Tag Archives: tree drawing

non-Traditional family structures and genomics

As I and my family await our 23andme kit to scan our genomes, family history has come back to the forefront of my thoughts. I used to be very fascinated by my own genealogy, and with adopted children, the concepts of descent, biology and culture have taken adjusted meanings for me. It’s why we have a ‘family map’ instead of a ‘family tree’. The difference between our cultural genealogy and our genetic genealogy has been become quite clear to me. Obtaining our family ancestry through these tests will bring a lot of these issues back to focus.

But there is a specific issue that is directly related to genomics, genomics tools and my family: same-gender headed household representation in pedigree and genealogy software. It’s non-existent or takes a difficult workaround to make it happen.

With the rising use of personal genomics data, there is a corresponding rise in the use of pedigree software for medical purposes and genealogy software for family history purposes. Neither of these handle non-traditional family structures well. I use ‘non-traditional’ lightly here though because even though same-gender headed households might be relatively new as a recognized family structure, the concept of family can be quite fluid across time and cultures. What is traditional and considered the ‘norm’ today in US culture (nuclear families of  two genders with children born to them) for ‘family’, is obviously not the case in the past, nor in contemporary cultures in other parts of the world.

A paper published last year entitled When Family Means More (or less) than Genetics by Burns and Edwards focuses on this inability of current tools to model family histories that aren’t within this norm. As they state:

One challenge in using family history as a health technology is that the geneticist or clinician defines family based on biology, whereas individuals often include those linked socially.

Genetic heritage and history is indeed important in determining disease susceptibilities, but ignoring or misunderstanding socially-defined kinship can lead to misdiagnosis, the lack of understanding of environmental influences and worse. Tools for modeling pedigrees must be able to flexibly model these family structures in order to be useful.

The researchers look at two groups and conclude that current tools are inadequate to model their family structures. Samoans were one group (Japanese-Americans the other):

When Samoan American participants were asked, “tell me about your family,” persons fulfilling social roles were described by that relationship. For example, an individual raised as a brother was identified as a brother whether or not there was a biological basis to the relationship. Similarly, individuals adopted in to or out of a family were described as the children of the family in which they were raised, not as offspring of the biological family. When further questioned, the participants could identify the biological link. But even when the biological relationship was known, the Samoan Americans reported family relationships based on social rather than biological ties.

They go in to good detail into why this is a problem. They also, early in the paper, suggest modern American society is changing. Americans already are one of the most ‘adopting’ nations in the world. And, as the authors note, our family structures are becoming more fluid (perhaps converging with Samoan concepts in some ways?):

For example, the Western postmodern family has looser kinship ties than in the past, with relationships that are diverse and fluid (Stacey, 1998). Blended, adoptive, and gay families, as well as those resulting from a variety of assisted reproductive technologies, place an emphasis on choice rather than genetics. For many, family is about social relationships and not solely concerned with the transfer of genes from one generation to the next (Finkler, 2001;Lévi-Strauss, 1969Peletz, 1995). Nonbiological social factors, such as role behavior, determine family membership, so that a mother’s sister’s son who has been raised with you is your brother (Finkler, 2001). Both formal and informal adoptions are traditional practices and very common in certain societies: Polynesia often being presented as the exemplar (Brady, 1976Carroll, 1970Levy, 1973).

So, let me side step adoption or other non-genetic descent issues for a moment, and hone in on gay families and representation in current pedigree tools available. Though the Recommendations for Standardized Human Pedigree Nomenclature (pdf)  mentions it in passing (“For example, information that is commonly recorded on a pedigree (e.g., same-sex relationships…)”) there is no standard suggested. In my and my colleague’s research so far we have yet to find a software or online medical pedigree tool that easily accepts same-gender parental groups, or represents them well.

I took at one excellent online tool, Madeline 2.0. If one enters a parent, entering a second parent automatically forces an opposite gender. Though there is the ability to model adoptive relationships, there is yet no way to model same-gender couples. I wrote the developers of the tool and received a thoughtful reply. No, there was ability to do this, but considering adopt-in and adopt-out relationships are model, it would make sense to include same-gender couples. They suggested they indeed will consider implementing this. Of course, as with all software and online tools, funding, timing and priorities I know will be an issue. I’ll definitely will keep an eye on developments. So as to not single Madeline out, no other tools that we know of (see here, here and here) allow for same-gender couples or headed families.

When going to family history modeling software for genealogy, the omission is as stark. Every individual has two family trees: a cultural/historical one and a genetic one. For most individuals, those histories overlap. The culture you received from your parents and they from theirs is pretty close to the genetic descent. Even then, its not a perfect overlap. What is important to who you are from a cultural or historical perspective might not at all be related to who are you from a genetic one, and who you are is as much cultural as it is genetic. I am as interested in where I got my cultural ancestry as where I got my genetic one, this has become quite clear to me as we’ve adopted children.

And in the future, descendants will look at their family genealogies and it will be very important to them that one of their ancestors was raised by two men, or two women whether adopted or biological from one parent. As these genealogies are built, those relationships which are very important to their family culture and histories should be represented. I know I personally will hope that this will be the case for our family history in the years to follow.

Yet, for software available it is impossible, a complicated workaround or awkward to allow for same-gender parents in the representation (not to mention paper family trees!). GEDCOM is the defacto standard for exchanging genealogical information. There is no simple standard in GEDCOM for including same-sex parents. That it was developed by the Mormon Church probably has something to do with that ‘oversight’, but frankly given the oversight across the board in pedigree and genealogy standards and software, I doubt that was a deliberate one.

So far I have found software that requires complicated workarounds, like Legacy, or it’s not easy to figure out (though once you do, it’s simple :). Of the many I’ve tried, none even allow it.

In a world where the number of same-sex couples is increasing annually (not to mention adoption, blended families and many other types of structures) and increased interest in family history through both genomics and culture and history, I look forward to seeing the software catch up to the ability to model my family for future researchers and historians.

Burns McGrath, B., & Edwards, K. (2009). When Family Means More (or Less) Than Genetics: The Intersection of Culture, Family, and Genomics Journal of Transcultural Nursing, 20 (3), 270-277 DOI: 10.1177/1043659609334931

Tip of the Week: PhyloWidget

Got phylogeny? So, you’ve created a phylogeny using some software and would like to draw the tree from the Newick formatted file* you exported. Of course there is no shortage of tree drawing programs out there (or phylogeny generating ones either). We found another one recently; a web-based, API-usable, opensource tree drawing tool that is quite intuitive and functional. It’s called PhyloWidget. The paper describing PhyloWidget is here and you can find some very nicely done step-by-step instructions here. I’ve done a quick 4 minute tutorial here to give you a quick overview. If it looks like something you could use, you might want to delve into it right away, or check out their ‘walk through.’ Happy climbing.

*Here’s the file I use in the tip: ((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,((monkey:100.85930,cat:47.14069):20.59201, weasel:18.87953):2.09460):3.87382,dog:25.46154);

Tip of the Week: Drawing a Tree

phylodendron_thumbSo, you’ve got your sequences aligned using Clustal, Muscle or T-Coffee (or other program), you’ve created a tree data file using PAUP, Phylip or one of the other many algorithms out there, now you want to draw and visualize those relationships. A good place to go to find a list of tools to do that is at the huge list of phylogeny tools at Department of Genome Sciences at the University of Washington (there is a lot more than just tree drawing of course!). Many of these tools are downloaded and feature rich, one might suit your needs, so check them out. One this tip points out is Phylodendron, which you can download, but also has a web interface. This will allow you to quickly draw a tree for viewing.