What are some researched examples of limitations in a species producing advantages gained phylogenically?

Define "limitation".

Then define "advantage gained phylogenetically".

I'd assume you're talking about species which have adaptations that are not unique, but also which are clearly not at the peaks of their adaptive landscapes. Every species qualifies here, because there is no empirical method to tell what a "limitation" is and because there are examples of positive or balancing selection everywhere.

All species have limitation in at least one or more factors or parameters. If an advantage is a condition which permits survival, then the evolved advantage lasts only as long as conditions do not change such that would exterminate the species. The limitations in many other species allow for the survival of their concurrent epoch member species.

There are no such examples of such research to my knowledge. If a species is gained phylogenically, then its limitations are gained phylogenically.

Reproductive traits are tightly linked to plant fitness and may therefore be mechanisms driving biological invasions, including the greater success of more phylogenetically novel introduced species in some systems. We present a phylogenetic comparative analysis of "Baker's law'', that introduced plants with the ability to reproduce autogamous or asexually may be better able to establish on introduction. We gathered data from both published and unpublished sources on pollen limitation of 141 species, including 26 introduced species and 115 native species. Our analysis compared differences in the proportion of autonomous autogamy, asexual reproduction, and pollen limitation among native, introduced noninvasive, and introduced invasive plant species, and included the phylogenetic novelty of the introduced species to the native species in that community. Introduced species were more likely to be autogamous than native species, consistent with Baker's law. On the other hand, introduced species were less likely to have the ability to reproduce asexually. Further, among species with no autonomous autogamy, pollen limitation was greater for introduced compared to native species. Such a result is consistent with the idea that plants entering a new continent receive lower quality or quantity of services from resident pollinators than species native to that continent. Finally, more phylogenetically novel invasive species had lower pollen limitation than less novel invasive species, potentially because they experience less competition for pollinators. This is the first evidence that enhanced pollination may be one mechanism driving the greater invasiveness of phylogenetically novel introduced species observed in some systems.

http://www.ncbi.nlm.nih.gov/pubmed/21328010

http://www.nature.com/scitable/topicpage/why-shoul...

http://www.uic.edu/classes/bios/bios101/x210_files...

chave.ups-tlse.fr/chave/gonzalez-jecol09.pdf