Why is Masechta Shekalim included in the Daf Yomi cycle?In the Talmud Bavli there is no gemara for Shekalim, but there is one in the Yerushalmi. However, there are gemaras for other massekhtot in the Yerushalmi for which there are none in the Bavli, and these did not become part of the Daf Yom cycle. So why should Shekalim alone jump borders and be included in the study schedule for the Babylonian Talmud? That is the question.
The answer is neatly summarized as follows: the Yerushalmi Shekalim has long been an honorary massekhet in Talmud Bavli. Thus, the Daf Yomi project begun in 1923 was not so much choosing to include a single Yerushalmi gemara, either arbitrarily or for a particular reason, as continuing a longstanding custom.
A good place to begin would be the famous manuscript Hebraicus 95, the Munich Babylonian Talmud manuscript from the 14th century. It included Shekalim.
Marvin Heller cites1 R. Saul Lieberman
a renowned authority on the Jerusalem Talmud [who], testifies2 to the frequent and early study of Shekalim as part of the Babylonian Talmud dating back to the time of the geonim. He writes that he has examined many manuscripts of Shekalim that were attached to codices of the Babylonian Talmud . . . . Lieberman also remarks that the text of the Jerusalem Talmud Shekalim attached to the Babylonian Talmud varies considerably from the text of Shekalim in the Jerusalem Talmud.
In Heller's survey of printed editions, he refers to an edition of Shekalim printed by Balthassar Wust in 1689 with the commentary of R. Elijah of Fulda. In the introduction R. Fulda wrote
וזה אשר יצא לי ראשונה להביא לבית הדפוס מסכת שקלים לבדה לפי שרבו עלי הוצאת הדפוס אפילו לסדר מן הסדרים בכן ראיתי להביא המסכת הלן לבית הדפוס כדי להשלים הסדר כפי אשר נדפס עם הש"ס בבלי בדפוס יוסטניאה
The reason why this tractate, Shekalim, was printed first and by itself is because of the expense of even printing one order [out of six]. Therefore I chose to have this tractate printed in order to
complete the order as it was printed in the Giustiniani edition [1540s].
1 Marvin J. Heller, "Printing the Talmud: A History of the Individual Treatises Printed from 1700 to 1750," pg. 21.
1 Saul Lieberman, "The Old Commentators of the Yerushalmi," Alexander Marx Jubilee Volume, pg. 295. n. 29.