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Abhilash Nair

University of Helsinki, Faculty of Biosciences, Post-Doc

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I am an evolutionary biologist, with a background in population and conservation genetics. My research interest is in understanding the factors that generate and maintain genetic diversity in wild populations and in understanding the genetic basis of adaptation in populations to varying environments. I have been involved in multiple projects some of which are on cryptic diversity of amphibians in south-east Asia, adaptation in sticklebacks in Baltic sea and spatial genetic structure of parasitoids of Glanville fritillary butterfly in Aland islands. In Husby’s lab, I will be working on the population structure and plasticity of wing-polymorphism in water-striders.

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Papers by Abhilash Nair

Long-term spatio-temporal genetic structure of an accidental introduction, and the population dynamics of its associated Wolbachia symbiont

Population bottlenecks associated with founder events strongly impact the establishment and genet... more Population bottlenecks associated with founder events strongly impact the establishment and genetic makeup of populations. In addition to their genotype, founding individuals also bring along symbionts that can manipulate the phenotype of their host, affecting the host population establishment, dynamics and evolution. Thus, to understand introduction, invasion, and spread, we should identify the roles played by accompanying symbionts. In 1991, the parasitoid wasp, Hyposoter horticola, and its associated hyperparasitoid were accidentally introduced from the main Åland islands, Finland, to an isolated island in the archipelago, along with their host, the Glanville fritillary butterfly. Though the receiving island was unoccupied, the butterfly was present on some of the small islands in the vicinity. The three species have persisted as small populations ever since. A strain of the endosymbiotic bacterium Wolbachia has an intermediate prevalence in the H. horticola across the main Åland population. The infection increases susceptibility of the parasitoid to hyperparasitism. We investigated the establishment and spread of the parasitoid, along with patterns of prevalence of its symbiont using 323 specimens collected between 1992 and 2013, from five localities across Åland, including the source and introduced populations. Using 14 microsatellites and one mitochondrial marker, we suggest that the relatively diverse founding population and occasional migration between islands might have facilitated the persistence of all isolated populations, despite multiple local population crashes. We also show local near-fixation of Wolbachia, where the hyperparasitoid is absent, and selection against infected wasp genotypes is relaxed.

Patterns of Cryptic Diversity and Phylogeography in Four Freshwater Copepod Crustaceans in European Lakes

Diversity, 2021

Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversit... more Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversity within widespread species and understanding how historical and biogeographical factors shape the modern patterns of their distribution. Most comparative phylogeographic studies so far focus on terrestrial and vertebrate taxa, while aquatic invertebrates (and especially freshwater invertebrates) remain unstudied. In this article, we explore and compare the patterns of molecular diversity and phylogeographic structure of four widespread freshwater copepod crustaceans in European water bodies: the harpacticoids Attheyella crassa, Canthocamptus staphylinus and Nitokra hibernica, and the cyclopoid Eucyclops serrulatus, using sequence data from mtDNA COI and nuclear ITS/18S rRNA genes. The three taxa A. crassa, C. staphylinus and E. serrulatus each consist of deeply diverged clusters and are deemed to represent complexes of species with largely (but not completely) non-overlapping distributi...

Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map

The Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulati... more The Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterfly’s genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO, indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,830 gene models using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.

The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host

BMC Genomics, 2019

Background: Adapting to changes in the environment is the foundation of species survival, and is ... more Background: Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra-and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict. Results: In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. Conclusion: We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.

Bats as potential suppressors of multiple agricultural pests: A case study from Madagascar

Agriculture, Ecosystems & Environment, 2019

The conversion of natural habitats to agriculture is one of the main drivers of biotic change. Ma... more The conversion of natural habitats to agriculture is one of the main drivers of biotic change. Madagascar is no exception and land-use change, mostly driven by slash-and-burn agriculture, is impacting the island's exceptional biodiversity. Although most species are negatively affected by agricultural expansion, some, such as synanthropic bats, are capable of exploring newly available resources and benefit from man-made agricultural ecosystems. As bats are known predators of agricultural pests it seems possible that Malagasy bats may be preferentially foraging within agricultural areas and therefore provide important pest suppression services. To investigate the potential role of bats as pest suppressors, we conducted acoustic surveys of insectivorous bats in and around Ranomafana National Park, Madagascar, during November and December 2015. We surveyed five landcover types: irrigated rice, hillside rice, secondary vegetation, forest fragment and continuous forest. 9,569 bat passes from a regional assemblage of 19 species were recorded. In parallel, we collected faeces from the six most common bat species to detect insect pest species in their diet using DNA metabarcoding. Total bat activity was higher over rice fields when compared to forest and bats belonging to the open space and edge space sonotypes were the most benefited by the conversion of forest to hillside and irrigated rice. Two economically important rice pests were detected in the faecal samples collected-the paddy swarming armyworm Spodoptera mauritia was detected in Mops leucogaster samples while the grass webworm Herpetogramma licarsisalis was detected from Mormopterus jugularis and Miniopterus majori samples. Other crops pests detected included the sugarcane cicada Yanga guttulata, the macadamia nut-borer Thaumatotibia batrachopa and the sober tabby Ericeia inangulata (a pest of citrus fruits). Samples from all bat species also contained reads from important insect disease vectors. In light of our results we argue that Malagasy insectivorous bats have the potential to suppress agricultural pests. It is important to retain and maximise Malagasy Benstead, 2005). However, despite its high level of endemism and species diversity, Madagascar's forests continue to face one of the highest rates of conversion in the world with approximately 1% of the island's forest cover being cleared each year (Rasolofoson et al., 2015; Eklund et al., 2016; Vieilledent et al., 2018). While most Malagasy biodiversity is adversely affected by agriculture-driven habitat modification, some 'winner' species benefit from habitat modification and increase their abundance in agricultural areas. Several of these are insectivorous birds (Martin et al., 2012; Rocha et al., 2015) and bats (López-Baucells et al., 2017b) that through the suppression of agricultural pests can provide valuable ecosystem services to local populations (Karp and Daily 2014; Maas et al. 2015). Rice (Oryza spp.) is one of the most important staple food crops worldwide (Muthayya et al., 2014). It is the main crop cultivated by Malagasy subsistence farmers (Kari and Korhonen-Kurki, 2013) throughout the island, and as in numerous other high-biodiversity regions across the tropics, much of the ongoing deforestation is due to agricultural expansion for rice production (McConnell et al., 2004; Neudert et al., 2017). Such a high dependency on rice creates problems when yields are affected by climatic events or pest outbreaks (Harvey et al., 2014). Insect rice pests are known to cause severe damage to rice crop yields (Oerke, 2006).

Rapid assessment of bat diversity in the Taita Hills Afromontane cloud forests, southeastern Kenya

Barbastella, 2016

Tropical mountain ranges are known to support high biodiversity. In addition to their role as ref... more Tropical mountain ranges are known to support high biodiversity. In addition to their role as refuge habitat, complex topography within these ecosystems promotes the development of diverse species traits and evolutionary divergence. However, species within these environments also face severe anthropological threats, most notably from habitat loss and degradation, invasive species, and climate change. A primary example is the Taita Hills in Kenya, which forms the northernmost portion of the biodiversity rich Eastern Arc Mountains. Despite the high biodiversity potential for the area, little is known regarding chiropteran diversity. In order to address this lack of knowledge, we conducted a rapid biological survey of bats during January-February 2016. Our trapping effort was focused on different habitat types (e.g. highland cloud rainforest fragments, lowland riverbeds and human structures) and diverse trapping methods were used (e.g. mist-netting and hand-netting). A total of 169 bats belonging to at least 19 species from 7 different families were captured across 16 sampling sites. We report 10 new species records for the Taita Hills region, including the first record of Miniopterus mossambicus for East Africa, with a major range expansion in its distribution, as well as the first echolocation call for Glauconycteris argentata in eastern Africa. Several cases of probable species complexes were also identified, which are the focus of ongoing molecular work. Together, our results demonstrate that the Taita Hills region is home to rich bat diversity, not yet completely assessed, and emphasizes the urgent need to conserve the remaining forest fragments.

Spatial and temporal genetic structure at the fourth trophic level in a fragmented landscape

Proceedings. Biological sciences / The Royal Society, May 25, 2016

A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such a... more A fragmented habitat becomes increasingly fragmented for species at higher trophic levels, such as parasitoids. To persist, these species are expected to possess life-history traits, such as high dispersal, that facilitate their ability to use resources that become scarce in fragmented landscapes. If a specialized parasitoid disperses widely to take advantage of a sparse host, then the parasitoid population should have lower genetic structure than the host. We investigated the temporal and spatial genetic structure of a hyperparasitoid (fourth trophic level) in a fragmented landscape over 50 × 70 km, using microsatellite markers, and compared it with the known structures of its host parasitoid, and the butterfly host which lives as a classic metapopulation. We found that population genetic structure decreases with increasing trophic level. The hyperparasitoid has fewer genetic clusters (K = 4), than its host parasitoid (K = 15), which in turn is less structured than the host butterf...

Testing the efficacy of a chilli-tobacco rope fence as a deterrent against crop-raiding elephants

Chilli-based repellents have shown promise as deterrents against crop-raiding elephants in Africa... more Chilli-based repellents have shown promise as deterrents against crop-raiding elephants in Africa. We experimented with ropes coated with chilli-based repellent as a cheap alternative to existing elephant cropraid deterrent methods in India. Three locations (Buxa Tiger Reserve, Wyanad Wildlife Sanctuary and Hosur Forest Division) representing varying rainfall regimes from high to low, and with histories of intense elephantagriculture conflict, were selected for the experiments that were conducted over 2-3 months during the preharvest period of the kharif season in late 2006. Chilli and tobacco powder mixed with waste oil was applied to ropes strung around agricultural fields of 1.4-5.5 km perimeter and elephant approaches were monitored. Elephants breached the rope fences a few times at all three study sites. Female-led herds were far more deterred (practically 100% reduction) than were solitary males (c. 50%) by the chilli-tobacco rope. Efficacy of this method as a deterrent was significantly better in the low-rainfall regime relative to medium and high-rainfall regimes. The initial promising results present a case for more rigorous experimentation; these would help determine if the elephants avoiding the rope are responding physiologically to the chillitobacco smell or merely reacting cautiously to a novel substance in their environment.

Microsatellite markers for a hyperparasitoid wasp from a fragmented landscape

Conservation Genetics Resources, 2015

Your article is protected by copyright and all rights are held exclusively by Springer Science +B... more Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media Dordrecht. This e-offprint is for personal use only and shall not be selfarchived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".

Increased fluctuation in a butterfly metapopulation leads to diploid males and decline of a hyperparasitoid

Proceedings. Biological sciences, Jan 22, 2018

Climate change can increase spatial synchrony of population dynamics, leading to large-scale fluc... more Climate change can increase spatial synchrony of population dynamics, leading to large-scale fluctuation that destabilizes communities. High trophic level species such as parasitoids are disproportionally affected because they depend on unstable resources. Most parasitoid wasps have complementary sex determination, producing sterile males when inbred, which can theoretically lead to population extinction via the diploid male vortex (DMV). We examined this process empirically using a hyperparasitoid population inhabiting a spatially structured host population in a large fragmented landscape. Over four years of high host butterfly metapopulation fluctuation, diploid male production by the wasp increased, and effective population size declined precipitously. Our multitrophic spatially structured model shows that host population fluctuation can cause local extinctions of the hyperparasitoid because of the DMV. However, regionally it persists because spatial structure allows for efficien...

A New Species of Frog (Anura: Dicroglossidae) Discovered from the Mega City of Dhaka

PloS one, 2016

We describe a new species of frog of the genus Zakerana discovered from the urban core of Dhaka, ... more We describe a new species of frog of the genus Zakerana discovered from the urban core of Dhaka, Bangladesh, one of the most densely populated cities in the world. Although the new species is morphologically similar to the geographically proximate congeners in the Bangladeshi cricket frog group, we show that it can be distinguished from all congeners on the basis of morphological characters, advertisement calls and variation in two mitochondrial DNA genes (12S rRNA and 16S rRNA). Apart from several diagnostic differences in body proportions, the new species differs from other Zakerana species in having a flattened snout (from ventral view) projecting over the lower jaw, and diagnostic trapezoid-shaped red markings on the vocal sac in males. Molecular genetic analyses show that the new species is highly divergent (3.1-20.1% sequence divergence) from all congeneric species, and forms a well-supported clade with its sister species, Zakerana asmati. The discovery of a new amphibian spec...

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks

BMC biology, Jan 24, 2015

The degree of genetic differentiation among populations experiencing high levels of gene flow is ... more The degree of genetic differentiation among populations experiencing high levels of gene flow is expected to be low for neutral genomic sites, but substantial divergence can occur in sites subject to directional selection. Studies of highly mobile marine fish populations provide an opportunity to investigate this kind of heterogeneous genomic differentiation, but most studies to this effect have focused on a relatively low number of genetic markers and/or few populations. Hence, the patterns and extent of genomic divergence in high-gene flow marine fish populations remain poorly understood. We here investigated genome-wide patterns of genetic variability and differentiation in 10 marine populations of three-spined stickleback (Gasterosteus aculeatus) distributed across a steep salinity and temperature gradient in the Baltic Sea, by utilizing > 30 000 single nucleotide polymorphisms obtained with a pooled RAD-seq approach. We found that genetic diversity and differentiation varied...

A New Species of Euphlyctis (Anura: Dicroglossidae) from Barisal, Bangladesh

PLOS ONE, 2015

A new species of the genus Euphlyctis is described from the Barisal district of Bangladesh and co... more A new species of the genus Euphlyctis is described from the Barisal district of Bangladesh and compared with its morphologically similar and geographically proximate congeners. The new species is highly divergent in comparison to other congeneric species on basis of sequence divergence in mitochondrial DNA gene sequences (ranging from 5.5% to 17.8% divergence). Euphlyctis kalasgramensis sp. nov. can be readily diagnosed by having the following combination of characters: snout-vent length (SVL) 30.44-37.88 mm, absence of mid-dorsal line, nostril-snout length 3% of SVL, nostril much closer to snout tip than eye, nostril-snout length 48% of distance from front of eyes to nostril, relative length of fingers (shortest to longest: 1 = 2 < 4 < 3), tibia length 59% of SVL, foot length 55% of SVL.

A new species of microhyla (anura: microhylidae) from nilphamari, bangladesh

PloS one, 2015

A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compa... more A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species - designated here as Microhyla nilphamariensis sp. nov. - forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7 - 13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril-snout length, internarial distance is roughly five times greater than nostril-snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermor...

A New Species of Frog (Anura: Dicroglossidae) Discovered from the Mega City of Dhaka

We describe a new species of frog of the genus Zakerana discovered from the urban core of Dhaka, ... more We describe a new species of frog of the genus Zakerana discovered from the urban core of Dhaka, Bangladesh, one of the most densely populated cities in the world. Although the new species is morphologically similar to the geographically proximate congeners in the Bangladeshi cricket frog group, we show that it can be distinguished from all congeners on the basis of morphological characters, advertisement calls and variation in two mitochon-drial DNA genes (12S rRNA and 16S rRNA). Apart from several diagnostic differences in body proportions, the new species differs from other Zakerana species in having a flattened snout (from ventral view) projecting over the lower jaw, and diagnostic trapezoid-shaped red markings on the vocal sac in males. Molecular genetic analyses show that the new species is highly divergent (3.1–20.1% sequence divergence) from all congeneric species, and forms a well-supported clade with its sister species, Zakerana asmati. The discovery of a new amphibian species from the urban core of Dhaka together with several recent descriptions of new amphibian species from Bangladesh may indicate that more amphibian species remain to be discovered from this country.

A New Species of Microhyla (Anura: Microhylidae) from Nilphamari, Bangladesh

A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compa... more A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species – designated here as Microhyla nilphamariensis sp. nov. – forms a clade with M. ornate , it is highly divergent from M. ornata and all of its congeners, with 5.7 – 13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril–snout length, internarial distance is roughly five times greater than nos-tril–snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatar-sal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.

A New Species of Euphlyctis (Anura: Dicroglossidae) from Barisal, Bangladesh

A new species of the genus Euphlyctis is described from the Barisal district of Bangladesh and co... more A new species of the genus Euphlyctis is described from the Barisal district of Bangladesh and compared with its morphologically similar and geographically proximate congeners. The new species is highly divergent in comparison to other congeneric species on basis of sequence divergence in mitochondrial DNA gene sequences (ranging from 5.5% to 17.8% divergence). Euphlyctis kalasgramensis sp. nov. can be readily diagnosed by having the following combination of characters: snout-vent length (SVL) 30.44 -37.88 mm, absence of mid-dorsal line, nostril-snout length 3% of SVL, nostril much closer to snout tip than eye, nostril-snout length 48% of distance from front of eyes to nostril, relative length of fingers (shortest to longest: 1 = 2 < 4 < 3), tibia length 59% of SVL, foot length 55% of SVL.

Microsatellite markers for a hyperparasitoid wasp from a fragmented landscape

Conservation genetics of endemic Indirana frogs of the Western Ghats biodiversity hotspot

To be presented for public examination with the permission of the Faculty of Biological and Envir... more

Cross-species testing and utility of microsatellite loci in Indirana frogs

BMC Research …, 2012

Background: Microsatellite loci are widely used in population and conservation genetic studies of... more Background: Microsatellite loci are widely used in population and conservation genetic studies of amphibians, but the availability of such markers for tropical and subtropical taxa is currently very limited. In order to develop resources for conservation genetic studies in the genus Indirana, we tested amplification success and polymorphism in 62 previously developed microsatellite loci, in eight Indirana species -including new candidate species. Developing genomic resources for this amphibian taxon is particularly important as it is endemic to the Western Ghats biodiversity hotspot, and harbours several endangered species. Findings: The cross-species amplification success rate varied from 11.3 % to 29.0 % depending on the species, with 29 -80 % of the amplifying loci being polymorphic. A strong negative correlation between cross-species amplification success (and polymorphism) and genetic distance separating target from source species was observed. Conclusions: Our results provide additional genetic support for the existence of genetically divergent cryptic species within the genus Indirana. The tested markers should be useful for population and conservation genetic studies in this genus, and in particular, for species closely related to the source species, I. beddomii.