Prepared for the Natural Rearing Breeder Community | August 2026

Author: Paula Vandervoort
Co-founder of Natural Rearing Breeder Connection Ltd, The Dog Breeder Store LLC, and Gentry Boxers LLC

How many generations does it take?

I often question whether the term "natural rearing" can apply when the primary animals in a breeding program who are fully naturally reared are the girls, and not the stud dogs. I must admit that finding naturally reared stud dogs can be almost impossible in today’s world. And those of us who are dedicated to raising animals very cleanly usually cannot breed to our own males, as they are too closely related to our girls. So what is the answer to this question of how many generations give us the right to claim that our program is truly "naturally reared"? In researching this question, I looked into the influences of the maternal line and found some information that I believe helps us to make that decision based on the facts of epigenetics, mitochondria and science. So here goes…

Mitochondria is all about her. Sperm need not apply.

Here is something that happens at the moment of conception that most breeders never hear about, and I find it fascinating every time I think about it. The sperm that fertilizes the egg carries its own mitochondria, the tiny energy-producing structures inside every cell. But those paternal mitochondria don't survive the process. Within hours of fertilization, the dam's body actively targets and destroys them, so that every puppy in the litter inherits its mitochondria exclusively from her side.¹ That is not a minor biological footnote. It means the metabolic engine inside every cell of every puppy she produces traces back through her own maternal line, generation after generation, regardless of which sire she is bred to.

For decades, scientists knew this happened but couldn't fully explain why. That changed in 2023, when researchers identified the actual mechanism.² During the formation of sperm cells, sperm produce a slightly different version of a protein called TFAM, whose normal job is to protect and maintain mitochondrial DNA. In a developing sperm cell, this protein holds onto a piece of itself that is supposed to be clipped off, and that leftover piece gets chemically tagged in a way that blocks the protein from ever entering the sperm's mitochondria. Without that protection, the sperm's mitochondrial DNA is eliminated before the sperm cell even matures. By the time fertilization happens, the sperm has essentially nothing left to contribute on the mitochondrial side. The entire mitochondrial genome of every puppy in the litter comes from the egg. From her.

This is why mitochondrial haplogroups exist at all; they are the signature of an unbroken maternal line. Because mitochondrial DNA passes down without mixing with the sire's genetics, it accumulates its own distinct pattern over generations, and researchers have sorted dogs worldwide into six of these haplogroups, labeled A through F. The vast majority of dogs, somewhere around seventy-two percent, carry haplogroup A, and haplogroups A, B, and C together account for roughly ninety-seven percent of dogs on the planet.³ When you follow dam to dam to dam across five generations, you are not just selecting for the traits you can see. You are propagating the exact same mitochondrial identity, unbroken, all the way back.

Here's something else worth understanding about her mitochondria, because it changes how you think about a maternal line that has thrown one questionable litter or one dog with a health issue nobody could quite explain. Not every mitochondrion in a dam's body necessarily carries an identical copy of her mitochondrial DNA. It is possible for her to carry two or more slightly different versions at once, a condition researchers call heteroplasmy, and the balance between those versions can shift from one generation to the next, sometimes quite a bit within just a handful of litters.⁴ A low-level variant that looks harmless in one generation can either fade back toward normal or become more prominent in the next, depending entirely on which puppies from that line you choose to breed forward. What that means for you as a breeder is that your dam-line choices are never just choices about temperament and structure today. They are choices about the mitochondrial makeup you are locking into your kennel for decades to come, for better or worse.

This matters because mitochondrial quality is not cosmetic. It is a real, measurable factor in how a dog ages. Researchers comparing cells from long-lived small breeds against short-lived large breeds found that the small-breed cells had what's called more "uncoupled" mitochondria. That sounds like a flaw, but it isn't. Mild uncoupling is a protective trait; it reduces the damaging byproducts of energy production while keeping the cell's respiration capacity strong. The long-lived breeds' cells produced less of the oxidative damage associated with aging and tolerated cellular stress better than the short-lived breeds' cells did.⁵ Mitochondrial quality, the thing that passes only through the dam, is tied directly to how well a dog's cells age. When I look at a bitch's dam and granddam and ask how long they lived and how well they aged, I am not being sentimental. I am looking at the mitochondrial inheritance every puppy in that litter is going to carry for life.

What she hands off at birth

The mitochondrial genome is not the only thing a dam passes down that a sire simply cannot. She also hands off something alive: the founding population of her puppies' gut microbiome.

In the hours surrounding birth, a puppy's gut, which is essentially sterile beforehand, gets colonized by bacteria, and the dam is the primary source of that colonization. A study out of the University of Turin collected meconium, the very first gut contents a puppy produces, immediately after natural vaginal delivery and before the puppies had any contact with the dam's mouth or milk.⁶ What they found was striking. Each dam's litter carried its own distinct microbial signature, clustering together and apart from other dams' litters even within the same kennel, on the same feeding program, in the same environment. The dam is not just present at colonization. She is the primary shaper of it.

How a puppy is born changes what gets handed off, too. A 2026 study out of Hungary followed eighty-nine purebred Pumi dogs from birth through eighty-one weeks of age, and in one particularly useful comparison, researchers looked at two litters from the very same dam, one delivered vaginally and one delivered by Cesarean section. The puppies born by C-section showed a significantly different microbial pattern during the eight-to-ten-week window than their vaginally delivered littermates.⁷ Passing through the birth canal gives a puppy a richer, more complex initial seeding from the dam's own vaginal and rectal microbiome, and puppies who miss that passage start life with a different founding community.

I know this is not just an academic point for a lot of you reading this, because I hear from breeders whose bitches need a Cesarean far more often than any of us would like. If that's you, you are not without options. Vaginal seeding is a real, usable protocol for exactly this situation, and I walk through it step by step in my video on The Dog Breeder Channel, "Vaginal Seeding: Microbiome Transfer for C-Section Puppies."⁸ For those of you who print these articles to keep in your whelping binder, the short version is this: Before surgery, a sterile cotton tipped applicator is placed in the dam's vagina to collect her natural secretions, and immediately after each puppy is delivered and dried, that material is used to swab the puppy's mouth, face, and body, mimicking the exposure they would have gotten passing through the birth canal. It is a simple procedure, it costs almost nothing, and it gives a C-section litter a meaningful piece of what nature would otherwise have provided.

None of this happens in isolation from what you feed. Diet shapes what a dam has in her gut to give in the first place, and there is now large-scale evidence for it. Researchers with the Dog Aging Project analyzed the gut microbiomes of over nine hundred companion dogs across the country and found that dogs on home-prepared diets, raw or cooked, carried a distinctly different microbial signature than dogs fed commercial food, with dozens of individual bacterial species and metabolic functions shifting along with what was in the bowl.⁹ The pattern lines up with everything I have watched play out in my own kennel and in the kennels of breeders I mentor. What a dam eats becomes what lives in her gut, and what lives in her gut is what she gives her puppies on the way into the world.

The life she lives becomes part of what she passes on

There is a third system worth understanding, and it is the one that took me the longest to wrap my head around, because it sounds at first like it shouldn't be possible. It is called epigenetics, and the easiest way I have found to explain it to breeders is this: the DNA sequence itself, the actual genetic code, does not change. What changes is which parts of that code get read, and which parts get quieted down, almost like a dimmer switch sitting on top of the genes themselves. Diet, chemical exposure, stress, and the conditions an animal is raised in can all move that dimmer switch up or down, turning certain genes more active or less active without ever touching the underlying DNA.

For a long time, the assumption was that all of this got wiped clean at conception, reset back to zero for the next generation. We now know that isn't entirely true. Some of those switches survive the reset and get passed down to offspring. Researchers studying dogs with difficult early histories, ones who had been rescued from neglectful or abusive situations, found measurable differences in the methylation patterns on genes that govern the stress response and the capacity for attachment, compared to dogs without that history. Methylation is the biggest factor in epigenetic influence. Those same dogs also showed differences in cortisol response and in how securely they bonded with their people.¹⁰ This is not a rodent study or a human study borrowed and applied to dogs by inference. This is dogs, showing that early life experience leaves a molecular mark that can be passed on to future generations.

For a breeder, that is not a small thing to sit with. It means the environment you raise your breeding stock in, the stress they carry, the chemicals they are exposed to, the quality of their early handling, is not only a welfare question. It may be part of what gets passed down the line, right alongside temperament and structure. This is exactly why natural rearing has always insisted that how an animal is raised matters beyond that individual animal. Science is only now catching up to explain why.

Generational results in natural rearing

We know from experience that it takes more than one generation of natural rearing to fully express its benefits. I believe that, and I have seen the first generation almost do what we call "detoxing" the pedigree ahead of it when we start feeding whole fresh foods and eliminating toxins. I have watched it happen in my own lines. But I also have to tell you plainly: No study has yet followed multiple generations of naturally reared dogs against multiple generations of conventionally raised dogs, measuring mitochondrial health, microbiome diversity, and long-term outcomes side by side. That study doesn't exist yet, but the experiences do.

What does exist is a body of biological plausibility that keeps getting stronger every year. The maternal-line pattern is not unique to dogs, either. In the thoroughbred world, where money and pedigree records go back centuries, researchers looked at the racing performance of six hundred seventy-five Australian thoroughbreds and found that a foal's performance correlated far more strongly with the dam's side than the sire's, a difference that was statistically significant.¹¹ I don't know of an equivalent controlled study in dogs yet. But between the mitochondrial science we now understand and what generations of breeders have observed firsthand, I don't think we need one to know where to put our attention.

Barbara "BJ" Andrews, a breeder I have long admired, put it better than the geneticists ever will: The strength of the sire is the power of the dam.¹² She spent decades convinced that it was the dam of a great sire who passed on his genetic prowess, and that if a stud was truly dominant in passing on quality, it would be his daughters, not his sons, who proved it out. She was saying, in plain breeder language, exactly what the mitochondrial research is now confirming in a laboratory.

Where this leaves us

The dam line is not a sentimental construct, and it never was. It is a biological superhighway, carrying a complete secondary genome that powers every cell's energy production, a living microbial community that seeds the next generation's immune system, and an epigenetic imprint shaped by the life she lives, all flowing almost exclusively through the female side of the pedigree, litter after litter, for as long as that line continues.

This is exactly what natural rearing has been telling breeders to pay attention to all along: Feed whole, species-appropriate food, avoid unnecessary chemical exposure, support natural whelping wherever you can, and know your maternal lines going back as many generations as you can trace. When I evaluate a sire, I don't stop at his own health record. I want to know about his dam and his granddam, because that tells me something about the mitochondrial quality he was built on. The breeders who understood that the dam line mattered were right long before the science caught up to them. Now it has. The only question left is whether we use it.

The answer to the question, "How many generations?"

I think each of us has to answer this original question of how many generations (and on which sides of the pedigree) give us the right to say that our program is truly “naturally reared”. This is really based on our own individual breeding program. But based on what I have learned researching this question and now living with multiple generations of naturally reared boxers, I believe that it takes at least 2, if not 3, generations on the dam’s side to shake out some of the inherited miasms coming through the pedigree, and thank goodness, there are homeopathic protocols that can help with clearing miasms more quickly if one wants to pursue those. (That’s another article, better written by a homeopath educated in constitutional homeopathy than me, but I would like to find someone who can write that for our community. If you are out there, let me know.)

If you have a different perspective on how many generations have passed in your own program for you to see substantial improvements, please comment below. We all would love to learn from you as well!

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¹ Song, Won-Hee, Young-Joo Yi, Miriam Sutovsky, Stuart Meyers, and Peter Sutovsky. "Autophagy and Ubiquitin–Proteasome System Contribute to Sperm Mitophagy After Mammalian Fertilization." Proceedings of the National Academy of Sciences 113, no. 36 (2016): E5261–E5270.

² Lee, W., et al. "Molecular Basis for Maternal Inheritance of Human Mitochondrial DNA." Nature Genetics 55 (2023): 1632–1639.

³ Thai, Quan Ke, Tuan Thanh Nguyen, and Hien Thi Thanh Pham. "mtDNA Haplotype Network Analysis: Exploring Genetic Relationships and Diversity in Dog Haplogroups." GSC Biological and Pharmaceutical Sciences 24, no. 1 (2023): 224–232.

⁴ Klütsch, Cornelya F. S., Elina H. Seppälä, Mathias Uhlén, Hannes Lohi, and Peter Savolainen. "Segregation of Point Mutation Heteroplasmy in the Control Region of Dog mtDNA Studied Systematically in Deep Generation Pedigrees." International Journal of Legal Medicine 125, no. 4 (2011): 527–535.

⁵ Nicholatos, Justin W., Timothy M. Robinette, Saurabh V. P. Tata, et al. "Cellular Energetics and Mitochondrial Uncoupling in Canine Aging." GeroScience 41, no. 2 (2019): 229–242.

⁶ Bertero, Alessia, Penelope Banchi, Angela Del Carro, et al. "Meconium Microbiota in Naturally Delivered Canine Puppies." BMC Veterinary Research 20 (2024): 363.

⁷ Asaduzzaman, Md, Péter Oláh, Natheer Jameel Yaseen, et al. "Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics." mSystems 11, no. 2 (2026).

⁸ Vandervoort, Paula. "Vaginal Seeding: Microbiome Transfer for C-Section Puppies." The Dog Breeder Channel.

⁹ Bamberger, Tal, Efrat Muller, Yadid M. Algavi, et al. "Mapping the Canine Gut Microbiome: Insights from the Dog Aging Project." Nature Communications 17 (2026): Article 6602.

¹⁰ "A Dog's Life: Early Life Histories Influence Methylation of Glucocorticoid (NR3C1) and Oxytocin (OXTR) Receptor Genes, Cortisol Levels, and Attachment Styles." Developmental Psychobiology 66 (2024): e22482.

¹¹ Lin, Xiang, Shi Zhou, Li Wen, Allan Davie, Xinkui Yao, Wujun Liu, and Yong Zhang. "Potential Role of Maternal Lineage in the Thoroughbred Breeding Strategy." Reproduction, Fertility and Development 28, no. 11 (2015): 1704–1711.

¹² Andrews, Barbara "BJ." "The Genetic X Factor. The Dog Place.