Applying molecular genetic tools
We have worked on a broad array of topics ranging from taxonomy to applied conservation management.
Hispaniolan solenodon, a highly threatened Caribbean ‘relict’ mammal
- Turvey, S.T., Peters, S., Brace, S., Young, R.P., Crumpton, N., Hansford, J., Nuñez-Miño, J.M., King, G., Tsalikidis, K., Ottenwalder, J.A., Timpson, A., Funk, S.M., Brocca, J.L., Thomas, M.G., Barnes, I., 2016. Independent evolutionary histories in allopatric populations of a threatened Caribbean land mammal. Diversity and Distributions 22, 589–602.
To determine the evolutionary history, relationships and distinctiveness of allopatric populations of Hispaniolan solenodon (Solenodon paradoxus), a highly threatened Caribbean ‘relict’ mammal, to understand spatio‐temporal patterns of gene flow and the distribution of diversity across complex large island landscapes and inform spatial conservation prioritization.
Historical and modern‐day solenodon specimens were analysed from sampling localities across Hispaniola, representing this geotectonically complex island's distinct northern, south‐eastern and south‐western biogeographic provinces.
We successfully amplified mitochondrial cytochrome b and control region sequences from 34 solenodon samples. Bayesian phylogenetic analyses were applied to assess the relationship between these sequence data, and coalescent simulation and approximate Bayesian computation were used to identify which model of solenodon intra‐island demographic history best explains the observed patterns of variation. We also conducted morphometric analysis of 110 solenodon specimens to investigate whether allopatric Hispaniolan populations can be differentiated using craniodental characteristics.
Unique haplotypes were identified in solenodon samples from each biogeographic region, with no haplotype sharing between regions. Higher marginal posterior probability values were found for a three‐population model comprising allopatric northern, south‐eastern and south‐western Hispaniolan populations, with exceptionally low migration rates inferred between all populations, indicating that they are genetically isolated. Modal estimates of long‐term effective female population size are extremely low for south‐western and south‐eastern populations. Morphometric differentiation is observed between all three populations.
Evolutionary differentiation of Hispaniolan solenodons into three distinct populations is congruent with phylogenetic patterns observed in several other Hispaniolan species, with population isolation possibly associated with past marine transgression. We interpret these populations as distinct subspecies, with the two genetically impoverished southern subspecies particularly vulnerable to environmental change. Our improved understanding of Hispaniolan solenodon evolutionary history provides an important baseline for identifying wider patterns of intra‐island diversification and prioritizing conservation attention for evolutionarily significant populations.
Translocation of Bojer’s skink in Mauritius
- Michaelides, S., Cole, N., Funk, S.M., 2015. Translocation retains genetic diversity of a threatened endemic reptile in Mauritius. Conserv Genet 16, 661–672.
The island of Mauritius has experienced five reptile extinctions since the 1600s. Approximately half of the remaining herpetofauna has been restricted to offshore islets, resulting in small populations at high risk of extinction. Under the combined pressures of invasive species, habitat loss and fragmentation and climate change, translocations are considered a powerful tool in conservation of threatened and endangered species. The Bojer’s skink, Gongylomorphus bojerii, on the offshore island on Ilot Vacoas represents the remnant population of the species in the southeast of Mauritius. Given the geographic isolation and its genetic distinctiveness, individuals were translocated to the neighbouring island of Ile aux Fouquets in order to re-establish historical range, minimize extinction risk and maintain genetic variation within the species.
Using fifteen microsatellite loci, we assessed the genetic structure of the population on Ilot Vacoas in relation to a northern offshore population (on Round Island) and evaluated the genetic consequences of the translocation.
Results revealed that the population on Ilot Vacoas exhibits significantly lower levels of genetic variation and strong differentiation (F ST = 0.16) compared to the northern population. The inbreeding coefficient was low and no recent bottleneck event was detected from its genetic signature. The translocation on Ile aux Fouquets did not provide evidence of negative genetic effects. The newly established population retained much of the source’s genetic material, though the effective population size was found to be relatively small.
These findings confirmed the importance of incorporating genetic management and continuous monitoring to detect changes in the long-term survival of translocated populations.
History of indigenous horse breeds in Croatia
- Galov, A., Byrne, K., Gomercic, T., Duras, M., Arbanasic, H., Sindicic, M., Mihelic, D., Kovacic, A., Funk, S.M., 2013. Genetic structure and admixture between the Posavina and Croatian Coldblood in contrast to Lipizzan horse from Croatia. Czech Journal of Animal Science 58, 71–78.
The Posavina and Croatian Coldblood are Croatian autochthonous horse breeds with interwoven breeding histories for which studbooks have only recently been established. The Lipizzan breed has the oldest formalized breeding and no record of recent genetic introgression from other breeds in Croatia.
We analyzed the genetic structure, interbreeding, and breed characteristics by genotyping nine dinucleotide microsatellite loci for 53 Posavina, 37 Croatian Coldblood, and 33 Lipizzan horses and showed that differing breeding schemes and histories have had a strong and measurable impact on the population genetic structure within and between the three breeds. A Bayesian clustering method demonstrated that two population clusters best explain the genetic structure. Samples from the pre-defined breeds of the Posavina and Croatian Coldblood were assigned to a separate genetic cluster, while Lipizzan specimens were assigned to another distinct genetic group. Twelve samples of the Posavina/Croatian Coldblood cluster (13%) showed admixed ancestry with Lipizzan horses. A test for heterozygosity excess, allele frequency distribution mode-shift, and M-ratio test were used to detect genetic evidence of recent population bottlenecks, none of which provided evidence for bottlenecks in the Posavina and Croatian Coldblood populations. In contrast, although somewhat ambiguous, evidence suggests a genetic bottleneck in the Lipizzan population in Croatia.
Conservation genetics of the Ethiopian wolf
- Gottelli, D., Sillero-Zubiri, C., Marino, J., Funk, S.M., Wang, J., 2013. Genetic structure and patterns of gene flow among populations of the endangered Ethiopian wolf: Ethiopian wolf population genetic structure. Anim Conserv 16, 234–247.
Populations of endangered mammals are often small, fragmented and have low genetic variability that can reduce the ability to evolve in response to environmental changes. The endangered Ethiopian wolf (Canis simensis) is a habitat specialist restricted to six small, isolated pockets of Afroalpine habitat, with a total population of fewer than 500 adult animals. The degradation of the Ethiopian highlands because of human expansion is ever increasing, potentially leading to further population fragmentation and local extinctions.
In order to assist Ethiopian wolf conservation management, we quantified the genetic diversity, population structure and patterns of gene flow of the species using up to 14 microsatellite loci.
FST, analysis of molecular variance, principal coordinates analysis and Bayesian clustering analyses revealed geographic population structuring delimited by three mountain ranges, in concert with a previous study based on mitochondrial DNA. Bayesian analysis showed that current gene flow is low, unidirectional and limited to geographically proximate populations.
Given the small census size and strong population structuring with low gene flow, demographic stochasticity is likely to be the highest threat to the long‐term persistence of this species. The protection of the remaining suitable habitat, especially narrow ridges linking habitat patches within mountain blocks, is therefore essential. The genetic survey presented by this study provides vital and much needed information for the future effective management of Ethiopian wolf populations.
Genetic description of a possibly new Salanoia mongoose species in Madagascar
- Durbin, J., Funk, S.M., Hawkins, F., Hills, D.M., Jenkins, P.D., Moncrieffe, C.B., Ralainasolo, F.B., 2010. Investigations into the status of a new taxon of Salanoia (Mammalia: Carnivora: Eupleridae) from the marshes of Lac Alaotra, Madagascar. Systematics and Biodiversity 8, 341–355.
Evidence is presented from morphological observations, multivariate and molecular analyses on the taxonomic status of specimens of Salanoia newly discovered at Lac Alaotra, Madagascar, which resemble but are phenotypically highly divergent from the monotypic species S. concolor.
A detailed comparative description is provided, together with information on the ecology of the region.
Principal Component and Canonical Variate Analyses of craniodental morphometrics revealed high divergence supporting the status of a new species. Conversely, genetic distances from S. concolor based on the mitochondrial cytochrome b locus are small, not supporting new species status. A literature review indicates that some accepted species also exhibit low genetic distances at cytochrome b, which might be caused by rapid recent evolution, hybridization or introgression of mtDNA between lineages that otherwise might be genetically more distinct.
Conflicting information from the analyses is discussed. Adaptation to highly divergent habitats might account for phenotypic plasticity, but the observed morphological difference is sufficiently great that the formal description as a new species is warranted. The biodiversity of Lac Alaotra and the importance of conservation issues are highlighted in relation to this discovery.
We captured two individuals of a population that is likely threatened because small population size, restricted distribution and the impact of habitat degradation. Therefore, we did not kill the animals, which would have made a formal taxonomic description more straightforward. We tool skin biopsies from each of the two individuals for genetic analysis and evaluated the skin, skull and skeleton of a museum sample. Taking these caveats (lack of a whole type specimen), we nevertheless have taken the decision to describe the new taxon as a species: Salanoia durrelli , Durrell´s salanoia. Since, no specimens were collected.
In a conservation assessment for the Red List, Hawkins (2016) interprets the morphological differences are minor and regards S. durrelli as synonym of S. concolor (I. Geoffroy Saint-Hilaire, 1837), the brown-tailed Vontsira. However, Hawkins stresses that the "synonym pending examination of further material. The population to which it refers is ecologically anomalous, occurring in marshland not the forest used by all other populations, and is highly threatened; clarifying its taxonomic status is therefore of urgent conservation importance."
Population genetic history of a Salangid icefish in China
- Zhao, L., Zhang, J., Liu, Z., Funk, S.M., Wei, F., Xu, M., Li, M., 2008. Complex population genetic and demographic history of the Salangid, Neosalanx taihuensis, based on cytochrome b sequences. BMC Evolutionary Biology 8, e201.
The Salangid icefish Neosalanx taihuensis (Salangidae) is an economically important fish, which is endemic to China, restricted to large freshwater systems (e.g. lakes, large rivers and estuaries) and typically exhibit low vagility. The continuous distribution ranges from the temperate region of the Huai and Yellow River basins to the subtropical region of the Pearl River basin. This wide ranging distribution makes the species an ideal model for the study of palaeoclimatic effects on population genetic structure and phylogeography. Here, we aim to analyze population genetic differentiation within and between river basins and demographic history in order to understand how this species responded to severe climatic oscillations, decline of the sea levels during the Pleistocene ice ages and tectonic activity.
We obtained the complete mtDNA cytochrome b sequences (1141 bp) of 354 individuals from 13 populations in the Pearl River, the Yangze River and the Huai River basin. Thirty-six haplotypes were detected. Haplotype frequency distributions were strongly skewed, with most haplotypes (n = 24) represented only in single samples each and thus restricted to a single population. The most common haplotype (H36) was found in 49.15% of all individuals. Analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. Significant levels of genetic subdivision were detected among populations within basins rather than between the three basins. Demographic analysis revealed that the population size in the Pearl River basin has remained relatively constant whereas the populations in the Yangze River and the Huai River basins expanded about 221 and 190 kyr ago, respectively, with the majority of mutations occurring after the last glacial maximum (LGM).
The observed complex genetic pattern of N. taihuensis is coherent with a scenario of multiple unrelated founding events by long-distance colonization and dispersal combined with contiguous population expansion and locally restricted gene flow. We also found that this species was likely severely impacted by past glaciations. More favourable climate and the formation of large suitable habitations together facilitated population expansion after the late Quaternary (especially the LGM). We proposed that all populations should be managed and conserved separately, especially for habitat protection.
Genetic differentiation golden brown mouse lemur populations in Madagascar
- Guschanski, K., Olivieri, G., Funk, S.M., Radespiel, U., 2007. MtDNA reveals strong genetic differentiation among geographically isolated populations of the golden brown mouse lemur, Microcebus ravelobensis. Conservation Genetics 8, 809–821.
Microcebus ravelobensis is an endangered nocturnal primate endemic to northwestern Madagascar. This part of the island is subject to extensive human intervention leading to massive habitat destruction and fragmentation.
We investigated the degree of genetic differentiation among remaining populations using mitochondrial control region sequences (479–482 bases). Nine populations were sampled from the hypothesized geographic range. The region is composed of three inter-river systems (IRSs). Samples were collected in three areas of continuous forests (CFs) and six isolated forest fragments (IFFs) of different sizes.
We identified 27 haplotypes in 114 animals, with CFs and IFFs harbouring 5–6 and 1–3 haplotypes, respectively. All IFFs were significantly differentiated from each other with high ΦST values and sets of unique haplotypes. The rivers constitute significant dispersal barriers with over 82% of the molecular variation being attributed to the divergence among the IRSs.
The data suggest a deep and so far unknown split within the rufous mouse lemurs of northwestern Madagascar. The limited data base and the lack of ecological and morphological data do not allow definite taxonomic classification at this stage. However, the results clearly indicate that M. ravelobensis consists of three evolutionary significant units, possibly cryptic species, which warrant urgent and separate conservation efforts.
Phylogeography the critically endangered golden monkey in China
- Li, M., Liu, Z., Gou, J., Ren, B., Pan, R., Su, Y., Funk, S.M., Wei, F., 2007. Phylogeography and Population Structure of the Golden Monkeys (Rhinopithecus roxellana): Inferred from Mitochondrial DNA Sequences. American Journal of Primatology 69, 1–15.
The golden monkey (Rhinopithecus roxellana) is one of the most endangered primate species due to its dramatically shrinking distribution during the past 400 years. Its populations are restricted to three isolated regions, Qinglin (QL), Sichuan/Gansu (SG), and Shennongjia (SNJ) in China. As with other snub‐nosed monkeys in China and Vietnam, the biology and evolution of this species is still poorly known.
To assess genetic differentiation and explore the relationships among populations of golden monkeys from different geographic locations, 379 bp of mitochondrial DNA control region (CR) hypervariable segment I (HVI) was studied from 60 individuals.
Twelve haplotypes were identified from seven populations within the three regions. Haplotype diversity was high (0.845), whereas nucleotide diversity among all haplotypes was low (0.0331). The most recent common ancestor (TMRCA) among mtDNA haplotypes was estimated to have lived approximately 0.48–0.32 million years ago. None of the haplotypes is shared among any of the three regions. Phylogenetic analysis and AMOVA revealed clear and significant phylogeographic structure between the three regions. However, only SG contained haplotypes of the two main clades, indicating either incomplete random sorting of haplotypes or a complex history with phases of population subdivisions and merging of populations.
The phylogeographic structure implies that R. roxellana should be regarded as separate management units (MUs) for each of the three regions. It is likely that recent phylogeographic history has shaped the pattern of genetic differentiation observed in the golden monkey and that its populations have suffered significant demographic fluctuation.
Phylogeography of the endemic St. Lucia whiptail lizard
- Funk, S.M., Fa, J.E., 2006. Phylogeography of the endemic St. Lucia whiptail lizard Cnemidophorus vanzoi: conservation genetics at the species boundary. Conservation Genetics 7, 651–663.
Vicariance and isolation leading to speciation of reptiles on islands is well exemplified in a number of taxa in the Caribbean. The St. Lucia whiptail (Cnemidophorus vanzoi), considered a single species, is found on two small islets (Maria Major and Maria Minor) off the main island of St. Lucia.
From lizards collected from both localities, we gathered morphological measurements and analysed the genetic divergence between populations, using a molecular survey of ∼2800 mtDNA base pairs and 8 microsatellites.
There are significant differences in body size and general form and fixed but small mtDNA differences between island populations. Microsatellites reveal low diversity within populations but very high differentiation between islands with non-overlapping allele size ranges at all except one microsatellite and two loci exhibiting single-base polymorphism, fixed between islands.
Based on these results, we examine published criteria to determine whether the studied island forms could be considered true species. According to the phylogenetic species concept and Moritz’s evolutionary significant unit (ESU) criteria, the two lizard populations can be considered separate entities. Crandall et al.’s (2000, Trends Ecol. Evol., 15, 290–295) broader categorization of population distinctiveness, based on concepts of ecological and genetic exchangeability, produces conflicting results depending on the interpretation of the observed ecological data. Following Fraser and Bernatchez’s (2001, Mol. Ecol., 10, 2741–2752) framework for management decisions when ecological data are not sufficient we propose that the lizard populations on the Maria islands are on differing evolutionary trajectories and thus at the species boundary.
The populations are of high priority to conservation, thus meriting separate management.