The Sister Islands rock iguana (
Cyclura nubila caymanensis
) is critically endangered and endemic to the Caribbean islands Little Cayman and Cayman Brac. The Cayman Brac population and indeed the ...entire species is under threat from habitat destruction, invasive species, and anthropogenic impacts on the island. We assessed the genetic diversity, estimated effective population sizes, and tested for differentiation of populations between these two islands to inform potential future translocation should this be needed for the Cayman Brac population. Two mitochondrial DNA markers (cytochrome b and NADH subunit 4) and seven DNA microsatellite markers were used to assess the genetic diversity, genetic structure, demographic history, and effective population size of the two iguana populations. Mitochondrial DNA showed no genetic differentiation between populations; however, we found little to moderate divergence with microsatellites. We compared multiple demographic scenarios and revealed that ongoing gene flow is likely. The demographic history implied a significant genetic bottleneck around 10,000 years ago, coinciding with the sea level rise at the close of the last glacial period, and the start of the Holocene. Estimates of current effective population sizes indicate a small-scale number of breeders on each island of similar magnitude to the census mature population size (between 100 and 800 individuals). The relatively low differentiation between populations supports the possible development of active genetic management plans to manage the declining populations of the Sister Islands rock iguana.
Living in a post-industrial landscape Osmond, Daniel R.; King, R. Andrew; Russo, Isa-Rita M. ...
Diversity & distributions,
07/2024, Letnik:
30, Številka:
7
Journal Article
Recenzirano
Odprti dostop
Aim
The British Isles have been worked for millennia to extract metal ores to feed industrial development, leaving a legacy of mine water pollution that continues to impact freshwater communities in ...many regions. Brown trout (Salmo trutta L.) have long been observed to persist in these metal‐impacted systems as apex predators, with previous studies showing a small number of impacted populations to be highly genetically divergent. We sought to understand the scale of genetic diversity across regions and the repeatability of genetic divergence in trout populations affected by metal pollution.
Location
We examined four mine water‐impacted regions across the British Isles: west Wales, northeast England, southwest England and southeast Ireland.
Methods
We employed a panel of 95 SNP loci to screen 1236 individuals from 71 sites representing paired metal‐impacted and clean sites from across the four regions. From these, we obtained diversity statistics, assessed genetic structuring of populations and modelled historical demographic scenarios to understand which factors most credibly explain genetic variation in divergent populations.
Results
We evidenced hierarchical population structure in the regions studied, in line with expectations from phylogeographic history. However, in a hierarchical analysis of genetic structuring the first level of differentiation was driven by the divergence of the metal‐impacted trout of Cornwall in southwest England. Within regions we observed reduced genetic diversity and repeated patterns of local genetic sub‐structuring between paired samples from metal‐impacted and relatively clean sites. Demographic history analyses suggested the timing of these splits to be relatively recent and to be associated with periods of peak mining activity.
Main conclusions
Our findings demonstrate distinct patterns of genetic isolation and reduced diversity arising from legacy pollution in freshwater ecosystems, with impacts being most apparent where both chemical pollution and physical barriers are present. Management should focus on the amelioration of mine water wash‐out and the removal of barriers to fish movement to safeguard genetic diversity in impacted populations.
The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding ...about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring.
Here, we report the draft genome of L. apterus, the first genome in the family Geotrupidae. The final assembly consisted of 286.93 Mbp in 66,933 scaffolds. Completeness analysis found the assembly contained 93.5% of the Endopterygota core BUSCO gene set. Ab initio gene prediction resulted in 25,385 coding genes, whereas homology-based analyses predicted 22,551 protein coding genes. After merging, 20,734 were found during functional annotation. Compared to other publicly available beetle genomes, 23,528 genes among the predicted genes were assigned to orthogroups of which 1664 were in species-specific groups. Additionally, reproduction related genes were found among the predicted genes based on which a reduction in the number of odorant- and pheromone-binding proteins was detected.
These genes can be used in further comparative and functional genomic researches which can advance our understanding of the genetic basis and hence the evolution of parental behaviour.
Abstract
Africa’s black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. ...Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa’s Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.
Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the ...genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates.
Landscape features may restricting dispersal and gene flow, and increase demographic isolation among sub-populations. In addition, landscape features may represent potential dispersal barriers ...depending on species vagility. To predict the persistence of populations and to formulate adequate conservation measures it is essential to understand the ability of species to transverse landscape barriers. Using population genetic techniques we assessed the importance of physical barriers along the Kinabatangan River for a suite of non-volant small mammals.
Cytochrome b
sequence variation was examined for each of the 19 species sampled across both riverbanks. Haplotype networks and molecular variance analyses indicated contrasting patterns of genetic isolation between riversides for different taxa. Genetic isolation between riversides ranged from moderate to complete in tree shrews and squirrels, whereas no isolating effect could be detected in murids and gymnures. Although genetic divergence between forest fragments on the same side of the river could only be studied in a subset of six species, the results suggest an additional dispersal barrier for two of these studied species. While barrier effects of a paved road and tributaries could not be verified, large oil palm plantations seem to have disrupted gene flow in these species. Furthermore, the findings suggest higher genetic connectivity on the more continuously forested compared to the more fragmented riverside, and underline the importance of forest corridors as essential conservation measures to maintain genetic diversity in a fragmented landscape such as that along the Kinabatangan River.
Sexual selection may act as a promotor of speciation since divergent mate choice and competition for mates can rapidly lead to reproductive isolation. Alternatively, sexual selection may also retard ...speciation since polygamous individuals can access additional mates by increased breeding dispersal. High breeding dispersal should hence increase gene flow and reduce diversification in polygamous species. Here, we test how polygamy predicts diversification in shorebirds using genetic differentiation and subspecies richness as proxies for population divergence. Examining microsatellite data from 79 populations in 10 plover species (Genus: Charadrius) we found that polygamous species display significantly less genetic structure and weaker isolation-by-distance effects than monogamous species. Consistent with this result, a comparative analysis including 136 shorebird species showed significantly fewer subspecies for polygamous than for monogamous species. By contrast, migratory behavior neither predicted genetic differentiation nor subspecies richness. Taken together, our results suggest that dispersal associated with polygamy may facilitate gene flow and limit population divergence. Therefore, intense sexual selection, as occurs in polygamous species, may act as a brake rather than an engine of speciation in shorebirds. We discuss alternative explanations for these results and call for further studies to understand the relationships between sexual selection, dispersal, and diversification.
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its ...numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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