting (i.e. the DNA sequences of both species are remarkably distinct). This finding is in sharp contrast to previous studies on Lake Malawi rock-dwelling cichlids which have shown that cichlid species share the same or very similar mtDNA haplotypes. Furthermore, the introduced populations showed a higher sequence and haplotype diversity than their native counterparts. This analysis suggests that elevated gene diversity was largely due to C. afra populations being founded by individuals from several genetically distinct and geographically separate populations. In Chapter 4, I discuss the role of introgressive hybridisation with native P. zebra, and its impact on mtDNA variation in the introduced C. afra gene pool.In Chapter 3, I show that in contrast to the signal obtained from the mtDNA, the genetic variation at the microsatellite loci exhibited a significant reduction in the introduced range. Introduced C. afra populations have a lower mean effective number of alleles (ne) than C. afra populations in their native range. I use an approximate Bayesian analysis and show compelling evidence that at least two independent introductions have contributed to the introduced C. afra gene pool, a conclusion that is supported by high probability values. This conclusion differs from that of previous studies which suggested a stepping stone introduction pattern around Thumbi West Island. Surprisingly, a population of C. afra at Domwe Island was founded by a source population from Thumbi West Island, and this stepping stone introduction pattern is supported with a high probability (95%).Microsatellite analysis furthermore suggests that the founder event of C. afra in Lake Malawi National Park was associated with strong genetic drift associated with a genetic bottleneck. I was not able to detect this signal from the mtDNA genetic marker alone, which showed an increase in genetic variation at the mtDNA due to different source populations contributing to the founder event (see Chapter 2). These combined studies reported in Chapter 2 and 3 thus demonstrate that microsatellites may be well-suited to investigate questions related to conservation issues such as bottlenecks associated with founder events, while mtDNA is more suited to reveal the evolutionary processes and establish different source populations that have contributed to the introduction.In Chapter 4, I analyse the level of genetic differentiation at microsatellite loci, and show that the introduced C. afra and native P. zebra populations at Thumbi West Island are genetically more similar (G'ST=0.36+/-0.05) than the species-pair at Otter point (G'ST=0.94+/-0.18) and Domwe Island (G'ST=0.55+/-0.09). In addition, C. afra and P. zebra at Thumbi West Island showed a lower genetic distance than allopatric C. afra or P. zebra populations from Otter point and Domwe Island. Further analysis using a Bayesian assignment approach supports previous findings and demonstrates the likelihood of introgressive hybridisation between an introduced C. afra and a native P. zebra population at Thumbi West Island. No evidence of introgression is found at Otter point and Domwe Island, where the C. afra and P. zebra populations show distinct genetic structure. The occurrence of introgressive hybridisation at Thumbi West between species from distinct genera shows that translocations can have a dramatic impact even on the gene pools of heterospecific recipient populations. The results from this work have crucial implications in evolution of cichlid fishes and in invasion biology when predicting the evolution of invasiveness.In summary, the thesis shows that hybridisation, as well as the introduction of multiple genetically differentiated source populations has increased the genetic diversity of introduced C. afra populations, and this may have facilitated their establishment in Lake Malawi National Park. Translocation of cichlid species in Lake Malawi can have a dramatic impact even on heterospecific gene pools
Genetic factors affecting establishment during invasions : the introduction of the topmouth gudgeon (Pseudorasbora parva) and the rainbow trout (Oncorhynchus mykiss) in Europe
No full textThe study of biological invasions is a major research topic, both because of the ecological and economical damage caused by invasive species and also as a great natural experiment to study evolutionary responses of non-native populations to their new environment, and the factors influencing invasions. Introduced species often evolve rapidly, despite the assumed loss of genetic variation associated with bottlenecks during the invasion process. In order examine the processes and mechanisms affecting the outcome invasions I studied two non-native fish species, the topmouth gudgeon (Pseudorasbora parva) is an Asian cyprinid that is found in most European countries as a result of accidental introductions. Rainbow trout (Oncorhynchus mykiss) has been introduced from the United States for aquaculture and angling, however, despite numerous introductions, it has only been able to establish in few European waters. I used mitochondrial DNA and microsatellite markers to understand the invasion history of these species and the factors that influence their establishment success/failure. Part of the cytochrome b gene was analysed in European and native Asian P. parva populations and microsatellite markers were used to investigate the source populations of the species. The analyses elucidated the colonisation pattern of P. parva in Europe and supported the hypothesis that the species spread through long-distance and stepping-stone methods and originate from admixed source populations. In O. mykiss, part of the d-loop region of the mitochondrial genome was analysed to compare the phylogeographic structure of native US and introduced European populations to examine the spread of the species outside its native range, as well as to find out whether the resistant Hofer strain is the source population of the European rainbow trout populations. I found that European populations are likely to originate from various sources, mainly from California. The Hofer strain is likely to have contributed to some of the wild European populations. Assessing the role of these processes is fundamental in understanding invasive species and finding suitable management practices to control them. From an evolutionary point of view, I was able to detect some of the processes that are important during invasions, in these studies particularly the role of multiple introductions and introduction from genetically admixed source populations
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