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My semi-cousin* has a five-year-old daughter named Adele. My cousin says they (mom/dad/grandparents) bring up the singer in conversations far more often than other people do, and nobody has ever assumed a pop culture reference in their child's name, despite the family's musical tendencies. It's a lovely choice, and a great fit with big sis, without boxing you in to any particular category for any subsequent sibling names.
I also know a young Juniper (age 7ish); she goes mostly by Junie. I keep meaning to ask her what she thinks of her name, but we only really meet once a year, so I haven't had a chance. As others have commented, Iris strongly "matches" both June and Juniper on some axis: great-grandma revival for June, botanical/hippie for Juniper. For some people, such a strong style match constrains any future sibling names into the same narrow category, but I think sibling names and name categories can be more flexible than that, especially when there's a nickname or short form that leans a different way, like June versus Juniper. I also think that the nicknaming can go either way: June nicknamed Juniper would be adorable.
On the "more interesting than you think" front: would you be surprised to learn that June is currently almost twice as popular as Juniper? (Almost 300/million versus 180/million, give or take.)
* Semi- being one step further than step-: we're technically not actually related, but we're family. The great-grandma Mária Adél after whom little Adele is named was married to my grandfather's brother, but he died in WWII, and Adele et al. are descended from her second marriage.
Brian probably derives from an old Celtic element meaning 'hill', and Scott is 'Scottish, Gaelic-speaking' (from/via a Latin name, but of unknown origin beyond that). Sir Hugh Munro wrote a catalog of Scotland's 3000-foot hills in 1891, and they're now known collectively as "the Munros". Other Scottish hill-names: Merrick, Galloway, Lowther, Moffat, Pentland, Moorfoot, Lammermuir, Corbett, Graham, Donald.
My daughter's best friend in kindergarten is Ava, who has a baby sister called Ellie (full name Ella). Middle child is Jake (Jacob). The baby is only five months old, so they naturally mostly use the nickname, but it's not because of the shared ending with big sister. (It's because the baby is the sort where you're surprised nobody has eaten her right up due to cuteness overload. :-)
I think maybe LLLN is thinking of this one?
I know two boys named Dante but only one girl named Charlotte. Don't let popularity dissuade you from a name you love! Names are much too varied nowadays for usage numbers to have any day-to-day meaning. The random factors governing your neighbors' tastes may mean that it's Leonora/Eleanor who shares her name with a classmate, not her sister. (But more likely, neither one will.)
Charlotte and Eleanor is a swoon-worthy pairing, in my book. So much in common! So distinct!
Edited to add: it occurs to me that I also know two young Eleanors (plus one old one). And three, count 'em, three, young girls named Lorelei. (Now there's a name that looks misspelled no matter what you do.) For comparison, the rankings from 2011 and 2010 (the average age of the children I know, and also as far back as the lists are up on BNW) are as follows:
27 (45) Charlotte (now 9th)150 (165) Eleanor (now 60th)268 (255) Dante (now 322nd)499 (531) Lorelei (now 448th)
In other words, no matter which specific year you look at, the numbers predict exactly the opposite of my actual experience.
I just heard of a baby girl named Melva, which was picked off the family tree. Behind the Name guesses that it's a feminization of Melville/Melvin. It definitely fits both the "never heard of anyone with that name" and the "not too weird" categories for me, but I don't know if it's at all the OP's style.
Just a heads up: most of the audience on this site is in the US, and almost all US accents are rhotic, meaning that for us, -er sounds nothing like the -uh or -ah at the end of many feminine names. In particular, "May-er" is the word 'mayor', not the name Maya, and "my-er" is the surname Meyer, like the lemons. :-)
May is one of the many traditional nicknames for Margaret, so you could go with Margaret Ursula and still have May available as a call name. If you're pronouncing Maya as MAY-a (i.e., like the name of the month plus an 'a'), then you could even plausibly use that as a nickname for Margaret.
On _Daniel Tiger's Neighborhood_ (animated PBS kid's show, basically the direct descendant of Mr. Rogers' Neighborhood), the little sister is called Margaret. This means that in the U.S., the name will be comfortably familiar to families with children, but without any sort of overwhelming association.
I adore the name Margaret, and I think it'd be easier to live with than Maya, because there's little chance of pronunciation confusion. (Whether you're saying MY-a or MAY-a, there is no unambiguous spelling for it in English.) But I'm also a sucker for honor names, with a particular soft spot for Ursula; hence my suggestion of Margaret Ursula.
Gah, I want specifics so I can research etymologies... :-)
I think you can absolutely use a sound-alike or look-alike name as a connection to an honor name. People do things like Renee in honor of Raymond, which share a first initial and pretty much nothing else, and nobody blinks an eye, so something like Theodore in honor of a Theodoric-derived name (like Derek) shouldn't cause any raised eyebrows.
Kohen is a Jewish hereditary position. Its use by random parents is offensive to many. Alternatives: Coen/Koen, which are Dutch short forms of Conrad, or Cowan, a form of the Irish surname MacOwen.
The repeated -a in first and middle is not really a problem -- my daughter's names both end in -a -- but what do you think of Cecily instead of Cecilia? It's a traditional English form of the name, but for some reason it has never made the top 1000 in the U.S. (Other English forms of Cecilia: Cicely/Sisely, Celia.)
Yeah, I was thoroughly surprised that they didn't name this one Wilberforce Henry. It still would not have been as bad as poor Sturgeon, oops, sorry, Surgeon, oh, wait, no, Spurge, wait, that's not it either...
Other commenters have touched on various aspects of this, but I'd like to address it directly: the best middle names have significance. They're not randomly picked out of a hat, or chosen merely because they sound good; if that's all you're doing, it's perhaps better to just skip the middle name. (I grew up without one. It was never a problem.) A good story attached to a name can even help overcome spousal objections.
You're already doing an honor name, so some other type of connection to the middle is an avenue to explore, but there's no law against two honor names. Is there perhaps a suitably-named ancestor on his side? We become accustomed to our relatives' names, so he'd be more likely to be OK with the choice, and if you go far enough back, the style of naming may include an "old lady" gem that suits your tastes.
You mentioned choir and books as interests you and your husband share. What sorts of books? Any mutually-favorite characters or authors?
This is the second time in as many weeks that this name has occurred to me as a suggestion on these forums: Philomela may derive from Greek words meaning 'friend' and 'song', and her story in Greek myth -- while violent -- ends with her turned into a nightingale. The name is often used in English poetry for the sweet-singing nocturnal bird, which is a nice connection to your choice of given name: Leila was Lord Byron's favored spelling of the name derived from the Arabic for 'night'.
The "musical" names list at Behind the Name (http://www.behindthename.com/names/gender/feminine/description/composer,musician,singer) reminded me that Cecilia/Cecily is the patron saint of music. Would this connection be enough for your husband to move it off the "too old" list?
Other choir-related names that occur to me: Harmony, Melody, Aria, Carol, Kalliope. Further afield: Aoide (Greek muse of song), Carmen (Latin for 'song'), Mavis (a bird-name: another name for the song thrush), Melpomene (from a Greek word meaning 'to sing'), Polymnia (from Greek 'much' and 'song'). Also, Behind the Name claims that one derivation of Ava is a Persian word meaning 'voice'. Would this connection be enough for you to move it off the "too common" list?
Names don't have meanings. They have derivations and associations.
Evan derives from a Welsh form of John, which is generally agreed to derive from Hebrew words meaning 'God' and 'grace, favor'. Theodore derives from Greek words meaning 'God' and 'gift'. These are slightly similar derivations, but the associations and history are vastly different: everyone knows someone named John or some variant of it, while most people have only heard of people named Theodore -- and this statement is true going back hundreds of years. (And if you asked one of those people named John/Ian/Sean/Evan about the "meaning" of his name, he'd probably look at you blankly.)
In short, don't rule out names because of etymology. Evan works as a brother to Nolan and Caden, and Theodore works as a middle name for it. Of course, so does Otto -- sound or "flow" with middle names is vastly overrated by imminent parents. :-)
I know a Juniper, nicknamed Junie; she's about eight years old now. The reason you don't know any adults with this name is that it has only recently made the top 1000 in the US. This means there's at least some risk of it sounding dated a few decades from now, but I think given the ability to shorten to the classic June -- which has reemerged in the top 1000 after a couple of decades of absence -- and the similarity to Jennifer are points in its favor; they are likely to make it a "new classic" rather than a flash-in-the-pan, short-lived fad.
As others have pointed out, a current Juniper will grow up to be an adult among people with a very large variety of names, including things like Harper, Mason, and Scarlett, and as such, she'll fit right in.
It sounds like you're looking for a sub-category (sub-species?) of the joke-name genre most famously employed by the "Dewey, Cheetham & Howe Staff List" of the radio program Car Talk (http://www.cartalk.com/content/staff-credits). Or are you hoping for actual examples that people have encountered in real life?
As others have noted, a triple-k-sound name easily ends up sounding like a joke, and can be difficult to say. Unfortunately, your top contender is also the top offender here, because with Clara as the middle name, you end up with k-r-k-r-k-r, which is just way over the top, and nearly unpronouncable. I think you need to choose just one of Keira or Clara, and pick a "softer" name for the other position. Have you considered using Clara as the first name? The /L/ sound in it helps soften the alliteration and makes it more pleasing to both hear and say with the surname than Keira.
My other comment concerns spelling. How to phrase this diplomatically... I agree with a previous comment in substance (if maybe not quite in delivery): Jordyn is just ...no. Just no. Don't do that to your defenseless child. Spell it correctly as Jordan, and save headaches while looking classy in the bargain. Maryn suffers the same problem, though to a lesser degree, because no spelling of /MA-rən/ is particularly well-established as a personal name. I'd either go with a different choice (Marian?), or spell it Maren. (If you want the stress on the second syllable, spell it Marin, like the county in California.)
There are no names that can't be mispronounced or misspelled. :-)
A few cases in point:
1. While Silvia is closer to the name's etymology -- Latin doesn't use the letter 'y' -- in English it's much more often written as Sylvia. You can see a graphic demonstration of this by typing 'lvia' into the 'Ending' field of Expert NameVoyager.
2. Nowadays, almost a third of parents bestowing the name /NO-ruh/ spell it Norah.
3. Clara can be pronounced more than one way. The different dialects/accents of English make it hard to describe the difference in writing, but for me, it's /CLAW-ruh/ versus /CLAIR-uh/, that is, the first vowel is either like the one in the word 'law', or like the one in the word 'lair'.
All that said, I can recommend my name: Julia. Most people know how to write it and say it, although of course there's variation in both: the Italian spelling is Giulia, and some people smush the pronunciation into two syllables, /JOOL-ya/, instead of my much-preferred three, /JOO-lee-ya/. (And there are a few people who automatically nickname it to Julie, which is Totally Not My Name, but luckily such people are pretty rare and getting rarer.)
For a boy, I really like Ezra for you: it has not just the -a, but the -ra of your daughters, and yet it's totally distinct in both sound and appearance.
I grew up with exactly the same name as my mother. Neither of us had a middle name. Compared to that, sharing a name with a great-aunt who (presumably) lives somewhere else is absolutely no big deal. (Sharing my name with my mother was mostly a non-issue, too, although I did decide to change my name at marriage because of it.)
Regarding the unintended name-match question: I've mentioned several times on these forums that if you announce the actually intended honor right up front, people will not make the wrong connection. (My late mother-in-law happened to have the same name as my mother's older sister, who is not a favorite relative. My mother tells about her momentary shock over her granddaughter's middle name as a favorite joke, now.)
Oh, we all agree that things can't stay as they are! I suggested a version of a fully-moderated forum: new accounts would have to wait for a moderator to approve their posts, but the regulars would be on an automatically-approved list. I don't know if the current infrastructure supports such a setup, however.