TL;DR: A transgender woman is unlikely to want her dead name in a publication. You can safely assume Jane wants to publish under "Jane" and under no other name. In the unlikely event that this is wrong, she's not going to be upset about her co-author thinking she would like to publish under her real name.
Allow me to offer my perspective (sorry, I didn't see the question earlier). I no longer consider myself transgender, but I've "been there".
Please accept that there is no "John". Jane has been falsely imprisoned in a male gender role since birth. Every time Jane is referred to by her dead name, she will think that she is not welcome, that people don't want her to exist, and she may even contemplate suicide. (Every time I've asked a transgender person about suicide, they have described detailed plans for how they would kill themselves.)
If you insist on deadnaming her, don't be surprised if she dumps the project, and severs contact with you. Other possibilities are jumping in front of a train, or filing a complaint of discrimination. (If people did this to me, I would catch a taxi to the airport, move to a new city/country and start a new life/career outside of academia. I have organized my life so that I can do this at any moment. However, I'm fortunate to have found a work environment where this is not an issue, and I'm now a very loyal employee [unwilling to leave even if somewhere else offered me a far higher salary].)
The best analogy I've found to explain how deadnaming feels: Imagine a husband referring to his wife by his ex-girlfriend's name, and then, when she gets angry, he tells her it's easier for him to refer to her by his ex's name, and that she's overreacting. His wife was never that person. Jane was never that person either.
From most transgender peoples' perspective, there is no "sex change" (it's one of many misleading terms non-transgender people use to describe transgender people [other popular ones include "woman trapped in a man's body" (instead of "woman") and "preferred name" (instead of "name")]). There's possibly a moment of realization ("Huh. I'm a girl.") followed by negotiating a pathway to being accepted in society as one's true gender (or a sufficiently close approximation to make life liveable). Often this involves adopting a gender-appropriate name, which will help her fit in and be one of the girls. Irrespective of which forms she's filled in, and irrespective of other people's opinions, Jane's name is Jane (until she says otherwise).
Jane may undergo medical procedures to correct her bodily mismatches (which are very expensive, probably will be the most physically painful experiences in her life, and might make her incapable of having children). She endures this partly to stop people mistaking her for a man; to live as Jane in every aspect of her life. Jane suffers greatly for the sake of being called Jane.
Jane will also be aware that if she refers to herself using her dead name, it gives others an excuse to follow suit. And when others see people deadnaming her, they think it's okay too, and it grows out of control quickly. (For this reason, I never use my dead name. Anyone who uses it is doing so against my will---they are backstabbing me. I have both threatened to sue or file a human rights complaint against those who have used it against my will.)
Being transgender should also be considered in a medical context---it's intimate and confidential, and not something she will want immortalized on permanent documents. However, one medical aspect is important to be aware of here: the real-life test. International guidelines for treatment of transgender people require that patients live a life consistent with their stipulated gender (the phrase is "consistent, insistent, and persistent"). As such, it's important for her to publish under the name "Jane" to access medical care, which is probably more important to her than the publication itself. (As it was for me. As another example, I deliberately stood at the front of this conference photo so I could later use it for the real-life test.)
With the above in mind, the idea that Jane would want that other word on a publication is preposterous to me. It would be a huge step backwards in life.
(Caveat: Transgender people are a diverse group, so there is no universal narrative.)
Some comments about Pete L. Clark's answer:
I'm not aware of a transgender person who considers themselves as a different person after transitioning (although they might use something along the lines of "the person I was" metaphorically). The typical transgender narrative is that they are affirming their gender; something along the lines of "I was always a girl, but was mistaken for a boy at birth". Some transgender people actually consider themselves as a different gender than prior to transitioning (which might be because of different interpretations of the word "gender"), but not a different person.
The ability to correct one's documents varies from document to document, state to state, country to country, and fluctuates with who's running the country/state you were born in, live in, or are a citizen of. While messy, it's perfectly legal. Keep in mind, however:
- Transgender people tend to value who someone is, rather than what's written on documents, and
There's also no such thing as e.g. "legally a woman": in a court of law, you are whatever the judge says you are. Outside of a court of law, it's ordinary for transgender people to have mismatches between their gender, driver's licence, passport, and birth certificate.
[I find it amusing when lawmakers talk about how simple it is to tell who's a man and who's a woman, then proceed to propose laws with definitions of "man" and "woman" inconsistent with the definitions in laws proposed by other lawmakers who also talk about how simple it is to tell who's a man and who's a woman. (99% of the time it is easy, and these definitions are consistent, but there's some exceptions, and this is what transgender people are---the exceptions.)]
Transgender people often avoid transitioning until the point where they become suicidal, where the choice becomes "transition or kill myself". They have no choice but to accept the consequences of transitioning, no matter how severe. They have likely accepted a host of negatives to live an authentic life, including a constant fear of being physically attacked, being arrested arbitrarily (and being raped in a gender-mismatched jail [along with forced prostitution]), being rejected by their families and religious groups, becoming homeless and having to turn to sex work to survive, unwanted sexual advances (trans people are often considered fetish objects, rather than human beings), and so on. Jane is probably unconcerned other people's momentary confusion about which papers she's authored.
By transitioning, Jane has accepted a lower chance at getting a job, and a lower salary if she does get it, all to live an authentic life. Her identity (who she is as a person) is more valuable to her than her career. Some of my stories:
I'm fairly sure I was turned down for a job for no other reason than my gender. The rejection letter was inaccurate, and I was even told I could not even give a seminar at that institution. While prior to transitioning, the professor would email me and be happy for me to visit (where I once gave a seminar), they have not returned my emails in about 3 years.
I was accepted for some short-term contract work. Admin requested my documents, but since they weren't corrected at that stage, I refused to supply them citing privacy reasons. They said that if I didn't supply the documents, I would be given a "without PhD qualifications" salary, to which I agreed explaining that my privacy was more important to me than money, but they eventually put me on the "with PhD qualifications" salary anyway.
My work under my dead name is listed on separate MathSciNet, Google Scholar, math.SE, etc., pages.
I had two (or maybe three?) papers in the "minor revisions" stage when I transitioned. It took me something like six months to actually make those changes. As the corresponding author of one paper, this is what I wrote to the journal editor:
I must apologize about this, as the delay [was] caused largely by myself (not my co-authors) due to personal reasons (which will be apparent from my change of name).
I've attached the relevant documents to this email. Please let me know if there's anything else required. Also please forgive me for not using the [submission system] to respond; I do not wish to use that account.
The editor asked me to create a new account, which I did, and the paper was transferred there. Noone said anything about the name.
I had a grant under my dead name. After transitioning, I claimed reimbursement for conference travel on that grant, and I was asked for proof of the change of name (a "linking document"), which I refused citing privacy reasons and told them not to worry about the reimbursement. They apologized for asking, and reimbursed me without the document.
There's workarounds in a lot of instances. It's not as bad as you might think. E.g. I've been publishing a lot recently, attempting to bury my dead-name publications; when applying for a job, I first email someone on the panel who I know from conferences; on my CV and website, I list surnames only; and here's a snippet from an email to someone I'll visit next week, who previously didn't know about my transition:
Hopefully you remember me (and can figure out
who this is---perhaps ask [another collaborator] if there's any
Anyway, I'm thinking of going to the Design Theory conference in
Many people have no difficulty with this. I'm starting to get emails about papers published under my dead name, but addressed to me. Journal editors are somehow still sending me referee requests. I've had two professors say they would write me letters of recommendation, which I've actually had to turn down (I guess they perceived me as having difficulty obtaining these).
And in response to some of the comments:
The idea of adding a footnote "previously known as John Doe" is just as preposterous to me as adding a dead name co-author (I would sooner write "I have genital herpes" as a footnote than my equivalent).
"If Jane didn't work on the project as Jane..." "What if, for example, John Doe's work on this project..." There is only Jane; there is only Jane's work. Please try to stop clinging onto the imaginary person, and see the real person.