John Lynch did an excellent job of demonstrating how many people are involved in a three-day draft.

The 49ers’ neophyte general manager cited executive Paraag Marathe for his role in the big Day 1 one trade that netted San Francisco three extra picks. He noted Kyle Shanahan’s work on Iowa quarterback C.J. Beathard, running back coach Bobby Turner’s diligence on Utah running back Joe Williams and the insight from personnel executive Martin Mayhew — who spent nine years as an NFL cornerback — on Colorado cornerback Ahkello Witherspoon.

Lynch mentioned his right-hand man in the front office, Adam Peters, four times from Thursday to Saturday.

But make no mistake, Lynch was the conductor of the 49ers’ orchestra, the one making the decisions and the one who articulated the team’s vision and thought process to the public.

Two picks in particular, Stanford defensive lineman Solomon Thomas and Witherspoon, may be most the most emblematic of the nascent Lynch era in San Francisco.

Some teams are turned off by Stanford players because they have a perceived know-it-all quality and because, frankly, they have other options. Are they willing to endure the monotony of NFL practices and the physical toll of a football career when they can join a Fortune 500 company or become a physician?

The same can be said of Witherspoon, who is talented enough to play baseball or soccer professionally and who aspires to go to medical school when his NFL career is over. During the run-up to the draft, Witherspoon was peppered with questions from teams about how important football is to him.

Lynch doesn’t have that bias.

“Having played at Stanford, sometimes people mistake smart football players,” he said. “They question (whether) smart guys love football, and I don’t think just because you have other interests and because you do well in school, you don’t love football.”

“Ahkello really communicated his love for the game and why he did so, and Kyle and I both got really comfortable with it,” Lynch continued. “And he was a guy, as I said, we went back (Friday) and really zeroed in on if he was there. It was a waiting game and we were hopeful that he would be there and sure enough, he was.”

A 2018 bonus — The 49ers went into the draft with 10 selections and came away with 10 players … as well as additional picks, one in the second and one in the third round, next year.

Defying their novice statuses, Lynch and Shanahan traded six times over the three-day period. Only the Vikings, with seven deals, traded more.

“I think of — when you trade, that means you go into a draft with 10 picks and you end up only getting six players,” Shanahan said. “To be able to do that that much and to get the players and that ammo for next year, that’s something I didn’t think happens very much.”

Those extra picks could be handy for maneuvering next year. The early indication is that the 2018 draft will be rich in quarterbacks, receivers and offensive tackles.

Late-round steal? He’ll likely get overlooked because he was drafted so late, but Mississippi defensive tackle D.J. Jones, who was taken in the sixth round, seems to be an excellent fit for the nose-tackle spot on the 49ers’ offensive line.

Jones is athletic for his size — 6-1, 319 pounds — and rarely got knocked to the ground in the rough-and-tumble SEC. Newcomer Earl Mitchell is the likely starter at the position; Jones will compete with Quinton Dial and Mike Purcell to be the main backup.

His selection also led to this exchange between Lynch and Shanahan:

“Lynch: “There’s two D.J. Joneses at Ole Miss. We were very clear that we wanted the defensive tackle from Ole Miss, not the other guy. We got the right guy.”

Shanahan: “… no offense …”

Lynch: “.. No offense to the other guy. He’s a heck of a player. We just didn’t want him at that point.”

Ward’s fifth year — When Lynch was asked last week whether the 49ers would pick up Jimmie Ward’s fifth-year option, he paused, blinked a couple of times and said he hadn’t thought about it because he’d been so consumed in the draft.

On Saturday, he admitted he didn’t know what a fifth-year option was. (Rookie contracts are for four years. For first-round picks like Ward, teams have the option of picking up a fifth year of their deal.)

Because the 49ers didn’t draft a free safety (seventh-round pick Adrian Colbert likely will start out as a cornerback), Ward is by far the team’s best option at the position, making him a shoe-in to get the fifth-year option, which would lock him up through 2018. The deadline for doing so is Wednesday.

“Yeah, it’s looking like that,” Lynch said. “Had no clue when you guys asked me that the other day. I had no idea.”

Single-high help — Though the 49ers did not draft a free safety, they appeared to land a good one following the draft.

Lorenzo Jerome had six interceptions and 11 pass break ups last year for St. Francis University. He also had two interceptions each in the NFLPA and Senior Bowl all-star games in which he was matched up against higher-caliber opponents than he faced at St. Francis. The university announced on Saturday that Jerome would sign a contract with the 49ers.

Local tight end — Witherspoon (Christian Brothers) wasn’t the only Sacramento area player the 49ers picked up. They also reportedly will sign tight end Cole Hikutini, who played at Pleasant Grove High School in Elk Grove, the same school that defensive lineman Arik Armstead attended.

Hikutini (6-4, 247) played at Sacramento State and City College of San Francisco before transferring to Louisville last year. He was productive in his only year there, catching 19 passes for 348 yards and three touchdowns.

He likely fits as the “move” tight end in the 49ers offense, a spot currently held by Vance McDonald, the subject of trade talks this weekend.

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