Nicola M. Anthony

The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa

The role of Pleistocene forest refugia and rivers in the evolutionary diversification of tropical biota has been the subject of considerable debate. A range-wide analysis of gorilla mitochondrial and nuclear variation was used to test the potential role of both refugia and rivers in shaping genetic diversity in current populations. Results reveal strong patterns of regional differentiation that are consistent with refugial hypotheses for central Africa. Four major mitochondrial haplogroups are evident with the greatest divergence between eastern (A, B) and western (C, D) gorillas. Coalescent simulations reject a model of recent east–west separation during the last glacial maximum but are consistent with a divergence time within the Pleistocene. Microsatellite data also support a similar regional pattern of population genetic structure. Signatures of demographic expansion were detected in eastern lowland (B) and Gabon/Congo (D3) mitochondrial haplogroups and are consistent with a history of postglacial expansion from formerly isolated refugia. Although most mitochondrial haplogroups are regionally defined, limited admixture is evident between neighboring haplogroups. Mantel tests reveal a significant isolation-by-distance effect among western lowland gorilla populations. However, mitochondrial genetic distances also correlate with the distance required to circumnavigate intervening rivers, indicating a possible role for rivers in partitioning gorilla genetic diversity. Comparative data are needed to evaluate the importance of both mechanisms of vicariance in other African rainforest taxa.

DUPLICATION OF THE RDL GABA RECEPTOR SUBUNIT GENE IN AN INSECTICIDE-RESISTANT APHID, MYZUS PERSICAE

Abstract Resistance to cyclodiene insecticides is associated with replacements of a single amino acid (alanine 302) in a γ-aminobutyric acid (GABA) receptor subunit encoded by the single-copy gene Resistance to dieldrin (Rdl). Alanine 302 is predicted to reside within the second membrane-spanning region of the Rdl receptor, a region that is thought to line the integral chloride ion channel pore. In all cyclodiene-resistant insects studied to date, this same alanine residue is replaced either by a serine, or, in some resistant strains of Drosophila simulans, a glycine residue. Therefore, individuals can carry only two different Rdl alleles. In contrast, here we report the presence of up to four different Rdl-like alleles in individual clones of the green peach aphid, Myzus persicae. In addition to the wild-type copy of Rdl gene (encoding A302 or allele A), M. persicae carries three other alleles with the following amino acid replacements: A302 → Glycine (allele G), A302 → SerineTCG (allele S) and A302 → SerineAGT (allele S′). Evidence from direct nucleotide sequencing and Single Stranded Conformational Polymorphism (SSCP) analysis shows that at least three of these different Rdl alleles (i.e. A, G and S) are commonly present in individual aphids or aphid clones. Southern analysis using allele-specific probes and analysis of sequences downstream of the exon containing the resistance-associated mutation confirm the presence of two independent Rdl-like loci in M. persicae. One locus carries the susceptible alanine (A) and/or resistant glycine (G) allele while the other carries the two serine alleles (S or S′). Whereas resistance levels are correlated with the glycine replacement, the S allele was present in all aphid clones, regardless of their resistance status. These results suggest that target site insensitivity is associated with replacements at the first (A/G) but not the second (S/S′) locus. Phylogenetic analysis of nucleotide sequences indicates that both putative aphid Rdl loci are monophyletic with respect to other insect Rdl genes and may have arisen through a recent gene duplication event. The implications of this duplication with respect to insecticide resistance and insect GABA receptor subunit diversity are discussed.

High mitochondrial diversity in geographically widespread butterflies of Madagascar: A test of the DNA barcoding approach

The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10x greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10x genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.

Mitochondrial DNA phylogeography of western lowland gorillas (Gorilla gorilla gorilla)

The geographical distribution of genetic variation within western lowland gorillas (Gorilla gorilla gorilla) was examined to clarify the population genetic structure and recent evolutionary history of this group. DNA was amplified from shed hair collected from sites across the range of the three traditionally recognized gorilla subspecies: western lowland (G. g. gorilla), eastern lowland (G. g. graueri) and mountain (G. g. beringei) gorillas. Nucleotide sequence variation was examined in the first hypervariable domain of the mitochondrial control region and was much higher in western lowland gorillas than in either of the other two subspecies. In addition to recapitulating the major evolutionary split between eastern and western lowland gorillas, phylogenetic analysis indicates a phylogeographical division within western lowland gorillas, one haplogroup comprising gorilla populations from eastern Nigeria through to southeast Cameroon and a second comprising all other western lowland gorillas. Within this second haplogroup, haplotypes appear to be partitioned geographically into three subgroups: (i) Equatorial Guinea, (ii) Central African Republic, and (iii) Gabon and adjacent Congo. There is also evidence of limited haplotype admixture in northeastern Gabon and southeast Cameroon. The phylogeographical patterns are broadly consistent with those predicted by current Pleistocene refuge hypotheses for the region and suggest that historical events have played an important role in shaping the population structure of this subspecies.

Cloning, sequencing and functional expression of an acetylcholinesterase gene from the yellow fever mosquito Aedes aegypti

A degenerate PCR strategy was used to isolate a fragment of the acetylcholinesterase gene (Ace) homolog from Aedes aegypti and screen for a cDNA clone containing the complete open reading frame of the gene. The predicted amino acid sequence of the Aedes gene shares 64% identify with Ace from Drosophila and 87% identity with the acetylcholinesterase gene from another mosquito species Anopheles stephensi. High levels of expression of the Aedes gene were achieved by infection of Sf21 cells with a recombinant baculovirus containing the Aedes Ace cDNA. The catalytic properties and sensitivity of the recombinant enzyme to insecticide inhibition are described and discussed in relation to the role of insensitive AChE in conferring resistance to organophosphorus and carbamate insecticides.

Comparative effectiveness of Longworth and Sherman live traps

Abstract Despite the widespread use of Sherman (H. B. Sherman Inc., Tallahassee, Flor.) and Longworth (Penlon Ltd., Oxford, U.K.) live traps in small-mammal-community assessment, few studies have directly compared the effectiveness of these 2 popular models. This study compared the relative efficacy of both trap types in capturing small mammals in southern Wisconsin grasslands. As trap size may cause capture bias, we compared Longworth traps with equal numbers of small and large, folding Sherman traps. We also deployed a small number of pitfalls. We carried out trapping at 12 sites over a 2-year period (1996–1997). We observed a significant year effect, so we analyzed differences in capture success, species diversity indices, and percent community similarity between trap types separately for each year. Two-way contingency table analyses indicated that all 3 trap types exhibited species-specific differences in capture rates. We assessed standardized deviates for each cell within this two-way design, and we considered departures greater than 2 standard deviations (SE±1.96) from the mean to show an either significantly positive (≥ + 1.96) or significantly negative (≤−1.96) association. In the first year, Longworth traps captured greater numbers of long-tailed shrews (Sorex spp.) whereas small Sherman traps captured more western harvest mice (Reithrodontomys megalotis) and white-footed or prairie deer mice (Peromyscus spp.). In the second year, small Sherman captures were greater for long-tailed shrews and western harvest mice while large Sherman traps captured more meadow voles (Microtus pennsylvanicus) and jumping mice (Zapus hudsonius). Although estimates of community diversity were similar between trap types, percent community similarity estimates were lowest for Longworth-Sherman trap comparisons. Mortality rates were highest for Longworth traps and small Sherman traps and lowest for large Sherman traps. Pitfalls caught proportionally more long-tailed shrews than conventional live traps in the first but not the second year of study. In general, body mass of the animal had little effect on trap capture rates. However, in the first year of this study, small Sherman traps caught lighter (P =0.028) long-tailed shrews than the large Sherman traps. Similarly, Longworth traps caught significantly lighter white-footed/prairie deer mice than either small (P=0.022) or large (P= 0.035) Shermans. When used in combination, both Longworth and Sherman traps can diminish overall sampling error and yield less biased estimates of species composition than either trap type alone. The use of new as opposed to used Sherman traps in the second year of this study might account for the greater capture efficacy of these traps and contribute to differences in relative trap type success between years.

The history and geography of diversification within the butterfly genus Lycaeides in North America.

The Lycaeides butterfly species complex in North America consists of two nominal, morphologically defined species. These butterflies are ecologically diverse and appear to be distributed as a geographically complex mosaic of locally differentiated populations that may be undergoing adaptive radiation. We asked whether patterns of molecular genetic variation within the species complex are congruent with currently recognized morphological species and whether the distribution of molecular variation is consistent with the hypothesis that Pleistocene climate changes contributed to the process of differentiation within the genus. Variation in the form of the genitalia from 726 males from 59 populations clearly distinguishes both species with only six populations containing morphologically intermediate or ambiguous individuals. However, partitioning of molecular variance in a 236 bp section of the mitochondrial AT‐rich region from 628 individuals (57 populations) surveyed using single strand conformation polymorphism analysis (SSCP) indicates that only 26% of the total genetic variation is distributed along nominal species boundaries as defined by morphology. Instead, three phylogeographical groups were detected, represented by three major haplotype clades, which account for 90% of the total genetic variance. Pleistocene glaciations appear to have fostered divergence during glacial maxima, while postglacial range expansions created opportunities for gene exchange and reticulation along suture zones between geographical groups. Data presented here allow us to make inferences about the history of the species complex. However, evidence of ancestral polymorphism and reticulation limit our ability to define species boundaries based on mitochondrial DNA sequence variation.

Effects of fragmentation on genetic diversity in island populations of the Aegean wall lizard Podarcis erhardii (Lacertidae, Reptilia).

Landbridge islands offer unique opportunities for understanding the effects of fragmentation history on genetic variation in island taxa. The formation of islands by rising sea levels can be likened to a population bottleneck whose magnitude and duration is determined by island area and time since isolation, respectively. The Holocene landbridge islands of the Aegean Sea (Greece) were formed since the last glacial maximum and constitute an ideal system for disentangling the effects of island area, age and geographic isolation on genetic variability. Of the many reptile species inhabiting this island system, the Aegean wall lizard Podarcis erhardii is an excellent indicator of fragmentation history due to its widespread distribution and poor over-water dispersal abilities. In this study, we utilize a detailed record of Holocene fragmentation to investigate the effects of island history on wall lizard mitochondrial and nuclear microsatellite diversity. Findings show that the spatial distribution of mitochondrial haplotypes reflects historical patterns of fragmentation rather than geographic proximity per se. In keeping with neutral bottleneck theory, larger and younger islands retain more nuclear genetic variation than smaller, older islands. Conversely, there is no evidence of an effect of isolation by distance or effect of distance to the nearest larger landmass on genetic variability, indicating little gene flow between islands. Lastly, population-specific measures of genetic differentiation are inversely correlated with island area, suggesting that smaller islands exhibit greater divergence due to their greater susceptibility to drift. Taken together, these results suggest that both island area and time since isolation are important predictors of genetic variation and that these patterns likely arose through the progressive fragmentation of ancestral diversity and the ensuing cumulative effects of drift.

A Comparative Approach Shows Differences in Patterns of Numt Insertion During Hominoid Evolution

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes, although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole-genome sequences of single species or, more recently, from genomic comparisons across vast phylogenetic distances. Here we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human–chimp divergence, which is significantly greater than the 37 numts observed in humans. By comparing these closely related species, we accurately reconstructed the preintegration target site sequence and deduced nucleotide changes associated with numt integration. From >100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements; however, the same was not seen in chimpanzees. From a separate data set, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a polymerase chain reaction–based screen. Last, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500 bp, and preferably >1 kb in length, to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion.

Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change

BackgroundThe Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios.ResultsEcological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations.ConclusionsThese findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century.