It is entirely characteristic of Charlotte Prodger’s gentle, subtle wit that she has used the sound of bagpipes in her new film, which is Scotland’s official offering for this year’s Venice Biennale. It is equally characteristic that she is completely uninterested in using a recognisable melody, preferring the low drone instead. “It is a means to an end,” she says. “Players need the drone for air to pass through the instrument in order to play notes. So I asked the player not to produce any notes. Then she happened to do this thing they call a pressure drop, which is where the instrument ‘gargles’, and which they are taught not to do. And I said, ‘Oh, please can you do some more of those?’”

Her film, SaF05, is full of moments when the eye or ear is drawn to something – such as the bagpipe pressure drop – that would normally be regarded as an error and discarded. One shot shows us the grubby smudges on Prodger’s laptop screen; others linger lovingly over the great sculptural mounds resembling “ghosts or shrouded human figures” that rise above termites’ nests – images captured when she was actually trying to shoot something quite different.

It is such “offcuts and extrusions” that interest Prodger in her new work: how the detritus of life can be a hint or a code for something deeply intimate, perhaps a key to understanding the self. In SaF05, Prodger delves into her memories of being a queer teenager in a village outside Aberdeen, but her material is also “cement and soil and fingerprints and bodies and touching and cigarettes”.

Facebook Twitter Pinterest On the prowl … an image from SaF05, in which Prodger searched for a lion exhibiting male characteristics. Photograph: Courtesy of the artist; Koppe Astner, Glasgow and Hollybush Gardens, London

Prodger, who is 45, has had an extraordinary few months. The Glasgow-based artist won the Turner prize last year with her film Bridgit, shot on her iPhone, which, among other things, lingered on the standing stones of Aberdeenshire, showed us churning Scottish seas, and brought the viewer her memories of being mistaken for a boy – a delicate, poetic meditation on the queer body and the landscape. Since then, there has been the “intense” challenge of completing the new work for Venice. “I am definitely still digesting this piece. I can’t even look back on the journey of making it.”

The work’s title refers to the name used by naturalists in the Okavango Delta in Botswana for a lioness that exhibits certain male characteristics. She has a mane, spends a great deal of time alone and roars. Prodger became fascinated by the idea of these maned lionesses. Several have been recorded in the area, though only one is thought still to survive – and she set out with a crew in the hope of filming her, though they never did see her. (Instead, Prodger came home with that termite-mound footage.)

The film opens with footage of SaF05 gleaned by local conservationists using a fixed camera activated for a few seconds when she strays nearby. We see her in the dark, a completely compelling presence, as flies swish around her. She plumps herself down on the ground, settling a paw beneath her enormous body, as grand as a duchess throwing herself into an armchair. Later she heaves herself up, arching her body and emitting a deep, throaty roar.

What is it about SaF05 that so captivated Prodger? She thinks about it, then laughs. “I’m attracted to her. As a being. I think because she’s got a big beard. I want a big beard! Maybe it’s just that which drew me to her. Maybe there is an identification in that sense: she’s like a butch. I don’t want to call animals queer, but I’m doing it, there’s a projection there. But there is also something about animals – that proximity and distance. In the footage, you can see her body right up next to the camera. You can see the dust on her tail, you can see the muscles and the flesh. I wanted to smell her. I asked the conservationists what she smelled like. But you can’t get truly close.”

Facebook Twitter Pinterest ‘I don’t want to call animals queer – but I am’ … one of the lionesses in Okavango Delta who grew a mane. Photograph: Pia Dierickx/BNPS/BNPS.co.uk

In the film, Prodger reads the conservation team’s descriptions of the lioness’s behaviour. It is a commentary as objective and oddly poetic as the shipping forecast. Prodger used a similarly dispassionate technique to record remembered moments of her adolescence in the 1980s – going to the austere, minimal Presbyterian church over the road for Bible study, and immersing herself in the magnificently strange and ecstatic Book of Revelation; watching teenage boys spitting and smoking, their cigarettes held between finger and thumb, facing their bodies; abandoning God for girls; making her first moves towards intimacy with a co-worker when she was earning cash as a cleaner at time-share apartments near Balmoral.

“It’s the idea of human behaviour being folded back into animal behaviour,” she says. “The materiality of it. All these little gestures. The hand in the pocket, moving. The boy flicking ash. I wanted it to feel on a similar register. These little vibrating behaviours, testing things, touching things.”

She disguises the names of characters with codes that echo the Botswana lioness’s. “I’m interested in naming, in codes,” she says. “Queerness is coded. When you’re growing up as a queer person, you are looking for signals, trying to transmit signals, but you don’t really know what the signals are. And if you transmit the wrong signals, that leads to moments of shame. Eventually, you start to learn the language, all of the little signifiers.”

Prodger and I are speaking in a spectacular location: Cove Park, an artists’ residence on the Rosneath peninsula near Glasgow; the organisation is running her Venice exhibition. On one side of the peninsula is Gare Loch, where the vast Faslane naval base sits alongside a tiny but persistent peace camp. On the other is the 80-metre-deep Loch Long, through which nuclear submarines cruise. It is a landscape that is both extraordinarily beautiful and deeply militarised, if you know how to read the signals.

Facebook Twitter Pinterest Big cat diary … an installation view of SaF05. Photograph: Cristiano Corte/courtesy of the artist and Koppe Astner and Hollybush Gardens galleries

The experience of seeing the dark shadow of a sub gliding through Loch Long is mentioned in SaF05. It resonates with the film’s deep concern with what can and can’t be seen clearly – the things hidden beneath the surface like a submarine, or the termites’ grand warren.

Like other aspects of the film, though, this passage might read differently in the context of Prodger “representing” her country in Venice, since the location of the UK’s nuclear deterrent is no small issue in the Scottish independence debate. “Representing Scotland is something I am trying not to think about,” she says, “because you can’t represent a country. Though obviously I feel very privileged and honoured and proud. But it is weird, the idea of the Biennale. It’s a strange time to be thinking about borders and hierarchies – who gets in and who doesn’t – and where those countries are, and who’s at the top of the avenue.”

She is, I suspect, referring to the British Pavilion, which this year is occupied by the official British artist Cathy Wilkes (who is also based in Glasgow). The British Pavilion stands grandly at the head of an avenue in Venice’s Giardini and dominates the surrounding landscape as if the British empire were still at its height. Scotland’s exhibition is officially a “collateral event”, not a formal national representation. “We didn’t vote for Brexit,” she says of Scotland. “So it’s nice to be somewhere that is not about that.”

English-born to English parents, but with roots now firmly in Glasgow, Prodger is pro-independence. “I don’t think we are left with a choice,” she says. “What was so exciting about the independence movement before the 2014 referendum was not so much the party politics, but the grassroots movement. For me, it was tied in with all kinds of ideas of self-determination. It’s a civic nationalism rather than an ethnic nationalism and it’s definitely about looking outward. For a lot of us, there is a real sense that independence would not be about this little inward-looking country but a way of looking towards, to our peers in other places – to our friends.”