Are any invertebrate nephridia (proto/meta) homologous with vertebrate kidneys in the sense that embryologically they also begin together with the genital system? When did the embryologic association between reproduction and osmoregulartion/metabolite elimination begin in terms of evolution?
The urogenital system as a cohesive functional unit probably evolved very early in vertebrate history. Hagfishes and lampreys have separate systems for reproduction and excretion. More derived groups of fishes use kidney tubules and ducts for sperm delivery outside the body (Helfman et al. 2009).
The vertebrate nephron may be homologous to the invertebrate nephridia (Ruppert 1994). The genetics underlying the development of vertebrate female reproductive organs shows many homologies with invertebrate reproductive organs (Kobayashi and Behringer 2003)
I would hypothesize that the both the reproductive and extrectory systems of vertebrates show corresponding homologies to invertebrate organ systems (at least genetic and developmental homologies) but evolution of the urogenital organ system did not evolve until the early vertebrates.
Helfman, G.S. et al. 2009. The Diversity of Fishes. Biology, Evolution and Ecology. Wiley-Blackwell, Oxford, UK.
Kobayashi, A. ad R.R. Behringer. 2003. Developmental genetics of the female reproductive tract in mammals. Nature Reviews Genetics 4: 969-980.
Ruppert, E.E. 1994. Evolutionary origin of the vertebrate nephron. American Zoologist 34: 542-553.