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List of pedigrees
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Ellis 1: Ellis of Norton, Ellis of Paunton, Ellis of Swineshead, Ellis Ellys of Wyham
Anthony or William Ellis of Swineshead
1. John Ellis of Swineshead
A. Thomas Ellis of Swineshead & Great Paunton d 1545/6
m Agnes Marshall a 1545, dau of Ralph Marshall of South Calrton
i. John Ellis of Swineshead & Great Paunton a 1546, dspsms
ii. Anthony Ellis of Swineshead & Paunton
m Anne Sherard dau of George or Thomas Sherard of Stainby and Stapleford
a. Thomas Ellis of Paunton
m Margaret Durant dau of William Durant of Cottesmore
1 Mary Ellis
m John Booth of Killingholme
b. Anthony Ellis
1 John Ellis
A Mary Ellis a 1639
2 William Ellis of Swineshead a 1639
m Jane a 1639
A+ issue a 1639 - John, William, Mary
3 Thomas Ellis of Swineshead d 1639/40, yeoman
A Frances Ellis a 1639
c.+ other issue a 1545 - Elizabeth, Ellen, Agnes
iii. Mary Ellis
m Thomas Haugh or Halghe of Wigtoft
iv. Jane Ellis bur 05.07.1549
m Richard Cony of Basingthorpe bur 12.04.1545
v. Mary Ellis
m1 Humphrey Walcott of Walcott
m2 _ Colville
m3. John Bothe
m4. Gabriel Saville of Newton bur 03.01.1619-20
B. ? Anthony Ellis
Presumed to have been connected to the above family, as he "bore the arms of Ellis of Swineshead" was ...
Thomas Ellys of Wyham
m Anne d before 25.06.1605
1. Sir Thomas Ellys or Ellis 'of Wyham' d 1605
m Jane Hutchinson d 1605, dau of William not John Hutchinson of Owthorpe
A. Sir Thomas Ellis of Grantham bur 07.09.1627
m before 1605 Jane Armstrong bur 25.11.1661, dau of Gabriel Armstrong of Wishall
i. Thomas Ellis of Wyham and Northill b c1605, d 06.04.1640
m 08.11.1627 Elizabeth Harding dau of _ Harding of Northill
a. Sir Thomas Ellis or Ellys, 1st Bart of Wyham bpt 08.10.1629
m Anne Stanhope dau of Sir John Stanhope of Elvaston, brother of 1st Earl of Chesterfield
1 Sir William Ellis or Ellys, 2nd Bart of Wyham & Norton b c1653, d 06.10.1727
m Isabella Hampden dau of Richard Hampden of Hampden, Chancellor
A Sir William Ellis or Ellys, 3rd Bart of Wyham & Norton dsp 14.01.1741-2, 2nd son
m1 Elizabeth Hussey dsp, dau of Sir Thomas Hussey of Dodington
m2 Sarah Gould d 02.02.1769, dau of Thomas Gould of Ivor, she m2. Sir Francis Dashwood, Bart
B Anne Ellis d 02.1722-3
m Edward Cheke or Check of Pergo
C Isabella Ellis
m Richard Hampden dsp
D+ other issue d unm - William b c1673, d 23.02.1680-1, Thomas, John, George, Sarah d 10.02.1735-6
2 Jane Ellis
m William Strode of Barrington, Somerset d before 05.06.1695
Thanks to a site visitor MF, 09.12.10 for pointing out the following connection, given by William's will..
A William Strode of Barrington
B Jane Strode
m Robert Austen
3+ other issue - John b c1662, d 02.05.1686, Dorothy bur30.06.1674
b. Anne Ellis bpt 02.09.1628, d 03.07.1662
m Thomas Yarborough of Campsall
c. Elizabeth Ellis of Campsall bpt 20.09.1631, d unm 1651-2
ii. Sir William Ellis of Grantham bpt 19.07.1607, d unm 03.12.1680, Attorney General, 3rd son
iii. John Ellis bpt 26.07.1614, 5th/6th son
m 1658 ??
The following comes from BLG1886 Ellis of Sea Park which reported that the following Thomas was son of John "stated to have been fifth son of Sir Thomas Ellis, of Wyham".
a. Thomas Ellis of Monaghan d 1714, to Ireland
m Mary
1 Francis Ellis b 1683, d 1773
m Joan Maxwell
A Henry Ellis, Governor of Georgia & Nova Scotia, Provost Marshal of Grendada, Tobago, etc. d unm 1806
B Robert Ellis of Arduncheon, co. Fermanagh b 1726, d 17820
m Penelope Leslie dau of Rev. Alexander Leslie of Portglenore
BLG1886 confuses the generations at this point, showing most of the following as siblings of Robert but the dates and confirmation that Henry was his 2nd son indicate that they were his children.
i Francis Ellis of Bath b 1772, d 1842 had issue
m Mary Kilbee dau of J. Kilbee
ii Henry Ellis of Mount Stewart b 1774, d 1848 had issue
m Elizabeth Cupples dau of Thomas Cupples of Lisburn
iii Jane Ellis
m Rev. William Maxwell of Falkland, co. Monaghan
iv Isabella Ellis d 1795
m William Mayne of Freame Mount
v Penelope Ellis d 1848
m Rev. Francis Lawrence Gore
vi+ other issue d unm - Robert d 1775, Alexander b 1776, d 1796, Sarah
2 Richard Ellis b 1684, d 1774
A ?? Ellis
i Thomas Ellis master in Chancery
a Richard Ellis of Abbeyfeale, co. Limerick
3+ other issue
iv. Margaret Ellis b before 1605, d before 16.02.1658-9
m 07.10.1624 William Adams of Owston b c1607, d before 09.1657
v. Elizabeth Ellis b before 1605, d before 27.09.1653
m 06.08.1618 Peter Ashton of Grantham d 1653
vi. Dorothy Ellis bpt 01.06.1612, a 09.1657
m William Ashurst of Ashurst
vii. Jane Ellis bpt 14.05.1618, d 01.08.1639
m 1637 Ridge John Locke of Hertfordshire
viii.+ other issue - Edmund bpt 29.06.1606, d young?, Gabriel bpt 06.01.1608-9, a 09.1628, George bpt 08.03.1609-10, a 09.1628, Henry bpt 13.06.1613, bur 09.04.1652, Joseph bpt 07.12.1616, d young?, Joseph bpt 13.10.1722, a 09.1628, Benjamin bpt 04.07.1624, a 09.1628, Judith bpt13.01.1619-20
B. George Ellis of Gresholme and Wyham d before 23.06.1643
m1 Frances Radley bpt 13.10.1566, d before 1629, dau of William Radley of Yarborough
i. Jane Ellis a 09.1657
m Sir William Bury of Grantham
ii. Anne Ellis
m Michael Clipham of Otteby
iii. Dorothy Ellis
m 29.11.1625 Isaac Knight of Lincoln
iv. Frances Ellis a 09.1657
m William Thornton of Grantham
v.+ other issue - William b c1611, Mary a 1634
m2 Alice a 1639
C. Jane Ellis a 06.1605
m ? _ Audley
D. Dorothy Ellis bur 01.01.1629-30
m after 11.1570 William Knight of Kirmington a 1625
E.+ other issue - Elizabeth a 11.1570, Anne a 11.1570
2. Elizabeth Ellys or Ellis
m Francis Ayscough son of Sir Francis of South Kelsey

Sources:
1 For upper section : Maddison's Lincolnshire Pedigrees 1906, Ellis of Swineshead
2 For lower section : Maddison's Lincolnshire Pedigrees 1906, Ellis of Wyham with some support from BEB1841 Ellys of Wyham
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